Merge pull request #2648 from akohlmey/next_lammps_version

Update version strings for the next patch release

LICENSE

@@ -1,6 +1,6 @@
 GNU GENERAL PUBLIC LICENSE
 
-Version 2, June 1991 
+Version 2, June 1991
 
 Copyright (C) 1989, 1991 Free Software Foundation, Inc.  
 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -301,9 +301,8 @@ one line to give the program's name and an idea of what it does.
 Copyright (C) yyyy  name of author
 
 This program is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 2 of the License, or (at
-your option) any later version.
+it under the terms of the GNU General Public License version 2 as
+published by the Free Software Foundation.
 
 This program is distributed in the hope that it will be useful, but
 WITHOUT ANY WARRANTY; without even the implied warranty of

cmake/CMakeLists.txt

@@ -26,7 +26,14 @@ find_package(Git)
 
 # by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed
 if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
-  set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "default install path" FORCE )
+  set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE)
+endif()
+
+# If enabled, no need to use LD_LIBRARY_PATH / DYLD_LIBRARY_PATH when installed
+option(LAMMPS_INSTALL_RPATH "Set runtime path for shared libraries linked to LAMMPS binaries" OFF)
+if (LAMMPS_INSTALL_RPATH)
+  set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR})
+  set(CMAKE_INSTALL_RPATH_USE_LINK_PATH ON)
 endif()
 
 # Cmake modules/macros are in a subdirectory to keep this file cleaner
@@ -156,8 +163,7 @@ if(BUILD_MPI)
     endif()
   endif()
 else()
-  enable_language(C)
-  file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
+  file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.cpp)
   add_library(mpi_stubs STATIC ${MPI_SOURCES})
   set_target_properties(mpi_stubs PROPERTIES OUTPUT_NAME lammps_mpi_stubs${LAMMPS_MACHINE})
   target_include_directories(mpi_stubs PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
@@ -778,9 +784,7 @@ if(PKG_GPU)
   message(STATUS "<<< GPU package settings >>>
 -- GPU API:          ${GPU_API}")
   if(GPU_API STREQUAL "CUDA")
-    message(STATUS "GPU architecture: ${GPU_ARCH}")
-  elseif(GPU_API STREQUAL "OPENCL")
-    message(STATUS "OpenCL tuning:    ${OCL_TUNE}")
+    message(STATUS "GPU default architecture: ${GPU_ARCH}")
   elseif(GPU_API STREQUAL "HIP")
     message(STATUS "HIP platform:     ${HIP_PLATFORM}")
     message(STATUS "HIP architecture: ${HIP_ARCH}")

cmake/Modules/Documentation.cmake

@@ -50,9 +50,9 @@ if(BUILD_DOC)
     OUTPUT ${DOC_BUILD_DIR}/requirements.txt
     DEPENDS docenv ${DOCENV_REQUIREMENTS_FILE}
     COMMAND ${CMAKE_COMMAND} -E copy ${DOCENV_REQUIREMENTS_FILE} ${DOC_BUILD_DIR}/requirements.txt
-    COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade pip
-    COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
-    COMMAND ${DOCENV_BINARY_DIR}/pip install --use-feature=2020-resolver -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
+    COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade pip
+    COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
+    COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
   )
 
   # download mathjax distribution and unpack to folder "mathjax"

cmake/Modules/GTest.cmake

@@ -20,10 +20,10 @@ ExternalProject_Add(googletest
                                     -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
                                     -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
                                     -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
-                    BUILD_BYPRODUCTS <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest${GTEST_LIB_POSTFIX}.a
-                                     <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock${GTEST_LIB_POSTFIX}.a
-                                     <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest_main${GTEST_LIB_POSTFIX}.a
-                                     <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock_main${GTEST_LIB_POSTFIX}.a
+                    BUILD_BYPRODUCTS <BINARY_DIR>/lib/libgtest${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
+                                     <BINARY_DIR>/lib/libgmock${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
+                                     <BINARY_DIR>/lib/libgtest_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
+                                     <BINARY_DIR>/lib/libgmock_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
                     LOG_DOWNLOAD ON
                     LOG_CONFIGURE ON
                     LOG_BUILD ON
@@ -39,10 +39,10 @@ file(MAKE_DIRECTORY ${GTEST_INCLUDE_DIR})
 file(MAKE_DIRECTORY ${GMOCK_INCLUDE_DIR})
 
 ExternalProject_Get_Property(googletest BINARY_DIR)
-set(GTEST_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest${GTEST_LIB_POSTFIX}.a)
-set(GMOCK_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock${GTEST_LIB_POSTFIX}.a)
-set(GTEST_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest_main${GTEST_LIB_POSTFIX}.a)
-set(GMOCK_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock_main${GTEST_LIB_POSTFIX}.a)
+set(GTEST_LIBRARY_PATH ${BINARY_DIR}/lib/libgtest${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
+set(GMOCK_LIBRARY_PATH ${BINARY_DIR}/lib/libgmock${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
+set(GTEST_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/libgtest_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
+set(GMOCK_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/libgmock_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
 
 # Prevent GoogleTest from overriding our compiler/linker options
 # when building with Visual Studio

cmake/Modules/OpenCLLoader.cmake

@@ -0,0 +1,48 @@
+message(STATUS "Downloading and building OpenCL loader library")
+
+include(ExternalProject)
+set(OPENCL_LOADER_URL "https://download.lammps.org/thirdparty/opencl-loader-2020.12.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
+mark_as_advanced(OPENCL_LOADER_URL)
+ExternalProject_Add(opencl_loader
+                    URL ${OPENCL_LOADER_URL}
+                    URL_MD5         011cdcbd41030be94f3fced6d763a52a
+                    SOURCE_DIR      "${CMAKE_BINARY_DIR}/opencl_loader-src"
+                    BINARY_DIR      "${CMAKE_BINARY_DIR}/opencl_loader-build"
+                    CMAKE_ARGS      ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_OPENCL_LOADER_OPTS}
+                                    -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+                                    -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+                                    -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+                                    -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
+                                    -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
+                    BUILD_BYPRODUCTS <BINARY_DIR>/libOpenCL${CMAKE_STATIC_LIBRARY_SUFFIX}
+                    LOG_DOWNLOAD ON
+                    LOG_CONFIGURE ON
+                    LOG_BUILD ON
+                    INSTALL_COMMAND ""
+                    TEST_COMMAND    "")
+
+ExternalProject_Get_Property(opencl_loader SOURCE_DIR)
+set(OPENCL_LOADER_INCLUDE_DIR ${SOURCE_DIR}/inc)
+
+# workaround for CMake 3.10 on ubuntu 18.04
+file(MAKE_DIRECTORY ${OPENCL_LOADER_INCLUDE_DIR})
+
+ExternalProject_Get_Property(opencl_loader BINARY_DIR)
+set(OPENCL_LOADER_LIBRARY_PATH "${BINARY_DIR}/libOpenCL${CMAKE_STATIC_LIBRARY_SUFFIX}")
+
+find_package(Threads QUIET)
+if(NOT WIN32)
+  set(OPENCL_LOADER_DEP_LIBS "Threads::Threads;${CMAKE_DL_LIBS}")
+else()
+  set(OPENCL_LOADER_DEP_LIBS "cfgmgr32;runtimeobject")
+endif()
+
+add_library(OpenCL::OpenCL UNKNOWN IMPORTED)
+add_dependencies(OpenCL::OpenCL opencl_loader)
+
+set_target_properties(OpenCL::OpenCL PROPERTIES
+  IMPORTED_LOCATION ${OPENCL_LOADER_LIBRARY_PATH}
+  INTERFACE_INCLUDE_DIRECTORIES ${OPENCL_LOADER_INCLUDE_DIR}
+  INTERFACE_LINK_LIBRARIES "${OPENCL_LOADER_DEP_LIBS}")
+
+

cmake/Modules/Packages/GPU.cmake

@@ -1,7 +1,9 @@
 set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
 set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
                 ${GPU_SOURCES_DIR}/fix_gpu.h
-                ${GPU_SOURCES_DIR}/fix_gpu.cpp)
+                ${GPU_SOURCES_DIR}/fix_gpu.cpp
+                ${GPU_SOURCES_DIR}/fix_nh_gpu.h
+                ${GPU_SOURCES_DIR}/fix_nh_gpu.cpp)
 target_compile_definitions(lammps PRIVATE -DLMP_GPU)
 
 set(GPU_API "opencl" CACHE STRING "API used by GPU package")
@@ -97,9 +99,13 @@ if(GPU_API STREQUAL "CUDA")
   if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
     string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
   endif()
-  # Ampere (GPU Arch 8.0 and 8.6) is supported by CUDA 11 and later
+  # Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
   if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
-    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80] -gencode arch=compute_86,code=[sm_86,compute_86]")
+    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
+  endif()
+  # Ampere (GPU Arch 8.6) is supported by CUDA 11.1 and later
+  if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
+    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
   endif()
   if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
     message(WARNING "Unsupported CUDA version. Use at your own risk.")
@@ -139,27 +145,13 @@ if(GPU_API STREQUAL "CUDA")
   target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
 
 elseif(GPU_API STREQUAL "OPENCL")
-  if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
-    # download and unpack support binaries for compilation of windows binaries.
-    set(LAMMPS_THIRDPARTY_URL "https://download.lammps.org/thirdparty")
-    file(DOWNLOAD "${LAMMPS_THIRDPARTY_URL}/opencl-win-devel.tar.gz" "${CMAKE_CURRENT_BINARY_DIR}/opencl-win-devel.tar.gz"
-            EXPECTED_MD5 2c00364888d5671195598b44c2e0d44d)
-    execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf opencl-win-devel.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
-    add_library(OpenCL::OpenCL UNKNOWN IMPORTED)
-    if(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86")
-      set_target_properties(OpenCL::OpenCL PROPERTIES IMPORTED_LOCATION "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win32/libOpenCL.dll")
-    elseif(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86_64")
-      set_target_properties(OpenCL::OpenCL PROPERTIES IMPORTED_LOCATION "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win64/libOpenCL.dll")
-    endif()
-    set_target_properties(OpenCL::OpenCL PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/include")
+  option(USE_STATIC_OPENCL_LOADER "Download and include a static OpenCL ICD loader" ON)
+  mark_as_advanced(USE_STATIC_OPENCL_LOADER)
+  if (USE_STATIC_OPENCL_LOADER)
+    include(OpenCLLoader)
   else()
     find_package(OpenCL REQUIRED)
   endif()
-  set(OCL_TUNE "generic" CACHE STRING "OpenCL Device Tuning")
-  set(OCL_TUNE_VALUES intel fermi kepler cypress generic)
-  set_property(CACHE OCL_TUNE PROPERTY STRINGS ${OCL_TUNE_VALUES})
-  validate_option(OCL_TUNE OCL_TUNE_VALUES)
-  string(TOUPPER ${OCL_TUNE} OCL_TUNE)
 
   include(OpenCLUtils)
   set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
@@ -203,7 +195,7 @@ elseif(GPU_API STREQUAL "OPENCL")
   add_library(gpu STATIC ${GPU_LIB_SOURCES})
   target_link_libraries(gpu PRIVATE OpenCL::OpenCL)
   target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu)
-  target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -D${OCL_TUNE}_OCL -DMPI_GERYON -DUCL_NO_EXIT)
+  target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DGERYON_NUMA_FISSION -DUCL_NO_EXIT)
   target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
 
   target_link_libraries(lammps PRIVATE gpu)
@@ -211,6 +203,7 @@ elseif(GPU_API STREQUAL "OPENCL")
   add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
   target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL)
   target_link_libraries(ocl_get_devices PRIVATE OpenCL::OpenCL)
+  add_dependencies(ocl_get_devices OpenCL::OpenCL)
 elseif(GPU_API STREQUAL "HIP")
   if(NOT DEFINED HIP_PATH)
       if(NOT DEFINED ENV{HIP_PATH})
@@ -393,13 +386,10 @@ elseif(GPU_API STREQUAL "HIP")
   target_link_libraries(lammps PRIVATE gpu)
 endif()
 
-# GPU package
-FindStyleHeaders(${GPU_SOURCES_DIR} FIX_CLASS fix_ FIX)
-
 set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
-
-# detects styles which have GPU version
+# detect styles which have a GPU version
 RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)
+RegisterFixStyle(${GPU_SOURCES_DIR}/fix_gpu.h)
 
 get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
 

cmake/Modules/Packages/KIM.cmake

@@ -69,14 +69,14 @@ if(DOWNLOAD_KIM)
     BUILD_RPATH "${_rpath_prefix}/kim_build-prefix/lib"
     )
 else()
-  if(KIM-API_FOUND AND KIM_API_VERSION VERSION_GREATER_EQUAL 2.2.0)
+  if(KIM-API_FOUND AND KIM-API_VERSION VERSION_GREATER_EQUAL 2.2.0)
     # For kim-api >= 2.2.0
-    find_package(KIM-API ${KIM-API_MIN_VERSION} CONFIG REQUIRED)
+    find_package(KIM-API 2.2.0 CONFIG REQUIRED)
     target_link_libraries(lammps PRIVATE KIM-API::kim-api)
   else()
     # For kim-api 2.1.3 (consistent with previous version of this file)
     find_package(PkgConfig REQUIRED)
-    pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=KIM-API_MIN_VERSION)
+    pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=${KIM-API_MIN_VERSION})
     target_link_libraries(lammps PRIVATE PkgConfig::KIM-API)
   endif()
 endif()

cmake/Modules/Packages/MESSAGE.cmake

@@ -2,9 +2,8 @@ if(LAMMPS_SIZES STREQUAL BIGBIG)
   message(FATAL_ERROR "The MESSAGE Package is not compatible with -DLAMMPS_BIGBIG")
 endif()
 option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
-file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F
-    ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c
-    ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
+file(GLOB_RECURSE cslib_SOURCES
+        ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
 
 add_library(cslib STATIC ${cslib_SOURCES})
 target_compile_definitions(cslib PRIVATE -DLAMMPS_${LAMMPS_SIZES})

cmake/Modules/YAML.cmake

@@ -12,7 +12,7 @@ ExternalProject_Add(libyaml
                                       CXX=${CMAKE_CXX_COMPILER}
                                       CC=${CMAKE_C_COMPILER}
                                       --prefix=<INSTALL_DIR> --disable-shared
-                    BUILD_BYPRODUCTS  <INSTALL_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}yaml.a
+                    BUILD_BYPRODUCTS  <INSTALL_DIR>/lib/libyaml${CMAKE_STATIC_LIBRARY_SUFFIX}
                     TEST_COMMAND      "")
 
 ExternalProject_Get_Property(libyaml INSTALL_DIR)
@@ -23,7 +23,7 @@ set(YAML_LIBRARY_DIR ${INSTALL_DIR}/lib)
 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)
+set(YAML_LIBRARY_PATH ${INSTALL_DIR}/lib/libyaml${CMAKE_STATIC_LIBRARY_SUFFIX})
 
 add_library(Yaml::Yaml UNKNOWN IMPORTED)
 set_target_properties(Yaml::Yaml PROPERTIES

doc/Makefile

@@ -47,6 +47,8 @@ HAS_PDFLATEX = YES
 endif
 endif
 
+# override settings for PIP commands
+# PIP_OPTIONS = --cert /etc/pki/ca-trust/extracted/openssl/ca-bundle.trust.crt --proxy http://proxy.mydomain.org
 
 #SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())') $(shell test -f $(BUILDDIR)/doxygen/xml/run.stamp && printf -- "-E")
 
@@ -228,13 +230,13 @@ $(VENV):
 	@( \
 		$(VIRTUALENV) -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
-		pip install --upgrade pip; \
-		pip install -r $(BUILDDIR)/utils/requirements.txt; \
+		pip $(PIP_OPTIONS) install --upgrade pip; \
+		pip $(PIP_OPTIONS) install -r $(BUILDDIR)/utils/requirements.txt; \
 		deactivate;\
 	)
 
 $(MATHJAX):
-	@git clone --depth 1 https://github.com/mathjax/MathJax.git $@
+	@git clone --depth 1 git://github.com/mathjax/MathJax.git $@
 
 $(TXT2RST) $(ANCHORCHECK): $(VENV)
 	@( \

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "10 February 2021" "2021-02-10"
+.TH LAMMPS "10 March 2021" "2021-03-10"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/src/Build_basics.rst

@@ -95,7 +95,7 @@ standard. A more detailed discussion of that is below.
 
       .. note::
 
-         The file ``src/STUBS/mpi.c`` provides a CPU timer function
+         The file ``src/STUBS/mpi.cpp`` provides a CPU timer function
          called ``MPI_Wtime()`` that calls ``gettimeofday()``.  If your
          operating system does not support ``gettimeofday()``, you will
          need to insert code to call another timer.  Note that the
@@ -526,6 +526,20 @@ you want to copy files to is protected.
          make                        # perform make after CMake command
          make install                # perform the installation into prefix
 
+      During the installation process CMake will by default remove any runtime
+      path settings for loading shared libraries.  Because of this you may
+      have to set or modify the ``LD_LIBRARY_PATH`` (or ``DYLD_LIBRARY_PATH``)
+      environment variable, if you are installing LAMMPS into a non-system
+      location and/or are linking to libraries in a non-system location that
+      depend on such runtime path settings.
+      As an alternative you may set the CMake variable ``LAMMPS_INSTALL_RPATH``
+      to ``on`` and then the runtime paths for any linked shared libraries
+      and the library installation folder for the LAMMPS library will be
+      embedded and thus the requirement to set environment variables is avoided.
+      The ``off`` setting is usually preferred for packaged binaries or when
+      setting up environment modules, the ``on`` setting is more convenient
+      for installing software into a non-system or personal folder.
+
    .. tab:: Traditional make
 
       There is no "install" option in the ``src/Makefile`` for LAMMPS.

doc/src/Build_extras.rst

@@ -120,8 +120,6 @@ CMake build
    -D GPU_API=value             # value = opencl (default) or cuda or hip
    -D GPU_PREC=value            # precision setting
                                 # value = double or mixed (default) or single
-   -D OCL_TUNE=value            # hardware choice for GPU_API=opencl
-                                # generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
    -D GPU_ARCH=value            # primary GPU hardware choice for GPU_API=cuda
                                 # value = sm_XX, see below
                                 # default is sm_50
@@ -135,6 +133,8 @@ CMake build
                                 # value = yes (default) or no
    -D CUDA_MPS_SUPPORT=value    # enables some tweaks required to run with active nvidia-cuda-mps daemon
                                 # value = yes or no (default)
+   -D USE_STATIC_OPENCL_LOADER=value  # downloads/includes OpenCL ICD loader library, no local OpenCL headers/libs needed
+                                      # value = yes (default) or no
 
 :code:`GPU_ARCH` settings for different GPU hardware is as follows:
 
@@ -161,6 +161,12 @@ When building with CMake, you **must NOT** build the GPU library in ``lib/gpu``
 using the traditional build procedure. CMake will detect files generated by that
 process and will terminate with an error and a suggestion for how to remove them.
 
+If you are compiling for OpenCL, the default setting is to download, build, and
+link with a static OpenCL ICD loader library and standard OpenCL headers.  This
+way no local OpenCL development headers or library needs to be present and only
+OpenCL compatible drivers need to be installed to use OpenCL.  If this is not
+desired, you can set :code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
+
 If you are compiling with HIP, note that before running CMake you will have to
 set appropriate environment variables. Some variables such as
 :code:`HCC_AMDGPU_TARGET` or :code:`CUDA_PATH` are necessary for :code:`hipcc`
@@ -258,18 +264,18 @@ To build with this package, the KIM library with API v2 must be downloaded
 and built on your system. It must include the KIM models that you want to
 use with LAMMPS.
 
-If you would like to use the :doc:`kim_query <kim_commands>`
+If you would like to use the :doc:`kim query <kim_commands>`
 command, you also need to have libcurl installed with the matching
 development headers and the curl-config tool.
 
-If you would like to use the :doc:`kim_property <kim_commands>`
+If you would like to use the :doc:`kim property <kim_commands>`
 command, you need 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. After successfully building LAMMPS with Python, you
-also need to install the kim-property Python package, 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:
+also need to install the ``kim-property`` Python package, 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>`_.
 
 In addition to installing the KIM API, it is also necessary to install the
@@ -309,7 +315,7 @@ minutes to hours) to build.  Of course you only need to do that once.)
 
       You can download and build the KIM library manually if you prefer;
       follow the instructions in ``lib/kim/README``.  You can also do
-      this in one step from the lammps/src dir, using a command like
+      this in one step from the lammps/src directory, using a command like
       these, which simply invoke the ``lib/kim/Install.py`` script with
       the specified args.
 
@@ -329,7 +335,7 @@ minutes to hours) to build.  Of course you only need to do that once.)
 
       .. code-block:: make
 
-         LMP_INC =       -DLMP_NO_SSL_CHECK
+         LMP_INC = -DLMP_NO_SSL_CHECK
 
 Debugging OpenKIM web queries in LAMMPS
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -377,10 +383,11 @@ Enabling the extra unit tests have some requirements,
   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.
+  ``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``,
+  ``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``, and
+  ``LennardJones612_UniversalShifted__MO_959249795837_003`` 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
+  to learn how to install a pre-built 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.

doc/src/Build_link.rst

@@ -20,16 +20,8 @@ the suffix ``.so.0`` (or some other number).
 .. note::
 
    Care should be taken to use the same MPI library for the calling code
-   and the LAMMPS library.  The ``library.h`` file includes ``mpi.h``
-   and uses definitions from it so those need to be available and
-   consistent.  When LAMMPS is compiled with the included STUBS MPI
-   library, then its ``mpi.h`` file needs to be included.  While it is
-   technically possible to use a full MPI library in the calling code
-   and link to a serial LAMMPS library compiled with MPI STUBS, it is
-   recommended to use the *same* MPI library for both, and then use
-   ``MPI_Comm_split()`` in the calling code to pass a suitable
-   communicator with a subset of MPI ranks to the function creating the
-   LAMMPS instance.
+   and the LAMMPS library unless LAMMPS is to be compiled without (real)
+   MPI support using the include STUBS MPI library.
 
 Link with LAMMPS as a static library
 ------------------------------------
@@ -110,7 +102,7 @@ executable, that are also required to link the LAMMPS executable.
 
       .. code-block:: bash
 
-         gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
+         gcc -c -O -I${HOME}/lammps/src -caller.c
          g++ -o caller caller.o -L${HOME}/lammps/lib/poems \
                       -L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src \
                       -llammps_serial -lpoems -lmpi_stubs
@@ -174,7 +166,7 @@ the POEMS package installed becomes:
 
       .. code-block:: bash
 
-         gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
+         gcc -c -O -I${HOME}/lammps/src -caller.c
          g++ -o caller caller.o -L${HOME}/lammps/src -llammps_serial
 
 Locating liblammps.so at runtime

doc/src/Build_manual.rst

@@ -74,7 +74,11 @@ For the documentation build a python virtual environment is set up in
 the folder ``doc/docenv`` and various python packages are installed into
 that virtual environment via the ``pip`` tool.  For rendering embedded
 LaTeX code also the `MathJax <https://www.mathjax.org/>`_ JavaScript
-engine needs to be downloaded.
+engine needs to be downloaded.  If you need to pass additional options
+to the pip commands to work (e.g. to use a web proxy or to point to
+additional SSL certificates) you can set them via the ``PIP_OPTIONS``
+environment variable or uncomment and edit the ``PIP_OPTIONS`` setting
+at beginning of the makefile.
 
 The actual translation is then done via ``make`` commands in the doc
 folder.  The following ``make`` commands are available:
@@ -108,7 +112,10 @@ installation of the HTML manual pages into the "install" step when
 installing LAMMPS after the CMake build via ``cmake --build . --target
 install``.  The documentation build is included in the default build
 target, but can also be requested independently with
-``cmake --build . --target doc``.
+``cmake --build . --target doc``.  If you need to pass additional options
+to the pip commands to work (e.g. to use a web proxy or to point to
+additional SSL certificates) you can set them via the ``PIP_OPTIONS``
+environment variable.
 
 .. code-block:: bash
 

doc/src/Commands_all.rst

@@ -60,11 +60,7 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`include <include>`
    * :doc:`info <info>`
    * :doc:`jump <jump>`
-   * :doc:`kim_init <kim_commands>`
-   * :doc:`kim_interactions <kim_commands>`
-   * :doc:`kim_param <kim_commands>`
-   * :doc:`kim_property <kim_commands>`
-   * :doc:`kim_query <kim_commands>`
+   * :doc:`kim <kim_commands>`
    * :doc:`kspace_modify <kspace_modify>`
    * :doc:`kspace_style <kspace_style>`
    * :doc:`label <label>`

doc/src/Commands_fix.rst

@@ -114,7 +114,7 @@ OPT.
    * :doc:`nph/eff <fix_nh_eff>`
    * :doc:`nph/sphere (o) <fix_nph_sphere>`
    * :doc:`nphug <fix_nphug>`
-   * :doc:`npt (iko) <fix_nh>`
+   * :doc:`npt (giko) <fix_nh>`
    * :doc:`npt/asphere (o) <fix_npt_asphere>`
    * :doc:`npt/body <fix_npt_body>`
    * :doc:`npt/cauchy <fix_npt_cauchy>`
@@ -122,8 +122,8 @@ OPT.
    * :doc:`npt/sphere (o) <fix_npt_sphere>`
    * :doc:`npt/uef <fix_nh_uef>`
    * :doc:`numdiff <fix_numdiff>`
-   * :doc:`nve (iko) <fix_nve>`
-   * :doc:`nve/asphere (i) <fix_nve_asphere>`
+   * :doc:`nve (giko) <fix_nve>`
+   * :doc:`nve/asphere (gi) <fix_nve_asphere>`
    * :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>`
    * :doc:`nve/awpmd <fix_nve_awpmd>`
    * :doc:`nve/body <fix_nve_body>`
@@ -138,7 +138,7 @@ OPT.
    * :doc:`nve/spin <fix_nve_spin>`
    * :doc:`nve/tri <fix_nve_tri>`
    * :doc:`nvk <fix_nvk>`
-   * :doc:`nvt (iko) <fix_nh>`
+   * :doc:`nvt (giko) <fix_nh>`
    * :doc:`nvt/asphere (o) <fix_nvt_asphere>`
    * :doc:`nvt/body <fix_nvt_body>`
    * :doc:`nvt/eff <fix_nh_eff>`

doc/src/Commands_pair.rst

@@ -122,7 +122,7 @@ OPT.
    * :doc:`lebedeva/z <pair_lebedeva_z>`
    * :doc:`lennard/mdf <pair_mdf>`
    * :doc:`line/lj <pair_line_lj>`
-   * :doc:`lj/charmm/coul/charmm (iko) <pair_charmm>`
+   * :doc:`lj/charmm/coul/charmm (giko) <pair_charmm>`
    * :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`
    * :doc:`lj/charmm/coul/long (gikot) <pair_charmm>`
    * :doc:`lj/charmm/coul/long/soft (o) <pair_fep_soft>`
@@ -163,6 +163,7 @@ OPT.
    * :doc:`lj/long/dipole/long <pair_dipole>`
    * :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
    * :doc:`lj/mdf <pair_mdf>`
+   * :doc:`lj/relres (o) <pair_lj_relres>`
    * :doc:`lj/sdk (gko) <pair_sdk>`
    * :doc:`lj/sdk/coul/long (go) <pair_sdk>`
    * :doc:`lj/sdk/coul/msm (o) <pair_sdk>`

doc/src/Developer_utils.rst

@@ -104,6 +104,9 @@ and parsing files or arguments.
 .. doxygenfunction:: strmatch
    :project: progguide
 
+.. doxygenfunction:: strfind
+   :project: progguide
+
 .. doxygenfunction:: is_integer
    :project: progguide
 

doc/src/Howto_cmake.rst

@@ -296,6 +296,8 @@ Some common CMake variables
      - Description
    * - ``CMAKE_INSTALL_PREFIX``
      - root directory of install location for ``make install``  (default: ``$HOME/.local``)
+   * - ``LAMMPS_INSTALL_RPATH``
+     - set or remove runtime path setting from binaries for ``make install`` (default: ``off``)
    * - ``CMAKE_BUILD_TYPE``
      - controls compilation options:
        one of ``RelWithDebInfo`` (default), ``Release``, ``Debug``, ``MinSizeRel``

doc/src/Install_tarball.rst

@@ -33,22 +33,19 @@ in its name, e.g. lammps-23Jun18.
 
 ----------
 
-You can also download a zip file via the "Clone or download" button on
-the `LAMMPS GitHub site <git_>`_.  The file name will be lammps-master.zip
-which can be unzipped with the following command, to create
-a lammps-master dir:
+You can also download a compressed tar or zip archives from the
+"Assets" sections of the `LAMMPS GitHub releases site <git_>`_.
+The file name will be lammps-<version>.zip which can be unzipped
+with the following command, to create a lammps-<version> dir:
 
 .. code-block:: bash
 
    $ unzip lammps*.zip
 
-This version is the most up-to-date LAMMPS development version.  It
-will have the date of the most recent patch release (see the file
-src/version.h).  But it will also include any new bug-fixes or
-features added since the last patch release.  They will be included in
-the next patch release tarball.
+This version corresponds to the selected LAMMPS patch or stable
+release.
 
-.. _git: https://github.com/lammps/lammps
+.. _git: https://github.com/lammps/lammps/releases
 
 ----------
 

doc/src/Intro_features.rst

@@ -85,7 +85,7 @@ commands)
 * water potentials: TIP3P, TIP4P, SPC
 * implicit solvent potentials: hydrodynamic lubrication, Debye
 * force-field compatibility with common CHARMM, AMBER, DREIDING,     OPLS, GROMACS, COMPASS options
-* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via     :doc:`kim_init, kim_interactions, and kim_query <kim_commands>` commands
+* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via     :doc:`kim command <kim_commands>`
 * hybrid potentials: multiple pair, bond, angle, dihedral, improper     potentials can be used in one simulation
 * overlaid potentials: superposition of multiple pair potentials
 

doc/src/Packages_details.rst

@@ -367,17 +367,19 @@ KIM package
 
 **Contents:**
 
-This package contains a set of commands that serve as a wrapper on the
+This package contains a command with a set of sub-commands that serve as a
+wrapper on the
 `Open Knowledgebase of Interatomic Models (OpenKIM) <https://openkim.org>`_
 repository of interatomic models (IMs) enabling compatible ones to be used in
 LAMMPS simulations.
 
-This includes :doc:`kim_init <kim_commands>`, and
-:doc:`kim_interactions <kim_commands>` commands to select, initialize and
-instantiate the IM, a :doc:`kim_query <kim_commands>` command to perform web
+
+This includes :doc:`kim init <kim_commands>`, and
+:doc:`kim interactions <kim_commands>` commands to select, initialize and
+instantiate the IM, a :doc:`kim query <kim_commands>` command to perform web
 queries for material property predictions of OpenKIM IMs, a
-:doc:`kim_param <kim_commands>` command to access KIM Model Parameters from
-LAMMPS, and a :doc:`kim_property <kim_commands>` command to write material
+:doc:`kim param <kim_commands>` command to access KIM Model Parameters from
+LAMMPS, and a :doc:`kim property <kim_commands>` command to write material
 properties computed in LAMMPS to standard KIM property instance format.
 
 Support for KIM IMs that conform to the
@@ -386,8 +388,8 @@ is provided by the :doc:`pair_style kim <pair_kim>` command.
 
 .. note::
 
-   The command *pair_style kim* is called by *kim_interactions* and
-   is not recommended to be directly used in input scripts.
+   The command *pair_style kim* is called by *kim interactions* and is not
+   recommended to be directly used in input scripts.
 
 To use this package you must have the KIM API library available on your
 system. The KIM API is available for download on the
@@ -404,7 +406,7 @@ and is funded by the `National Science Foundation <https://www.nsf.gov/>`_.
 API and the *pair_style kim* command. Yaser Afshar (U Minnesota),
 Axel Kohlmeyer (Temple U), Ellad Tadmor (U Minnesota), and
 Daniel Karls (U Minnesota) contributed to the
-:doc:`kim_commands <kim_commands>` interface in close collaboration with
+:doc:`kim command <kim_commands>` interface in close collaboration with
 Ryan Elliott.
 
 **Install:**
@@ -414,7 +416,7 @@ This package has :ref:`specific installation instructions <kim>` on the
 
 **Supporting info:**
 
-* :doc:`kim_commands <kim_commands>`
+* :doc:`kim command <kim_commands>`
 * :doc:`pair_style kim <pair_kim>`
 * src/KIM: filenames -> commands
 * src/KIM/README
@@ -1430,8 +1432,8 @@ oscillators as a model of polarization.  See the :doc:`Howto drude <Howto_drude>
 for an overview of how to use the package.  There are auxiliary tools
 for using this package in tools/drude.
 
-**Authors:** Alain Dequidt (U Blaise Pascal Clermont-Ferrand), Julien
-Devemy (CNRS), and Agilio Padua (U Blaise Pascal).
+**Authors:** Alain Dequidt (U Clermont Auvergne), Julien
+Devemy (CNRS), and Agilio Padua (ENS de Lyon).
 
 **Supporting info:**
 
@@ -1498,7 +1500,7 @@ methods for performing FEP simulations by using a :doc:`fix adapt/fep <fix_adapt
 which have a "soft" in their style name.  There are auxiliary tools
 for using this package in tools/fep; see its README file.
 
-**Author:** Agilio Padua (Universite Blaise Pascal Clermont-Ferrand)
+**Author:** Agilio Padua (ENS de Lyon)
 
 **Supporting info:**
 

doc/src/Python_atoms.rst

@@ -50,7 +50,7 @@ against invalid accesses.
 
       **Numpy Methods**:
 
-      * :py:meth:`numpy.extract_atom() <lammps.numpy_wrapper.extract_atom()>`: extract a per-atom quantity as numpy array
+      * :py:meth:`numpy.extract_atom() <lammps.numpy_wrapper.numpy_wrapper.extract_atom()>`: extract a per-atom quantity as numpy array
 
    .. tab:: PyLammps/IPyLammps API
 

doc/src/Python_formats.rst

@@ -0,0 +1,11 @@
+Output Readers
+==============
+
+.. py:module:: lammps.formats
+
+The Python package contains the :py:mod:`lammps.formats` module, which
+provides classes to post-process some of the output files generated by LAMMPS.
+
+.. automodule:: lammps.formats
+   :members:
+   :noindex:

doc/src/Python_head.rst

@@ -13,6 +13,7 @@ together.
    Python_module
    Python_ext
    Python_call
+   Python_formats
    Python_examples
    Python_error
    Python_trouble

doc/src/Python_module.rst

@@ -61,7 +61,7 @@ functions. Below is a detailed documentation of the API.
 .. autoclass:: lammps.lammps
    :members:
 
-.. autoclass:: lammps.numpy::numpy_wrapper
+.. autoclass:: lammps.numpy_wrapper::numpy_wrapper
    :members:
 
 ----------
@@ -134,8 +134,8 @@ 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() <lammps.numpy.numpy_wrapper.extract_compute>` and
-   :py:func:`lammps.numpy.extract_fix() <lammps.numpy.numpy_wrapper.extract_fix>`.
+   :py:func:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute>` and
+   :py:func:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix>`.
 
 .. _py_type_constants:
 
@@ -149,8 +149,8 @@ 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() <lammps.numpy.numpy_wrapper.extract_compute>` and
-   :py:func:`lammps.numpy.extract_fix() <lammps.numpy.numpy_wrapper.extract_fix>`.
+   :py:func:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute>` and
+   :py:func:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix>`.
 
 .. _py_vartype_constants:
 
@@ -170,6 +170,6 @@ Classes representing internal objects
    :members:
    :no-undoc-members:
 
-.. autoclass:: lammps.numpy::NumPyNeighList
+.. autoclass:: lammps.numpy_wrapper::NumPyNeighList
    :members:
    :no-undoc-members:

doc/src/Python_neighbor.rst

@@ -14,5 +14,5 @@ Neighbor list access
 
 **NumPy Methods:**
 
-* :py:meth:`lammps.numpy.get_neighlist() <lammps.numpy_wrapper.get_neighlist()>`: Get neighbor list for given index, which uses NumPy arrays for its element neighbor arrays
-* :py:meth:`lammps.numpy.get_neighlist_element_neighbors() <lammps.numpy_wrapper.get_neighlist_element_neighbors()>`: Get element in neighbor list and its neighbors (as numpy array)
+* :py:meth:`lammps.numpy.get_neighlist() <lammps.numpy_wrapper.numpy_wrapper.get_neighlist()>`: Get neighbor list for given index, which uses NumPy arrays for its element neighbor arrays
+* :py:meth:`lammps.numpy.get_neighlist_element_neighbors() <lammps.numpy_wrapper.numpy_wrapper.get_neighlist_element_neighbors()>`: Get element in neighbor list and its neighbors (as numpy array)

doc/src/Python_objects.rst

@@ -36,9 +36,9 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module.
       Python subscripting. The values will be zero for atoms not in the
       specified group.
 
-      :py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.extract_compute()>`,
-      :py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.extract_fix()>`, and
-      :py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.extract_variable()>` are
+      :py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute()>`,
+      :py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix()>`, and
+      :py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.numpy_wrapper.extract_variable()>` are
       equivalent NumPy implementations that return NumPy arrays instead of ``ctypes`` pointers.
 
       The :py:meth:`lammps.set_variable() <lammps.lammps.set_variable()>` method sets an
@@ -54,9 +54,9 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module.
 
       **NumPy Methods**:
 
-      * :py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.extract_compute()>`: extract value(s) from a compute, return arrays as numpy arrays
-      * :py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.extract_fix()>`: extract value(s) from a fix, return arrays as numpy arrays
-      * :py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.extract_variable()>`: extract value(s) from a variable, return arrays as numpy arrays
+      * :py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute()>`: extract value(s) from a compute, return arrays as numpy arrays
+      * :py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix()>`: extract value(s) from a fix, return arrays as numpy arrays
+      * :py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.numpy_wrapper.extract_variable()>`: extract value(s) from a variable, return arrays as numpy arrays
 
 
    .. tab:: PyLammps/IPyLammps API

doc/src/Speed_gpu.rst

@@ -1,11 +1,14 @@
 GPU package
 ===========
 
-The GPU package was developed by Mike Brown while at SNL and ORNL
-and his collaborators, particularly Trung Nguyen (now at Northwestern).
-It provides GPU versions of many pair styles and for parts of the
-:doc:`kspace_style pppm <kspace_style>` for long-range Coulombics.
-It has the following general features:
+The GPU package was developed by Mike Brown while at SNL and ORNL (now
+at Intel Corp.) and his collaborators, particularly Trung Nguyen (now at
+Northwestern).  Support for AMD GPUs via HIP was added by Vsevolod Nikolskiy
+and coworkers at HSE University.
+
+The GPU package provides GPU versions of many pair styles and for
+parts of the :doc:`kspace_style pppm <kspace_style>` for long-range
+Coulombics.  It has the following general features:
 
 * It is designed to exploit common GPU hardware configurations where one
   or more GPUs are coupled to many cores of one or more multi-core CPUs,
@@ -24,8 +27,9 @@ It has the following general features:
   force vectors.
 * LAMMPS-specific code is in the GPU package.  It makes calls to a
   generic GPU library in the lib/gpu directory.  This library provides
-  NVIDIA support as well as more general OpenCL support, so that the
-  same functionality is supported on a variety of hardware.
+  either Nvidia support, AMD support, or more general OpenCL support
+  (for Nvidia GPUs, AMD GPUs, Intel GPUs, and multi-core CPUs).
+  so that the same functionality is supported on a variety of hardware.
 
 **Required hardware/software:**
 
@@ -45,12 +49,23 @@ to have the OpenCL headers and the (vendor neutral) OpenCL library installed.
 In OpenCL mode, the acceleration depends on having an `OpenCL Installable Client Driver (ICD) <https://www.khronos.org/news/permalink/opencl-installable-client-driver-icd-loader>`_
 installed. There can be multiple of them for the same or different hardware
 (GPUs, CPUs, Accelerators) installed at the same time. OpenCL refers to those
-as 'platforms'.  The GPU library will select the **first** suitable platform,
-but this can be overridden using the device option of the :doc:`package <package>`
+as 'platforms'.  The GPU library will try to auto-select the best suitable platform,
+but this can be overridden using the platform option of the :doc:`package <package>`
 command. run lammps/lib/gpu/ocl_get_devices to get a list of available
 platforms and devices with a suitable ICD available.
 
-To compute and use this package in HIP mode, you have to have the AMD ROCm
+To compile and use this package for Intel GPUs, OpenCL or the Intel oneAPI
+HPC Toolkit can be installed using linux package managers. The latter also
+provides optimized C++, MPI, and many other libraries and tools. See:
+
+* https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit/download.html
+
+If you do not have a discrete GPU card installed, this package can still provide
+significant speedups on some CPUs that include integrated GPUs. Additionally, for
+many macs, OpenCL is already included with the OS and Makefiles are available
+in the lib/gpu directory.
+
+To compile and use this package in HIP mode, you have to have the AMD ROCm
 software installed. Versions of ROCm older than 3.5 are currently deprecated
 by AMD.
 
@@ -75,10 +90,20 @@ automatically if you create more MPI tasks/node than there are
 GPUs/mode.  E.g. with 8 MPI tasks/node and 2 GPUs, each GPU will be
 shared by 4 MPI tasks.
 
+The GPU package also has limited support for OpenMP for both
+multi-threading and vectorization of routines that are run on the CPUs.
+This requires that the GPU library and LAMMPS are built with flags to
+enable OpenMP support (e.g. -fopenmp). Some styles for time integration
+are also available in the GPU package. These run completely on the CPUs
+in full double precision, but exploit multi-threading and vectorization
+for faster performance.
+
 Use the "-sf gpu" :doc:`command-line switch <Run_options>`, which will
 automatically append "gpu" to styles that support it.  Use the "-pk
 gpu Ng" :doc:`command-line switch <Run_options>` to set Ng = # of
-GPUs/node to use.
+GPUs/node to use. If Ng is 0, the number is selected automatically as
+the number of matching GPUs that have the highest number of compute
+cores.
 
 .. code-block:: bash
 
@@ -87,8 +112,8 @@ GPUs/node to use.
    mpirun -np 48 -ppn 12 lmp_machine -sf gpu -pk gpu 2 -in in.script   # ditto on 4 16-core nodes
 
 Note that if the "-sf gpu" switch is used, it also issues a default
-:doc:`package gpu 1 <package>` command, which sets the number of
-GPUs/node to 1.
+:doc:`package gpu 0 <package>` command, which will result in
+automatic selection of the number of GPUs to use.
 
 Using the "-pk" switch explicitly allows for setting of the number of
 GPUs/node to use and additional options.  Its syntax is the same as
@@ -138,6 +163,13 @@ Likewise, you should experiment with the precision setting for the GPU
 library to see if single or mixed precision will give accurate
 results, since they will typically be faster.
 
+MPI parallelism typically outperforms OpenMP parallelism, but in some
+cases using fewer MPI tasks and multiple OpenMP threads with the GPU
+package can give better performance. 3-body potentials can often perform
+better with multiple OMP threads because the inter-process communication
+is higher for these styles with the GPU package in order to allow
+deterministic results.
+
 **Guidelines for best performance:**
 
 * Using multiple MPI tasks per GPU will often give the best performance,
@@ -161,6 +193,12 @@ results, since they will typically be faster.
   :doc:`angle <angle_style>`, :doc:`dihedral <dihedral_style>`,
   :doc:`improper <improper_style>`, and :doc:`long-range <kspace_style>`
   calculations will not be included in the "Pair" time.
+* Since only part of the pppm kspace style is GPU accelerated, it
+  may be faster to only use GPU acceleration for Pair styles with
+  long-range electrostatics.  See the "pair/only" keyword of the
+  package command for a shortcut to do that.  The work between kspace
+  on the CPU and non-bonded interactions on the GPU can be balanced
+  through adjusting the coulomb cutoff without loss of accuracy.
 * When the *mode* setting for the package gpu command is force/neigh,
   the time for neighbor list calculations on the GPU will be added into
   the "Pair" time, not the "Neigh" time.  An additional breakdown of the

doc/src/Speed_packages.rst

@@ -16,7 +16,7 @@ These are the accelerator packages currently in LAMMPS, either as
 standard or user packages:
 
 +-----------------------------------------+-------------------------------------------------------+
-| :doc:`GPU Package <Speed_gpu>`          | for NVIDIA GPUs as well as OpenCL support             |
+| :doc:`GPU Package <Speed_gpu>`          | for GPUs via CUDA, OpenCL, or ROCm HIP                |
 +-----------------------------------------+-------------------------------------------------------+
 | :doc:`USER-INTEL Package <Speed_intel>` | for Intel CPUs and Intel Xeon Phi                     |
 +-----------------------------------------+-------------------------------------------------------+
@@ -43,7 +43,7 @@ three kinds of hardware, via the listed packages:
 +-----------------+-----------------------------------------------------------------------------------------------------------------------------+
 | Many-core CPUs  | :doc:`USER-INTEL <Speed_intel>`, :doc:`KOKKOS <Speed_kokkos>`, :doc:`USER-OMP <Speed_omp>`, :doc:`OPT <Speed_opt>` packages |
 +-----------------+-----------------------------------------------------------------------------------------------------------------------------+
-| NVIDIA/AMD GPUs | :doc:`GPU <Speed_gpu>`, :doc:`KOKKOS <Speed_kokkos>` packages                                                               |
+| GPUs            | :doc:`GPU <Speed_gpu>`, :doc:`KOKKOS <Speed_kokkos>` packages                                                               |
 +-----------------+-----------------------------------------------------------------------------------------------------------------------------+
 | Intel Phi/AVX   | :doc:`USER-INTEL <Speed_intel>`, :doc:`KOKKOS <Speed_kokkos>` packages                                                      |
 +-----------------+-----------------------------------------------------------------------------------------------------------------------------+
@@ -154,8 +154,8 @@ Here is a brief summary of what the various packages provide.  Details
 are in the individual accelerator sections.
 
 * Styles with a "gpu" suffix are part of the GPU package and can be run
-  on NVIDIA or AMD GPUs.  The speed-up on a GPU depends on a variety of
-  factors, discussed in the accelerator sections.
+  on Intel, NVIDIA, or AMD GPUs.  The speed-up on a GPU depends on a
+  variety of factors, discussed in the accelerator sections.
 * Styles with an "intel" suffix are part of the USER-INTEL
   package. These styles support vectorized single and mixed precision
   calculations, in addition to full double precision.  In extreme cases,

doc/src/Tools.rst

@@ -267,7 +267,7 @@ data file in the required format.
 See the header of the polarizer.py file for details.
 
 The tool is authored by Agilio Padua and Alain Dequidt: agilio.padua
-at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr
+at ens-lyon.fr, alain.dequidt at uca.fr
 
 ----------
 
@@ -341,8 +341,7 @@ The tools/fep directory contains Python scripts useful for
 post-processing results from performing free-energy perturbation
 simulations using the USER-FEP package.
 
-The scripts were contributed by Agilio Padua (Universite Blaise
-Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr.
+The scripts were contributed by Agilio Padua (ENS de Lyon), agilio.padua at ens-lyon.fr.
 
 See README file in the tools/fep directory.
 

doc/src/compute_fep.rst

@@ -163,7 +163,7 @@ the meaning of these parameters:
 +------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`born <pair_born>`                                                      | a,b,c                   | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
-| :doc:`buck <pair_buck>`                                                      | a,c                     | type pairs |
+| :doc:`buck, buck/coul/cut, buck/coul/long, buck/coul/msm  <pair_buck>`       | a,c                     | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`buck/mdf <pair_mdf>`                                                   | a,c                     | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+

doc/src/compute_temp_chunk.rst

@@ -153,7 +153,7 @@ temp/chunk calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>
 
    compute cc1 all chunk/atom molecule
    compute myChunk all temp/chunk cc1 temp
-   fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
+   fix 1 all ave/time 100 1 100 c_myChunk[1] file tmp.out mode vector
 
 ----------
 

doc/src/create_box.rst

@@ -13,7 +13,7 @@ Syntax
 * N = # of atom types to use in this simulation
 * region-ID = ID of region to use as simulation domain
 * zero or more keyword/value pairs may be appended
-* keyword = *bond/types* or *angle/types* or *dihedral/types* or *improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom*
+* keyword = *bond/types* or *angle/types* or *dihedral/types* or *improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* or *extra/special/per/atom*
 
   .. parsed-literal::
 

doc/src/fix_adapt.rst

@@ -128,9 +128,9 @@ formulas for the meaning of these parameters:
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`born/coul/long, born/coul/msm <pair_born>`                             | coulombic_cutoff                                 | type global |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
-| :doc:`buck <pair_buck>`                                                      | a,c                                              | type pairs  |
+| :doc:`buck, buck/coul/cut  <pair_buck>`                                      | a,c                                              | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
-| :doc:`buck/coul/long, buck/coul/msm <pair_buck>`                             | coulombic_cutoff                                 | type global |
+| :doc:`buck/coul/long, buck/coul/msm <pair_buck>`                             | a,c,coulombic_cutoff                             | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`buck/mdf <pair_mdf>`                                                   | a,c                                              | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+

doc/src/fix_adapt_fep.rst

@@ -120,7 +120,7 @@ styles and their energy formulas for the meaning of these parameters:
 +------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`born <pair_born>`                                                      | a,b,c                   | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
-| :doc:`buck <pair_buck>`                                                      | a,c                     | type pairs |
+| :doc:`buck, buck/coul/cut, buck/coul/long, buck/coul/msm  <pair_buck>`       | a,c                     | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`buck/mdf <pair_mdf>`                                                   | a,c                     | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+

doc/src/fix_nh.rst

@@ -1,8 +1,10 @@
 .. index:: fix nvt
+.. index:: fix nvt/gpu
 .. index:: fix nvt/intel
 .. index:: fix nvt/kk
 .. index:: fix nvt/omp
 .. index:: fix npt
+.. index:: fix npt/gpu
 .. index:: fix npt/intel
 .. index:: fix npt/kk
 .. index:: fix npt/omp
@@ -13,12 +15,12 @@
 fix nvt command
 ===============
 
-Accelerator Variants: *nvt/intel*, *nvt/kk*, *nvt/omp*
+Accelerator Variants: *nvt/gpu*, *nvt/intel*, *nvt/kk*, *nvt/omp*
 
 fix npt command
 ===============
 
-Accelerator Variants: *npt/intel*, *npt/kk*, *npt/omp*
+Accelerator Variants: *npt/gpu*, *npt/intel*, *npt/kk*, *npt/omp*
 
 fix nph command
 ===============

doc/src/fix_nve.rst

@@ -1,4 +1,5 @@
 .. index:: fix nve
+.. index:: fix nve/gpu
 .. index:: fix nve/intel
 .. index:: fix nve/kk
 .. index:: fix nve/omp
@@ -6,7 +7,7 @@
 fix nve command
 ===============
 
-Accelerator Variants: *nve/intel*, *nve/kk*, *nve/omp*
+Accelerator Variants: *nve/gpu*, *nve/intel*, *nve/kk*, *nve/omp*
 
 Syntax
 """"""

doc/src/fix_nve_asphere.rst

@@ -1,10 +1,11 @@
 .. index:: fix nve/asphere
+.. index:: fix nve/asphere/gpu
 .. index:: fix nve/asphere/intel
 
 fix nve/asphere command
 =======================
 
-Accelerator Variants: *nve/asphere/intel*
+Accelerator Variants: *nve/asphere/gpu*, *nve/asphere/intel*
 
 Syntax
 """"""

doc/src/fix_wall_body_polygon.rst

@@ -15,7 +15,7 @@ Syntax
 * k_n = normal repulsion strength (force/distance or pressure units)
 * c_n = normal damping coefficient (force/distance or pressure units)
 * c_t = tangential damping coefficient (force/distance or pressure units)
-* wallstyle = *xplane* or *yplane* or *zplane* or *zcylinder*
+* wallstyle = *xplane* or *yplane* or *zcylinder*
 * args = list of arguments for a particular style
 
   .. parsed-literal::

doc/src/fix_wall_gran.rst

@@ -199,11 +199,11 @@ the following table:
 |     1 | 1.0 if particle is in contact with wall,           |                |
 |       | 0.0 otherwise                                      |                |
 +-------+----------------------------------------------------+----------------+
-|     2 | Force :math:`f_x` exerted on the wall              | force units    |
+|     2 | Force :math:`f_x` exerted by the wall              | force units    |
 +-------+----------------------------------------------------+----------------+
-|     3 | Force :math:`f_y` exerted on the wall              | force units    |
+|     3 | Force :math:`f_y` exerted by the wall              | force units    |
 +-------+----------------------------------------------------+----------------+
-|     4 | Force :math:`f_z` exerted on the wall              | force units    |
+|     4 | Force :math:`f_z` exerted by the wall              | force units    |
 +-------+----------------------------------------------------+----------------+
 |     5 | :math:`x`-coordinate of contact point on wall      | distance units |
 +-------+----------------------------------------------------+----------------+

doc/src/fix_wall_gran_region.rst

@@ -240,11 +240,11 @@ the following table:
 |     1 | 1.0 if particle is in contact with wall,           |                |
 |       | 0.0 otherwise                                      |                |
 +-------+----------------------------------------------------+----------------+
-|     2 | Force :math:`f_x` exerted on the wall              | force units    |
+|     2 | Force :math:`f_x` exerted by the wall              | force units    |
 +-------+----------------------------------------------------+----------------+
-|     3 | Force :math:`f_y` exerted on the wall              | force units    |
+|     3 | Force :math:`f_y` exerted by the wall              | force units    |
 +-------+----------------------------------------------------+----------------+
-|     4 | Force :math:`f_z` exerted on the wall              | force units    |
+|     4 | Force :math:`f_z` exerted by the wall              | force units    |
 +-------+----------------------------------------------------+----------------+
 |     5 | :math:`x`-coordinate of contact point on wall      | distance units |
 +-------+----------------------------------------------------+----------------+

doc/src/package.rst

@@ -18,7 +18,7 @@ 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 *pair/only* 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 *blocksize* or *platform* or *device_type* or *ocl_args*
            *neigh* value = *yes* or *no*
              yes = neighbor list build on GPU (default)
              no = neighbor list build on CPU
@@ -32,17 +32,20 @@ Syntax
              size = bin size for neighbor list construction (distance units)
            *split* = fraction
              fraction = fraction of atoms assigned to GPU (default = 1.0)
-           *gpuID* values = first last
-             first = ID of first GPU to be used on each node
-             last = ID of last GPU to be used on each node
-           *tpa* value = Nthreads
-             Nthreads = # of GPU threads used per atom
-           *device* value = device_type or platform_id:device_type or platform_id:custom,val1,val2,val3,..,val13
-             platform_id = numerical OpenCL platform id (default: -1)
-             device_type = *kepler* or *fermi* or *cypress* or *intel* or *phi* or *generic* or *custom*
-             val1,val2,... = custom OpenCL tune parameters (see below for details)
+           *tpa* value = Nlanes
+             Nlanes = # of GPU vector lanes (CUDA threads) used per atom
            *blocksize* value = size
              size = thread block size for pair force computation
+           *omp* value = Nthreads
+             Nthreads = number of OpenMP threads to use on CPU (default = 0)
+           *platform* value = id
+             id = For OpenCL, platform ID for the GPU or accelerator
+           *gpuID* values = id
+             id = ID of first GPU to be used on each node
+           *device_type* value = *intelgpu* or *nvidiagpu* or *amdgpu* or *applegpu* or *generic* or *custom,val1,val2,...*
+             val1,val2,... = custom OpenCL accelerator configuration parameters (see below for details)
+           *ocl_args* value = args
+             args = List of additional OpenCL compiler arguments delimited by colons
        *intel* args = NPhi keyword value ...
          Nphi = # of co-processors per node
          zero or more keyword/value pairs may be appended
@@ -100,7 +103,7 @@ Syntax
              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
+         Nthreads = # of OpenMP threads to associate with each MPI process
          zero or more keyword/value pairs may be appended
          keywords = *neigh*
            *neigh* value = *yes* or *no*
@@ -112,12 +115,10 @@ Examples
 
 .. code-block:: LAMMPS
 
-   package gpu 1
+   package gpu 0
    package gpu 1 split 0.75
    package gpu 2 split -1.0
-   package gpu 1 device kepler
-   package gpu 1 device 2:generic
-   package gpu 1 device custom,32,4,8,256,11,128,256,128,32,64,8,128,128
+   package gpu 0 omp 2 device_type intelgpu
    package kokkos neigh half comm device
    package omp 0 neigh no
    package omp 4
@@ -174,10 +175,18 @@ simulations.
 The *gpu* style invokes settings associated with the use of the GPU
 package.
 
-The *Ngpu* argument sets the number of GPUs per node.  There must be
-at least as many MPI tasks per node as GPUs, as set by the mpirun or
-mpiexec command.  If there are more MPI tasks (per node)
-than GPUs, multiple MPI tasks will share each GPU.
+The *Ngpu* argument sets the number of GPUs per node. If *Ngpu* is 0
+and no other keywords are specified, GPU or accelerator devices are
+auto-selected. In this process, all platforms are searched for
+accelerator devices and GPUs are chosen if available. The device with
+the highest number of compute cores is selected. The number of devices
+is increased to be the number of matching accelerators with the same
+number of compute cores. If there are more devices than MPI tasks,
+the additional devices will be unused. The auto-selection of GPUs/
+accelerator devices and platforms can be restricted by specifying
+a non-zero value for *Ngpu* and / or using the *gpuID*, *platform*,
+and *device_type* keywords as described below. If there are more MPI
+tasks (per node) than GPUs, multiple MPI tasks will share each GPU.
 
 Optional keyword/value pairs can also be specified.  Each has a
 default value as listed below.
@@ -212,18 +221,8 @@ 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
-pairwise cutoff + neighbor skin distance.  This is 2x larger than the
-LAMMPS default used for neighbor list building on the CPU.  This will
-be close to optimal for the GPU, so you do not normally need to use
-this keyword.  Note that if you use a longer-than-usual pairwise
-cutoff, e.g. to allow for a smaller fraction of KSpace work with a
-:doc:`long-range Coulombic solver <kspace_style>` because the GPU is
-faster at performing pairwise interactions, then it may be optimal to
-make the *binsize* smaller than the default.  For example, with a
-cutoff of 20\*sigma in LJ :doc:`units <units>` and a neighbor skin
-distance of sigma, a *binsize* = 5.25\*sigma can be more efficient than
-the default.
+If *binsize* is set to 0.0 (the default), then the binsize is set
+automatically using heuristics in the GPU package.
 
 The *split* keyword can be used for load balancing force calculations
 between CPU and GPU cores in GPU-enabled pair styles. If 0 < *split* <
@@ -257,63 +256,79 @@ cores would perform force calculations for some fraction of the
 particles at the same time the GPUs performed force calculation for
 the other particles.
 
-The *gpuID* keyword allows selection of which GPUs on each node will
-be used for a simulation.  The *first* and *last* values specify the
-GPU IDs to use (from 0 to Ngpu-1).  By default, first = 0 and last =
-Ngpu-1, so that all GPUs are used, assuming Ngpu is set to the number
-of physical GPUs.  If you only wish to use a subset, set Ngpu to a
-smaller number and first/last to a sub-range of the available GPUs.
+The *gpuID* keyword is used to specify the first ID for the GPU or
+other accelerator that LAMMPS will use. For example, if the ID is
+1 and *Ngpu* is 3, GPUs 1-3 will be used. Device IDs should be
+determined from the output of nvc_get_devices, ocl_get_devices,
+or hip_get_devices
+as provided in the lib/gpu directory. When using OpenCL with
+accelerators that have main memory NUMA, the accelerators can be
+split into smaller virtual accelerators for more efficient use
+with MPI.
 
-The *tpa* keyword sets the number of GPU thread per atom used to
+The *tpa* keyword sets the number of GPU vector lanes per atom used to
 perform force calculations.  With a default value of 1, the number of
-threads will be chosen based on the pair style, however, the value can
+lanes will be chosen based on the pair style, however, the value can
 be set explicitly with this keyword to fine-tune performance.  For
 large cutoffs or with a small number of particles per GPU, increasing
-the value can improve performance. The number of threads per atom must
-be a power of 2 and currently cannot be greater than 32.
-
-The *device* keyword can be used to tune parameters optimized for a
-specific accelerator and platform when using OpenCL. OpenCL supports
-the concept of a **platform**\ , which represents one or more devices that
-share the same driver (e.g. there would be a different platform for
-GPUs from different vendors or for CPU based accelerator support).
-In LAMMPS only one platform can be active at a time and by default
-the first platform with an accelerator is selected. This is equivalent
-to using a platform ID of -1. The platform ID is a number corresponding
-to the output of the ocl_get_devices tool. The platform ID is passed
-to the GPU library, by prefixing the *device* keyword with that number
-separated by a colon. For CUDA, the *device* keyword is ignored.
-Currently, the device tuning support is limited to NVIDIA Kepler, NVIDIA
-Fermi, AMD Cypress, Intel x86_64 CPU, Intel Xeon Phi, or a generic device.
-More devices may be added later.  The default device type can be
-specified when building LAMMPS with the GPU library, via setting a
-variable in the lib/gpu/Makefile that is used.
-
-In addition, a device type *custom* is available, which is followed by
-13 comma separated numbers, which allows to set those tweakable parameters
-from the package command. It can be combined with the (colon separated)
-platform id. The individual settings are:
-
-* MEM_THREADS
-* THREADS_PER_ATOM
-* THREADS_PER_CHARGE
-* BLOCK_PAIR
-* MAX_SHARED_TYPES
-* BLOCK_NBOR_BUILD
-* BLOCK_BIO_PAIR
-* BLOCK_ELLIPSE
-* WARP_SIZE
-* PPPM_BLOCK_1D
-* BLOCK_CELL_2D
-* BLOCK_CELL_ID
-* MAX_BIO_SHARED_TYPES
+the value can improve performance. The number of lanes per atom must
+be a power of 2 and currently cannot be greater than the SIMD width
+for the GPU / accelerator. In the case it exceeds the SIMD width, it
+will automatically be decreased to meet the restriction.
 
 The *blocksize* keyword allows you to tweak the number of threads used
 per thread block. This number should be a multiple of 32 (for GPUs)
 and its maximum depends on the specific GPU hardware. Typical choices
 are 64, 128, or 256. A larger block size increases occupancy of
 individual GPU cores, but reduces the total number of thread blocks,
-thus may lead to load imbalance.
+thus may lead to load imbalance. On modern hardware, the sensitivity
+to the blocksize is typically low.
+
+The *Nthreads* value for the *omp* keyword sets the number of OpenMP
+threads allocated for each MPI task. This setting controls OpenMP
+parallelism only for routines run on the CPUs. For more details on
+setting the number of OpenMP threads, see the discussion of the
+*Nthreads* setting on this doc page for the "package omp" command.
+The meaning of *Nthreads* is exactly the same for the GPU, USER-INTEL,
+and GPU packages.
+
+The *platform* keyword is only used with OpenCL to specify the ID for
+an OpenCL platform. See the output from ocl_get_devices in the lib/gpu
+directory. In LAMMPS only one platform can be active at a time and by
+default (id=-1) the platform is auto-selected to find the GPU with the
+most compute cores. When *Ngpu* or other keywords are specified, the
+auto-selection is appropriately restricted. For example, if *Ngpu* is
+3, only platforms with at least 3 accelerators are considered. Similar
+restrictions can be enforced by the *gpuID* and *device_type* keywords.
+
+The *device_type* keyword can be used for OpenCL to specify the type of
+GPU to use or specify a custom configuration for an accelerator. In most
+cases this selection will be automatic and there is no need to use the
+keyword. The *applegpu* type is not specific to a particular GPU vendor,
+but is separate due to the more restrictive Apple OpenCL implementation.
+For expert users, to specify a custom configuration, the *custom* keyword
+followed by the next parameters can be specified:
+
+CONFIG_ID, SIMD_SIZE, MEM_THREADS, SHUFFLE_AVAIL, FAST_MATH,
+THREADS_PER_ATOM, THREADS_PER_CHARGE, THREADS_PER_THREE, BLOCK_PAIR,
+BLOCK_BIO_PAIR, BLOCK_ELLIPSE, PPPM_BLOCK_1D, BLOCK_NBOR_BUILD,
+BLOCK_CELL_2D, BLOCK_CELL_ID, MAX_SHARED_TYPES, MAX_BIO_SHARED_TYPES,
+PPPM_MAX_SPLINE.
+
+CONFIG_ID can be 0. SHUFFLE_AVAIL in {0,1} indicates that inline-PTX
+(NVIDIA) or OpenCL extensions (Intel) should be used for horizontal
+vector operations. FAST_MATH in {0,1} indicates that OpenCL fast math
+optimizations are used during the build and hardware-accelerated
+transcendental functions are used when available. THREADS_PER_* give the
+default *tpa* values for ellipsoidal models, styles using charge, and
+any other styles. The BLOCK_* parameters specify the block sizes for
+various kernel calls and the MAX_*SHARED*_ parameters are used to
+determine the amount of local shared memory to use for storing model
+parameters.
+
+For OpenCL, the routines are compiled at runtime for the specified GPU
+or accelerator architecture. The *ocl_args* keyword can be used to
+specify additional flags for the runtime build.
 
 ----------
 
@@ -331,44 +346,13 @@ built with co-processor support.
 Optional keyword/value pairs can also be specified.  Each has a
 default value as listed below.
 
-The *omp* keyword determines the number of OpenMP threads allocated
-for each MPI task when any portion of the interactions computed by a
-USER-INTEL pair style are run on the CPU.  This can be the case even
-if LAMMPS was built with co-processor support; see the *balance*
-keyword discussion below.  If you are running with less MPI tasks/node
-than there are CPUs, it can be advantageous to use OpenMP threading on
-the CPUs.
-
-.. note::
-
-   The *omp* keyword has nothing to do with co-processor threads on
-   the Xeon Phi; see the *tpc* and *tptask* keywords below for a
-   discussion of co-processor threads.
-
-The *Nthread* value for the *omp* keyword sets the number of OpenMP
-threads allocated for each MPI task.  Setting *Nthread* = 0 (the
-default) instructs LAMMPS to use whatever value is the default for the
-given OpenMP environment. This is usually determined via the
-*OMP_NUM_THREADS* environment variable or the compiler runtime, which
-is usually a value of 1.
-
-For more details, including examples of how to set the OMP_NUM_THREADS
-environment variable, see the discussion of the *Nthreads* setting on
-this doc page for the "package omp" command.  Nthreads is a required
-argument for the USER-OMP package.  Its meaning is exactly the same
-for the USER-INTEL package.
-
-.. note::
-
-   If you build LAMMPS with both the USER-INTEL and USER-OMP
-   packages, be aware that both packages allow setting of the *Nthreads*
-   value via their package commands, but there is only a single global
-   *Nthreads* value used by OpenMP.  Thus if both package commands are
-   invoked, you should insure the two values are consistent.  If they are
-   not, the last one invoked will take precedence, for both packages.
-   Also note that if the :doc:`-sf hybrid intel omp command-line switch <Run_options>` is used, it invokes a "package intel"
-   command, followed by a "package omp" command, both with a setting of
-   *Nthreads* = 0.
+The *Nthreads* value for the *omp* keyword sets the number of OpenMP
+threads allocated for each MPI task. This setting controls OpenMP
+parallelism only for routines run on the CPUs. For more details on
+setting the number of OpenMP threads, see the discussion of the
+*Nthreads* setting on this doc page for the "package omp" command.
+The meaning of *Nthreads* is exactly the same for the GPU, USER-INTEL,
+and GPU packages.
 
 The *mode* keyword determines the precision mode to use for
 computing pair style forces, either on the CPU or on the co-processor,
@@ -574,7 +558,7 @@ result in better performance for certain configurations and system sizes.
 The *omp* style invokes settings associated with the use of the
 USER-OMP package.
 
-The *Nthread* argument sets the number of OpenMP threads allocated for
+The *Nthreads* argument sets the number of OpenMP threads allocated for
 each MPI task.  For example, if your system has nodes with dual
 quad-core processors, it has a total of 8 cores per node.  You could
 use two MPI tasks per node (e.g. using the -ppn option of the mpirun
@@ -583,7 +567,7 @@ This would use all 8 cores on each node.  Note that the product of MPI
 tasks \* threads/task should not exceed the physical number of cores
 (on a node), otherwise performance will suffer.
 
-Setting *Nthread* = 0 instructs LAMMPS to use whatever value is the
+Setting *Nthreads* = 0 instructs LAMMPS to use whatever value is the
 default for the given OpenMP environment. This is usually determined
 via the *OMP_NUM_THREADS* environment variable or the compiler
 runtime.  Note that in most cases the default for OpenMP capable
@@ -614,6 +598,24 @@ input.  Not all features of LAMMPS support OpenMP threading via the
 USER-OMP package and the parallel efficiency can be very different,
 too.
 
+.. note::
+
+   If you build LAMMPS with the GPU, USER-INTEL, and / or USER-OMP
+   packages, be aware these packages all allow setting of the *Nthreads*
+   value via their package commands, but there is only a single global
+   *Nthreads* value used by OpenMP.  Thus if multiple package commands are
+   invoked, you should insure the values are consistent.  If they are
+   not, the last one invoked will take precedence, for all packages.
+   Also note that if the :doc:`-sf hybrid intel omp command-line switch <Run_options>` is used, it invokes a "package intel" command, followed by a
+   "package omp" command, both with a setting of *Nthreads* = 0. Likewise
+   for a hybrid suffix for gpu and omp. Note that KOKKOS also supports
+   setting the number of OpenMP threads from the command line using the
+   "-k on" :doc:`command-line switch <Run_options>`. The default for
+   KOKKOS is 1 thread per MPI task, so any other number of threads should
+   be explicitly set using the "-k on" command-line switch (and this
+   setting should be consistent with settings from any other packages
+   used).
+
 Optional keyword/value pairs can also be specified.  Each has a
 default value as listed below.
 
@@ -658,9 +660,9 @@ Related commands
 Default
 """""""
 
-For the GPU package, the default is Ngpu = 1 and the option defaults
+For the GPU package, the default is Ngpu = 0 and the option defaults
 are neigh = yes, newton = off, binsize = 0.0, split = 1.0, gpuID = 0
-to Ngpu-1, tpa = 1, and device = not used.  These settings are made
+to Ngpu-1, tpa = 1, omp = 0, and platform=-1.  These settings are made
 automatically if the "-sf gpu" :doc:`command-line switch <Run_options>`
 is used.  If it is not used, you must invoke the package gpu command
 in your input script or via the "-pk gpu" :doc:`command-line switch <Run_options>`.

doc/src/pair_adp.rst

@@ -59,7 +59,7 @@ command to specify them.
 * The OpenKIM Project at
   `https://openkim.org/browse/models/by-type <https://openkim.org/browse/models/by-type>`_
   provides ADP potentials that can be used directly in LAMMPS with the
-  :doc:`kim_commands <kim_commands>` interface.
+  :doc:`kim command <kim_commands>` interface.
 
 ----------
 

doc/src/pair_charmm.rst

@@ -1,4 +1,5 @@
 .. index:: pair_style lj/charmm/coul/charmm
+.. index:: pair_style lj/charmm/coul/charmm/gpu
 .. index:: pair_style lj/charmm/coul/charmm/intel
 .. index:: pair_style lj/charmm/coul/charmm/kk
 .. index:: pair_style lj/charmm/coul/charmm/omp
@@ -19,7 +20,7 @@
 pair_style lj/charmm/coul/charmm command
 ========================================
 
-Accelerator Variants: *lj/charmm/coul/charmm/intel*, *lj/charmm/coul/charmm/kk*, *lj/charmm/coul/charmm/omp*
+Accelerator Variants: *lj/charmm/coul/charmm/gpu*, *lj/charmm/coul/charmm/intel*, *lj/charmm/coul/charmm/kk*, *lj/charmm/coul/charmm/omp*
 
 pair_style lj/charmm/coul/charmm/implicit command
 =================================================

doc/src/pair_eam.rst

@@ -141,7 +141,7 @@ interatomic potentials and file formats.
 The OpenKIM Project at
 `https://openkim.org/browse/models/by-type <https://openkim.org/browse/models/by-type>`_
 provides EAM potentials that can be used directly in LAMMPS with the
-:doc:`kim_commands <kim_commands>` interface.
+:doc:`kim command <kim_commands>` interface.
 
 ----------
 

doc/src/pair_kim.rst

@@ -23,29 +23,30 @@ Examples
 Description
 """""""""""
 
-This pair style is a wrapper on the `Open Knowledgebase of Interatomic Models (OpenKIM) <https://openkim.org>`_ repository of interatomic
-potentials to enable their use in LAMMPS scripts.
+This pair style is a wrapper on the
+`Open Knowledgebase of Interatomic Models (OpenKIM) <https://openkim.org>`_
+repository of interatomic potentials to enable their use in LAMMPS scripts.
 
 The preferred interface for using interatomic models archived in
-OpenKIM is the :doc:`kim_commands interface <kim_commands>`. That
+OpenKIM is the :doc:`kim command <kim_commands>` interface. That
 interface supports both "KIM Portable Models" (PMs) that conform to the
 KIM API Portable Model Interface (PMI) and can be used by any
 simulation code that conforms to the KIM API/PMI, and
-"KIM Simulator Models" that are natively implemented within a single
+"KIM Simulator Models" (SMs) that are natively implemented within a single
 simulation code (like LAMMPS) and can only be used with it.
 The *pair_style kim* command is limited to KIM PMs. It is
-used by the :doc:`kim_commands interface <kim_commands>` as needed.
+used by the :doc:`kim command <kim_commands>` interface as needed.
 
 .. note::
 
-   Since *pair_style kim* is called by *kim_interactions* as needed,
-   is not recommended to be directly used in input scripts.
+   Since *pair_style kim* is called by *kim interactions* as needed,
+   it is not recommended to be directly used in input scripts.
 
 ----------
 
 The argument *model* is the name of the KIM PM.
 For potentials archived in OpenKIM
-this is the extended KIM ID (see :doc:`kim_commands <kim_commands>`
+this is the extended KIM ID (see :doc:`kim command <kim_commands>`
 for details). LAMMPS can invoke any KIM PM, however there can
 be incompatibilities (for example due to unit matching issues).
 In the event of an incompatibility, the code will terminate with
@@ -106,7 +107,7 @@ Restrictions
 """"""""""""
 
 This pair style is part of the KIM package. See details on
-restrictions in :doc:`kim_commands <kim_commands>`.
+restrictions in :doc:`kim command <kim_commands>`.
 
 This current version of pair_style kim is compatible with the
 kim-api package version 2.0.0 and higher.
@@ -114,7 +115,7 @@ kim-api package version 2.0.0 and higher.
 Related commands
 """"""""""""""""
 
-:doc:`pair_coeff <pair_coeff>`, :doc:`kim_commands <kim_commands>`
+:doc:`pair_coeff <pair_coeff>`, :doc:`kim command <kim_commands>`
 
 Default
 """""""

doc/src/pair_lj_relres.rst

@@ -0,0 +1,291 @@
+.. index:: pair_style lj/relres
+.. index:: pair_style lj/relres/omp
+
+pair_style lj/relres command
+============================
+
+Accelerator Variants: *lj/relres/omp*
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style lj/relres Rsi Rso Rci Rco
+
+* Rsi = inner switching cutoff between the fine-grained and coarse-grained potentials (distance units)
+* Rso = outer switching cutoff between the fine-grained and coarse-grained potentials (distance units)
+* Rci = inner cutoff beyond which the force smoothing for all interactions is applied (distance units)
+* Rco = outer cutoff for all interactions (distance units)
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style lj/relres 4.0 5.0 8.0 10.0
+   pair_coeff 1 1 0.5 1.0 1.5 1.1
+   pair_coeff 2 2 0.5 1.0 0.0 0.0 3.0 3.5 6.0 7.0
+
+Description
+"""""""""""
+
+Pair style *lj/relres* computes a LJ interaction using the Relative
+Resolution (RelRes) framework which applies a fine-grained (FG)
+potential between near neighbors and a coarse-grained (CG) potential
+between far neighbors :ref:`(Chaimovich1) <Chaimovich1>`. This approach
+can improve the computational efficiency by almost an order of
+magnitude, while maintaining the correct static and dynamic behavior of
+a reference system :ref:`(Chaimovich2) <Chaimovich2>`.
+
+.. math::
+
+   E = \left\{\begin{array}{lr}
+        4 \epsilon^{\scriptscriptstyle FG} \left[ \left(\frac{\sigma^{FG}}{r}\right)^{12} - \left(\frac{\sigma^{FG}}{r}\right)^6 \right]-\Gamma_{si}, & \quad\mathrm{if}\quad  r< r_{si}, \\
+        \sum_{m=0}^{4} \gamma_{sm}\left(r-r_{si}\right)^m-\Gamma_{so} ,   & \quad\mathrm{if}\quad  r_{si}\leq r< r_{so}, \\
+        4 \epsilon^{\scriptscriptstyle CG} \left[ \left(\frac{\sigma^{CG}}{r}\right)^{12} -     \left(\frac{\sigma^{CG}}{r}\right)^6 \right]-\Gamma_c, &  \quad\mathrm{if}\quad  r_{so}\leq r<r_{ci}, \\
+        \sum_{m=0}^{4} \gamma_{cm}\left(r-r_{ci}\right)^m -\Gamma_c, & \quad\mathrm{if}\quad  r_{ci}\leq r< r_{co}, \\
+        0, & \quad\mathrm{if}\quad  r\geq r_{co}.\end{array}\right.
+
+The FG parameters of the LJ potential (:math:`\epsilon^{FG}` and
+:math:`\sigma^{FG}`) are applied up to the inner switching cutoff,
+:math:`r_{si}`, while the CG parameters of the LJ potential
+(:math:`\epsilon^{CG}` and :math:`\sigma^{CG}`) are applied beyond the
+outer switching cutoff, :math:`r_{so}`. Between :math:`r_{si}` and
+:math:`r_{so}` a polynomial smoothing function is applied so that the
+force and its derivative are continuous between the FG and CG
+potentials.  An analogous smoothing function is applied between the
+inner and outer cutoffs (:math:`r_{ci}` and :math:`r_{co}`).
+The offsets :math:`\Gamma_{si}`, :math:`\Gamma_{so}` and
+:math:`\Gamma_{c}` ensure the continuity of the energy over the entire
+domain.  The corresponding polynomial coefficients :math:`\gamma_{sm}`
+and :math:`\gamma_{cm}`, as well as the offsets are automatically
+computed by LAMMPS.
+
+.. note::
+
+   Energy and force resulting from this methodology can be plotted via the
+   :doc:`pair_write <pair_write>` command.
+
+The following coefficients must be defined for each pair of atom types
+via the :doc:`pair_coeff <pair_coeff>` command as in the examples above,
+or in the data file or restart files read by the :doc:`read_data
+<read_data>` or :doc:`read_restart <read_restart>` commands, or by
+mixing as will be described below:
+
+* :math:`\epsilon^{FG}` (energy units)
+* :math:`\sigma^{FG}` (distance units)
+* :math:`\epsilon^{CG}` (energy units)
+* :math:`\sigma^{CG}` (distance units)
+
+Additional parameters can be defined to specify different
+:math:`r_{si}`, :math:`r_{so}`, :math:`r_{ci}`, :math:`r_{co}` for
+a particular set of atom types:
+
+* :math:`r_{si}` (distance units)
+* :math:`r_{so}` (distance units)
+* :math:`r_{ci}` (distance units)
+* :math:`r_{co}` (distance units)
+
+These parameters are optional, and they are used to override the global
+cutoffs as defined in the pair_style command.  If not specified, the
+global values for :math:`r_{si}`, :math:`r_{so}`, :math:`r_{ci}`, and
+:math:`r_{co}` are used.  If this override option is employed, all four
+arguments must be specified.
+
+----------
+
+Here are some guidelines for using the pair_style *lj/relres* command.
+
+In general, RelRes focuses on the speedup of pairwise interactions between
+all LJ sites. Importantly, it works with any settings and flags (e.g.,
+:doc:`special_bonds <special_bonds>` settings and :doc:`newton <newton>`
+flags) that can be used in a molecular simulation with the
+conventional LJ potential. In particular, all intramolecular topology
+with its energetics (i.e., bonds, angles, etc.) remains unaltered.
+
+At the most basic level in the RelRes framework, all sites are mapped into
+clusters. Each cluster is just a collection of sites bonded together (the
+bonds themselves are not part of the cluster). In general, a molecule may
+be comprised of several clusters, and preferably, no two sites in a cluster
+are separated by more than two bonds. There are two categories of sites in
+RelRes: "hybrid" sites embody both FG and CG models, while "ordinary" sites
+embody just FG characteristics with no CG features. A given cluster has
+a single hybrid site (typically its central site) and several ordinary sites
+(typically its peripheral sites). Notice that while clusters are necessary
+for the RelRes parameterization (discussed below), they are not actually
+defined in LAMMPS. Besides, the total number of sites in the cluster are
+called the "mapping ratio", and this substantially impacts the computational
+efficiency of RelRes: For a mapping ratio of 3, the efficiency factor is
+around 4, and for a mapping ratio of 5, the efficiency factor is around 5
+:ref:`(Chaimovich2) <Chaimovich2>`.
+
+The flexibility of LAMMPS allows placing any values for the LJ
+parameters in the input script. However, here are the optimal
+recommendations for the RelRes parameters, which yield the correct
+structural and thermal behavior in a system of interest
+:ref:`(Chaimovich1) <Chaimovich1>`.  One must first assign a complete set of
+parameters for the FG interactions that are applicable to all atom types.
+Regarding the parameters for the CG interactions, the rules rely on the
+site category (if it is a hybrid or an ordinary site). For atom types of
+ordinary sites, :math:`\epsilon^{CG}` must be set to 0 (zero) while the
+specific value of :math:`\sigma^{CG}` is irrelevant. For atom types of
+hybrid sites, the CG parameters should be generally calculated using the
+following equations:
+
+.. math::
+
+   \sigma_I^{CG}=\frac{\left((\sum_{\alpha\in A}\sqrt{\epsilon_\alpha^{FG}\left(\sigma_\alpha^{FG}\right)^{12}}\right)^{1/2}}{\left((\sum_{\alpha\in A}\sqrt{\epsilon_\alpha^{FG}\left(\sigma_\alpha^{FG}\right)^6}\right)^{1/3}}
+   \quad\mathrm{and}\quad
+   \epsilon_I^{CG}=\frac{\left((\sum_{\alpha\in A}\sqrt{\epsilon_\alpha^{FG}\left(\sigma_\alpha^{FG}\right)^6}\right)^4}{\left((\sum_{\alpha\in A}\sqrt{\epsilon_\alpha^{FG}\left(\sigma_\alpha^{FG}\right)^{12}}\right)^2}
+
+where :math:`I` is an atom type of a hybrid site of a particular cluster
+:math:`A`, and corresponding with this cluster, the summation proceeds over
+all of its sites :math:`\alpha`.  These equations are derived from the
+monopole term in the underlying Taylor series, and they are indeed relevant
+only if geometric mixing is applicable for the FG model; if this is not the
+case, Ref. :ref:`(Chaimovich2) <Chaimovich2>` discusses the alternative
+formula, and in such a situation, the pair_coeff command should be explicitly
+used for all combinations of atom types :math:`I\;!=J`.
+
+The switching distance (the midpoint between inner and outer switching
+cutoffs) is another crucial factor in RelRes: decreasing it improves the
+computational efficiency, yet if it is too small, the molecular simulations
+may not capture the system behavior correctly.  As a rule of thumb,
+the switching distance should be approximately :math:`\,\sim\! 1.5\sigma`
+:ref:`(Chaimovich1) <Chaimovich1>`; recommendations can be found in
+Ref. :ref:`(Chaimovich2) <Chaimovich2>`.
+Regarding the switching smoothing zone, :math:`\,\sim\!0.1\sigma` is
+recommended; if desired, smoothing can be eliminated by setting
+the inner switching cutoff, :math:`r_{si}`, equal to the outer
+switching cutoff, :math:`r_{so}` (the same is true for the other cutoffs
+:math:`r_{ci}` and :math:`r_{co}`).
+
+----------
+
+As an example, imagine that in your system, a molecule is comprised just
+of one cluster such that one atom type (#1) is associated with
+its hybrid site, and another atom type (#2) is associated with its ordinary
+sites (in total, there are 2 atom types). If geometric mixing is applicable,
+the following commands should be used:
+
+.. code-block:: LAMMPS
+
+   pair_style lj/relres Rsi Rso Rci Rco
+   pair_coeff 1 1 epsilon_FG1 sigma_FG1 epsilon_CG1 sigma_CG1
+   pair_coeff 2 2 epsilon_FG2 sigma_FG2 0.0         0.0
+   pair_modify shift yes
+
+In a more complex situation, there may be two distinct clusters in a system
+(these two clusters may be on same molecule or on different molecules),
+each with its own switching cutoffs.  If there are still two atom types
+in each cluster as in the earlier example, the commands should be:
+
+.. code-block:: LAMMPS
+
+   pair_style lj/relres Rsi Rso Rci Rco
+   pair_coeff 1 1 epsilon_FG1 sigma_FG1 epsilon_CG1 sigma_CG1 Rsi1 Rso1 Rci Rco
+   pair_coeff 2 2 epsilon_FG2 sigma_FG2 0.0         0.0       Rsi1 Rso1 Rci Rco
+   pair_coeff 3 3 epsilon_FG3 sigma_FG3 epsilon_CG3 sigma_CG3
+   pair_coeff 4 4 epsilon_FG4 sigma_FG4 0.0         0.0
+   pair_modify shift yes
+
+In this example, the switching cutoffs for the first cluster (atom types 1
+and 2) is defined explicitly in the pair_coeff command which overrides the
+global values, while the second cluster (atom types 3 and 4) uses the global
+definition from the pair_style command. The emphasis here is that the atom
+types that belong to a specific cluster should have the same switching/cutoff
+arguments.
+
+In the case that geometric mixing is not applicable, for simulating the
+system from the previous example, we recommend using the following commands:
+
+.. code-block:: LAMMPS
+
+   pair_style lj/relres Rsi Rso Rci Rco
+   pair_coeff 1 1 epsilon_FG1  sigma_FG1  epsilon_CG1  sigma_CG1  Rsi1  Rso1  Rci Rco
+   pair_coeff 1 2 epsilon_FG12 sigma_FG12 0.0          0.0        Rsi1  Rso1  Rci Rco
+   pair_coeff 1 3 epsilon_FG13 sigma_FG13 epsilon_CG13 sigma_CG13 Rsi13 Rso13 Rci Rco
+   pair_coeff 1 4 epsilon_FG14 sigma_FG14 0.0          0.0        Rsi13 Rso13 Rci Rco
+   pair_coeff 2 2 epsilon_FG2  sigma_FG2  0.0          0.0        Rsi1  Rso1  Rci Rco
+   pair_coeff 2 3 epsilon_FG23 sigma_FG23 0.0          0.0        Rsi13 Rso13 Rci Rco
+   pair_coeff 2 4 epsilon_FG24 sigma_FG24 0.0          0.0        Rsi13 Rso13 Rci Rco
+   pair_coeff 3 3 epsilon_FG3  sigma_FG3  epsilon_CG3  sigma_CG3
+   pair_coeff 3 4 epsilon_FG34 sigma_FG34 0.0          0.0
+   pair_coeff 4 4 epsilon_FG4  sigma_FG4  0.0          0.0
+   pair_modify shift yes
+
+Notice that the CG parameters are mixed only for interactions between atom
+types associated with hybrid sites, and that the cutoffs are
+mixed on the cluster basis.
+
+More examples can be found in the *examples/relres* folder.
+
+----------
+
+.. include:: accel_styles.rst
+
+----------
+
+Mixing, shift, table, tail correction, restart, rRESPA info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+For atom type pairs :math:`I,\:J` with :math:`I\;!=J`, the
+:math:`\epsilon^{FG}`, :math:`\sigma^{FG}`, :math:`\epsilon^{CG}`,
+:math:`\sigma^{CG}`, :math:`r_{si}`, :math:`r_{so}`, :math:`r_{ci}`,
+and :math:`r_{co}` parameters for this pair style can be mixed, if
+not defined explicitly. All parameters are mixed according to the
+pair_modify mix option.  The default mix value is *geometric*\ ,
+and it is recommended to use with this *lj/relres* style.  See the
+"pair_modify" command for details.
+
+This pair style supports the :doc:`pair_modify <pair_modify>` shift
+option for the energy of the pair interaction. It is recommended to set
+this option to *yes*\ .  Otherwise, the offset :math:`\Gamma_{c}`
+is set to zero. Constants :math:`\Gamma_{si}` and :math:`\Gamma_{so}` are
+not impacted by this option.
+
+The :doc:`pair_modify <pair_modify>` table option is not relevant
+for this pair style.
+
+This pair style does not support the :doc:`pair_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and
+pressure, since the energy of the pair interaction is smoothed to 0.0
+at the cutoff.
+
+This pair style writes its information to :doc:`binary restart files
+<restart>`, so pair_style and pair_coeff commands do not need to be
+specified in an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+----------
+
+Restrictions
+""""""""""""
+none
+
+Related commands
+""""""""""""""""
+
+:doc:`pair_coeff <pair_coeff>`
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _Chaimovich1:
+
+**(Chaimovich1)** A. Chaimovich, C. Peter and K. Kremer, J. Chem. Phys. 143,
+243107 (2015).
+
+.. _Chaimovich2:
+
+**(Chaimovich2)** M. Chaimovich and A. Chaimovich, J. Chem. Theory Comput. 17,
+1045-1059 (2021).
+

doc/src/pair_mliap.rst

@@ -16,7 +16,7 @@ Syntax
   .. parsed-literal::
 
        *model* values = style filename
-         style = *linear* or *quadratic* or *mliappy*
+         style = *linear* or *quadratic* or *nn* or *mliappy*
          filename = name of file containing model definitions
        *descriptor* values = style filename
          style = *sna*
@@ -45,7 +45,7 @@ pair style currently supports just one descriptor style, but it is
 is straightforward to add new descriptor styles.
 The SNAP descriptor style *sna* is the same as that used by :doc:`pair_style snap <pair_snap>`,
 including the linear, quadratic, and chem variants.
-The available models are *linear*, *quadratic*, and *mliappy*.
+The available models are *linear*, *quadratic*, *nn*, and *mliappy*.
 The *mliappy* style can be used to couple python models,
 e.g. PyTorch neural network energy models, and requires building
 LAMMPS with the PYTHON package (see below).
@@ -77,13 +77,32 @@ line must contain two integers:
 * nelems  = Number of elements
 * nparams = Number of parameters
 
-This is followed by one block for each of the *nelem* elements.
+When the *model* keyword is *linear* or *quadratic*,
+this is followed by one block for each of the *nelem* elements.
 Each block consists of *nparams* parameters, one per line.
 Note that this format is similar, but not identical to that used
 for the :doc:`pair_style snap <pair_snap>` coefficient file.
 Specifically, the line containing the element weight and radius is omitted,
 since these are handled by the *descriptor*.
 
+When the *model* keyword is *nn* (neural networks), the model file can contain
+blank and comment lines (start with #) anywhere. The second non-blank non-comment
+line must contain the string NET, followed by two integers:
+
+* ndescriptors = Number of descriptors
+* nlayers      = Number of layers (including the hidden layers and the output layer)
+
+and followed by a sequence of a string and an integer for each layer:
+
+* Activation function (linear, sigmoid, tanh or relu)
+* nnodes = Number of nodes
+
+This is followed by one block for each of the *nelem* elements. Each block consists
+of *scale0* minimum value, *scale1* (maximum - minimum) value,
+in order to normalize the descriptors, followed by *nparams* parameters,
+including *bias* and *weights* of the model, starting with the first node of the first layer
+and so on, with a maximum of 30 values per line.
+
 Notes on mliappy models:
 When the *model* keyword is *mliappy*, the filename should end in '.pt',
 '.pth' for pytorch models, or be a pickle file. To load a model from

doc/src/pair_snap.rst

@@ -88,9 +88,12 @@ that will be used with other potentials.
 
 The name of the SNAP coefficient file usually ends in the
 ".snapcoeff" extension. It may contain coefficients
-for many SNAP elements. The only requirement is that it
-contain at least those element names appearing in the
-LAMMPS mapping list.
+for many SNAP elements. The only requirement is that
+each of the unique element names appearing in the
+LAMMPS pair_coeff command appear exactly once in
+the SNAP coefficient file. It is okay if the SNAP coefficient file
+contains additional elements not in the pair_coeff command,
+except when using *chemflag* (see below).
 The name of the SNAP parameter file usually ends in the ".snapparam"
 extension. It contains a small number
 of parameters that define the overall form of the SNAP potential.
@@ -129,7 +132,7 @@ line must contain two integers:
 This is followed by one block for each of the *nelem* elements.
 The first line of each block contains three entries:
 
-* Element symbol (text string)
+* Element name (text string)
 * R = Element radius (distance units)
 * w = Element weight (dimensionless)
 
@@ -166,8 +169,8 @@ where :math:`\mathbf{B}_i` is the *K*-vector of bispectrum components,
 :math:`\boldsymbol{\beta}^{\mu_i}` is the *K*-vector of linear coefficients
 for element :math:`\mu_i`, and :math:`\boldsymbol{\alpha}^{\mu_i}`
 is the symmetric *K* by *K* matrix of quadratic coefficients.
-The SNAP element file should contain *K*\ (\ *K*\ +1)/2 additional coefficients
-for each element, the upper-triangular elements of :math:`\boldsymbol{\alpha}^{\mu_i}`.
+The SNAP coefficient file should contain *K*\ (\ *K*\ +1)/2 additional coefficients
+in each element block, the upper-triangular elements of :math:`\boldsymbol{\alpha}^{\mu_i}`.
 
 If *chemflag* is set to 1, then the energy expression is written in terms of explicit multi-element bispectrum
 components indexed on ordered triplets of elements, which has been shown to increase the ability of the SNAP
@@ -181,8 +184,12 @@ at the expense of a significant increase in computational cost :ref:`(Cusentino)
 where :math:`\mathbf{B}^{\kappa\lambda\mu}_i` is the *K*-vector of bispectrum components
 for neighbors of elements :math:`\kappa`, :math:`\lambda`, and :math:`\mu` and
 :math:`\boldsymbol{\beta}^{\kappa\lambda\mu}_{\mu_i}` is the corresponding *K*-vector
-of linear coefficients for element :math:`\mu_i`. The SNAP element file should contain
-a total of :math:`K N_{elem}^3` coefficients for each of the :math:`N_{elem}` elements.
+of linear coefficients for element :math:`\mu_i`. The SNAP coefficient file should contain
+a total of :math:`K N_{elem}^3` coefficients in each element block,
+where :math:`N_{elem}` is the number of elements in the SNAP coefficient file,
+which must equal the number of unique elements appearing in the
+LAMMPS pair_coeff command, to avoid ambiguity in the
+number of coefficients.
 
 The keyword *chunksize* is only applicable when using the
 pair style *snap* with the KOKKOS package and is ignored otherwise.

doc/src/pair_style.rst

@@ -227,6 +227,7 @@ accelerated styles exist.
 * :doc:`lj/long/dipole/long <pair_dipole>` - long-range LJ and long-range point dipoles
 * :doc:`lj/long/tip4p/long <pair_lj_long>` - long-range LJ and long-range Coulomb for TIP4P water
 * :doc:`lj/mdf <pair_mdf>` - LJ potential with a taper function
+* :doc:`lj/relres <pair_lj_relres>` - LJ using multiscale Relative Resolution (RelRes) methodology :ref:`(Chaimovich) <Chaimovich2>`.
 * :doc:`lj/sdk <pair_sdk>` - LJ for SDK coarse-graining
 * :doc:`lj/sdk/coul/long <pair_sdk>` - LJ for SDK coarse-graining with long-range Coulomb
 * :doc:`lj/sdk/coul/msm <pair_sdk>` - LJ for SDK coarse-graining with long-range Coulomb via MSM

doc/utils/requirements.txt

@@ -1,6 +1,6 @@
 Sphinx
 sphinxcontrib-spelling
-git+https://github.com/akohlmey/sphinx-fortran@parallel-read
+git+git://github.com/akohlmey/sphinx-fortran@parallel-read
 sphinx_tabs
 breathe
 Pygments

doc/utils/sphinx-config/LAMMPSLexer.py

@@ -8,8 +8,8 @@ LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify", "atom_style",
 "delete_bonds", "dielectric", "dihedral_coeff", "dihedral_style", "dimension",
 "displace_atoms", "dump_modify", "dynamical_matrix", "echo",
 "fix_modify", "group2ndx", "hyper", "if", "improper_coeff",
-"improper_style", "include", "info", "jump", "kim_init", "kim_interactions",
-"kim_param", "kim_query", "kspace_modify", "kspace_style", "label", "lattice",
+"improper_style", "include", "info", "jump", "kim",
+"kspace_modify", "kspace_style", "label", "lattice",
 "log", "mass", "message", "minimize", "min_modify", "min_style", "molecule",
 "ndx2group", "neb", "neb/spin", "neighbor", "neigh_modify", "newton", "next",
 "package", "pair_coeff", "pair_modify", "pair_style", "pair_write",

doc/utils/sphinx-config/false_positives.txt

@@ -384,6 +384,7 @@ CGDNA
 cgs
 cgsdk
 CGSDK
+Chaimovich
 Chalopin
 Champaign
 charmm
@@ -1953,6 +1954,7 @@ Monaghan
 Monaghans
 monodisperse
 monodispersity
+monopole
 monovalent
 Montalenti
 Montero
@@ -2096,6 +2098,7 @@ ncol
 ncorr
 ncount
 nd
+ndescriptors
 ndihedrals
 ndihedraltypes
 Ndihedraltype
@@ -2156,6 +2159,7 @@ niu
 Nk
 nktv
 nl
+nlayers
 nlen
 Nlines
 nlo
@@ -2171,6 +2175,7 @@ Nmin
 nmin
 Nmols
 nn
+nnodes
 Nocedal
 nocite
 nocoeff
@@ -2297,6 +2302,7 @@ omegaz
 Omelyan
 omp
 OMP
+oneAPI
 onelevel
 oneway
 onn
@@ -2366,6 +2372,7 @@ parmin
 Parrinello
 Partay
 Particuology
+Pascuet
 pastewka
 Pastewka
 pathangle
@@ -2528,6 +2535,7 @@ ptm
 PTM
 ptol
 ptr
+PTX
 pu
 purdue
 Purohit
@@ -2620,10 +2628,12 @@ Rappe
 Ravelo
 rc
 Rc
+Rci
 Rcm
 rcmax
 Rcmx
 Rcmy
+Rco
 Rcut
 rcutfac
 rdc
@@ -2650,7 +2660,9 @@ Reinders
 reinit
 relaxbox
 relink
+relres
 relTol
+relu
 remappings
 remd
 Ren
@@ -2762,6 +2774,8 @@ rozero
 Rperp
 Rr
 rRESPA
+Rsi
+Rso
 Rspace
 rsq
 rst
@@ -2878,6 +2892,7 @@ si
 SiC
 Siepmann
 Sievers
+sigmoid
 Sij
 Sikandar
 Silbert

examples/USER/fep/C7inEthanol/fep01/data.init_conf_with_heptane

@@ -26,7 +26,7 @@ Masses
 7 12.0112
 8 1.00797
 
-Pair Coeffs # lj/class2/coul/long
+Pair Coeffs # hybrid
 
 1 lj/class2/coul/long 0.054 4.01
 2 lj/class2/coul/long 0.054 4.01

examples/USER/fep/C7inEthanol/fep01/in.insertion

@@ -12,7 +12,7 @@ improper_style  class2
 pair_modify     mix sixthpower tail yes
 special_bonds   lj/coul 0 0 1
 
-read_data       data.init_conf_without_heptane
+read_data       data.init_conf_with_heptane
 
 pair_coeff    1    6  lj/class2/coul/long/soft   0.054 4.01 0.0
 pair_coeff    2    6  lj/class2/coul/long/soft   0.054 4.01 0.0
@@ -47,7 +47,7 @@ fix ADAPT all adapt/fep 10 &
   atom charge 8 v_q3 &
   after yes
 
-thermo_style custom step spcpu temp press vol etotal pe v_lambda v_q1 v_q2 v_q3
+thermo_style custom step temp press vol etotal pe v_lambda v_q1 v_q2 v_q3
 thermo_modify line one
 thermo          100
 

examples/USER/fep/C7inEthanol/fep10/data.init_conf_with_heptane

@@ -26,7 +26,7 @@ Masses
 7 12.0112
 8 1.00797
 
-Pair Coeffs # lj/class2/coul/long
+Pair Coeffs # hybrid
 
 1 lj/class2/coul/long 0.054 4.01
 2 lj/class2/coul/long 0.054 4.01

examples/USER/fep/C7inEthanol/fep10/in.deletion

@@ -47,7 +47,7 @@ fix ADAPT all adapt/fep 10 &
   atom charge 8 v_q3 &
   after yes
 
-thermo_style custom step spcpu temp press vol etotal pe v_lambda v_q1 v_q2 v_q3
+thermo_style custom step temp press vol etotal pe v_lambda v_q1 v_q2 v_q3
 thermo_modify line one
 thermo          100
 

examples/USER/fep/CC-CO/README.md

@@ -2,14 +2,14 @@ Ethane to Methanol in Water
 ===========================
 
 Example calculation of the difference in free energy of hydration upon
-transforming ethane into methanol with LAMMPS using *compute fep* and
-*fix adapt/fep*.
+transforming ethane into methanol with LAMMPS using *compute fep*,
+*fix adapt/fep* and *pair lj/cut/coul/long/soft*.
 
 Ethane and methanol are represented by the OPLS-AA force field (1
 molecule). Water is represented by the 3-site SPC/E model (360
 molecules).
 
-The strategy used to perform the alchemical transformation is the
+The procedure used to perform the alchemical transformation is the
 following:
 
 * The dual topology approach is used, therefore all the atoms of
@@ -18,13 +18,20 @@ following:
   transformation. Masses and intramolecular terms (bond lengths,
   angles, dihedrals) are not changed.
 
-* Interactions of sites that are being created (from dummy sites) or
-  deleted (to become dummy sites) are treated using soft-core verions
+* Interactions of sites that are being created (from dummy sites, XD-) or
+  deleted (to become dummy sites, X-D) are treated using soft-core verions
   of the Lennard-Jones and Coulomb potentials (*pair
   lj/cut/coul/long/soft*) in order to avoid singularities. The
   exponent of the coupling parameter lambda in the soft-core pair
   potentials was in this example n = 1.
 
+* In order to avoid catastrophic overlaps between the fragments being created
+  and being deleted, interactions between certain atoms need to be zeroed.
+  In this case this concerns the H atoms of the methyl group and the O atom
+  of the OH group involved in the transformation. Other pairs of atoms
+  belonging to these fragments are either within the 1-2 and 1-3 neighbor
+  relations, or are H atoms with no LJ site (H of the OH group).
+
 * Eletrostatic charges that are modified are varied linearly from the
   initial to the final values. This keeps the overall charge of the
   molecule constant, which is good for the long range electrostatics
@@ -44,42 +51,20 @@ integration (TI/FDTI) and Bennet's acceptance ratio methods:
 * `fep10` -- Calculation using FEP, multi-stage transformation of a
   methanol molecule into ethane. Results in `fep10.lmp`
 
-* `fdti01` -- Calculation using FDTI, transformation of an
-  ethane molecule into methanol. Results in `fdti01.lmp`
-
-* `fdti10` -- Calculation using FDTI, transformation of a
-  methanol molecule into ethane. Results in `fdti10.lmp`
-
-* `bar01` -- Calculation using BAR, 1-step transformation of an
-  ethane molecule into methanol. Results in `bar01.lmp`
-
-* `bar10` -- Calculation using BAR, 1-step transformation of a
-  methanol molecule into ethane. Results in `bar10.lmp`
-
 The free-energy profiles can be observed by plotting the values in the
-third column of the results files. The Python scripts `fep.py`,
-`nti.py`, `fdti.py`, and `bar.py` found in the `tools` directory can
-be used to calculate the free-energy differences corresponding to the
-above transformations:
+third column of the results files. The Python script `fep.py`, found in
+the `tools` directory, can be used to calculate the free-energy differences
+corresponding to the above transformations:
 
     fep.py 300 < fep01.lmp
 
     fep.py 300 < fep10.lmp
 
-    nti.py 300 0.002 < fdti01.lmp
-
-    nti.py 300 0.002 < fdti10.lmp
-
-    fdti.py 300 0.002 < fdti01.lmp
-
-    fdti.py 300 0.002 < fdti10.lmp
-
-    bar.py 300 bar01.lmp bar10.lmp
-
 The outputs are in kcal/mol and can be compared with the experimental
-value of -6.93 kcal/mol and with simulation value from the literature:
--6.7 kcal/mol [Jorgensen, Ravimohan, J Chem Phys 83 (1985) 3050], -6.8
-kcal/mol [Goette, Grubmüller, J Comp Chem 30 (2007) 447].
+value of -6.93 kcal/mol and with simulation value from the literature
+(obtained with different force field parameters):
+-6.7 kcal/mol [Jorgensen, Ravimohan, J Chem Phys 83 (1985) 3050](https://doi.org/10.1063/1.449208),
+-6.8 kcal/mol [Goette, Grubmüller, J Comp Chem 30 (2007) 447](https://doi.org/10.1002/jcc.21073).
 
 These example calculations are for tutorial purposes only. The results
 may not be of research quality (not enough sampling, size of the step

examples/USER/fep/CC-CO/bar01/in.bar01.lmp

@@ -1,120 +0,0 @@
-# created by fftool
-
-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
-
-read_data data.0.lmp
-# read_restart restart.*.lmp
-# reset_timestep 0
-
-pair_style hybrid lj/cut/coul/long 10.0 10.0 &
-  lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
-pair_modify tail no
-kspace_style pppm 1.0e-4
-
-pair_coeff    1    1  none  # C-CO C-CO
-pair_coeff    1    2  none  # C-CO C-D
-pair_coeff    1    3  none  # C-CO H-D
-pair_coeff    1    4  none  # C-CO H-H1
-pair_coeff    1    5  none  # C-CO OHD-
-pair_coeff    1    6  none  # C-CO HOD-
-pair_coeff    1    7  lj/cut/coul/long    0.0000   1.0000  # C-CO Hw
-pair_coeff    1    8  lj/cut/coul/long    0.1013   3.3286  # C-CO Ow
-pair_coeff    2    2  none  # C-D C-D
-pair_coeff    2    3  none  # C-D H-D
-pair_coeff    2    4  none  # C-D H-H1
-pair_coeff    2    5  none  # C-D OHD-
-pair_coeff    2    6  none  # C-D HOD-
-pair_coeff    2    7  lj/cut/coul/long/soft    0.0000   1.0000  1.0  # C-D Hw
-pair_coeff    2    8  lj/cut/coul/long/soft    0.1013   3.3286  1.0  # C-D Ow
-pair_coeff    3    3  none  # H-D H-D
-pair_coeff    3    4  lj/cut/coul/long/soft    0.0300   2.5000  1.0  # H-D H-H1
-pair_coeff    3    5  none  # H-D OHD-
-pair_coeff    3    6  none  # H-D HOD-
-pair_coeff    3    7  lj/cut/coul/long/soft    0.0000   1.0000  1.0  # H-D Hw
-pair_coeff    3    8  lj/cut/coul/long/soft    0.0683   2.8131  1.0  # H-D Ow
-pair_coeff    4    4  none  # H-H1 H-H1
-pair_coeff    4    5  none  # H-H1 OHD-
-pair_coeff    4    6  lj/cut/coul/long/soft    0.0000   1.0000  0.0 # H-H1 HOD-
-pair_coeff    4    7  lj/cut/coul/long    0.0000   1.0000  # H-H1 Hw
-pair_coeff    4    8  lj/cut/coul/long    0.0683   2.8131  # H-H1 Ow
-pair_coeff    5    5  none  # OHD- OHD-
-pair_coeff    5    6  none  # OHD- HOD-
-pair_coeff    5    7  lj/cut/coul/long/soft    0.0000   1.0000  0.0  # OHD- Hw
-pair_coeff    5    8  lj/cut/coul/long/soft    0.1625   3.1427  0.0  # OHD- Ow
-pair_coeff    6    6  none  # HOD- HOD-
-pair_coeff    6    7  lj/cut/coul/long/soft    0.0000   1.0000  0.0  # HOD- Hw
-pair_coeff    6    8  lj/cut/coul/long/soft    0.0000   1.7792  0.0  # HOD- Ow
-pair_coeff    7    7  lj/cut/coul/long    0.0000   1.0000  # Hw Hw
-pair_coeff    7    8  lj/cut/coul/long    0.0000   1.0000  # Hw Ow
-pair_coeff    8    8  lj/cut/coul/long    0.1554   3.1655  # Ow Ow
-
-variable nsteps equal 500000
-variable nprint equal ${nsteps}/500
-variable ndump equal ${nsteps}/100
-# variable nrestart equal ${nsteps}/10
-
-variable temp equal 300.0
-variable press equal 1.0
-
-neighbor 2.0 bin
-
-timestep 2.0
-
-# velocity all create ${temp} 12345
-
-thermo_style multi
-thermo ${nprint}
-
-fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
-
-fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
-
-run 100000
-reset_timestep 0
-
-
-variable dlambda equal 1.0
-variable minusdl equal -1.0
-variable dq1 equal  0.145*v_dlambda+0.180*v_dlambda
-variable dq2 equal  0.180*v_dlambda
-variable dq3 equal -0.060*v_dlambda
-variable dq4 equal  0.040*v_dlambda-0.060*v_dlambda
-variable dq5 equal -0.683*v_dlambda
-variable dq6 equal  0.418*v_dlambda
-
-compute cFEP all fep ${temp} &
-    pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusdl &
-    pair lj/cut/coul/long/soft lambda 3 4 v_minusdl &
-    pair lj/cut/coul/long/soft lambda 4 6 v_dlambda &
-    pair lj/cut/coul/long/soft lambda 5*6 7*8 v_dlambda &
-    atom charge 1 v_dq1 &
-    atom charge 2 v_dq2 &
-    atom charge 3 v_dq3 &
-    atom charge 4 v_dq4 &
-    atom charge 5 v_dq5 &
-    atom charge 6 v_dq6
-
-fix fFEP all ave/time 1 1 100 c_cFEP[1] c_cFEP[2] file bar01.lmp
-
-# compute cRDF all rdf 100 1 1
-# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
-
-# compute cMSD all msd
-# fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
-
-dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
-dump_modify dCONF element C C H H O H H O
-
-# restart ${nrestart} restart.*.lmp
-
-run ${nsteps}
-
-write_restart restart.*.lmp
-write_data data.*.lmp

examples/USER/fep/CC-CO/bar10/in.bar10.lmp

@@ -1,120 +0,0 @@
-# created by fftool
-
-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
-
-read_data data.1.lmp
-# read_restart restart.*.lmp
-# reset_timestep 0
-
-pair_style hybrid lj/cut/coul/long 10.0 10.0 &
-  lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
-pair_modify tail no
-kspace_style pppm 1.0e-4
-
-pair_coeff    1    1  none  # CO-C CO-C
-pair_coeff    1    2  none  # CO-C CD-
-pair_coeff    1    3  none  # CO-C HD-
-pair_coeff    1    4  none  # CO-C H1-H
-pair_coeff    1    5  none  # CO-C OH-D
-pair_coeff    1    6  none  # CO-C HO-D
-pair_coeff    1    7  lj/cut/coul/long    0.0000   1.0000  # CO-C Hw
-pair_coeff    1    8  lj/cut/coul/long    0.1013   3.3286  # CO-C Ow
-pair_coeff    2    2  none  # CD- CD-
-pair_coeff    2    3  none  # CD- HD-
-pair_coeff    2    4  none  # CD- H1-H
-pair_coeff    2    5  none  # CD- OH-D
-pair_coeff    2    6  none  # CD- HO-D
-pair_coeff    2    7  lj/cut/coul/long/soft    0.0000   1.0000  0.0  # CD- Hw
-pair_coeff    2    8  lj/cut/coul/long/soft    0.1013   3.3286  0.0  # CD- Ow
-pair_coeff    3    3  none  # HD- HD-
-pair_coeff    3    4  lj/cut/coul/long/soft    0.0300   2.5000  0.0  # HD- H1-H
-pair_coeff    3    5  none  # HD- OH-D
-pair_coeff    3    6  none  # HD- HO-D
-pair_coeff    3    7  lj/cut/coul/long/soft    0.0000   1.0000  0.0  # HD- Hw
-pair_coeff    3    8  lj/cut/coul/long/soft    0.0683   2.8131  0.0  # HD- Ow
-pair_coeff    4    4  none  # H1-H H1-H
-pair_coeff    4    5  none  # H1-H OH-D
-pair_coeff    4    6  lj/cut/coul/long/soft    0.0000   1.0000  1.0 # H1-H HO-D
-pair_coeff    4    7  lj/cut/coul/long    0.0000   1.0000  # H1-H Hw
-pair_coeff    4    8  lj/cut/coul/long    0.0683   2.8131  # H1-H Ow
-pair_coeff    5    5  none  # OH-D OH-D
-pair_coeff    5    6  none  # OH-D HO-D
-pair_coeff    5    7  lj/cut/coul/long/soft    0.0000   1.0000  1.0  # OH-D Hw
-pair_coeff    5    8  lj/cut/coul/long/soft    0.1625   3.1427  1.0  # OH-D Ow
-pair_coeff    6    6  none  # HO-D HO-D
-pair_coeff    6    7  lj/cut/coul/long/soft    0.0000   1.0000  1.0  # HO-D Hw
-pair_coeff    6    8  lj/cut/coul/long/soft    0.0000   1.7792  1.0  # HO-D Ow
-pair_coeff    7    7  lj/cut/coul/long    0.0000   1.0000  # Hw Hw
-pair_coeff    7    8  lj/cut/coul/long    0.0000   1.0000  # Hw Ow
-pair_coeff    8    8  lj/cut/coul/long    0.1554   3.1655  # Ow Ow
-
-variable nsteps equal 500000
-variable nprint equal ${nsteps}/500
-variable ndump equal ${nsteps}/100
-# variable nrestart equal ${nsteps}/10
-
-variable temp equal 300.0
-variable press equal 1.0
-
-neighbor 2.0 bin
-
-timestep 2.0
-
-# velocity all create ${temp} 12345
-
-thermo_style multi
-thermo ${nprint}
-
-fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
-
-fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
-
-run 100000
-reset_timestep 0
-
-
-variable dlambda equal -1.0
-variable minusdl equal 1.0
-variable dq1 equal  0.145*v_dlambda+0.180*v_dlambda
-variable dq2 equal  0.180*v_dlambda
-variable dq3 equal -0.060*v_dlambda
-variable dq4 equal  0.040*v_dlambda-0.060*v_dlambda
-variable dq5 equal -0.683*v_dlambda
-variable dq6 equal  0.418*v_dlambda
-
-compute cFEP all fep ${temp} &
-    pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusdl &
-    pair lj/cut/coul/long/soft lambda 3 4 v_minusdl &
-    pair lj/cut/coul/long/soft lambda 4 6 v_dlambda &
-    pair lj/cut/coul/long/soft lambda 5*6 7*8 v_dlambda &
-    atom charge 1 v_dq1 &
-    atom charge 2 v_dq2 &
-    atom charge 3 v_dq3 &
-    atom charge 4 v_dq4 &
-    atom charge 5 v_dq5 &
-    atom charge 6 v_dq6
-
-fix fFEP all ave/time 1 1 100 c_cFEP[1] c_cFEP[2] file bar10.lmp
-
-# compute cRDF all rdf 100 1 1
-# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
-
-# compute cMSD all msd
-# fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
-
-dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
-dump_modify dCONF element C C H H O H H O
-
-# restart ${nrestart} restart.*.lmp
-
-run ${nsteps}
-
-write_restart restart.*.lmp
-write_data data.*.lmp

examples/USER/fep/CC-CO/fdti01/fdti01.lmp

@@ -1,22 +0,0 @@
-# Time-averaged data for fix fFEP
-# TimeStep c_cFEP[1] c_cFEP[2]
-125000 0.00871763 0.985497
-250000 0.00705519 0.98825
-375000 0.00568771 0.99052
-500000 0.00429336 0.992842
-625000 0.00308675 0.994856
-750000 0.00169928 0.997181
-875000 0.000144366 0.999789
-1000000 -0.00112539 1.00193
-1125000 -0.0026842 1.00456
-1250000 -0.00474318 1.00805
-1375000 -0.00571651 1.0097
-1500000 -0.0073978 1.01256
-1625000 -0.00966334 1.01644
-1750000 -0.011584 1.01972
-1875000 -0.0148498 1.02535
-2000000 -0.0192874 1.03307
-2125000 -0.0257123 1.04433
-2250000 -0.035944 1.06249
-2375000 -0.046465 1.08144
-2500000 -0.0558595 1.09863

examples/USER/fep/CC-CO/fdti01/in.fdti01.lmp

@@ -1,142 +0,0 @@
-# created by fftool
-
-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
-
-read_data data.0.lmp
-# read_restart restart.*.lmp
-# reset_timestep 0
-
-pair_style hybrid lj/cut/coul/long 10.0 10.0 &
-  lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
-pair_modify tail no
-kspace_style pppm 1.0e-4
-
-pair_coeff    1    1  none  # C-CO C-CO
-pair_coeff    1    2  none  # C-CO C-D
-pair_coeff    1    3  none  # C-CO H-D
-pair_coeff    1    4  none  # C-CO H-H1
-pair_coeff    1    5  none  # C-CO OHD-
-pair_coeff    1    6  none  # C-CO HOD-
-pair_coeff    1    7  lj/cut/coul/long    0.0000   1.0000  # C-CO Hw
-pair_coeff    1    8  lj/cut/coul/long    0.1013   3.3286  # C-CO Ow
-pair_coeff    2    2  none  # C-D C-D
-pair_coeff    2    3  none  # C-D H-D
-pair_coeff    2    4  none  # C-D H-H1
-pair_coeff    2    5  none  # C-D OHD-
-pair_coeff    2    6  none  # C-D HOD-
-pair_coeff    2    7  lj/cut/coul/long/soft    0.0000   1.0000  1.0  # C-D Hw
-pair_coeff    2    8  lj/cut/coul/long/soft    0.1013   3.3286  1.0  # C-D Ow
-pair_coeff    3    3  none  # H-D H-D
-pair_coeff    3    4  lj/cut/coul/long/soft    0.0300   2.5000  1.0  # H-D H-H1
-pair_coeff    3    5  none  # H-D OHD-
-pair_coeff    3    6  none  # H-D HOD-
-pair_coeff    3    7  lj/cut/coul/long/soft    0.0000   1.0000  1.0  # H-D Hw
-pair_coeff    3    8  lj/cut/coul/long/soft    0.0683   2.8131  1.0  # H-D Ow
-pair_coeff    4    4  none  # H-H1 H-H1
-pair_coeff    4    5  none  # H-H1 OHD-
-pair_coeff    4    6  lj/cut/coul/long/soft    0.0000   1.0000  0.0 # H-H1 HOD-
-pair_coeff    4    7  lj/cut/coul/long    0.0000   1.0000  # H-H1 Hw
-pair_coeff    4    8  lj/cut/coul/long    0.0683   2.8131  # H-H1 Ow
-pair_coeff    5    5  none  # OHD- OHD-
-pair_coeff    5    6  none  # OHD- HOD-
-pair_coeff    5    7  lj/cut/coul/long/soft    0.0000   1.0000  0.0  # OHD- Hw
-pair_coeff    5    8  lj/cut/coul/long/soft    0.1625   3.1427  0.0  # OHD- Ow
-pair_coeff    6    6  none  # HOD- HOD-
-pair_coeff    6    7  lj/cut/coul/long/soft    0.0000   1.0000  0.0  # HOD- Hw
-pair_coeff    6    8  lj/cut/coul/long/soft    0.0000   1.7792  0.0  # HOD- Ow
-pair_coeff    7    7  lj/cut/coul/long    0.0000   1.0000  # Hw Hw
-pair_coeff    7    8  lj/cut/coul/long    0.0000   1.0000  # Hw Ow
-pair_coeff    8    8  lj/cut/coul/long    0.1554   3.1655  # Ow Ow
-
-variable nsteps equal 2500000
-variable nprint equal ${nsteps}/500
-variable ndump equal ${nsteps}/100
-# variable nrestart equal ${nsteps}/10
-
-variable temp equal 300.0
-variable press equal 1.0
-
-neighbor 2.0 bin
-
-timestep 2.0
-
-velocity all create ${temp} 12345
-
-thermo_style multi
-thermo ${nprint}
-
-fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
-
-fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
-
-run 250000
-reset_timestep 0
-
-
-variable lambda equal ramp(0.0,1.0)
-variable minusl equal 1.0-v_lambda
-variable q1 equal  0.145*v_lambda-0.180*(1.0-v_lambda)
-variable q2 equal -0.180*(1.0-v_lambda)
-variable q3 equal  0.060*(1.0-v_lambda)
-variable q4 equal  0.040*v_lambda+0.060*(1.0-v_lambda)
-variable q5 equal -0.683*v_lambda
-variable q6 equal  0.418*v_lambda
-
-fix fADAPT all adapt/fep 125000 &
-    pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusl &
-    pair lj/cut/coul/long/soft lambda 3 4 v_minusl &
-    pair lj/cut/coul/long/soft lambda 4 6 v_lambda &
-    pair lj/cut/coul/long/soft lambda 5*6 7*8 v_lambda &
-    atom charge 1 v_q1 &
-    atom charge 2 v_q2 &
-    atom charge 3 v_q3 &
-    atom charge 4 v_q4 &
-    atom charge 5 v_q5 &
-    atom charge 6 v_q6 &
-    after yes
-
-variable dlambda equal 0.002
-variable minusdl equal -0.002
-variable dq1 equal  0.145*v_dlambda+0.180*v_dlambda
-variable dq2 equal  0.180*v_dlambda
-variable dq3 equal -0.060*v_dlambda
-variable dq4 equal  0.040*v_dlambda-0.060*v_dlambda
-variable dq5 equal -0.683*v_dlambda
-variable dq6 equal  0.418*v_dlambda
-
-compute cFEP all fep ${temp} &
-    pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusdl &
-    pair lj/cut/coul/long/soft lambda 3 4 v_minusdl &
-    pair lj/cut/coul/long/soft lambda 4 6 v_dlambda &
-    pair lj/cut/coul/long/soft lambda 5*6 7*8 v_dlambda &
-    atom charge 1 v_dq1 &
-    atom charge 2 v_dq2 &
-    atom charge 3 v_dq3 &
-    atom charge 4 v_dq4 &
-    atom charge 5 v_dq5 &
-    atom charge 6 v_dq6
-
-fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fdti01.lmp
-
-# compute cRDF all rdf 100 1 1
-# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
-
-compute cMSD all msd
-fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
-
-dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
-dump_modify dCONF element C C H H O H H O
-
-# restart ${nrestart} restart.*.lmp
-
-run ${nsteps}
-
-write_restart restart.*.lmp
-write_data data.*.lmp

examples/USER/fep/CC-CO/fdti10/fdti10.lmp

@@ -1,22 +0,0 @@
-# Time-averaged data for fix fFEP
-# TimeStep c_cFEP[1] c_cFEP[2]
-125000 0.0632017 0.899723
-250000 0.0561376 0.910429
-375000 0.0471384 0.924277
-500000 0.0349153 0.943416
-625000 0.0244399 0.960071
-750000 0.019451 0.968073
-875000 0.0134728 0.977767
-1000000 0.011723 0.980628
-1125000 0.00945656 0.984351
-1250000 0.00790634 0.986905
-1375000 0.00564311 0.990642
-1500000 0.00376572 0.993753
-1625000 0.00238483 0.996053
-1750000 0.00085649 0.9986
-1875000 -0.000515888 1.0009
-2000000 -0.00151569 1.00257
-2125000 -0.00325174 1.00549
-2250000 -0.00472612 1.00798
-2375000 -0.00578231 1.00976
-2500000 -0.00729864 1.01233

examples/USER/fep/CC-CO/fdti10/in.fdti10.lmp

@@ -1,142 +0,0 @@
-# created by fftool
-
-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
-
-read_data data.1.lmp
-# read_restart restart.*.lmp
-# reset_timestep 0
-
-pair_style hybrid lj/cut/coul/long 10.0 10.0 &
-  lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
-pair_modify tail no
-kspace_style pppm 1.0e-4
-
-pair_coeff    1    1  none  # CO-C CO-C
-pair_coeff    1    2  none  # CO-C CD-
-pair_coeff    1    3  none  # CO-C HD-
-pair_coeff    1    4  none  # CO-C H1-H
-pair_coeff    1    5  none  # CO-C OH-D
-pair_coeff    1    6  none  # CO-C HO-D
-pair_coeff    1    7  lj/cut/coul/long    0.0000   1.0000  # CO-C Hw
-pair_coeff    1    8  lj/cut/coul/long    0.1013   3.3286  # CO-C Ow
-pair_coeff    2    2  none  # CD- CD-
-pair_coeff    2    3  none  # CD- HD-
-pair_coeff    2    4  none  # CD- H1-H
-pair_coeff    2    5  none  # CD- OH-D
-pair_coeff    2    6  none  # CD- HO-D
-pair_coeff    2    7  lj/cut/coul/long/soft    0.0000   1.0000  0.0  # CD- Hw
-pair_coeff    2    8  lj/cut/coul/long/soft    0.1013   3.3286  0.0  # CD- Ow
-pair_coeff    3    3  none  # HD- HD-
-pair_coeff    3    4  lj/cut/coul/long/soft    0.0300   2.5000  0.0  # HD- H1-H
-pair_coeff    3    5  none  # HD- OH-D
-pair_coeff    3    6  none  # HD- HO-D
-pair_coeff    3    7  lj/cut/coul/long/soft    0.0000   1.0000  0.0  # HD- Hw
-pair_coeff    3    8  lj/cut/coul/long/soft    0.0683   2.8131  0.0  # HD- Ow
-pair_coeff    4    4  none  # H1-H H1-H
-pair_coeff    4    5  none  # H1-H OH-D
-pair_coeff    4    6  lj/cut/coul/long/soft    0.0000   1.0000  1.0 # H1-H HO-D
-pair_coeff    4    7  lj/cut/coul/long    0.0000   1.0000  # H1-H Hw
-pair_coeff    4    8  lj/cut/coul/long    0.0683   2.8131  # H1-H Ow
-pair_coeff    5    5  none  # OH-D OH-D
-pair_coeff    5    6  none  # OH-D HO-D
-pair_coeff    5    7  lj/cut/coul/long/soft    0.0000   1.0000  1.0  # OH-D Hw
-pair_coeff    5    8  lj/cut/coul/long/soft    0.1625   3.1427  1.0  # OH-D Ow
-pair_coeff    6    6  none  # HO-D HO-D
-pair_coeff    6    7  lj/cut/coul/long/soft    0.0000   1.0000  1.0  # HO-D Hw
-pair_coeff    6    8  lj/cut/coul/long/soft    0.0000   1.7792  1.0  # HO-D Ow
-pair_coeff    7    7  lj/cut/coul/long    0.0000   1.0000  # Hw Hw
-pair_coeff    7    8  lj/cut/coul/long    0.0000   1.0000  # Hw Ow
-pair_coeff    8    8  lj/cut/coul/long    0.1554   3.1655  # Ow Ow
-
-variable nsteps equal 2500000
-variable nprint equal ${nsteps}/500
-variable ndump equal ${nsteps}/100
-# variable nrestart equal ${nsteps}/10
-
-variable temp equal 300.0
-variable press equal 1.0
-
-neighbor 2.0 bin
-
-timestep 2.0
-
-velocity all create ${temp} 12345
-
-thermo_style multi
-thermo ${nprint}
-
-fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
-
-fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
-
-run 250000
-reset_timestep 0
-
-
-variable lambda equal ramp(1.0,0.0)
-variable minusl equal 1.0-v_lambda
-variable q1 equal  0.145*v_lambda-0.180*(1.0-v_lambda)
-variable q2 equal -0.180*(1.0-v_lambda)
-variable q3 equal  0.060*(1.0-v_lambda)
-variable q4 equal  0.040*v_lambda+0.060*(1.0-v_lambda)
-variable q5 equal -0.683*v_lambda
-variable q6 equal  0.418*v_lambda
-
-fix fADAPT all adapt/fep 125000 &
-    pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusl &
-    pair lj/cut/coul/long/soft lambda 3 4 v_minusl &
-    pair lj/cut/coul/long/soft lambda 4 6 v_lambda &
-    pair lj/cut/coul/long/soft lambda 5*6 7*8 v_lambda &
-    atom charge 1 v_q1 &
-    atom charge 2 v_q2 &
-    atom charge 3 v_q3 &
-    atom charge 4 v_q4 &
-    atom charge 5 v_q5 &
-    atom charge 6 v_q6 &
-    after yes
-
-variable dlambda equal -0.002
-variable minusdl equal 0.002
-variable dq1 equal  0.145*v_dlambda+0.180*v_dlambda
-variable dq2 equal  0.180*v_dlambda
-variable dq3 equal -0.060*v_dlambda
-variable dq4 equal  0.040*v_dlambda-0.060*v_dlambda
-variable dq5 equal -0.683*v_dlambda
-variable dq6 equal  0.418*v_dlambda
-
-compute cFEP all fep ${temp} &
-    pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusdl &
-    pair lj/cut/coul/long/soft lambda 3 4 v_minusdl &
-    pair lj/cut/coul/long/soft lambda 4 6 v_dlambda &
-    pair lj/cut/coul/long/soft lambda 5*6 7*8 v_dlambda &
-    atom charge 1 v_dq1 &
-    atom charge 2 v_dq2 &
-    atom charge 3 v_dq3 &
-    atom charge 4 v_dq4 &
-    atom charge 5 v_dq5 &
-    atom charge 6 v_dq6
-
-fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fdti10.lmp
-
-# compute cRDF all rdf 100 1 1
-# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
-
-compute cMSD all msd
-fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
-
-dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
-dump_modify dCONF element C C H H O H H O
-
-# restart ${nrestart} restart.*.lmp
-
-run ${nsteps}
-
-write_restart restart.*.lmp
-write_data data.*.lmp

examples/USER/fep/CC-CO/fep01/fep01.fep

@@ -0,0 +1,22 @@
+# Time-averaged data for fix FEP
+# TimeStep c_FEP[1] c_FEP[2] c_FEP[3]
+100000 0.367224 7226.74 10972.3
+200000 0.117221 9775.91 10969.8
+300000 0.0327981 10833 10957.1
+400000 -0.00682693 11431.4 10973.1
+500000 -0.0346601 11895.3 10970.6
+600000 -0.047293 12165.7 10994.3
+700000 -0.0571432 12366.1 10992.6
+800000 -0.0643234 12487.6 10947.9
+900000 -0.0673497 12638 10962.3
+1000000 -0.0821333 13059.7 10957.9
+1100000 -0.0652233 12737.3 10966.8
+1200000 -0.10943 13955.7 10961
+1300000 -0.105325 13902.4 10950.4
+1400000 -0.133363 14687.1 10966.7
+1500000 -0.171816 16217.4 10959.1
+1600000 -0.271532 19801.5 10980.3
+1700000 -0.370116 24272.1 10962.7
+1800000 -0.58429 36064.2 10939.8
+1900000 -0.899593 63323 10933
+2000000 -1.12815 101729 10915.2

examples/USER/fep/CC-CO/fep01/fep01.lmp

@@ -1,22 +0,0 @@
-# Time-averaged data for fix fFEP
-# TimeStep c_cFEP[1] c_cFEP[2]
-125000 0.205889 0.714253
-250000 0.164934 0.765732
-375000 0.131935 0.809532
-500000 0.09771 0.859006
-625000 0.0688602 0.903005
-750000 0.0356141 0.958919
-875000 -0.00180317 1.02349
-1000000 -0.0317681 1.08115
-1125000 -0.0686221 1.15601
-1250000 -0.117495 1.2677
-1375000 -0.140627 1.31823
-1500000 -0.179791 1.41782
-1625000 -0.233651 1.57071
-1750000 -0.284345 1.71981
-1875000 -0.367527 2.01219
-2000000 -0.480496 2.54915
-2125000 -0.644218 3.47978
-2250000 -0.898797 5.57997
-2375000 -1.1516 8.56702
-2500000 -1.36364 12.2295

examples/USER/fep/CC-CO/fep01/in.fep01

@@ -1,143 +0,0 @@
-# created by fftool
-
-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
-
-read_data data.0.lmp
-# read_restart restart.*.lmp
-# reset_timestep 0
-
-pair_style hybrid lj/cut/coul/long 10.0 10.0 &
-  lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
-pair_modify tail no
-kspace_style pppm 1.0e-4
-
-pair_coeff    1    1  none  # C-CO C-CO
-pair_coeff    1    2  none  # C-CO C-D
-pair_coeff    1    3  none  # C-CO H-D
-pair_coeff    1    4  none  # C-CO H-H1
-pair_coeff    1    5  none  # C-CO OHD-
-pair_coeff    1    6  none  # C-CO HOD-
-pair_coeff    1    7  lj/cut/coul/long    0.0000   1.0000  # C-CO Hw
-pair_coeff    1    8  lj/cut/coul/long    0.1013   3.3286  # C-CO Ow
-pair_coeff    2    2  none  # C-D C-D
-pair_coeff    2    3  none  # C-D H-D
-pair_coeff    2    4  none  # C-D H-H1
-pair_coeff    2    5  none  # C-D OHD-
-pair_coeff    2    6  none  # C-D HOD-
-pair_coeff    2    7  lj/cut/coul/long/soft    0.0000   1.0000  1.0  # C-D Hw
-pair_coeff    2    8  lj/cut/coul/long/soft    0.1013   3.3286  1.0  # C-D Ow
-pair_coeff    3    3  none  # H-D H-D
-pair_coeff    3    4  lj/cut/coul/long/soft    0.0300   2.5000  1.0  # H-D H-H1
-pair_coeff    3    5  none  # H-D OHD-
-pair_coeff    3    6  none  # H-D HOD-
-pair_coeff    3    7  lj/cut/coul/long/soft    0.0000   1.0000  1.0  # H-D Hw
-pair_coeff    3    8  lj/cut/coul/long/soft    0.0683   2.8131  1.0  # H-D Ow
-pair_coeff    4    4  none  # H-H1 H-H1
-pair_coeff    4    5  none  # H-H1 OHD-
-pair_coeff    4    6  lj/cut/coul/long/soft    0.0000   1.0000  0.0 # H-H1 HOD-
-pair_coeff    4    7  lj/cut/coul/long    0.0000   1.0000  # H-H1 Hw
-pair_coeff    4    8  lj/cut/coul/long    0.0683   2.8131  # H-H1 Ow
-pair_coeff    5    5  none  # OHD- OHD-
-pair_coeff    5    6  none  # OHD- HOD-
-pair_coeff    5    7  lj/cut/coul/long/soft    0.0000   1.0000  0.0  # OHD- Hw
-pair_coeff    5    8  lj/cut/coul/long/soft    0.1625   3.1427  0.0  # OHD- Ow
-pair_coeff    6    6  none  # HOD- HOD-
-pair_coeff    6    7  lj/cut/coul/long/soft    0.0000   1.0000  0.0  # HOD- Hw
-pair_coeff    6    8  lj/cut/coul/long/soft    0.0000   1.7792  0.0  # HOD- Ow
-pair_coeff    7    7  lj/cut/coul/long    0.0000   1.0000  # Hw Hw
-pair_coeff    7    8  lj/cut/coul/long    0.0000   1.0000  # Hw Ow
-pair_coeff    8    8  lj/cut/coul/long    0.1554   3.1655  # Ow Ow
-
-variable nsteps equal 25000
-variable nprint equal ${nsteps}/500
-variable ndump equal ${nsteps}/100
-# variable nrestart equal ${nsteps}/10
-
-variable temp equal 300.0
-variable press equal 1.0
-
-neighbor 2.0 bin
-
-timestep 2.0
-
-# velocity all create ${temp} 12345
-
-thermo_style multi
-thermo ${nprint}
-
-fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
-
-fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
-
-run 10000
-reset_timestep 0
-write_restart  init.restart
-
-
-variable lambda equal ramp(0.0,1.0)
-variable minusl equal 1.0-v_lambda
-variable q1 equal  0.145*v_lambda-0.180*(1.0-v_lambda)
-variable q2 equal -0.180*(1.0-v_lambda)
-variable q3 equal  0.060*(1.0-v_lambda)
-variable q4 equal  0.040*v_lambda+0.060*(1.0-v_lambda)
-variable q5 equal -0.683*v_lambda
-variable q6 equal  0.418*v_lambda
-
-fix fADAPT all adapt/fep 125000 &
-    pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusl &
-    pair lj/cut/coul/long/soft lambda 3 4 v_minusl &
-    pair lj/cut/coul/long/soft lambda 4 6 v_lambda &
-    pair lj/cut/coul/long/soft lambda 5*6 7*8 v_lambda &
-    atom charge 1 v_q1 &
-    atom charge 2 v_q2 &
-    atom charge 3 v_q3 &
-    atom charge 4 v_q4 &
-    atom charge 5 v_q5 &
-    atom charge 6 v_q6 &
-    after yes
-
-variable dlambda equal 0.05
-variable minusdl equal -0.05
-variable dq1 equal  0.145*v_dlambda+0.180*v_dlambda
-variable dq2 equal  0.180*v_dlambda
-variable dq3 equal -0.060*v_dlambda
-variable dq4 equal  0.040*v_dlambda-0.060*v_dlambda
-variable dq5 equal -0.683*v_dlambda
-variable dq6 equal  0.418*v_dlambda
-
-compute cFEP all fep ${temp} &
-    pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusdl &
-    pair lj/cut/coul/long/soft lambda 3 4 v_minusdl &
-    pair lj/cut/coul/long/soft lambda 4 6 v_dlambda &
-    pair lj/cut/coul/long/soft lambda 5*6 7*8 v_dlambda &
-    atom charge 1 v_dq1 &
-    atom charge 2 v_dq2 &
-    atom charge 3 v_dq3 &
-    atom charge 4 v_dq4 &
-    atom charge 5 v_dq5 &
-    atom charge 6 v_dq6
-
-fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fep01.lmp
-
-# compute cRDF all rdf 100 1 1
-# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
-
-compute cMSD all msd
-fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
-
-dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
-dump_modify dCONF element C C H H O H H O
-
-# restart ${nrestart} restart.*.lmp
-
-run ${nsteps}
-
-write_restart restart.*.lmp
-write_data data.*.lmp

examples/USER/fep/CC-CO/fep01/in.fep01.lmp

@@ -16,70 +16,67 @@ read_data data.0.lmp
 pair_style hybrid lj/cut/coul/long 10.0 10.0 &
   lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
 pair_modify tail no
-kspace_style pppm 1.0e-4
+kspace_style pppm 1.0e-5
 
-pair_coeff    1    1  none  # C-CO C-CO
-pair_coeff    1    2  none  # C-CO C-D
-pair_coeff    1    3  none  # C-CO H-D
-pair_coeff    1    4  none  # C-CO H-H1
-pair_coeff    1    5  none  # C-CO OHD-
-pair_coeff    1    6  none  # C-CO HOD-
-pair_coeff    1    7  lj/cut/coul/long    0.0000   1.0000  # C-CO Hw
-pair_coeff    1    8  lj/cut/coul/long    0.1013   3.3286  # C-CO Ow
-pair_coeff    2    2  none  # C-D C-D
-pair_coeff    2    3  none  # C-D H-D
-pair_coeff    2    4  none  # C-D H-H1
-pair_coeff    2    5  none  # C-D OHD-
-pair_coeff    2    6  none  # C-D HOD-
-pair_coeff    2    7  lj/cut/coul/long/soft    0.0000   1.0000  1.0  # C-D Hw
-pair_coeff    2    8  lj/cut/coul/long/soft    0.1013   3.3286  1.0  # C-D Ow
-pair_coeff    3    3  none  # H-D H-D
-pair_coeff    3    4  lj/cut/coul/long/soft    0.0300   2.5000  1.0  # H-D H-H1
-pair_coeff    3    5  none  # H-D OHD-
-pair_coeff    3    6  none  # H-D HOD-
-pair_coeff    3    7  lj/cut/coul/long/soft    0.0000   1.0000  1.0  # H-D Hw
-pair_coeff    3    8  lj/cut/coul/long/soft    0.0683   2.8131  1.0  # H-D Ow
-pair_coeff    4    4  none  # H-H1 H-H1
-pair_coeff    4    5  none  # H-H1 OHD-
-pair_coeff    4    6  lj/cut/coul/long/soft    0.0000   1.0000  0.0 # H-H1 HOD-
-pair_coeff    4    7  lj/cut/coul/long    0.0000   1.0000  # H-H1 Hw
-pair_coeff    4    8  lj/cut/coul/long    0.0683   2.8131  # H-H1 Ow
-pair_coeff    5    5  none  # OHD- OHD-
-pair_coeff    5    6  none  # OHD- HOD-
-pair_coeff    5    7  lj/cut/coul/long/soft    0.0000   1.0000  0.0  # OHD- Hw
-pair_coeff    5    8  lj/cut/coul/long/soft    0.1625   3.1427  0.0  # OHD- Ow
-pair_coeff    6    6  none  # HOD- HOD-
-pair_coeff    6    7  lj/cut/coul/long/soft    0.0000   1.0000  0.0  # HOD- Hw
-pair_coeff    6    8  lj/cut/coul/long/soft    0.0000   1.7792  0.0  # HOD- Ow
-pair_coeff    7    7  lj/cut/coul/long    0.0000   1.0000  # Hw Hw
-pair_coeff    7    8  lj/cut/coul/long    0.0000   1.0000  # Hw Ow
-pair_coeff    8    8  lj/cut/coul/long    0.1554   3.1655  # Ow Ow
+# use pair soft for atoms that may overlap
+# zero epsilon between appearing and desappearing sites: 2-5 3-5 
+pair_coeff    1    1 lj/cut/coul/long     0.065999     3.500000  # C-CO C-CO
+pair_coeff    1    2 lj/cut/coul/long     0.065999     3.500000  # C-CO C-D
+pair_coeff    1    3 lj/cut/coul/long     0.044497     2.958040  # C-CO H-D
+pair_coeff    1    4 lj/cut/coul/long     0.044497     2.958040  # C-CO H-H1
+pair_coeff    1    5 lj/cut/coul/long     0.105924     3.304542  # C-CO OHD-
+pair_coeff    1    6 lj/cut/coul/long     0.000000     1.870829  # C-CO HOD-
+pair_coeff    1    7 lj/cut/coul/long     0.000000     1.870829  # C-CO Hw
+pair_coeff    1    8 lj/cut/coul/long     0.101281     3.328551  # C-CO Ow
+pair_coeff    2    2 lj/cut/coul/long     0.065999     3.500000  # C-D C-D
+pair_coeff    2    3 lj/cut/coul/long     0.044497     2.958040  # C-D H-D
+pair_coeff    2    4 lj/cut/coul/long     0.044497     2.958040  # C-D H-H1
+pair_coeff    2    5 lj/cut/coul/long     0.000000     3.304542  # C-D OHD-
+pair_coeff    2    6 lj/cut/coul/long     0.000000     1.870829  # C-D HOD-
+pair_coeff    2    7 lj/cut/coul/long/soft     0.000000     1.870829  1.0  # C-D Hw
+pair_coeff    2    8 lj/cut/coul/long/soft     0.101281     3.328551  1.0  # C-D Ow
+pair_coeff    3    3 lj/cut/coul/long     0.030000     2.500000  # H-D H-D
+pair_coeff    3    4 lj/cut/coul/long/soft     0.030000     2.500000  1.0  # H-D H-H1
+pair_coeff    3    5 lj/cut/coul/long     0.000000     2.792848  # H-D OHD-
+pair_coeff    3    6 lj/cut/coul/long     0.000000     1.581139  # H-D HOD-
+pair_coeff    3    7 lj/cut/coul/long/soft     0.000000     1.581139  1.0  # H-D Hw
+pair_coeff    3    8 lj/cut/coul/long/soft     0.068284     2.813139  1.0  # H-D Ow
+pair_coeff    4    4 lj/cut/coul/long     0.030000     2.500000  # H-H1 H-H1
+pair_coeff    4    5 lj/cut/coul/long     0.071414     2.792848  # H-H1 OHD-
+pair_coeff    4    6 lj/cut/coul/long/soft     0.000000     1.581139  0.0  # H-H1 HOD-
+pair_coeff    4    7 lj/cut/coul/long     0.000000     1.581139  # H-H1 Hw
+pair_coeff    4    8 lj/cut/coul/long     0.068284     2.813139  # H-H1 Ow
+pair_coeff    5    5 lj/cut/coul/long     0.170000     3.120000  # OHD- OHD-
+pair_coeff    5    6 lj/cut/coul/long     0.000000     1.766352  # OHD- HOD-
+pair_coeff    5    7 lj/cut/coul/long/soft     0.000000     1.766352  0.0  # OHD- Hw
+pair_coeff    5    8 lj/cut/coul/long/soft     0.162549     3.142668  0.0  # OHD- Ow
+pair_coeff    6    6 lj/cut/coul/long     0.000000     1.000000  # HOD- HOD-
+pair_coeff    6    7 lj/cut/coul/long/soft     0.000000     1.000000  0.0  # HOD- Hw
+pair_coeff    6    8 lj/cut/coul/long/soft     0.000000     1.779185  0.0  # HOD- Ow
+pair_coeff    7    7 lj/cut/coul/long     0.000000     1.000000  # Hw Hw
+pair_coeff    7    8 lj/cut/coul/long     0.000000     1.779185  # Hw Ow
+pair_coeff    8    8 lj/cut/coul/long     0.155425     3.165500  # Ow Ow
 
-variable nsteps equal 2500000
-variable nprint equal ${nsteps}/500
-variable ndump equal ${nsteps}/100
-# variable nrestart equal ${nsteps}/10
-
-variable temp equal 300.0
-variable press equal 1.0
+variable TK equal 300.0
+variable PBAR equal 1.0
 
 neighbor 2.0 bin
 
-timestep 2.0
+timestep 1.0
 
-velocity all create ${temp} 12345
+velocity all create ${TK} 12345
 
-thermo_style multi
-thermo ${nprint}
+fix SHAKE all shake 0.0001 20 0 b 2 4 5 a 6
 
-fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
+fix NPT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500
 
-fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
+thermo_style custom step cpu epair emol etotal temp press density
+thermo 1000
+
+run 200000
 
-run 250000
 reset_timestep 0
 
-
 variable lambda equal ramp(0.0,1.0)
 variable minusl equal 1.0-v_lambda
 variable q1 equal  0.145*v_lambda-0.180*(1.0-v_lambda)
@@ -89,7 +86,7 @@ variable q4 equal  0.040*v_lambda+0.060*(1.0-v_lambda)
 variable q5 equal -0.683*v_lambda
 variable q6 equal  0.418*v_lambda
 
-fix fADAPT all adapt/fep 125000 &
+fix ADAPT all adapt/fep 100000 &
     pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusl &
     pair lj/cut/coul/long/soft lambda 3 4 v_minusl &
     pair lj/cut/coul/long/soft lambda 4 6 v_lambda &
@@ -102,16 +99,16 @@ fix fADAPT all adapt/fep 125000 &
     atom charge 6 v_q6 &
     after yes
 
-variable dlambda equal 0.05
+variable dlambda equal  0.05
 variable minusdl equal -0.05
-variable dq1 equal  0.145*v_dlambda+0.180*v_dlambda
+variable dq1 equal (0.145+0.180)*v_dlambda
 variable dq2 equal  0.180*v_dlambda
 variable dq3 equal -0.060*v_dlambda
-variable dq4 equal  0.040*v_dlambda-0.060*v_dlambda
+variable dq4 equal (0.040-0.060)*v_dlambda
 variable dq5 equal -0.683*v_dlambda
 variable dq6 equal  0.418*v_dlambda
 
-compute cFEP all fep ${temp} &
+compute FEP all fep ${TK} &
     pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusdl &
     pair lj/cut/coul/long/soft lambda 3 4 v_minusdl &
     pair lj/cut/coul/long/soft lambda 4 6 v_dlambda &
@@ -121,22 +118,18 @@ compute cFEP all fep ${temp} &
     atom charge 3 v_dq3 &
     atom charge 4 v_dq4 &
     atom charge 5 v_dq5 &
-    atom charge 6 v_dq6
+    atom charge 6 v_dq6 &
+    volume yes
 
-fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fep01.lmp
+fix FEP all ave/time 20 4000 100000 c_FEP[*] file fep01.fep
 
-# compute cRDF all rdf 100 1 1
-# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
+thermo_style custom step cpu epair emol etotal temp press density v_lambda
 
-compute cMSD all msd
-fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
+dump TRAJ all custom 20000 dump.lammpstrj id mol type element xu yu zu
+dump_modify TRAJ element C C H H O H H O
 
-dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
-dump_modify dCONF element C C H H O H H O
+#restart 20000 restart1.lmp restart2.lmp
 
-# restart ${nrestart} restart.*.lmp
+run 2000000
 
-run ${nsteps}
-
-write_restart restart.*.lmp
 write_data data.*.lmp

examples/USER/fep/CC-CO/fep01/log.reference

@@ -1,285 +0,0 @@
-LAMMPS (18 Apr 2014-ICMS)
-WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
-  using 1 OpenMP thread(s) per MPI task
-# created by fftool
-
-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
-
-read_data data.0.lmp
-  orthogonal box = (-13.4438 -13.4438 -13.4438) to (13.4438 13.4438 13.4438)
-  2 by 2 by 2 MPI processor grid
-  reading atoms ...
-  1090 atoms
-  scanning bonds ...
-  1 = max bonds/atom
-  scanning angles ...
-  10 = max angles/atom
-  scanning dihedrals ...
-  12 = max dihedrals/atom
-  reading bonds ...
-  729 bonds
-  reading angles ...
-  377 angles
-  reading dihedrals ...
-  16 dihedrals
-  5 = max # of 1-2 neighbors
-  4 = max # of 1-3 neighbors
-  8 = max # of 1-4 neighbors
-  9 = max # of special neighbors
-# read_restart restart.*.lmp
-# reset_timestep 0
-
-pair_style hybrid lj/cut/coul/long 10.0 10.0   lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
-pair_modify tail no
-kspace_style pppm 1.0e-4
-
-pair_coeff    1    1  none  # C-CO C-CO
-pair_coeff    1    2  none  # C-CO C-D
-pair_coeff    1    3  none  # C-CO H-D
-pair_coeff    1    4  none  # C-CO H-H1
-pair_coeff    1    5  none  # C-CO OHD-
-pair_coeff    1    6  none  # C-CO HOD-
-pair_coeff    1    7  lj/cut/coul/long    0.0000   1.0000  # C-CO Hw
-pair_coeff    1    8  lj/cut/coul/long    0.1013   3.3286  # C-CO Ow
-pair_coeff    2    2  none  # C-D C-D
-pair_coeff    2    3  none  # C-D H-D
-pair_coeff    2    4  none  # C-D H-H1
-pair_coeff    2    5  none  # C-D OHD-
-pair_coeff    2    6  none  # C-D HOD-
-pair_coeff    2    7  lj/cut/coul/long/soft    0.0000   1.0000  1.0  # C-D Hw
-pair_coeff    2    8  lj/cut/coul/long/soft    0.1013   3.3286  1.0  # C-D Ow
-pair_coeff    3    3  none  # H-D H-D
-pair_coeff    3    4  lj/cut/coul/long/soft    0.0300   2.5000  1.0  # H-D H-H1
-pair_coeff    3    5  none  # H-D OHD-
-pair_coeff    3    6  none  # H-D HOD-
-pair_coeff    3    7  lj/cut/coul/long/soft    0.0000   1.0000  1.0  # H-D Hw
-pair_coeff    3    8  lj/cut/coul/long/soft    0.0683   2.8131  1.0  # H-D Ow
-pair_coeff    4    4  none  # H-H1 H-H1
-pair_coeff    4    5  none  # H-H1 OHD-
-pair_coeff    4    6  lj/cut/coul/long/soft    0.0000   1.0000  0.0 # H-H1 HOD-
-pair_coeff    4    7  lj/cut/coul/long    0.0000   1.0000  # H-H1 Hw
-pair_coeff    4    8  lj/cut/coul/long    0.0683   2.8131  # H-H1 Ow
-pair_coeff    5    5  none  # OHD- OHD-
-pair_coeff    5    6  none  # OHD- HOD-
-pair_coeff    5    7  lj/cut/coul/long/soft    0.0000   1.0000  0.0  # OHD- Hw
-pair_coeff    5    8  lj/cut/coul/long/soft    0.1625   3.1427  0.0  # OHD- Ow
-pair_coeff    6    6  none  # HOD- HOD-
-pair_coeff    6    7  lj/cut/coul/long/soft    0.0000   1.0000  0.0  # HOD- Hw
-pair_coeff    6    8  lj/cut/coul/long/soft    0.0000   1.7792  0.0  # HOD- Ow
-pair_coeff    7    7  lj/cut/coul/long    0.0000   1.0000  # Hw Hw
-pair_coeff    7    8  lj/cut/coul/long    0.0000   1.0000  # Hw Ow
-pair_coeff    8    8  lj/cut/coul/long    0.1554   3.1655  # Ow Ow
-
-variable nsteps equal 2500000
-variable nprint equal ${nsteps}/500
-variable nprint equal 2500000/500
-variable ndump equal ${nsteps}/100
-variable ndump equal 2500000/100
-# variable nrestart equal ${nsteps}/10
-
-variable temp equal 300.0
-variable press equal 1.0
-
-neighbor 2.0 bin
-
-timestep 2.0
-
-# velocity all create ${temp} 12345
-
-thermo_style multi
-thermo ${nprint}
-thermo 5000
-
-fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
-fix fSHAKE all shake 0.0001 20 5000 b 2 4 5 a 6
-  1 = # of size 2 clusters
-  0 = # of size 3 clusters
-  2 = # of size 4 clusters
-  360 = # of frozen angles
-
-fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
-fix fNPT all npt temp 300 ${temp} 100 iso ${press} ${press} 500
-fix fNPT all npt temp 300 300 100 iso ${press} ${press} 500
-fix fNPT all npt temp 300 300 100 iso 1 ${press} 500
-fix fNPT all npt temp 300 300 100 iso 1 1 500
-
-run 250000
-PPPM initialization ...
-  G vector (1/distance) = 0.270213
-  grid = 15 15 15
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0169033
-  estimated relative force accuracy = 5.09037e-05
-  using double precision FFTs
-  3d grid and FFT values/proc = 2744 512
-SHAKE stats (type/ave/delta) on step 0
-  2 1.09 4.99625e-06
-  4 0.945001 0
-  5 1 1.58341e-05
-  6 109.47 0.0012593
-Memory usage per processor = 8.38576 Mbytes
----------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
-TotEng   =      -236.7999 KinEng   =         0.0000 Temp     =         0.0000 
-PotEng   =      -236.7999 E_bond   =         0.0000 E_angle  =         0.3094 
-E_dihed  =         0.0001 E_impro  =         0.0000 E_vdwl   =      -192.9285 
-E_coul   =     19402.7702 E_long   =    -19446.9511 Press    =       406.6448 
-Volume   =     19438.0383 
-SHAKE stats (type/ave/delta) on step 5000
-  2 1.09006 8.6791e-07
-  4 0.945054 0
-  5 1.00006 3.8639e-06
-  6 109.47 0.000376049
----------------- Step     5000 ----- CPU =     16.4963 (sec) ----------------
-TotEng   =     -3314.5713 KinEng   =       650.7183 Temp     =       300.4163 
-PotEng   =     -3965.2896 E_bond   =         0.0875 E_angle  =         1.4729 
-E_dihed  =         0.4749 E_impro  =         0.0000 E_vdwl   =       774.1508 
-E_coul   =     14908.3382 E_long   =    -19649.8139 Press    =       358.7253 
-Volume   =     10987.1076 
-SHAKE stats (type/ave/delta) on step 10000
-  2 1.08998 2.43077e-07
-  4 0.944985 0
-  5 0.999985 4.10972e-06
-  6 109.47 0.000514527
----------------- Step    10000 ----- CPU =     34.0488 (sec) ----------------
-TotEng   =     -3279.4541 KinEng   =       689.4215 Temp     =       318.2843 
-PotEng   =     -3968.8755 E_bond   =         0.2040 E_angle  =         1.8441 
-E_dihed  =         0.1574 E_impro  =         0.0000 E_vdwl   =       703.3180 
-E_coul   =     14976.4466 E_long   =    -19650.8457 Press    =      -983.5171 
-Volume   =     10927.3524 
-SHAKE stats (type/ave/delta) on step 15000
-  2 1.09002 1.0199e-06
-  4 0.945017 0
-  5 1.00002 5.08944e-06
-  6 109.47 0.00042735
----------------- Step    15000 ----- CPU =     53.1541 (sec) ----------------
-TotEng   =     -3368.2566 KinEng   =       686.6827 Temp     =       317.0199 
-PotEng   =     -4054.9393 E_bond   =         0.4514 E_angle  =         1.5194 
-E_dihed  =         2.4125 E_impro  =         0.0000 E_vdwl   =       709.7507 
-E_coul   =     14880.7025 E_long   =    -19649.7759 Press    =     -1277.1945 
-Volume   =     10817.2760 
-SHAKE stats (type/ave/delta) on step 20000
-  2 1.09005 3.84509e-06
-  4 0.945044 0
-  5 1.00005 1.15463e-05
-  6 109.47 0.000893174
----------------- Step    20000 ----- CPU =     67.0658 (sec) ----------------
-TotEng   =     -3401.0672 KinEng   =       639.1818 Temp     =       295.0902 
-PotEng   =     -4040.2490 E_bond   =         0.8254 E_angle  =         4.2422 
-E_dihed  =         0.6223 E_impro  =         0.0000 E_vdwl   =       777.7799 
-E_coul   =     14826.3237 E_long   =    -19650.0425 Press    =      -268.5153 
-Volume   =     10911.3140 
-SHAKE stats (type/ave/delta) on step 25000
-  2 1.09 3.16085e-06
-  4 0.945002 0
-  5 1 6.82105e-06
-  6 109.47 0.000683982
----------------- Step    25000 ----- CPU =     83.1242 (sec) ----------------
-TotEng   =     -3331.9648 KinEng   =       658.5638 Temp     =       304.0383 
-PotEng   =     -3990.5287 E_bond   =         0.0504 E_angle  =         4.8757 
-E_dihed  =         0.9548 E_impro  =         0.0000 E_vdwl   =       742.1312 
-E_coul   =     14907.2989 E_long   =    -19645.8396 Press    =      -803.8894 
-Volume   =     11243.5807 
-SHAKE stats (type/ave/delta) on step 30000
-  2 1.08995 5.90921e-08
-  4 0.944954 0
-  5 0.999952 5.01043e-06
-  6 109.47 0.000369665
----------------- Step    30000 ----- CPU =     96.1911 (sec) ----------------
-TotEng   =     -3321.5197 KinEng   =       681.8132 Temp     =       314.7718 
-PotEng   =     -4003.3328 E_bond   =         0.5162 E_angle  =         6.2281 
-E_dihed  =         1.2145 E_impro  =         0.0000 E_vdwl   =       767.4719 
-E_coul   =     14871.6899 E_long   =    -19650.4535 Press    =        63.7724 
-Volume   =     10913.5775 
-SHAKE stats (type/ave/delta) on step 35000
-  2 1.08996 3.93868e-07
-  4 0.944963 0
-  5 0.999961 4.01003e-06
-  6 109.47 0.000492251
----------------- Step    35000 ----- CPU =    111.1547 (sec) ----------------
-TotEng   =     -3376.3100 KinEng   =       652.5134 Temp     =       301.2450 
-PotEng   =     -4028.8234 E_bond   =         0.6940 E_angle  =         3.8874 
-E_dihed  =         0.6796 E_impro  =         0.0000 E_vdwl   =       811.7936 
-E_coul   =     14803.9468 E_long   =    -19649.8247 Press    =       957.3673 
-Volume   =     10810.8812 
-SHAKE stats (type/ave/delta) on step 40000
-  2 1.08993 1.84911e-06
-  4 0.944937 0
-  5 0.999934 4.48159e-06
-  6 109.47 0.000423379
----------------- Step    40000 ----- CPU =    127.8336 (sec) ----------------
-TotEng   =     -3342.5048 KinEng   =       641.0827 Temp     =       295.9678 
-PotEng   =     -3983.5875 E_bond   =         1.4592 E_angle  =         3.3579 
-E_dihed  =         0.1250 E_impro  =         0.0000 E_vdwl   =       714.5090 
-E_coul   =     14945.5914 E_long   =    -19648.6299 Press    =     -1146.3509 
-Volume   =     10993.6945 
-SHAKE stats (type/ave/delta) on step 45000
-  2 1.09004 2.52413e-06
-  4 0.945038 0
-  5 1.00004 7.30752e-06
-  6 109.47 0.000660905
----------------- Step    45000 ----- CPU =    141.7030 (sec) ----------------
-TotEng   =     -3368.5223 KinEng   =       640.7082 Temp     =       295.7949 
-PotEng   =     -4009.2305 E_bond   =         0.0226 E_angle  =         2.7492 
-E_dihed  =         0.8929 E_impro  =         0.0000 E_vdwl   =       820.3025 
-E_coul   =     14817.6347 E_long   =    -19650.8325 Press    =       388.8981 
-Volume   =     11292.9397 
-SHAKE stats (type/ave/delta) on step 50000
-  2 1.09006 2.89749e-06
-  4 0.945051 0
-  5 1.00006 6.08927e-06
-  6 109.47 0.000779845
----------------- Step    50000 ----- CPU =    156.2936 (sec) ----------------
-TotEng   =     -3253.6028 KinEng   =       683.0893 Temp     =       315.3610 
-PotEng   =     -3936.6921 E_bond   =         0.4303 E_angle  =         5.1773 
-E_dihed  =         1.1538 E_impro  =         0.0000 E_vdwl   =       722.3282 
-E_coul   =     14982.9162 E_long   =    -19648.6979 Press    =      -338.7238 
-Volume   =     11230.1507 
-SHAKE stats (type/ave/delta) on step 55000
-  2 1.09007 9.95472e-07
-  4 0.945062 0
-  5 1.00007 3.93786e-06
-  6 109.47 0.000436645
----------------- Step    55000 ----- CPU =    176.2674 (sec) ----------------
-TotEng   =     -3332.0820 KinEng   =       662.9270 Temp     =       306.0527 
-PotEng   =     -3995.0090 E_bond   =         0.8395 E_angle  =         1.9527 
-E_dihed  =         1.0770 E_impro  =         0.0000 E_vdwl   =       750.6359 
-E_coul   =     14899.3802 E_long   =    -19648.8943 Press    =      -498.7755 
-Volume   =     11082.6763 
-SHAKE stats (type/ave/delta) on step 60000
-  2 1.09006 7.79087e-08
-  4 0.945052 1.22125e-15
-  5 1.00006 3.87615e-06
-  6 109.47 0.000355506
----------------- Step    60000 ----- CPU =    193.3379 (sec) ----------------
-TotEng   =     -3296.5834 KinEng   =       679.6746 Temp     =       313.7845 
-PotEng   =     -3976.2580 E_bond   =         2.4610 E_angle  =         2.9231 
-E_dihed  =         0.8719 E_impro  =         0.0000 E_vdwl   =       803.1348 
-E_coul   =     14863.3163 E_long   =    -19648.9651 Press    =      1009.2429 
-Volume   =     11125.1736 
-SHAKE stats (type/ave/delta) on step 65000
-  2 1.09003 1.05995e-06
-  4 0.945023 1.22125e-15
-  5 1.00003 4.3471e-06
-  6 109.47 0.000511365
----------------- Step    65000 ----- CPU =    210.3194 (sec) ----------------
-TotEng   =     -3322.0496 KinEng   =       666.5091 Temp     =       307.7064 
-PotEng   =     -3988.5587 E_bond   =         0.8728 E_angle  =         5.7476 
-E_dihed  =         0.9783 E_impro  =         0.0000 E_vdwl   =       743.8165 
-E_coul   =     14910.0426 E_long   =    -19650.0166 Press    =      -421.7167 
-Volume   =     10902.5998 
-SHAKE stats (type/ave/delta) on step 70000
-  2 1.0901 1.09831e-06
-  4 0.94509 0
-  5 1.0001 3.59309e-06
-  6 109.47 0.000361318
----------------- Step    70000 ----- CPU =    228.7878 (sec) ----------------
-TotEng   =     -3395.7912 KinEng   =       667.4514 Temp     =       308.1414 
-PotEng   =     -4063.2426 E_bond   =         0.6965 E_angle  =         5.1350 
-E_dihed  

examples/USER/fep/CC-CO/fep01/log.reference-omp

@@ -1,287 +0,0 @@
-LAMMPS (18 Apr 2014-ICMS)
-WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
-  using 1 OpenMP thread(s) per MPI task
-package omp *
-using multi-threaded neighbor list subroutines
-prefer double precision OpenMP force kernels
-# created by fftool
-
-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
-
-read_data data.0.lmp
-  orthogonal box = (-13.4438 -13.4438 -13.4438) to (13.4438 13.4438 13.4438)
-  2 by 2 by 2 MPI processor grid
-  reading atoms ...
-  1090 atoms
-  scanning bonds ...
-  1 = max bonds/atom
-  scanning angles ...
-  10 = max angles/atom
-  scanning dihedrals ...
-  12 = max dihedrals/atom
-  reading bonds ...
-  729 bonds
-  reading angles ...
-  377 angles
-  reading dihedrals ...
-  16 dihedrals
-  5 = max # of 1-2 neighbors
-  4 = max # of 1-3 neighbors
-  8 = max # of 1-4 neighbors
-  9 = max # of special neighbors
-# read_restart restart.*.lmp
-# reset_timestep 0
-
-pair_style hybrid lj/cut/coul/long 10.0 10.0   lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
-pair_modify tail no
-kspace_style pppm 1.0e-4
-
-pair_coeff    1    1  none  # C-CO C-CO
-pair_coeff    1    2  none  # C-CO C-D
-pair_coeff    1    3  none  # C-CO H-D
-pair_coeff    1    4  none  # C-CO H-H1
-pair_coeff    1    5  none  # C-CO OHD-
-pair_coeff    1    6  none  # C-CO HOD-
-pair_coeff    1    7  lj/cut/coul/long    0.0000   1.0000  # C-CO Hw
-pair_coeff    1    8  lj/cut/coul/long    0.1013   3.3286  # C-CO Ow
-pair_coeff    2    2  none  # C-D C-D
-pair_coeff    2    3  none  # C-D H-D
-pair_coeff    2    4  none  # C-D H-H1
-pair_coeff    2    5  none  # C-D OHD-
-pair_coeff    2    6  none  # C-D HOD-
-pair_coeff    2    7  lj/cut/coul/long/soft    0.0000   1.0000  1.0  # C-D Hw
-pair_coeff    2    8  lj/cut/coul/long/soft    0.1013   3.3286  1.0  # C-D Ow
-pair_coeff    3    3  none  # H-D H-D
-pair_coeff    3    4  lj/cut/coul/long/soft    0.0300   2.5000  1.0  # H-D H-H1
-pair_coeff    3    5  none  # H-D OHD-
-pair_coeff    3    6  none  # H-D HOD-
-pair_coeff    3    7  lj/cut/coul/long/soft    0.0000   1.0000  1.0  # H-D Hw
-pair_coeff    3    8  lj/cut/coul/long/soft    0.0683   2.8131  1.0  # H-D Ow
-pair_coeff    4    4  none  # H-H1 H-H1
-pair_coeff    4    5  none  # H-H1 OHD-
-pair_coeff    4    6  lj/cut/coul/long/soft    0.0000   1.0000  0.0 # H-H1 HOD-
-pair_coeff    4    7  lj/cut/coul/long    0.0000   1.0000  # H-H1 Hw
-pair_coeff    4    8  lj/cut/coul/long    0.0683   2.8131  # H-H1 Ow
-pair_coeff    5    5  none  # OHD- OHD-
-pair_coeff    5    6  none  # OHD- HOD-
-pair_coeff    5    7  lj/cut/coul/long/soft    0.0000   1.0000  0.0  # OHD- Hw
-pair_coeff    5    8  lj/cut/coul/long/soft    0.1625   3.1427  0.0  # OHD- Ow
-pair_coeff    6    6  none  # HOD- HOD-
-pair_coeff    6    7  lj/cut/coul/long/soft    0.0000   1.0000  0.0  # HOD- Hw
-pair_coeff    6    8  lj/cut/coul/long/soft    0.0000   1.7792  0.0  # HOD- Ow
-pair_coeff    7    7  lj/cut/coul/long    0.0000   1.0000  # Hw Hw
-pair_coeff    7    8  lj/cut/coul/long    0.0000   1.0000  # Hw Ow
-pair_coeff    8    8  lj/cut/coul/long    0.1554   3.1655  # Ow Ow
-
-variable nsteps equal 2500000
-variable nprint equal ${nsteps}/500
-variable nprint equal 2500000/500
-variable ndump equal ${nsteps}/100
-variable ndump equal 2500000/100
-# variable nrestart equal ${nsteps}/10
-
-variable temp equal 300.0
-variable press equal 1.0
-
-neighbor 2.0 bin
-
-timestep 2.0
-
-# velocity all create ${temp} 12345
-
-thermo_style multi
-thermo ${nprint}
-thermo 5000
-
-fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
-fix fSHAKE all shake 0.0001 20 5000 b 2 4 5 a 6
-  1 = # of size 2 clusters
-  0 = # of size 3 clusters
-  2 = # of size 4 clusters
-  360 = # of frozen angles
-
-fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
-fix fNPT all npt temp 300 ${temp} 100 iso ${press} ${press} 500
-fix fNPT all npt temp 300 300 100 iso ${press} ${press} 500
-fix fNPT all npt temp 300 300 100 iso 1 ${press} 500
-fix fNPT all npt temp 300 300 100 iso 1 1 500
-
-run 250000
-PPPM initialization ...
-  G vector (1/distance) = 0.270213
-  grid = 15 15 15
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0169033
-  estimated relative force accuracy = 5.09037e-05
-  using double precision FFTs
-  3d grid and FFT values/proc = 2744 512
-Hybrid pair style last /omp style lj/cut/coul/long/soft
-Last active /omp style is kspace_style pppm/omp
-SHAKE stats (type/ave/delta) on step 0
-  2 1.09 4.99625e-06
-  4 0.945001 0
-  5 1 1.58341e-05
-  6 109.47 0.0012593
-Memory usage per processor = 8.38667 Mbytes
----------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
-TotEng   =      -236.7999 KinEng   =         0.0000 Temp     =         0.0000 
-PotEng   =      -236.7999 E_bond   =         0.0000 E_angle  =         0.3094 
-E_dihed  =         0.0001 E_impro  =         0.0000 E_vdwl   =      -192.9285 
-E_coul   =     19402.7702 E_long   =    -19446.9511 Press    =       406.6448 
-Volume   =     19438.0383 
-SHAKE stats (type/ave/delta) on step 5000
-  2 1.09009 2.87398e-07
-  4 0.945079 0
-  5 1.00008 3.9811e-06
-  6 109.47 0.000369321
----------------- Step     5000 ----- CPU =     11.8253 (sec) ----------------
-TotEng   =     -3307.2904 KinEng   =       658.6061 Temp     =       304.0578 
-PotEng   =     -3965.8965 E_bond   =         0.0083 E_angle  =         0.6669 
-E_dihed  =         0.2569 E_impro  =         0.0000 E_vdwl   =       734.5556 
-E_coul   =     14945.5504 E_long   =    -19646.9346 Press    =      -401.3652 
-Volume   =     10990.0279 
-SHAKE stats (type/ave/delta) on step 10000
-  2 1.08991 8.10164e-07
-  4 0.944925 0
-  5 0.999922 7.76553e-06
-  6 109.47 0.000694232
----------------- Step    10000 ----- CPU =     23.7032 (sec) ----------------
-TotEng   =     -3381.5340 KinEng   =       646.2577 Temp     =       298.3570 
-PotEng   =     -4027.7917 E_bond   =         0.2113 E_angle  =         1.2103 
-E_dihed  =         0.8831 E_impro  =         0.0000 E_vdwl   =       807.4931 
-E_coul   =     14812.7871 E_long   =    -19650.3766 Press    =      1168.7845 
-Volume   =     10591.5096 
-SHAKE stats (type/ave/delta) on step 15000
-  2 1.08988 6.96695e-07
-  4 0.944894 0
-  5 0.999889 7.87681e-06
-  6 109.47 0.000849755
----------------- Step    15000 ----- CPU =     37.0159 (sec) ----------------
-TotEng   =     -3391.4919 KinEng   =       640.6926 Temp     =       295.7878 
-PotEng   =     -4032.1845 E_bond   =         0.3271 E_angle  =         2.4027 
-E_dihed  =         0.2102 E_impro  =         0.0000 E_vdwl   =       833.3641 
-E_coul   =     14781.8806 E_long   =    -19650.3692 Press    =      1246.1602 
-Volume   =     10806.8631 
-SHAKE stats (type/ave/delta) on step 20000
-  2 1.09009 5.35061e-07
-  4 0.945076 0
-  5 1.00008 5.8947e-06
-  6 109.47 0.000481652
----------------- Step    20000 ----- CPU =     49.5427 (sec) ----------------
-TotEng   =     -3340.9663 KinEng   =       649.0129 Temp     =       299.6290 
-PotEng   =     -3989.9791 E_bond   =         0.2338 E_angle  =         1.4422 
-E_dihed  =         0.7066 E_impro  =         0.0000 E_vdwl   =       823.4408 
-E_coul   =     14835.4457 E_long   =    -19651.2482 Press    =      1369.0812 
-Volume   =     10984.3808 
-SHAKE stats (type/ave/delta) on step 25000
-  2 1.09003 1.29003e-06
-  4 0.945026 0
-  5 1.00003 5.08541e-06
-  6 109.47 0.000543653
----------------- Step    25000 ----- CPU =     61.5352 (sec) ----------------
-TotEng   =     -3350.1301 KinEng   =       628.6694 Temp     =       290.2370 
-PotEng   =     -3978.7994 E_bond   =         0.5250 E_angle  =         3.3362 
-E_dihed  =         1.1997 E_impro  =         0.0000 E_vdwl   =       753.6460 
-E_coul   =     14908.8825 E_long   =    -19646.3890 Press    =      -107.3383 
-Volume   =     10858.4423 
-SHAKE stats (type/ave/delta) on step 30000
-  2 1.09012 2.15723e-06
-  4 0.945104 0
-  5 1.00011 7.30223e-06
-  6 109.47 0.000722195
----------------- Step    30000 ----- CPU =     75.1590 (sec) ----------------
-TotEng   =     -3291.1533 KinEng   =       662.9659 Temp     =       306.0706 
-PotEng   =     -3954.1192 E_bond   =         0.0386 E_angle  =         3.4541 
-E_dihed  =         0.3158 E_impro  =         0.0000 E_vdwl   =       745.0479 
-E_coul   =     14947.2099 E_long   =    -19650.1856 Press    =      -296.2930 
-Volume   =     11301.5139 
-SHAKE stats (type/ave/delta) on step 35000
-  2 1.08998 1.28162e-06
-  4 0.944981 0
-  5 0.999982 8.25561e-06
-  6 109.47 0.000790911
----------------- Step    35000 ----- CPU =     86.8870 (sec) ----------------
-TotEng   =     -3370.6689 KinEng   =       637.0075 Temp     =       294.0864 
-PotEng   =     -4007.6763 E_bond   =         0.2585 E_angle  =         2.7426 
-E_dihed  =         0.2288 E_impro  =         0.0000 E_vdwl   =       766.3429 
-E_coul   =     14871.1344 E_long   =    -19648.3835 Press    =      -434.1739 
-Volume   =     11077.2342 
-SHAKE stats (type/ave/delta) on step 40000
-  2 1.09005 3.30799e-07
-  4 0.945044 0
-  5 1.00005 4.39187e-06
-  6 109.47 0.000367325
----------------- Step    40000 ----- CPU =    102.1257 (sec) ----------------
-TotEng   =     -3318.0442 KinEng   =       694.3948 Temp     =       320.5803 
-PotEng   =     -4012.4390 E_bond   =         0.3986 E_angle  =         4.3594 
-E_dihed  =         1.0551 E_impro  =         0.0000 E_vdwl   =       716.6662 
-E_coul   =     14914.0530 E_long   =    -19648.9712 Press    =     -1177.4188 
-Volume   =     11087.6184 
-SHAKE stats (type/ave/delta) on step 45000
-  2 1.08997 7.63663e-06
-  4 0.944973 0
-  5 0.999973 2.30441e-05
-  6 109.47 0.00155851
----------------- Step    45000 ----- CPU =    119.3648 (sec) ----------------
-TotEng   =     -3371.5332 KinEng   =       660.1645 Temp     =       304.7773 
-PotEng   =     -4031.6977 E_bond   =         1.3352 E_angle  =         2.6760 
-E_dihed  =         1.0255 E_impro  =         0.0000 E_vdwl   =       734.4320 
-E_coul   =     14878.0777 E_long   =    -19649.2440 Press    =      -978.3955 
-Volume   =     11108.5059 
-SHAKE stats (type/ave/delta) on step 50000
-  2 1.09015 1.28872e-06
-  4 0.945128 0
-  5 1.00014 5.27234e-06
-  6 109.47 0.000408939
----------------- Step    50000 ----- CPU =    132.4029 (sec) ----------------
-TotEng   =     -3345.1117 KinEng   =       660.2366 Temp     =       304.8106 
-PotEng   =     -4005.3482 E_bond   =         0.9878 E_angle  =         3.3427 
-E_dihed  =         0.4740 E_impro  =         0.0000 E_vdwl   =       763.3350 
-E_coul   =     14874.5886 E_long   =    -19648.0763 Press    =       257.8221 
-Volume   =     10750.8743 
-SHAKE stats (type/ave/delta) on step 55000
-  2 1.09006 1.79853e-06
-  4 0.945055 0
-  5 1.00006 8.96473e-06
-  6 109.47 0.000604022
----------------- Step    55000 ----- CPU =    144.3965 (sec) ----------------
-TotEng   =     -3329.0112 KinEng   =       639.1918 Temp     =       295.0949 
-PotEng   =     -3968.2030 E_bond   =         0.3779 E_angle  =         4.2627 
-E_dihed  =         0.1647 E_impro  =         0.0000 E_vdwl   =       775.0143 
-E_coul   =     14900.7482 E_long   =    -19648.7708 Press    =       384.3466 
-Volume   =     10943.9465 
-SHAKE stats (type/ave/delta) on step 60000
-  2 1.09006 5.76725e-07
-  4 0.94505 0
-  5 1.00005 4.15938e-06
-  6 109.47 0.000456895
----------------- Step    60000 ----- CPU =    158.9285 (sec) ----------------
-TotEng   =     -3337.6373 KinEng   =       686.3391 Temp     =       316.8613 
-PotEng   =     -4023.9764 E_bond   =         0.1951 E_angle  =         3.2295 
-E_dihed  =         0.2227 E_impro  =         0.0000 E_vdwl   =       803.8460 
-E_coul   =     14822.5916 E_long   =    -19654.0613 Press    =       343.2839 
-Volume   =     11053.5476 
-SHAKE stats (type/ave/delta) on step 65000
-  2 1.08992 1.92627e-06
-  4 0.944928 0
-  5 0.999925 9.65284e-06
-  6 109.47 0.000982037
----------------- Step    65000 ----- CPU =    171.6679 (sec) ----------------
-TotEng   =     -3286.1431 KinEng   =       655.6296 Temp     =       302.6837 
-PotEng   =     -3941.7726 E_bond   =         0.8912 E_angle  =         5.2439 
-E_dihed  =         1.0392 E_impro  =         0.0000 E_vdwl   =       723.8338 
-E_coul   =     14977.3056 E_long   =    -19650.0863 Press    =      -610.8426 
-Volume   =     11125.9793 
-SHAKE stats (type/ave/delta) on step 70000
-  2 1.08995 3.49023e-07
-  4 0.944954 0
-  5 0.999952 3.62092e-06
-  6 109.47 0.000402967
----------------- Step    70000 ----- CPU

examples/USER/fep/CC-CO/fep10/fep10.fep

@@ -0,0 +1,22 @@
+# Time-averaged data for fix FEP
+# TimeStep c_FEP[1] c_FEP[2] c_FEP[3]
+100000 1.55561 1173.35 10967.2
+200000 1.26758 1706.42 10917.2
+300000 0.91231 3045.94 10923.2
+400000 0.639111 4499.99 10961.2
+500000 0.40046 6497.21 10962.2
+600000 0.279001 7565.63 10963.9
+700000 0.233332 8053.37 10927.2
+800000 0.150123 9047.58 10949.7
+900000 0.159809 8841.01 10966.4
+1000000 0.146608 9019.04 10941.9
+1100000 0.121731 9308.38 10929.3
+1200000 0.10571 9530.24 10970.7
+1300000 0.0851774 9781.09 10983.2
+1400000 0.0889958 9711.62 10952.8
+1500000 0.0758179 9904.38 10962.1
+1600000 0.0687379 10005.4 10953.8
+1700000 0.0500615 10342.1 10928
+1800000 0.0165215 11146.2 10997
+1900000 -0.0358799 12457.9 11003.3
+2000000 -0.136771 16018.6 10954

examples/USER/fep/CC-CO/fep10/fep10.lmp

@@ -1,22 +0,0 @@
-# Time-averaged data for fix fFEP
-# TimeStep c_cFEP[1] c_cFEP[2]
-125000 1.6302 0.0823708
-250000 1.42237 0.11283
-375000 1.1798 0.168088
-500000 0.869449 0.279336
-625000 0.610803 0.412455
-750000 0.489597 0.486584
-875000 0.34439 0.601048
-1000000 0.303411 0.640696
-1125000 0.244627 0.70206
-1250000 0.204737 0.746389
-1375000 0.144716 0.816302
-1500000 0.0941156 0.880968
-1625000 0.0575351 0.933564
-1750000 0.0171831 0.992497
-1875000 -0.018964 1.05078
-2000000 -0.0457397 1.09726
-2125000 -0.0904898 1.17888
-2250000 -0.128205 1.25226
-2375000 -0.155891 1.31122
-2500000 -0.194237 1.3965

examples/USER/fep/CC-CO/fep10/in.fep10.lmp

@@ -16,70 +16,67 @@ read_data data.1.lmp
 pair_style hybrid lj/cut/coul/long 10.0 10.0 &
   lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
 pair_modify tail no
-kspace_style pppm 1.0e-4
+kspace_style pppm 1.0e-5
 
-pair_coeff    1    1  none  # CO-C CO-C
-pair_coeff    1    2  none  # CO-C CD-
-pair_coeff    1    3  none  # CO-C HD-
-pair_coeff    1    4  none  # CO-C H1-H
-pair_coeff    1    5  none  # CO-C OH-D
-pair_coeff    1    6  none  # CO-C HO-D
-pair_coeff    1    7  lj/cut/coul/long    0.0000   1.0000  # CO-C Hw
-pair_coeff    1    8  lj/cut/coul/long    0.1013   3.3286  # CO-C Ow
-pair_coeff    2    2  none  # CD- CD-
-pair_coeff    2    3  none  # CD- HD-
-pair_coeff    2    4  none  # CD- H1-H
-pair_coeff    2    5  none  # CD- OH-D
-pair_coeff    2    6  none  # CD- HO-D
-pair_coeff    2    7  lj/cut/coul/long/soft    0.0000   1.0000  0.0  # CD- Hw
-pair_coeff    2    8  lj/cut/coul/long/soft    0.1013   3.3286  0.0  # CD- Ow
-pair_coeff    3    3  none  # HD- HD-
-pair_coeff    3    4  lj/cut/coul/long/soft    0.0300   2.5000  0.0  # HD- H1-H
-pair_coeff    3    5  none  # HD- OH-D
-pair_coeff    3    6  none  # HD- HO-D
-pair_coeff    3    7  lj/cut/coul/long/soft    0.0000   1.0000  0.0  # HD- Hw
-pair_coeff    3    8  lj/cut/coul/long/soft    0.0683   2.8131  0.0  # HD- Ow
-pair_coeff    4    4  none  # H1-H H1-H
-pair_coeff    4    5  none  # H1-H OH-D
-pair_coeff    4    6  lj/cut/coul/long/soft    0.0000   1.0000  1.0 # H1-H HO-D
-pair_coeff    4    7  lj/cut/coul/long    0.0000   1.0000  # H1-H Hw
-pair_coeff    4    8  lj/cut/coul/long    0.0683   2.8131  # H1-H Ow
-pair_coeff    5    5  none  # OH-D OH-D
-pair_coeff    5    6  none  # OH-D HO-D
-pair_coeff    5    7  lj/cut/coul/long/soft    0.0000   1.0000  1.0  # OH-D Hw
-pair_coeff    5    8  lj/cut/coul/long/soft    0.1625   3.1427  1.0  # OH-D Ow
-pair_coeff    6    6  none  # HO-D HO-D
-pair_coeff    6    7  lj/cut/coul/long/soft    0.0000   1.0000  1.0  # HO-D Hw
-pair_coeff    6    8  lj/cut/coul/long/soft    0.0000   1.7792  1.0  # HO-D Ow
-pair_coeff    7    7  lj/cut/coul/long    0.0000   1.0000  # Hw Hw
-pair_coeff    7    8  lj/cut/coul/long    0.0000   1.0000  # Hw Ow
-pair_coeff    8    8  lj/cut/coul/long    0.1554   3.1655  # Ow Ow
+# use pair soft for atoms that may overlap
+# zero epsilon between appearing and desappearing sites: 2-5 3-5
+pair_coeff    1    1 lj/cut/coul/long     0.065999     3.500000  # CO-C CO-C
+pair_coeff    1    2 lj/cut/coul/long     0.065999     3.500000  # CO-C CD-
+pair_coeff    1    3 lj/cut/coul/long     0.044497     2.958040  # CO-C HD-
+pair_coeff    1    4 lj/cut/coul/long     0.044497     2.958040  # CO-C H1-H
+pair_coeff    1    5 lj/cut/coul/long     0.105924     3.304542  # CO-C OH-D
+pair_coeff    1    6 lj/cut/coul/long     0.000000     1.870829  # CO-C HO-D
+pair_coeff    1    7 lj/cut/coul/long     0.000000     1.870829  # CO-C Hw
+pair_coeff    1    8 lj/cut/coul/long     0.101281     3.328551  # CO-C Ow
+pair_coeff    2    2 lj/cut/coul/long     0.065999     3.500000  # CD- CD-
+pair_coeff    2    3 lj/cut/coul/long     0.044497     2.958040  # CD- HD-
+pair_coeff    2    4 lj/cut/coul/long     0.044497     2.958040  # CD- H1-H
+pair_coeff    2    5 lj/cut/coul/long     0.000000     3.304542  # CD- OH-D
+pair_coeff    2    6 lj/cut/coul/long     0.000000     1.870829  # CD- HO-D
+pair_coeff    2    7 lj/cut/coul/long/soft     0.000000     1.870829  0.0  # CD- Hw
+pair_coeff    2    8 lj/cut/coul/long/soft     0.101281     3.328551  0.0  # CD- Ow
+pair_coeff    3    3 lj/cut/coul/long     0.030000     2.500000  # HD- HD-
+pair_coeff    3    4 lj/cut/coul/long/soft     0.030000     2.500000  0.0  # HD- H1-H
+pair_coeff    3    5 lj/cut/coul/long     0.000000     2.792848  # HD- OH-D
+pair_coeff    3    6 lj/cut/coul/long     0.000000     1.581139  # HD- HO-D
+pair_coeff    3    7 lj/cut/coul/long/soft     0.000000     1.581139  0.0  # HD- Hw
+pair_coeff    3    8 lj/cut/coul/long/soft     0.068284     2.813139  0.0  # HD- Ow
+pair_coeff    4    4 lj/cut/coul/long     0.030000     2.500000  # H1-H H1-H
+pair_coeff    4    5 lj/cut/coul/long     0.071414     2.792848  # H1-H OH-D
+pair_coeff    4    6 lj/cut/coul/long/soft     0.000000     1.581139  1.0  # H1-H HO-D
+pair_coeff    4    7 lj/cut/coul/long     0.000000     1.581139  # H1-H Hw
+pair_coeff    4    8 lj/cut/coul/long     0.068284     2.813139  # H1-H Ow
+pair_coeff    5    5 lj/cut/coul/long     0.170000     3.120000  # OH-D OH-D
+pair_coeff    5    6 lj/cut/coul/long     0.000000     1.766352  # OH-D HO-D
+pair_coeff    5    7 lj/cut/coul/long/soft     0.000000     1.766352  1.0  # OH-D Hw
+pair_coeff    5    8 lj/cut/coul/long/soft     0.162549     3.142668  1.0  # OH-D Ow
+pair_coeff    6    6 lj/cut/coul/long     0.000000     1.000000  # HO-D HO-D
+pair_coeff    6    7 lj/cut/coul/long/soft     0.000000     1.000000  1.0  # HO-D Hw
+pair_coeff    6    8 lj/cut/coul/long/soft     0.000000     1.779185  1.0  # HO-D Ow
+pair_coeff    7    7 lj/cut/coul/long     0.000000     1.000000  # Hw Hw
+pair_coeff    7    8 lj/cut/coul/long     0.000000     1.779185  # Hw Ow
+pair_coeff    8    8 lj/cut/coul/long     0.155425     3.165500  # Ow Ow
 
-variable nsteps equal 2500000
-variable nprint equal ${nsteps}/500
-variable ndump equal ${nsteps}/100
-# variable nrestart equal ${nsteps}/10
-
-variable temp equal 300.0
-variable press equal 1.0
+variable TK equal 300.0
+variable PBAR equal 1.0
 
 neighbor 2.0 bin
 
-timestep 2.0
+timestep 1.0
 
-velocity all create ${temp} 12345
+velocity all create ${TK} 12345
 
-thermo_style multi
-thermo ${nprint}
+fix SHAKE all shake 0.0001 20 0 b 2 4 5 a 6
 
-fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
+fix NPT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500
 
-fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
+thermo_style custom step cpu epair emol etotal temp press density
+thermo 1000
+
+run 200000
 
-run 250000
 reset_timestep 0
 
-
 variable lambda equal ramp(1.0,0.0)
 variable minusl equal 1.0-v_lambda
 variable q1 equal  0.145*v_lambda-0.180*(1.0-v_lambda)
@@ -89,7 +86,7 @@ variable q4 equal  0.040*v_lambda+0.060*(1.0-v_lambda)
 variable q5 equal -0.683*v_lambda
 variable q6 equal  0.418*v_lambda
 
-fix fADAPT all adapt/fep 125000 &
+fix ADAPT all adapt/fep 100000 &
     pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusl &
     pair lj/cut/coul/long/soft lambda 3 4 v_minusl &
     pair lj/cut/coul/long/soft lambda 4 6 v_lambda &
@@ -103,15 +100,15 @@ fix fADAPT all adapt/fep 125000 &
     after yes
 
 variable dlambda equal -0.05
-variable minusdl equal 0.05
-variable dq1 equal  0.145*v_dlambda+0.180*v_dlambda
+variable minusdl equal  0.05
+variable dq1 equal (0.145+0.180)*v_dlambda
 variable dq2 equal  0.180*v_dlambda
 variable dq3 equal -0.060*v_dlambda
-variable dq4 equal  0.040*v_dlambda-0.060*v_dlambda
+variable dq4 equal (0.040-0.060)*v_dlambda
 variable dq5 equal -0.683*v_dlambda
 variable dq6 equal  0.418*v_dlambda
 
-compute cFEP all fep ${temp} &
+compute FEP all fep ${TK} &
     pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusdl &
     pair lj/cut/coul/long/soft lambda 3 4 v_minusdl &
     pair lj/cut/coul/long/soft lambda 4 6 v_dlambda &
@@ -121,22 +118,18 @@ compute cFEP all fep ${temp} &
     atom charge 3 v_dq3 &
     atom charge 4 v_dq4 &
     atom charge 5 v_dq5 &
-    atom charge 6 v_dq6
+    atom charge 6 v_dq6 &
+    volume yes
 
-fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fep10.lmp
+fix FEP all ave/time 20 4000 100000 c_FEP[*] file fep10.fep
 
-# compute cRDF all rdf 100 1 1
-# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
+thermo_style custom step cpu epair emol etotal temp press density v_lambda
 
-compute cMSD all msd
-fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
+dump TRAJ all custom 20000 dump.lammpstrj id mol type element xu yu zu
+dump_modify TRAJ element C C H H O H H O
 
-dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
-dump_modify dCONF element C C H H O H H O
+#restart 20000 restart1.lmp restart2.lmp
 
-# restart ${nrestart} restart.*.lmp
+run 2000000
 
-run ${nsteps}
-
-write_restart restart.*.lmp
 write_data data.*.lmp

examples/USER/fep/CH4-CF4/README

@@ -1,57 +0,0 @@
-Methane to Tetrafluoromethane in Water
-======================================
-
-Example calculation of the difference in free energy of hydration upon
-transforming methane into tetrafluoromethane with LAMMPS using
-*compute fep* and *fix adapt*.
-
-Methane and tetrafluoromethane are represented by the OPLS-AA force
-field (1 molecule). Water is represented by the 3-site SPC/E model
-(360 molecules).
-
-The strategy used to perform the alchemical transformation is the
-following:
-
-* The dual topology approach is used, therefore all the atoms of
-  methane and perfluorommethane are present throughout the simulation,
-  only some of them are dummy sites at the endpoints of the
-  transformation. Masses and intramolecular terms (bond lengths,
-  angles, dihedrals) are not changed.
-
-* Interactions of sites that are being created (from dummy sites) or
-  deleted (to become dummy sites) are treated using soft-core verions
-  of the Lennard-Jones and Coulomb potentials (*pair
-  lj/cut/coul/long/soft*) in order to avoid singularities. The
-  exponent of the coupling parameter lambda in the soft-core pair
-  potentials was in this example n = 1.
-
-* Eletrostatic charges that are modified are varied linearly from the
-  initial to the final values. This keeps the overall charge of the
-  molecule constant, which is good for the long range electrostatics
-  (the coupling parameter lambda has no effect on the kspace terms).
-
-The following directories contain input files and results for
-calculations using Bennet's acceptance ratio (BAR) method:
-
-* `bar01` -- Calculation using BAR, 1-step transformation of a CH4
-  molecule into CF4. Results in `bar01.lmp`
-
-* `bar10` -- Calculation using BAR, 1-step transformation of a
-  CF4 molecule into CH4. Results in `bar10.lmp`
-
-The Python script `bar.py` found in the `tools` directory can
-be used to calculate the free-energy difference corresponding to the
-transformation:
-
-    bar.py 300 bar01.lmp bar10.lmp
-
-The outputs are in kcal/mol and can be compared with the experimental
-value of 1.2 kcal/mol and with a simulation value from the literature
-(using a different force field): 0.8 kcal/mol
-[Gough, Pearlman, Kolmann, J Chem Phys 99 (1993) 9103]. This small
-free energy difference is difficult to predict.
-
-These example calculations are for tutorial purposes only. The results
-may not be of research quality (not enough sampling, size of the step
-in lambda or of the delta for numerical derivative not optimized, no
-evaluation of ideal-gas contributions, etc.)

examples/USER/fep/CH4-CF4/README.md

@@ -0,0 +1,77 @@
+Methane to Tetrafluoromethane in Water
+======================================
+
+Example calculation of the difference in free energy of hydration upon
+transforming methane into tetrafluoromethane with LAMMPS using
+*compute fep*, *fix adapt/fep* and *pair lj/cut/coul/long/soft*.
+
+Methane and tetrafluoromethane are represented by the OPLS-AA force
+field (1 molecule). Water is represented by the 3-site SPC/E model
+(360 molecules).
+
+The procedure used to perform the alchemical transformation is the
+following:
+
+* The dual topology approach is used, therefore all the atoms of
+  methane and perfluorommethane are present throughout the simulation,
+  only some of them are dummy sites at the endpoints of the
+  transformation. Masses and intramolecular terms (bonds, angles, dihedrals)
+  are not changed.
+
+* Interactions of sites that are being created (from dummy sites, XD-) or
+  deleted (to become dummy sites X-D) are treated using soft-core versions
+  of the Lennard-Jones and Coulomb potentials (*pair
+  lj/cut/coul/long/soft*) in order to avoid singularities. The
+  exponent of the coupling parameter lambda in the soft-core pair
+  potentials was in this example n = 1.
+
+* Atoms of the fragments being created should not interact with atoms being
+  deleted. In this small solute this is guaranteed by the exclusion of 1-2
+  and 1-3 interactions, so no modifications of the *pair_coeff* are needed.
+  Otherwise the LJ epsilon of those interactions should be zeroed.
+
+* Eletrostatic charges that are modified are varied linearly from the
+  initial to the final values. This keeps the overall charge of the
+  molecule constant, which is good for the long range electrostatics
+  (the coupling parameter lambda has no effect on the kspace terms).
+
+The following directories contain input files and results for
+calculations using the free-energy perturbation and Bennet's acceptance
+ratio (BAR) method:
+
+* `mols` -- molecule description files and force field database used
+  to create the initial configurations used for the simulations
+  `data.0.lmp` and `data.1.lmp`
+
+* `fep01` -- Calculation using FEP, 20-step transformation of a CH4
+  molecule into CF4, constant NpT. Results in `fep01.fep`
+
+* `fep10` -- Calculation using FEP, 20-step transformation of a
+  CF4 molecule into CH4, constant NpT. Results in `fep10.fep`
+
+* `bar01` -- Calculation using BAR, 1-step transformation of a CH4
+  molecule into CF4, constant NVT, Results in `bar01.fep`
+
+* `bar10` -- Calculation using BAR, 1-step transformation of a
+  CF4 molecule into CH4, constant NVT. Results in `bar10.fep`
+
+The Python scripts `fep.py` and  `bar.py` found in the `tools` directory
+can be used to calculate the free-energy difference corresponding to the
+transformation:
+
+    fep.py 300 < fep01.fep
+
+    fep.py 300 < fep10.fep
+
+    bar.py 300 bar01.lmp bar10.lmp
+
+The outputs are in kcal/mol and can be compared with the experimental
+value of 1.2 kcal/mol, and also with a simulation value from the literature
+using a different force field): 0.8 kcal/mol
+[Gough, Pearlman, Kolmann, J Chem Phys 99 (1993) 9103](https://doi.org/10.1063/1.465525).
+This is a small free energy difference so consider the absolute discrepancies.
+
+These example calculations are for tutorial purposes only. The results
+may not be of research quality (not enough sampling, size of the step
+in lambda or of the delta for numerical derivative not optimized, no
+evaluation of ideal-gas contributions, etc.)

examples/USER/fep/CH4-CF4/bar01/in.bar01.lmp

@@ -16,74 +16,63 @@ pair_style hybrid lj/cut/coul/long 10.0 10.0 lj/cut/coul/long/soft 1 0.5 10.0 10
 pair_modify tail yes
 kspace_style pppm 1.0e-4
 
-pair_coeff    1    1  none  # C-CF C-CF
-pair_coeff    1    2  none  # C-CF H-D
-pair_coeff    1    3  none  # C-CF FD-
+pair_coeff    1    1  lj/cut/coul/long    0.0660   3.5000  # C-CF C-CF
+pair_coeff    1    2  lj/cut/coul/long    0.0445   2.9580  # C-CF H-D
+pair_coeff    1    3  lj/cut/coul/long    0.0591   3.2133  # C-CF FD-
 pair_coeff    1    4  lj/cut/coul/long    0.0000   1.8708  # C-CF Hw
 pair_coeff    1    5  lj/cut/coul/long    0.1013   3.3286  # C-CF Ow
-pair_coeff    2    2  none  # H-D H-D
-pair_coeff    2    3  none  # H-D FD-
+pair_coeff    2    2  lj/cut/coul/long    0.0300   2.5000  # H-D H-D
+pair_coeff    2    3  lj/cut/coul/long    0.0399   2.7157  # H-D FD-
 pair_coeff    2    4  lj/cut/coul/long/soft    0.0000   1.5811  1.0  # H-D Hw
 pair_coeff    2    5  lj/cut/coul/long/soft    0.0683   2.8131  1.0  # H-D Ow
-pair_coeff    3    3  none  # FD- FD-
+pair_coeff    3    3  lj/cut/coul/long    0.0530   2.9500  # FD- FD-
 pair_coeff    3    4  lj/cut/coul/long/soft    0.0000   1.7176  0.0  # FD- Hw
 pair_coeff    3    5  lj/cut/coul/long/soft    0.0908   3.0559  0.0  # FD- Ow
 pair_coeff    4    4  lj/cut/coul/long    0.0000   1.0000  # Hw Hw
 pair_coeff    4    5  lj/cut/coul/long    0.0000   1.7792  # Hw Ow
 pair_coeff    5    5  lj/cut/coul/long    0.1554   3.1655  # Ow Ow
 
-variable nsteps equal 500000
-variable nprint equal ${nsteps}/500
-variable ndump equal ${nsteps}/100
-# variable nrestart equal ${nsteps}/10
-
-variable temp equal 300.0
-variable press equal 1.0
+variable TK equal 300.0
+variable PBAR equal 1.0
 
 neighbor 2.0 bin
 
-timestep 2.0
+timestep 1.0
 
-velocity all create ${temp} 12345
+velocity all create ${TK} 12345
 
-thermo_style multi
-thermo ${nprint}
+fix SHAKE all shake 0.0001 20 0 b 3 a 4
 
-fix fSHAKE all shake 0.0001 20 ${nprint} b 3 a 4
+fix NPT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500
 
-fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
+thermo_style custom step cpu etotal ke pe evdwl ecoul elong temp press vol density
+thermo 1000
 
 run 200000
+
 reset_timestep 0
+unfix NPT
+fix NVT all nvt temp ${TK} ${TK} 100
 
 variable dlambda equal  1.0
 variable minusdl equal -1.0
-variable dqC equal  0.48*v_dlambda-0.24*(1.0-v_dlambda)
-variable dqH equal  0.06*(1.0-v_dlambda)
+variable dqC equal  (0.48+0.24)*v_dlambda
+variable dqH equal -0.06*v_dlambda
 variable dqF equal -0.12*v_dlambda
 
-compute cFEP all fep ${temp} &
+compute FEP all fep ${TK} &
     pair lj/cut/coul/long/soft lambda 2 4*5 v_minusdl &
     pair lj/cut/coul/long/soft lambda 3 4*5 v_dlambda &
     atom charge 1 v_dqC &
     atom charge 2 v_dqH &
     atom charge 3 v_dqF
 
-fix fFEP all ave/time 1 1 100 c_cFEP[1] c_cFEP[2] file bar01.lmp
+fix FEP all ave/time 1 1 100 c_FEP[1] c_FEP[2] file bar01.fep
 
+dump TRAJ all custom 5000 dump.lammpstrj id mol type element xu yu zu
+dump_modify TRAJ element C H F H O
 
-# compute cRDF all rdf 100 1 1
-# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
-
-# compute cMSD all msd
-# fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
-
-dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
-dump_modify dCONF element C H F H O
-
-# restart ${nrestart} restart.*.lmp
-
-run ${nsteps}
+run 500000
 
 # write_restart restart.*.lmp
 write_data data.*.lmp

examples/USER/fep/CH4-CF4/bar01/log.bar01

@@ -0,0 +1,978 @@
+LAMMPS (29 Oct 2020)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/lammps/src/comm.cpp:94)
+  using 1 OpenMP thread(s) per MPI task
+# created by fftool
+
+units real
+boundary p p p
+
+atom_style full
+bond_style harmonic
+angle_style harmonic
+special_bonds lj/coul 0.0 0.0 0.5
+
+read_data data.0.lmp
+Reading data file ...
+  orthogonal box = (-13.443762 -13.443762 -13.443762) to (13.443762 13.443762 13.443762)
+  2 by 2 by 3 MPI processor grid
+  reading atoms ...
+  1089 atoms
+  scanning bonds ...
+  1 = max bonds/atom
+  scanning angles ...
+  28 = max angles/atom
+  reading bonds ...
+  728 bonds
+  reading angles ...
+  388 angles
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0.5     
+  special bond factors coul:  0        0        0.5     
+     8 = max # of 1-2 neighbors
+     7 = max # of 1-3 neighbors
+     7 = max # of 1-4 neighbors
+     8 = max # of special neighbors
+  special bonds CPU = 0.001 seconds
+  read_data CPU = 0.014 seconds
+# read_restart restart.*.lmp
+# reset_timestep 0
+
+pair_style hybrid lj/cut/coul/long 10.0 10.0 lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
+pair_modify tail yes
+kspace_style pppm 1.0e-4
+
+pair_coeff    1    1  lj/cut/coul/long    0.0660   3.5000  # C-CF C-CF
+pair_coeff    1    2  lj/cut/coul/long    0.0445   2.9580  # C-CF H-D
+pair_coeff    1    3  lj/cut/coul/long    0.0591   3.2133  # C-CF FD-
+pair_coeff    1    4  lj/cut/coul/long    0.0000   1.8708  # C-CF Hw
+pair_coeff    1    5  lj/cut/coul/long    0.1013   3.3286  # C-CF Ow
+pair_coeff    2    2  lj/cut/coul/long    0.0300   2.5000  # H-D H-D
+pair_coeff    2    3  lj/cut/coul/long    0.0399   2.7157  # H-D FD-
+pair_coeff    2    4  lj/cut/coul/long/soft    0.0000   1.5811  1.0  # H-D Hw
+pair_coeff    2    5  lj/cut/coul/long/soft    0.0683   2.8131  1.0  # H-D Ow
+pair_coeff    3    3  lj/cut/coul/long    0.0530   2.9500  # FD- FD-
+pair_coeff    3    4  lj/cut/coul/long/soft    0.0000   1.7176  0.0  # FD- Hw
+pair_coeff    3    5  lj/cut/coul/long/soft    0.0908   3.0559  0.0  # FD- Ow
+pair_coeff    4    4  lj/cut/coul/long    0.0000   1.0000  # Hw Hw
+pair_coeff    4    5  lj/cut/coul/long    0.0000   1.7792  # Hw Ow
+pair_coeff    5    5  lj/cut/coul/long    0.1554   3.1655  # Ow Ow
+
+variable TK equal 300.0
+variable PBAR equal 1.0
+
+neighbor 2.0 bin
+
+timestep 1.0
+
+velocity all create ${TK} 12345
+velocity all create 300 12345
+
+fix SHAKE all shake 0.0001 20 0 b 3 a 4
+       0 = # of size 2 clusters
+       0 = # of size 3 clusters
+       0 = # of size 4 clusters
+     360 = # of frozen angles
+  find clusters CPU = 0.001 seconds
+
+fix NPT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500
+fix NPT all npt temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 500
+fix NPT all npt temp 300 300 100 iso ${PBAR} ${PBAR} 500
+fix NPT all npt temp 300 300 100 iso 1 ${PBAR} 500
+fix NPT all npt temp 300 300 100 iso 1 1 500
+
+thermo_style custom step cpu etotal ke pe evdwl ecoul elong temp press vol density
+thermo 1000
+
+run 200000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
+  G vector (1/distance) = 0.27021276
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.016910392
+  estimated relative force accuracy = 5.0925143e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 2352 450
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 5 5 5
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair lj/cut/coul/long, perpetual, skip from (3)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (2) pair lj/cut/coul/long/soft, perpetual, skip from (3)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 16.37 | 16.38 | 16.39 Mbytes
+Step CPU TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Volume Density 
+       0            0    798.08888     972.9364   -174.84752    -201.6326    19449.757    -19423.16    448.35165    1094.5342    19438.038   0.56189244 
+    1000    1.6227639   -3135.9243    629.54322   -3765.4676    732.54113     15141.62   -19640.497    290.10811   -234.59752    13323.595   0.81975524 
+    2000    4.3550149   -3333.4048    628.81546   -3962.2203    771.57676    14914.189   -19648.873    289.77274   -306.28703    11774.436   0.92761017 
+    3000    7.2743737   -3309.7195    677.89703   -3987.6166    757.99659    14902.361   -19649.323    312.39067     383.0691    10832.367    1.0082825 
+    4000    10.112018   -3314.5067    641.13741   -3955.6441    769.70713    14921.613   -19647.838    295.45098    510.27803    10888.206    1.0031117 
+    5000    12.706124   -3371.0779    621.77548   -3992.8534    790.65314    14864.613   -19649.217    286.52855    954.94335    10827.277    1.0087566 
+    6000    15.489237   -3353.7143    662.53154   -4016.2459    744.67602    14889.993     -19652.3    305.30989   -422.11945    10980.311   0.99469738 
+    7000    18.236457   -3360.1226    638.50387   -3998.6265    739.96323     14908.61   -19648.408    294.23739   -397.77334     10917.97    1.0003771 
+    8000    21.113473   -3350.5189    659.78194   -4010.3009    763.57322    14874.976   -19650.722    304.04281    58.154192    10905.304    1.0015389 
+    9000    23.987032    -3396.809    626.60232   -4023.4113    776.04899    14849.476    -19650.05    288.75287    263.83864    10861.498    1.0055783 
+   10000    27.076899   -3394.4848    642.63639   -4037.1212     711.4545    14901.365   -19651.143    296.14175    -1267.145    10904.447    1.0016176 
+   11000    30.184956   -3297.1389    686.72595   -3983.8649    753.45058     14907.57   -19646.446    316.45924    441.31675    10709.186    1.0198802 
+   12000    32.719707   -3411.7157    634.98327    -4046.699    757.47342    14841.968   -19647.665    292.61501   -70.867985    10726.666    1.0182182 
+   13000    35.727222   -3374.9645    634.51906   -4009.4836    715.92455    14921.027   -19648.011    292.40109   -665.68165    10807.776    1.0105767 
+   14000    38.770042   -3438.3513    638.93389   -4077.2852    724.17831    14845.131   -19648.377    294.43555   -1171.5416    10807.455    1.0106067 
+   15000     41.35641   -3365.0228    644.87938   -4009.9021    827.30298    14811.105   -19649.786    297.17537     1095.495    10900.078    1.0020191 
+   16000    44.198681   -3365.6605    640.00578   -4005.6663    733.30864    14911.539   -19651.433     294.9295   -893.58882    11099.467   0.98401905 
+   17000    47.004999   -3412.1185     652.8766   -4064.9951    808.29086    14774.583   -19649.833    300.86067    775.16386    10832.393    1.0082802 
+   18000    49.307934   -3413.1241    642.52146   -4055.6455    779.41048    14813.756   -19650.103    296.08878    239.37739    10770.676    1.0140577 
+   19000    52.516104   -3392.8412    652.52618   -4045.3674    780.92671    14821.147   -19649.131    300.69919   -21.897655    10966.136   0.99598314 
+   20000    55.649319   -3330.7426    663.82659   -3994.5692    737.44583    14915.667   -19651.054    305.90668   -465.12194    10903.468    1.0017076 
+   21000    58.277268   -3329.3496    676.78976   -4006.1393    709.91532    14929.303   -19647.492    311.88041   -877.40985     10982.77   0.99447473 
+   22000    60.472235   -3370.5698    636.53863   -4007.1085    773.13288    14865.407    -19649.07    293.33176    563.27108    10931.735   0.99911745 
+   23000    62.767962   -3349.9273    656.01208   -4005.9394    756.49013    14886.996   -19651.417    302.30557    34.763751    10860.428    1.0056774 
+   24000    65.937963   -3325.3063    672.60215   -3997.9084    760.64327    14886.531   -19647.632    309.95067   -164.43976    10936.076   0.99872082 
+   25000    69.103421    -3358.178    677.71691   -4035.8949    755.15482    14857.343   -19650.872    312.30766    -84.92193    10843.837    1.0072161 
+   26000    71.851329    -3347.382     672.1553   -4019.5373    750.87566    14875.682   -19648.128    309.74474   -450.18098    11156.794   0.97896283 
+   27000    74.118636   -3373.0732    664.42954   -4037.5027    805.42361    14801.784   -19647.775    306.18454    615.21813    11013.134   0.99173282 
+   28000     76.02629   -3405.9581    640.38635   -4046.3444    755.70742     14842.59   -19647.534    295.10488   -682.91397    10977.214   0.99497801 
+   29000     77.94268   -3391.7825    660.70223   -4052.4848    741.10988    14850.358   -19646.019     304.4669   -335.54942    10759.014    1.0151568 
+   30000    79.874011   -3420.3523    619.13732   -4039.4897    748.84158    14856.835   -19647.895    285.31283   -555.95656    10817.844    1.0096362 
+   31000    82.529485   -3418.7423    636.16294   -4054.9052    743.02294    14850.469   -19651.029    293.15863   -960.36278    11038.486   0.98945511 
+   32000    85.405709   -3298.6451    710.74972   -4009.3948    713.81064    14923.742   -19648.983    327.52995   -906.58524    10949.584   0.99748877 
+   33000     88.43898   -3345.6779    666.60707    -4012.285    733.59753      14901.4   -19650.877    307.18799   -612.23666    10913.444     1.000792 
+   34000     91.49661   -3398.4259    651.70407     -4050.13    728.38362    14868.157   -19648.637    300.32034   -949.57274    10826.612    1.0088185 
+   35000    94.396664   -3335.5822    679.38748   -4014.9697    748.94256    14883.767   -19650.181     313.0775   -113.94404    10846.052    1.0070104 
+   36000    96.385906    -3444.994    658.12175   -4103.1157    774.99324    14770.478   -19651.116    303.27776    -101.7667    10635.157    1.0269793 
+   37000    98.378928   -3404.8312    649.64154   -4054.4727    876.87186    14716.949   -19649.753    299.36988    2649.1268    10507.427    1.0394635 
+   38000     101.3117   -3344.8928    655.38456   -4000.2773    719.20801    14926.744   -19649.132     302.0164   -504.44754    10717.894    1.0190516 
+   39000    104.48293   -3352.8954    643.29653   -3996.1919    725.72981    14923.677   -19647.526    296.44595   -585.78876    10905.137    1.0015543 
+   40000    107.62957   -3369.9101    637.39998     -4007.31    746.91058    14895.384   -19651.745    293.72869    26.094236    10776.242    1.0135339 
+   41000    110.73764   -3281.4951    648.37198    -3929.867    726.88832     14990.21   -19649.256    298.78484    122.07948    10811.983    1.0101835 
+   42000    113.89317   -3352.4718      637.776   -3990.2478     698.8244    14953.386   -19645.083    293.90197   -323.99367    10553.334    1.0349419 
+   43000    116.98708   -3417.1937    648.96364   -4066.1573    810.87183    14771.133   -19649.478    299.05749    954.79757    10653.129    1.0252468 
+   44000    120.11947    -3399.018    651.38047   -4050.3985    748.86042    14846.364   -19648.669    300.17122    -128.0086    10720.429    1.0188106 
+   45000    123.18405   -3316.4994    663.83111   -3980.3305    730.84729    14933.283   -19646.334    305.90877   -471.03351    10999.966   0.99292005 
+   46000    126.34266   -3379.5773    634.41148   -4013.9888    726.68572    14907.788   -19650.575    292.35152   -362.34441    10704.492    1.0203274 
+   47000    129.39545   -3299.3383    678.74581   -3978.0841    808.75365    14860.115   -19650.314     312.7818    1105.5628    11016.741   0.99140817 
+   48000    132.36242   -3328.0267    663.94989   -3991.9766       738.84    14918.287   -19651.128     305.9635   -149.85725    10954.863   0.99700805 
+   49000     135.4771   -3393.8602    664.10659   -4057.9668      778.728    14808.309   -19648.368    306.03571    367.98933    10714.776    1.0193482 
+   50000    138.67527   -3327.2702    665.60161   -3992.8718    730.52205    14921.662   -19649.656    306.72465   -507.98309    10972.496   0.99540583 
+   51000    141.78402   -3408.9553    647.78836   -4056.7436    800.11595    14792.953   -19651.622     298.5159    733.58442    10770.401    1.0140836 
+   52000    144.97759   -3346.0292    674.59159   -4020.6208     741.7902    14885.791     -19651.2    310.86744   -253.31211    10771.224    1.0140061 
+   53000    148.10596   -3403.6702    647.30126   -4050.9714    702.44537    14892.703   -19650.153    298.29142   -1455.3963    10887.242    1.0032006 
+   54000    151.27561   -3402.2708    635.30832   -4037.5791    784.06045      14824.2   -19649.122     292.7648    456.18379    10895.154     1.002472 
+   55000    154.31059   -3356.8544    658.92367   -4015.7781     763.9178    14867.309   -19649.791     303.6473    383.12741    10764.652    1.0146252 
+   56000    157.35988   -3367.0719    647.68934   -4014.7613    795.24439    14836.387   -19650.473    298.47026    629.99251    10898.792    1.0021374 
+   57000    160.41422    -3331.368     668.9516   -4000.3196    755.42796    14890.939   -19649.119     308.2684    197.64025    10828.027    1.0086867 
+   58000    163.43492   -3419.3941    603.03817   -4022.4323    770.31208    14856.552   -19652.191    277.89397    193.13804    10905.861    1.0014878 
+   59000    166.48169    -3443.906    615.62832   -4059.5343    830.66206    14753.628   -19646.219     283.6958    746.99913    10943.948    0.9980024 
+   60000    169.36167   -3352.4508    639.91257   -3992.3633    756.76722    14897.558   -19648.528    294.88655   -351.80447     11091.83   0.98469655 
+   61000    172.15329   -3332.3304    654.29338   -3986.6238    738.23788    14921.388   -19648.685    301.51356   -412.09881    11155.118   0.97910992 
+   62000    175.18581   -3318.3617    659.16412   -3977.5258    743.21533    14926.246   -19649.542    303.75811   -249.54472    10898.661    1.0021494 
+   63000    178.33253   -3311.1132    642.26966   -3953.3829    723.58338    14967.469   -19647.287    295.97275   -385.33656    10884.406    1.0034619 
+   64000    181.60183   -3383.0314    629.93214   -4012.9636    730.04342    14904.941   -19649.613    290.28733   -969.93156    11056.015    0.9878864 
+   65000    184.69713   -3308.2098    674.52711    -3982.737    747.85911    14913.345   -19646.694    310.83773   -165.84809      11111.7   0.98293571 
+   66000    187.65407   -3364.2868     652.0621   -4016.3489    799.42941    14832.934    -19650.75    300.48533    917.61356    10805.021    1.0108344 
+   67000    190.77911   -3363.9885    638.70705   -4002.6955    761.21697    14884.338   -19650.305    294.33102    635.45937    10546.969    1.0355664 
+   68000    193.86146   -3334.0791    636.44049   -3970.5196    739.73877    14937.166   -19649.614    293.28653    68.912387    10726.537    1.0182304 
+   69000    196.94314   -3418.4919    634.00423   -4052.4961    820.51179    14773.769    -19648.83    292.16385    747.20053    10922.388   0.99997246 
+   70000    199.80403    -3373.947    631.42486   -4005.3719    711.02529    14931.736   -19650.858    290.97521   -1000.4585    11049.818   0.98844045 
+   71000    202.92351   -3343.3809    681.76184   -4025.1427    710.22237    14909.644    -19648.07    314.17166   -1169.1237    10925.148   0.99971979 
+   72000    206.16718   -3370.6387     671.8063    -4042.445    809.06517    14794.279   -19647.383    309.58392    1029.3304    10718.336    1.0190096 
+   73000    209.25575   -3363.0344    648.99348   -4012.0279    752.87791    14883.425   -19650.369    299.07124   -86.557401    10803.898    1.0109394 
+   74000    212.34845   -3344.0362    656.35024   -4000.3864    765.46402    14883.809   -19650.893    302.46141    811.73493    10654.411    1.0251235 
+   75000    215.42493   -3441.0221    643.37193    -4084.394    747.00535    14815.788   -19648.971     296.4807   -687.99101    10758.163    1.0152371 
+   76000    218.18937   -3368.2667    659.91054   -4028.1772    714.27352    14902.671   -19647.297    304.10208   -1093.9805    10977.453   0.99495638 
+   77000    220.42222   -3358.7851    646.86982   -4005.6549    760.48103    14880.703   -19648.521    298.09261   -42.803257    11010.743   0.99194822 
+   78000    222.87324   -3405.3542    646.26899   -4051.6232    751.04556    14847.343   -19651.631    297.81573     -366.845    10836.053    1.0079396 
+   79000    225.85253    -3334.737    652.95347   -3987.6905    773.64001    14886.896    -19649.86     300.8961    739.14565    10643.412    1.0261828 
+   80000    228.94092   -3364.4996    635.46853   -3999.9681    746.74747    14902.651   -19651.381    292.83863     27.34912    10632.941    1.0271934 
+   81000    232.12064   -3336.9105    626.37349    -3963.284    718.41756    14965.831   -19649.999    288.64743   -482.82365    10903.607    1.0016949 
+   82000    235.20638   -3294.8229    639.79024   -3934.6131    765.39251    14946.022   -19647.838    294.83018    937.00266    10804.659    1.0108683 
+   83000    238.13385   -3353.1695    650.04806   -4003.2176    770.82681    14873.109   -19648.497    299.55722    723.14608    10699.458    1.0208075 
+   84000    241.13583   -3401.9404    636.42544   -4038.3659     756.6727    14852.968   -19650.268     293.2796    42.460588     10803.51    1.0109758 
+   85000    243.33306    -3367.905     640.1287   -4008.0337    734.92136    14906.233   -19651.455    294.98614     83.80666    10584.659    1.0318789 
+   86000    245.97371   -3392.4387     646.2809   -4038.7196     806.8106     14801.83   -19649.186    297.82122    438.85782    11015.687   0.99150301 
+   87000    248.12829   -3384.7716    651.77287   -4036.5445    813.19595    14799.513    -19650.99    300.35205    798.80286    10880.565    1.0038162 
+   88000     250.0307   -3377.3051    657.90541   -4035.2105    821.94479    14791.328   -19650.478    303.17806    901.78308    10815.707    1.0098357 
+   89000    251.99639   -3342.4027    670.73846   -4013.1412    804.18895    14822.309   -19644.383    309.09183    1284.3841     10671.02    1.0235279 
+   90000    254.19997   -3420.2163    615.64957   -4035.8659    754.92363    14856.769   -19652.088    283.70559   -269.37533    10945.889   0.99782546 
+   91000    256.93525   -3328.1675    659.51188   -3987.6793    795.80348    14860.244   -19647.865    303.91836    215.60569     11260.45   0.96995114 
+   92000    259.66669   -3358.2213    656.90946   -4015.1307    801.52461    14825.995   -19648.965    302.71911    793.31406    10837.102    1.0078421 
+   93000    262.49811   -3373.1305    631.19068   -4004.3212    743.90076    14898.618   -19650.669     290.8673   -244.18726    10934.883   0.99882981 
+   94000    265.27422   -3417.4348    620.68383   -4038.1186    729.51892    14876.758   -19648.529     286.0255    -988.8428    10948.711   0.99756826 
+   95000    268.02755   -3360.5218    637.85203   -3998.3738    720.68596    14925.393   -19650.463      293.937     14.71448    10617.634    1.0286742 
+   96000    271.08994   -3314.0216    657.16917   -3971.1908    736.14127    14936.736   -19647.832    302.83879    254.74282    10664.142    1.0241881 
+   97000    274.29641   -3347.2386    654.74153   -4001.9801    737.48065    14906.209   -19650.784    301.72007   -392.11361    10859.047    1.0058053 
+   98000     277.5295   -3399.6443    645.62027   -4045.2646    805.86756    14795.989   -19650.991    297.51679    622.88014    10815.931    1.0098148 
+   99000    280.69542   -3409.0821    632.97743   -4042.0595    764.60187    14841.751   -19652.313    291.69067   -26.842273    10728.354     1.018058 
+  100000     283.8378   -3339.8374    658.30631   -3998.1437    761.06109    14888.636   -19652.093    303.36281   -6.0703178    11090.189   0.98484226 
+  101000    286.87721   -3362.1186    661.94979   -4024.0684    742.99972     14878.86   -19649.336    305.04181   -563.29767    11014.995   0.99156528 
+  102000    290.07789   -3386.5733    606.90665     -3993.48    772.90614     14877.66   -19648.487    279.67666    364.80743    10858.193    1.0058843 
+  103000    293.29033   -3324.9554    659.76653   -3984.7219    769.15339    14889.287   -19646.675    304.03571    513.48317     10953.61   0.99712208 
+  104000     296.5465   -3397.1866    620.62139    -4017.808     795.9375    14828.662   -19647.968    285.99672     907.0442    10837.588    1.0077968 
+  105000     299.6883   -3382.4995    648.25877   -4030.7583    797.25655    14816.713   -19649.467    298.73267    412.87326    10959.672   0.99657057 
+  106000     302.8692   -3333.7645    678.18678   -4011.9513    751.75647    14880.712   -19650.503    312.52419   -346.13564    11128.759   0.98142904 
+  107000     305.9912   -3354.9009    648.70234   -4003.6033    814.22481    14828.018   -19651.832    298.93708    1326.7249    10804.094    1.0109212 
+  108000     309.1072   -3323.7826    676.27053   -4000.0531    757.66342    14883.633    -19647.48    311.64114   -14.394857    10890.887    1.0028648 
+  109000    312.30662   -3355.5416    654.20276   -4009.7444    784.10263     14849.23   -19649.707     301.4718    1187.0686    10639.679    1.0265429 
+  110000    315.47373   -3380.3752    631.31939   -4011.6946    745.60134    14883.493   -19646.482    290.92661   -48.374809    10795.436    1.0117319 
+  111000    318.59032   -3401.8334    638.94498   -4040.7784    766.96923    14836.431   -19649.555    294.44066   -354.50407    11003.022   0.99264426 
+  112000    321.59996   -3413.5057    662.60937   -4076.1151    819.41803    14749.595   -19649.635    305.34576    659.18933    10854.637    1.0062139 
+  113000    324.67915   -3370.1107    632.33094   -4002.4416    772.99396    14868.719   -19650.231    291.39276    515.02396    10717.486    1.0190904 
+  114000    327.87951   -3354.0328    673.83429   -4027.8671    812.63712    14801.595   -19648.243    310.51846    985.88879    10790.828     1.012164 
+  115000    331.09494   -3270.8582    652.33372    -3923.192    709.91663    15011.308    -19648.42     300.6105   -514.77178     11022.22   0.99091535 
+  116000    334.36494   -3326.0255    649.26272   -3975.2882    765.32922    14904.188   -19650.521    299.19531    89.704998    11030.013   0.99021519 
+  117000    337.60043   -3314.6976    690.48407   -4005.1817    739.31178    14898.625   -19648.293    318.19107   -706.01302    11136.645   0.98073407 
+  118000    340.73023   -3395.3039    646.25987   -4041.5638    782.89725    14821.981   -19650.706    297.81153    469.89183    10725.427    1.0183358 
+  119000    343.85716   -3352.8785     648.9704   -4001.8489    743.77601    14896.931   -19649.255    299.06061   -72.754473    10827.626    1.0087241 
+  120000    347.02799    -3376.287    646.47293   -4022.7599    780.16074     14841.24   -19649.425    297.90972    677.92401    10559.084    1.0343783 
+  121000    350.14087   -3334.2648    653.54886   -3987.8137    807.03694    14847.086   -19647.143    301.17047    1231.7405    10834.347    1.0080983 
+  122000     353.2703   -3392.1736    659.25807   -4051.4317    790.08415    14802.976   -19648.342     303.8014    608.48434    10755.876     1.015453 
+  123000    356.50134   -3351.3844    661.13084   -4012.5152    765.68373     14865.89   -19647.859    304.66442    455.96449    10769.393    1.0141785 
+  124000    359.75143   -3399.7389    645.59268   -4045.3316    838.17932    14758.228   -19646.284    297.50407    1366.4127    10766.994    1.0144045 
+  125000    362.99561   -3377.9557    642.40716   -4020.3629    764.85444     14856.98   -19648.707    296.03611    50.832713    10833.286     1.008197 
+  126000    366.34009   -3430.9334    620.76964    -4051.703    819.17048    14776.823    -19651.21    286.06504    786.80724    10959.845   0.99655482 
+  127000    369.65576   -3304.0337    657.36979   -3961.4035    722.09865    14961.098   -19650.383    302.93124   -617.63058    11002.927   0.99265288 
+  128000    372.89106   -3350.4912    650.11432   -4000.6055    730.81891    14911.363   -19647.549    299.58775   -345.07238    10848.892    1.0067467 
+  129000     375.9395   -3352.3377    659.05496   -4011.3927     801.5679    14827.902   -19648.553     303.7078    1024.8803    10761.064    1.0149634 
+  130000    379.05924   -3331.3316    646.16758   -3977.4992    702.45572    14961.396   -19648.868      297.769   -813.36433    10734.344    1.0174899 
+  131000    382.24409   -3378.3014    654.56592   -4032.8673    783.17916    14827.183   -19646.825    301.63915    314.88338    10797.279    1.0115592 
+  132000    385.44093   -3294.3184    685.17163   -3979.4901    648.96238    15017.565   -19650.224    315.74297   -2184.2676    11184.021   0.97657963 
+  133000    388.68642   -3343.5645    683.09706   -4026.6615     735.6572    14883.576     -19651.4    314.78696   -1185.4466    10996.315   0.99324975 
+  134000    391.61811   -3362.5165    663.41639   -4025.9329    723.85251    14894.769   -19650.647    305.71765   -1275.2595     11191.14   0.97595841 
+  135000    394.67542   -3415.5801    631.64607   -4047.2262     737.9634    14860.936   -19650.533    291.07715   -1173.4651    10946.547   0.99776548 
+  136000    397.86076   -3387.9696    642.28653   -4030.2562    803.92941    14810.291   -19649.027    295.98052     558.5236    10880.977    1.0037781 
+  137000    400.95476   -3306.5591    669.23431   -3975.7934    765.46865    14899.052   -19648.694    308.39869   -144.69146    11093.497   0.98454859 
+  138000     404.0148   -3436.8724    604.66442   -4041.5368     827.0866    14774.497   -19649.223    278.64338    1039.4942    10877.528    1.0040964 
+  139000    406.90658   -3316.7286    642.07761   -3958.8062    770.14988    14910.151   -19647.123    295.88425    586.61636    10830.229    1.0084817 
+  140000      410.139   -3435.4909    646.60473   -4082.0956    742.88993    14819.762   -19649.242    297.97045    -924.6196    10763.567    1.0147274 
+  141000    412.97397   -3349.8621    665.88867   -4015.7508     824.0151    14802.572    -19649.88    306.85693    1437.0343    10815.766    1.0098301 
+  142000    415.69334   -3389.4803    656.80813   -4046.2884     815.9995    14783.418   -19649.538    302.67241    618.52893    10888.803    1.0030567 
+  143000    418.35581   -3353.9126    657.39556   -4011.3081    754.07514    14876.046   -19648.455    302.94312   -761.67008    11210.215   0.97429771 
+  144000    421.09581   -3399.1395    648.34596   -4047.4854     757.3745     14842.47   -19650.302    298.77285   -290.76144    10918.994    1.0002832 
+  145000    423.89736   -3321.4046    672.82697   -3994.2315    727.01005    14923.103   -19648.023    310.05426   -94.548607    10776.144    1.0135431 
+  146000    426.88246   -3334.4314    646.05182   -3980.4832    718.68787    14945.962   -19650.513    297.71566   -765.92932    10954.651   0.99702734 
+  147000    429.03205   -3354.2563    655.47531   -4009.7316    732.63749    14902.593   -19649.108    302.05822    -430.8045    10725.851    1.0182956 
+  148000    431.18588   -3337.8871    654.61295      -3992.5    769.42856    14880.899   -19650.086    301.66082     755.7811    10683.384    1.0223434 
+  149000    434.07276    -3376.242    641.83503   -4018.0771    774.77423    14853.885   -19649.601    295.77246    361.77483    10814.831    1.0099174 
+  150000    437.03956   -3361.8006    636.53661   -3998.3372    794.62666    14850.839   -19648.304    293.33083    621.45504    10840.943    1.0074849 
+  151000    439.38767   -3385.8031     660.1222   -4045.9253    787.26849    14814.229   -19650.391    304.19961    540.19133    10758.994    1.0151587 
+  152000    442.26277   -3343.2856     669.2682   -4012.5538    753.90842    14877.678   -19648.544     308.4143   -75.500409     10842.74     1.007318 
+  153000    445.11162   -3302.9056     655.9137   -3958.8193    727.60445    14959.349   -19649.544    302.26024   -542.06617    11257.085   0.97024109 
+  154000    447.79634   -3364.4801    640.01767   -4004.4977    786.40365    14853.443   -19648.083    294.93498    167.89008    11070.961   0.98655272 
+  155000    450.80494   -3381.1697    648.14661   -4029.3163    745.34994    14870.872   -19649.681    298.68099   -484.22067    10953.454   0.99713629 
+  156000    453.78255   -3355.8323    690.06687   -4045.8991    801.03438    14796.077   -19647.031    317.99881    646.55058    10808.799     1.010481 
+  157000    456.74023   -3358.0471    624.66039   -3982.7075    751.73555    14908.971   -19646.858    287.85799    -171.8557    10800.265    1.0112796 
+  158000    459.95793   -3361.8345    615.05113   -3976.8857    756.69986    14910.547   -19648.063    283.42982    565.78305    10581.632    1.0321741 
+  159000    463.07595   -3354.6895    650.23744   -4004.9269    814.77489    14825.419   -19649.058    299.64448    1870.0288    10539.543    1.0362961 
+  160000    465.61057   -3387.3316    642.27094   -4029.6026    756.42682    14859.059    -19648.66    295.97334   -306.78395    10898.921    1.0021255 
+  161000    468.44261   -3343.0814    653.61712   -3996.6986    800.28065    14847.812   -19647.964    301.20192    595.15208    11010.736   0.99194886 
+  162000     470.7058   -3324.2673    657.09555   -3981.3628    792.19065    14870.232    -19648.33    302.80486    1199.9282    10744.365     1.016541 
+  163000    473.09732   -3342.7775    679.83215   -4022.6096    727.18841    14897.208   -19650.549    313.28241   -997.06935    11210.914   0.97423699 
+  164000    475.81005   -3379.4848    625.20354   -4004.6883    757.14884    14881.551   -19648.134    288.10828   -76.040761    11090.621    0.9848039 
+  165000    478.15052   -3386.1281    628.34429   -4014.4724    734.93844    14895.393   -19648.215    289.55562   -464.67688     11010.29   0.99198902 
+  166000     480.8469   -3424.9866    658.25206   -4083.2387    818.88571    14746.189   -19651.579    303.33781    614.68026    10849.995    1.0066444 
+  167000    483.26895   -3302.9751    671.15602   -3974.1311    685.34376    14987.713   -19650.202    309.28425   -1418.9099    11021.782   0.99095467 
+  168000      485.209   -3327.7241    643.48556   -3971.2097     721.1792    14953.493   -19648.175    296.53306   -446.08256    10937.132   0.99862443 
+  169000    487.10676   -3431.0038    640.85754   -4071.8613    803.41985    14771.642   -19650.096    295.32201    376.19715    10859.958    1.0057209 
+  170000    489.25367   -3392.2951    632.96022   -4025.2553    780.55886    14838.676   -19647.453    291.68274    56.696342    10877.572    1.0040923 
+  171000    492.07922   -3345.5847    636.41469   -3981.9994    714.60203    14949.089    -19649.18    293.27464   -1535.0279    11266.565   0.96942474 
+  172000    494.84722   -3412.7904    624.36129   -4037.1517    797.10144    14813.176   -19649.883    287.72016    770.10845     10813.91    1.0100035 
+  173000    497.32327   -3332.2803    635.28695   -3967.5672    704.08272    14974.011   -19650.007    292.75495   -1081.8724    11342.367   0.96294601 
+  174000    499.19226   -3372.3767    600.06605   -3972.4427     711.3376    14958.707   -19647.835    276.52435   -963.09077     11005.88   0.99238652 
+  175000    501.11676   -3378.6046    669.43573   -4048.0404    769.70451    14830.409   -19650.915     308.4915   -171.35864    10854.568    1.0062203 
+  176000    503.01936   -3394.9346    634.14852   -4029.0831    693.23185    14923.391   -19648.477    292.23034   -1420.7325    10872.075       1.0046 
+  177000    505.06396   -3411.4372    652.44563   -4063.8828    816.49405    14765.108   -19649.331    300.66207    808.65833    10842.157    1.0073721 
+  178000    508.26742   -3366.5327    658.07457   -4024.6072    737.87074    14884.423   -19650.094    303.25602   -491.38544     11016.79   0.99140371 
+  179000    511.57476   -3434.1251    629.75987    -4063.885      773.094    14804.889   -19647.271    290.20795   -650.98858    10960.219   0.99652083 
+  180000    514.70512   -3383.3969    679.47789   -4062.8748    791.28905    14794.776   -19652.651    313.11917    390.13227    10803.493    1.0109774 
+  181000    517.97242    -3388.246    636.14319   -4024.3892    823.56405    14798.147   -19650.585    293.14953    1415.4269    10861.759    1.0055541 
+  182000    521.23139   -3408.0717    650.85109   -4058.9228    787.82137    14799.668   -19650.028    299.92727   -53.738357    10976.988   0.99499849 
+  183000    524.54272   -3340.7676    643.08656   -3983.8542     743.8686     14917.46   -19648.747     296.3492   -242.82649    11011.924   0.99184185 
+  184000    527.74844   -3433.1964    607.55441   -4040.7509    760.56557    14846.307    -19651.15    279.97516   -197.28739    10818.803    1.0095467 
+  185000    530.94582   -3401.7191    644.98431   -4046.7034    753.52973    14846.192   -19648.963    297.22372    13.718959    10734.268    1.0174971 
+  186000    534.12608    -3423.214    645.14548   -4068.3595    824.69067    14753.103   -19649.007      297.298    897.60049    10756.426    1.0154011 
+  187000    537.23581   -3344.7412    649.84528   -3994.5864     752.1529     14901.88   -19652.455    299.46377   -316.55785    10904.143    1.0016456 
+  188000    539.86768   -3324.6336    669.85221   -3994.4858    782.33881    14869.239   -19648.467    308.68343     344.3233    10934.187   0.99889334 
+  189000    542.81487    -3337.352    659.23929   -3996.5913    737.23792    14910.279   -19647.745    303.79275   -427.15321    11004.478   0.99251298 
+  190000    545.85026   -3408.1123    677.18274    -4085.295    814.76646    14747.084   -19649.094     312.0615    265.85399    10972.917   0.99536771 
+  191000    548.22635   -3374.5792    652.43146   -4027.0106    798.72937    14819.149   -19648.559    300.65554    589.27577    10894.944    1.0024913 
+  192000    550.15801   -3380.4072    663.81497   -4044.2222    764.97864    14837.259   -19648.504    305.90133    24.769315     10859.15    1.0057958 
+  193000    552.10156   -3333.7718    665.59132   -3999.3631     777.8822    14869.312   -19650.441    306.71991    341.07365    10920.172    1.0001753 
+  194000    554.11349   -3353.0683    659.14773   -4012.2161    728.41507    14904.858   -19649.309    303.75055   -526.17181    10900.056    1.0020212 
+  195000     556.0744   -3353.3614    680.88951   -4034.2509    733.19005    14881.482   -19651.024    313.76967   -818.00122    10917.711    1.0004008 
+  196000    558.79417   -3344.6073    652.72643   -3997.3337    746.06025    14902.023   -19648.103    300.79147    -542.4291    10965.793   0.99601433 
+  197000    561.88103   -3361.3955    649.81715   -4011.2127    778.20383    14857.622   -19650.459    299.45081    758.15369    10855.892    1.0060976 
+  198000    564.71123   -3375.0547    639.90978   -4014.9644    769.46044    14864.345   -19651.635    294.88526    541.36956    10764.059    1.0146811 
+  199000    566.62662   -3340.6462    680.56676   -4021.2129    742.41536    14883.325   -19650.541    313.62094   -242.81889    10781.093    1.0130778 
+  200000     568.5192   -3392.5132    655.59989   -4048.1131    788.37821    14810.426    -19650.31    302.11563    452.50967    10884.769    1.0034285 
+Loop time of 568.519 on 12 procs for 200000 steps with 1089 atoms
+
+Performance: 30.395 ns/day, 0.790 hours/ns, 351.791 timesteps/s
+93.1% CPU use with 12 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 225.29     | 244.44     | 283.93     | 111.9 | 43.00
+Bond    | 0.13517    | 0.2753     | 1.2102     |  54.4 |  0.05
+Kspace  | 121.44     | 161.43     | 181.09     | 137.9 | 28.40
+Neigh   | 20.445     | 20.505     | 20.539     |   0.7 |  3.61
+Comm    | 53.62      | 59.557     | 62.217     |  42.3 | 10.48
+Output  | 0.012041   | 0.012435   | 0.016413   |   1.1 |  0.00
+Modify  | 57.983     | 65.646     | 81.081     | 108.2 | 11.55
+Other   |            | 16.66      |            |       |  2.93
+
+Nlocal:        90.7500 ave         101 max          83 min
+Histogram: 3 1 1 2 0 1 0 1 1 2
+Nghost:        3759.42 ave        3809 max        3712 min
+Histogram: 2 0 0 3 2 1 1 0 2 1
+Neighs:        32260.6 ave       36917 max       28405 min
+Histogram: 1 1 2 4 0 0 1 1 0 2
+
+Total # of neighbors = 387127
+Ave neighs/atom = 355.48852
+Ave special neighs/atom = 2.0495868
+Neighbor list builds = 8468
+Dangerous builds = 4
+
+reset_timestep 0
+unfix NPT
+fix NVT all nvt temp ${TK} ${TK} 100
+fix NVT all nvt temp 300 ${TK} 100
+fix NVT all nvt temp 300 300 100
+
+variable dlambda equal  1.0
+variable minusdl equal -1.0
+variable dqC equal  (0.48+0.24)*v_dlambda
+variable dqH equal -0.06*v_dlambda
+variable dqF equal -0.12*v_dlambda
+
+compute FEP all fep ${TK}     pair lj/cut/coul/long/soft lambda 2 4*5 v_minusdl     pair lj/cut/coul/long/soft lambda 3 4*5 v_dlambda     atom charge 1 v_dqC     atom charge 2 v_dqH     atom charge 3 v_dqF
+compute FEP all fep 300     pair lj/cut/coul/long/soft lambda 2 4*5 v_minusdl     pair lj/cut/coul/long/soft lambda 3 4*5 v_dlambda     atom charge 1 v_dqC     atom charge 2 v_dqH     atom charge 3 v_dqF
+
+fix FEP all ave/time 1 1 100 c_FEP[1] c_FEP[2] file bar01.fep
+
+dump TRAJ all custom 5000 dump.lammpstrj id mol type element xu yu zu
+dump_modify TRAJ element C H F H O
+
+run 500000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
+  G vector (1/distance) = 0.26771633
+  grid = 12 12 12
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.025848288
+  estimated relative force accuracy = 7.7841351e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 1859 144
+FEP settings ...
+  temperature = 300.000000
+  tail no
+  lj/cut/coul/long/soft lambda 2-2 4-5
+  lj/cut/coul/long/soft lambda 3-3 4-5
+  1-1 charge
+  2-2 charge
+  3-3 charge
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 4 4 4
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair lj/cut/coul/long, perpetual, skip from (3)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (2) pair lj/cut/coul/long/soft, perpetual, skip from (3)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 17.62 | 17.63 | 17.63 Mbytes
+Step CPU TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Volume Density 
+       0            0   -3392.5233    655.59989   -4048.1232    788.37821    14629.081   -19468.975    302.11563    66.207268    10884.769    1.0034285 
+    1000    1.6811173   -3299.5075    692.20562   -3991.7131    778.25752    14691.657   -19467.153     318.9844    531.54794    10884.769    1.0034285 
+    2000    3.4266793   -3345.8401    672.15357   -4017.9937    754.89913     14692.39   -19468.044    309.74395   -147.16589    10884.769    1.0034285 
+    3000    5.6563153   -3347.3876    680.24737    -4027.635    801.32207    14634.959   -19469.614    313.47376    608.24729    10884.769    1.0034285 
+    4000    8.3285509   -3422.8843    642.07627   -4064.9605    749.54977    14646.739   -19465.434    295.88363    -798.2545    10884.769    1.0034285 
+    5000    11.003447   -3395.7269    651.90953   -4047.6364    794.41883    14625.696   -19470.699    300.41502    424.90838    10884.769    1.0034285 
+    6000    13.554516   -3379.3207    658.82739   -4038.1481    774.56484    14650.196   -19467.307    303.60294    264.50083    10884.769    1.0034285 
+    7000     16.06654   -3328.1712    672.06632   -4000.2376    770.43733    14691.469   -19467.518    309.70374    374.91512    10884.769    1.0034285 
+    8000    18.586977   -3346.4967    669.43289   -4015.9296    713.43009    14734.686   -19468.413    308.49019   -994.22271    10884.769    1.0034285 
+    9000    21.139807   -3421.4727    630.54971   -4052.0224     736.3754     14677.94   -19470.208    290.57192   -796.49483    10884.769    1.0034285 
+   10000    23.693652   -3358.3053    637.70114   -3996.0064    727.79701    14741.394   -19469.333    293.86747   -489.17242    10884.769    1.0034285 
+   11000    26.356224   -3382.4087    618.63949   -4001.0482    741.78751    14716.947   -19465.321    285.08342    -330.3192    10884.769    1.0034285 
+   12000    29.112214   -3334.5468    638.43918    -3972.986    747.02393    14738.603   -19465.776    294.20758   -68.170368    10884.769    1.0034285 
+   13000    31.812909   -3371.0486    647.96184   -4019.0104    765.94159    14678.816   -19469.352    298.59584   -97.249564    10884.769    1.0034285 
+   14000    34.538916   -3297.7217    678.51414   -3976.2359    668.98723    14819.716   -19468.779    312.67505   -1268.1136    10884.769    1.0034285 
+   15000    37.266623    -3373.087    639.38201    -4012.469    767.32979    14680.789   -19468.002    294.64205    171.53467    10884.769    1.0034285 
+   16000    40.009645   -3402.4215    652.00299   -4054.4245    771.91001    14636.237   -19469.143    300.45809   -197.81675    10884.769    1.0034285 
+   17000    42.748199   -3354.9429    642.32354   -3997.2664    782.37106    14681.343   -19466.539    295.99758    514.80071    10884.769    1.0034285 
+   18000    45.577128   -3344.8765    654.36132   -3999.2378    753.06347    14710.625   -19468.472    301.54486    26.607457    10884.769    1.0034285 
+   19000     48.37701   -3369.9861    651.23758   -4021.2236    682.11084    14757.597   -19469.739    300.10537   -1381.4838    10884.769    1.0034285 
+   20000    51.238304     -3372.16    644.79106   -4016.9511    761.96533    14683.158   -19468.941    297.13467    33.694074    10884.769    1.0034285 
+   21000    54.015707   -3391.5503    634.23099   -4025.7813    728.48913    14708.684    -19469.76    292.26834   -694.66683    10884.769    1.0034285 
+   22000    56.748778    -3332.257    649.13725   -3981.3943    739.20186     14741.91   -19467.548    299.13749   0.53749352    10884.769    1.0034285 
+   23000    59.447737   -3334.7011    648.36185    -3983.063    763.34358    14713.701   -19466.712    298.78017    351.84157    10884.769    1.0034285 
+   24000    62.111912   -3311.1433    671.52415   -3982.6675     741.0101    14733.039   -19466.072     309.4539   -399.81499    10884.769    1.0034285 
+   25000    64.685375   -3386.7822    632.09186   -4018.8741    740.02281    14704.199   -19470.911    291.28258   -1002.7393    10884.769    1.0034285 
+   26000    67.048266   -3430.0077    621.11236     -4051.12    816.18615    14595.604   -19467.786    286.22297    850.44682    10884.769    1.0034285 
+   27000      69.2054   -3417.9883    652.66224   -4070.6505    746.17234    14644.289   -19468.924    300.76189   -501.95941    10884.769    1.0034285 
+   28000    71.879128    -3352.973    634.50476   -3987.4777    792.88584    14678.588   -19466.619     292.3945    529.47638    10884.769    1.0034285 
+   29000    74.522808   -3418.1756    641.58878   -4059.7643     821.6061    14579.297   -19465.982    295.65899    805.47244    10884.769    1.0034285 
+   30000    77.171838   -3343.4995    663.09171   -4006.5912    753.23767    14701.935    -19467.09    305.56803    157.34857    10884.769    1.0034285 
+   31000    79.798534   -3362.1992    607.29189   -3969.4911    719.52107    14770.077   -19466.154    279.85418   -872.39699    10884.769    1.0034285 
+   32000    82.481369   -3377.2456    642.72578   -4019.9714    777.98481    14664.043   -19467.043    296.18294    70.648441    10884.769    1.0034285 
+   33000    85.125024   -3374.4755    677.62709   -4052.1026    776.50672    14634.382    -19467.03    312.26627   -118.61804    10884.769    1.0034285 
+   34000    87.693977   -3391.7554     630.0941   -4021.8495    793.58227    14647.164   -19468.672    290.36197     336.4751    10884.769    1.0034285 
+   35000    89.550172   -3363.8961    653.24835   -4017.1445    783.07559    14658.706   -19466.708    301.03198    831.25835    10884.769    1.0034285 
+   36000    92.042449    -3378.157    630.28905   -4008.4461    749.13541    14702.888   -19465.523    290.45181   -435.24553    10884.769    1.0034285 
+   37000    94.675515   -3396.8788    636.51966   -4033.3984    786.47438     14640.41   -19466.285    293.32302    180.31598    10884.769    1.0034285 
+   38000    97.317783   -3369.1654    656.56119   -4025.7265     820.3147    14615.021   -19466.701    302.55862    848.43605    10884.769    1.0034285 
+   39000    99.949448   -3377.1989    661.29735   -4038.4963    780.48734    14642.238   -19468.079    304.74115    255.92285    10884.769    1.0034285 
+   40000    102.60942   -3390.9886    647.44653   -4038.4351    757.42692    14668.825   -19468.007    298.35837   -475.42316    10884.769    1.0034285 
+   41000    105.28411   -3350.2253    658.81357   -4009.0389    730.42814    14719.114   -19464.283    303.59657   -903.03585    10884.769    1.0034285 
+   42000    107.89321   -3355.1829    634.64919   -3989.8321    717.07127    14753.812   -19467.937    292.46106   -820.68512    10884.769    1.0034285 
+   43000     110.2896   -3373.1254    662.48847   -4035.6139    797.42473    14630.014   -19469.184    305.29005     732.6283    10884.769    1.0034285 
+   44000    112.96943   -3342.8197    643.15451   -3985.9742    762.76344    14711.295   -19467.518    296.38051    252.72321    10884.769    1.0034285 
+   45000    115.66085   -3392.7496    643.46918   -4036.2187    795.50991      14628.5   -19466.034    296.52551    460.31078    10884.769    1.0034285 
+   46000    118.28419   -3345.3294    647.45671   -3992.7862    751.60875    14720.847   -19469.691    298.36306   -67.285324    10884.769    1.0034285 
+   47000    120.92672   -3374.6939    650.82643   -4025.5203    803.91747    14632.871   -19469.068     299.9159    885.67175    10884.769    1.0034285 
+   48000    123.54131   -3376.5834     656.4403   -4033.0237    728.45645    14702.693    -19469.04    302.50291   -592.86252    10884.769    1.0034285 
+   49000    126.16474   -3302.6257    677.14869   -3979.7744    763.27829    14719.458   -19466.816    312.04582    579.20607    10884.769    1.0034285 
+   50000    128.80017   -3394.6384    642.49782   -4037.1362    766.45009    14659.889   -19468.203    296.07789   -418.98788    10884.769    1.0034285 
+   51000    131.48223   -3403.5465    631.70758   -4035.2541    771.11904    14657.269   -19467.996     291.1055    17.264108    10884.769    1.0034285 
+   52000    134.22028    -3369.879    620.83184   -3990.7108    736.45855    14735.253   -19467.571    286.09371    -79.30133    10884.769    1.0034285 
+   53000    137.03314    -3355.713    667.45254   -4023.1655    750.49151    14687.892   -19464.642     307.5776   -204.76425    10884.769    1.0034285 
+   54000     140.0659   -3339.4836    644.53634   -3984.0199    774.20855    14704.183    -19469.11    297.01729   -21.870424    10884.769    1.0034285 
+   55000     142.8789   -3248.5052    709.42519   -3957.9304    707.80441    14794.891    -19468.98    326.91957   -165.74795    10884.769    1.0034285 
+   56000    145.47586   -3301.0284    658.78202   -3959.8105    704.22566    14798.124   -19467.571    303.58203   -276.54505    10884.769    1.0034285 
+   57000    148.04988   -3352.8114    649.85313   -4002.6645    718.43598    14742.119   -19469.268    299.46739   -803.50287    10884.769    1.0034285 
+   58000    150.62787   -3435.8725    630.39743     -4066.27    770.59375    14625.095   -19468.445    290.50175   -794.47088    10884.769    1.0034285 
+   59000    153.23446   -3343.2966    661.03067   -4004.3273    788.14877    14670.463   -19466.965    304.61826    715.38661    10884.769    1.0034285 
+   60000    155.86291   -3388.4494    662.45218   -4050.9016    771.51382    14637.842   -19468.024    305.27332    228.70354    10884.769    1.0034285 
+   61000    158.41542    -3341.684    656.71252   -3998.3965    710.02044    14756.957   -19469.342    302.62835   -939.67674    10884.769    1.0034285 
+   62000    160.90203   -3317.5062    633.12081    -3950.627    756.91435    14754.893   -19467.791    291.75675   -116.56738    10884.769    1.0034285 
+   63000    163.46632    -3349.249    665.61313   -4014.8621    781.57201    14667.451   -19469.657    306.72996    137.78175    10884.769    1.0034285 
+   64000    166.12552   -3296.4818    688.03213   -3984.5139    740.17128    14737.654   -19468.095    317.06115    320.87241    10884.769    1.0034285 
+   65000    168.67528   -3316.3065    672.07188   -3988.3784    777.23737    14696.693   -19467.354     309.7063    636.33474    10884.769    1.0034285 
+   66000    170.35008   -3381.5748    665.59937   -4047.1742    753.27584    14663.084   -19468.005    306.72362   -611.51143    10884.769    1.0034285 
+   67000    172.36153   -3436.1104    638.38336   -4074.4938     771.9136    14620.585    -19469.51    294.18185   -624.63906    10884.769    1.0034285 
+   68000     174.4599   -3331.1812    667.82988    -3999.011    748.29988    14717.236   -19469.158    307.75149    266.97949    10884.769    1.0034285 
+   69000    177.08185   -3353.5416    659.14109   -4012.6827    768.60823    14682.912   -19467.344    303.74749    386.21889    10884.769    1.0034285 
+   70000     179.6983   -3404.6246    632.16162   -4036.7862    813.50016    14614.534   -19469.311    291.31473    749.62239    10884.769    1.0034285 
+   71000     182.3267   -3384.8668    636.17053   -4021.0373    736.18673    14706.881   -19468.253    293.16213   -621.97708    10884.769    1.0034285 
+   72000    184.97665   -3406.7832    639.97066   -4046.7539    802.95794      14614.5   -19468.425    294.91332    747.74532    10884.769    1.0034285 
+   73000    187.63822   -3350.1839    656.01408   -4006.1979    796.29969    14662.092   -19468.075     302.3065    1094.7749    10884.769    1.0034285 
+   74000    190.31152   -3364.0697    641.24144   -4005.3111     708.3915    14751.579   -19468.594    295.49892   -1060.3998    10884.769    1.0034285 
+   75000    192.94703   -3344.0246    619.05004   -3963.0746    714.57627    14787.263   -19469.194    285.27261   -695.76735    10884.769    1.0034285 
+   76000    195.58904   -3348.1396    658.00002   -4006.1396    724.11817     14733.46   -19465.887    303.22166   -500.54075    10884.769    1.0034285 
+   77000    198.23386   -3302.3014    683.31477   -3985.6162    799.39383    14677.221   -19466.192    314.88728    1169.1764    10884.769    1.0034285 
+   78000    200.91817   -3355.1494    652.84212   -4007.9915    766.02973    14691.262   -19469.202    300.84478   -89.602404    10884.769    1.0034285 
+   79000    203.18307   -3338.1582    663.94322   -4002.1014    731.94742    14730.828   -19469.086    305.96043   -514.05802    10884.769    1.0034285 
+   80000    205.54876   -3305.6879    657.27741   -3962.9653    724.63653    14776.787   -19468.885    302.88867   -85.315398    10884.769    1.0034285 
+   81000    208.20428   -3420.5065    649.28955   -4069.7961    825.56991     14569.69   -19469.393    299.20768    900.03551    10884.769    1.0034285 
+   82000    210.96477   -3371.4178    650.22749   -4021.6453      718.597    14725.782   -19469.387     299.6399   -869.42154    10884.769    1.0034285 
+   83000    213.62045     -3413.08    644.35951   -4057.4395    799.05883    14609.683   -19470.186     296.9358    159.67984    10884.769    1.0034285 
+   84000    216.12916   -3387.3358     648.4488   -4035.7846    737.86969    14690.171    -19466.51    298.82024   -448.98917    10884.769    1.0034285 
+   85000    217.78977   -3355.3349    651.60638   -4006.9412    763.37146    14691.793   -19467.511    300.27533    211.15989    10884.769    1.0034285 
+   86000    220.24331    -3392.521    649.59384   -4042.1148    731.63559    14691.855   -19469.003     299.3479   -783.61319    10884.769    1.0034285 
+   87000    222.85728   -3346.3695    649.33458   -3995.7041    742.91425    14725.386   -19469.239    299.22843   -339.24385    10884.769    1.0034285 
+   88000    225.03915   -3352.5714    666.78268   -4019.3541    687.63084    14757.357   -19468.462    307.26892   -1587.4069    10884.769    1.0034285 
+   89000    227.65977   -3404.9342    603.96862   -4008.9029    761.27643    14693.623   -19467.157    278.32274   -9.6654117    10884.769    1.0034285 
+   90000    230.33312   -3388.3658    650.41591   -4038.7817    782.96102    14642.793   -19467.954    299.72673    35.503993    10884.769    1.0034285 
+   91000    232.97093   -3345.3341    682.11092    -4027.445    756.44601    14681.236   -19468.634    314.33252   -299.00279    10884.769    1.0034285 
+   92000    235.61364   -3358.6697    681.92535    -4040.595    757.04448    14669.511   -19469.866    314.24701   -352.88605    10884.769    1.0034285 
+   93000    238.19708   -3398.8534    622.43523   -4021.2886    746.45093    14697.035   -19468.344    286.83258   -293.99367    10884.769    1.0034285 
+   94000    240.91931   -3387.6874    625.71972   -4013.4071    785.29423    14668.442   -19469.791    288.34615    380.29332    10884.769    1.0034285 
+   95000    243.45274   -3338.2567    657.14629    -3995.403    707.60283    14757.373   -19466.122    302.82824   -1259.7291    10884.769    1.0034285 
+   96000    245.12248   -3346.2709     643.8836   -3990.1545    723.21226    14750.182    -19466.67    296.71649    -545.5226    10884.769    1.0034285 
+   97000    246.87645    -3304.122    661.68987   -3965.8119    718.72307    14779.498   -19468.737    304.92203   -185.89581    10884.769    1.0034285 
+   98000    248.95971   -3384.1246    633.68902   -4017.8136    713.00288    14734.686   -19468.944    292.01859   -851.96113    10884.769    1.0034285 
+   99000    251.61686    -3317.834    694.86722   -4012.7012    708.60818    14743.924   -19468.702    320.21093   -1099.8099    10884.769    1.0034285 
+  100000    254.37772   -3372.7172    649.88143   -4022.5987    733.96698     14707.79    -19467.51    299.48043   -597.95684    10884.769    1.0034285 
+  101000    256.34824   -3435.4402    625.03479    -4060.475    789.53059     14615.97   -19470.526    288.03052    225.99984    10884.769    1.0034285 
+  102000    258.79934   -3425.5736    639.52625   -4065.0999    750.05378     14650.15   -19467.654    294.70852   -572.89126    10884.769    1.0034285 
+  103000    260.46195    -3333.926    659.51738   -3993.4434    757.30801    14710.804    -19466.38     303.9209   -358.44401    10884.769    1.0034285 
+  104000    262.54144   -3389.8992      631.351   -4021.2502    752.08137    14694.458   -19470.392    290.94118   -237.00267    10884.769    1.0034285 
+  105000     264.6734   -3415.1147    625.29265   -4040.4073    756.35163    14669.962   -19470.415    288.14935   -281.84399    10884.769    1.0034285 
+  106000    266.35046   -3362.2713    666.64093   -4028.9122     728.0197    14707.008   -19467.447    307.20359   -668.83961    10884.769    1.0034285 
+  107000    268.22001   -3430.7377     655.6673    -4086.405    803.62099    14577.727   -19470.435    302.14669    226.49862    10884.769    1.0034285 
+  108000    269.88995   -3361.2862    631.43629   -3992.7225    738.09167    14735.144   -19468.752    290.98048   -382.52042    10884.769    1.0034285 
+  109000     272.0943   -3391.7549    656.64697   -4048.4019    731.46183    14686.123   -19469.336    302.59815   -637.73354    10884.769    1.0034285 
+  110000    274.69862   -3402.8856    654.59929   -4057.4849    754.83158    14652.555   -19468.706    301.65453   -470.27119    10884.769    1.0034285 
+  111000    277.34594   -3407.6623    637.27419   -4044.9365    743.58123      14675.4     -19466.6    293.67072   -760.83259    10884.769    1.0034285 
+  112000    279.95177   -3373.2725    669.32743   -4042.5999    797.16485    14624.093   -19467.521    308.44159    451.16773    10884.769    1.0034285 
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+  114000    285.15729   -3355.1053    672.59494   -4027.7002    808.32237    14629.692   -19469.661    309.94734    1002.8272    10884.769    1.0034285 
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+  463000    1185.9343   -3353.9724    654.21985   -4008.1923    753.41299    14702.337   -19466.777    301.47968    -38.01484    10884.769    1.0034285 
+  464000    1188.5947   -3367.9482    647.70878   -4015.6569    726.02045    14722.772   -19467.551    298.47922   -746.46033    10884.769    1.0034285 
+  465000    1191.3234   -3375.9438    647.43884   -4023.3827     737.8556    14699.946   -19466.301    298.35483   -762.47592    10884.769    1.0034285 
+  466000     1194.148   -3382.0565    633.88101   -4015.9375    728.14268    14719.033   -19467.501    292.10707   -815.52081    10884.769    1.0034285 
+  467000    1196.9729   -3352.4659    660.95022   -4013.4161    720.84255     14731.47   -19468.821    304.58118   -675.61959    10884.769    1.0034285 
+  468000    1199.7465   -3358.6234    652.51372   -4011.1371    726.76551    14723.721   -19468.476    300.69345    -596.5145    10884.769    1.0034285 
+  469000    1202.4646   -3398.6766    639.12087   -4037.7975    761.92233    14665.696   -19467.917    294.52171   -114.65072    10884.769    1.0034285 
+  470000    1205.1556   -3375.5333    653.08366    -4028.617    747.49005    14687.379   -19467.981    300.95609   -560.00991    10884.769    1.0034285 
+  471000    1207.8286   -3373.3315    648.09883   -4021.4303    738.20986    14702.862   -19467.953    298.65897   -172.19402    10884.769    1.0034285 
+  472000    1210.4971   -3332.1041    673.84369   -4005.9478    724.82747     14734.53   -19468.862    310.52279   -328.77865    10884.769    1.0034285 
+  473000    1213.1828   -3330.0829    681.87274   -4011.9556    768.46848    14683.806   -19468.092    314.22276    123.72622    10884.769    1.0034285 
+  474000    1215.8929    -3346.435    642.00938   -3988.4444    758.61878    14714.661   -19469.159    295.85281   -125.13242    10884.769    1.0034285 
+  475000    1218.5329   -3443.8357    614.83964   -4058.6754    781.61539    14624.416   -19468.477    283.33236    -111.5801    10884.769    1.0034285 
+  476000     1221.178   -3400.7974    638.63917   -4039.4366    784.79512    14641.855   -19469.076    294.29974    517.41905    10884.769    1.0034285 
+  477000    1223.8523   -3320.0342    653.14369   -3973.1779    716.07877    14773.753   -19468.532    300.98376   -458.16557    10884.769    1.0034285 
+  478000    1226.5547   -3399.4442    640.11785   -4039.5621    771.08147    14651.622   -19466.562    294.98115   -197.74698    10884.769    1.0034285 
+  479000    1229.1658   -3326.6496    695.49682   -4022.1464    808.20733    14631.903   -19468.159    320.50106    634.31531    10884.769    1.0034285 
+  480000    1231.8425   -3334.6791    658.32148   -3993.0006    773.22972    14697.373   -19468.715     303.3698    446.26474    10884.769    1.0034285 
+  481000    1234.5644   -3359.0137    662.25789   -4021.2716    794.57799    14646.408   -19467.738    305.18379    886.12083    10884.769    1.0034285 
+  482000    1237.2816   -3364.2843    619.48039   -3983.7646    731.30777    14748.159   -19468.063    285.47092   -620.63473    10884.769    1.0034285 
+  483000    1239.8325   -3322.9451    661.28309   -3984.2282    742.40976    14734.131   -19466.312    304.73458   -222.24701    10884.769    1.0034285 
+  484000    1242.6089   -3375.2908    645.07137   -4020.3622    744.66198    14697.014   -19468.175    297.26384   -136.11832    10884.769    1.0034285 
+  485000    1245.3754   -3378.1938    652.70779   -4030.9016    771.21368    14662.803    -19468.64    300.78288    179.33884    10884.769    1.0034285 
+  486000    1248.1668   -3353.6944    663.96968   -4017.6641    747.96436    14695.385   -19467.156    305.97262   -204.89716    10884.769    1.0034285 
+  487000    1250.9451   -3378.5985    618.19475   -3996.7933    802.27888    14660.268    -19465.25    284.87847    758.55561    10884.769    1.0034285 
+  488000    1253.8242   -3383.4314    628.64496   -4012.0763    695.60474     14755.36   -19468.271    289.69417   -1440.2954    10884.769    1.0034285 
+  489000    1256.7123   -3353.4337    639.18453   -3992.6183    776.60327    14693.087   -19469.167    294.55105    679.63676    10884.769    1.0034285 
+  490000    1259.5889   -3402.9615    644.52942   -4047.4909    791.04054    14624.437   -19466.425     297.0141    261.43904    10884.769    1.0034285 
+  491000    1262.4351   -3365.8526    649.37639    -4015.229    759.05805    14688.834   -19468.725     299.2477   -246.75688    10884.769    1.0034285 
+  492000    1265.3213   -3329.7038    665.28344   -3994.9872    756.07131    14712.004   -19468.819    306.57803   -27.238249    10884.769    1.0034285 
+  493000    1268.1117   -3376.8648    643.42854   -4020.2933    794.79336    14647.846   -19467.803    296.50679     636.6427    10884.769    1.0034285 
+  494000    1270.9762   -3365.5727    627.78783   -3993.3605    785.11016     14682.83   -19467.596    289.29919    657.20701    10884.769    1.0034285 
+  495000    1273.8675   -3360.4436    651.89842    -4012.342    699.51635     14748.52   -19466.495    300.40991   -1445.6517    10884.769    1.0034285 
+  496000    1276.7102   -3364.6024    643.94023   -4008.5427    754.26362    14697.764   -19467.441    296.74259   -122.47872    10884.769    1.0034285 
+  497000    1279.5134   -3295.1345     653.2039   -3948.3384    799.24543    14711.358   -19465.575     301.0115     1418.332    10884.769    1.0034285 
+  498000    1282.3841   -3367.7301    630.59081   -3998.3209    761.83084     14703.35   -19468.711    290.59086    99.969115    10884.769    1.0034285 
+  499000    1285.1837   -3309.0757    652.60901   -3961.6847     760.3183    14738.726   -19467.155    300.73736    352.38315    10884.769    1.0034285 
+  500000    1288.0731     -3360.42    669.85238   -4030.2724    780.88169    14655.258   -19469.761    308.68351    410.74767    10884.769    1.0034285 
+Loop time of 1288.07 on 12 procs for 500000 steps with 1089 atoms
+
+Performance: 33.538 ns/day, 0.716 hours/ns, 388.177 timesteps/s
+92.8% CPU use with 12 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 586.82     | 650.28     | 723.75     | 172.7 | 50.49
+Bond    | 0.21603    | 0.47536    | 1.0816     |  38.6 |  0.04
+Kspace  | 261.99     | 333.22     | 394.35     | 230.9 | 25.87
+Neigh   | 52.434     | 52.566     | 52.723     |   1.3 |  4.08
+Comm    | 134.36     | 137.58     | 140.67     |  18.6 | 10.68
+Output  | 0.088694   | 0.094951   | 0.095607   |   0.6 |  0.01
+Modify  | 91.711     | 92.795     | 93.695     |   7.3 |  7.20
+Other   |            | 21.06      |            |       |  1.63
+
+Nlocal:        90.7500 ave          99 max          84 min
+Histogram: 2 1 2 0 0 3 2 0 1 1
+Nghost:        3801.33 ave        3848 max        3759 min
+Histogram: 1 1 2 2 1 0 1 3 0 1
+Neighs:        32343.8 ave       35671 max       30135 min
+Histogram: 3 1 2 1 0 1 2 0 1 1
+
+Total # of neighbors = 388125
+Ave neighs/atom = 356.40496
+Ave special neighs/atom = 2.0495868
+Neighbor list builds = 20690
+Dangerous builds = 0
+
+# write_restart restart.*.lmp
+write_data data.*.lmp
+System init for write_data ...
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
+  G vector (1/distance) = 0.26771633
+  grid = 12 12 12
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.025848288
+  estimated relative force accuracy = 7.7841351e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 1859 144
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 4 4 4
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair lj/cut/coul/long, perpetual, skip from (3)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (2) pair lj/cut/coul/long/soft, perpetual, skip from (3)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Total wall time: 0:30:56