Merge branch 'develop' into snann_slcsa

.github/CODEOWNERS

@@ -61,6 +61,7 @@ src/GPU/pair_vashishta_gpu.*        @andeplane
 src/KOKKOS/pair_vashishta_kokkos.*  @andeplane
 src/MANYBODY/pair_vashishta_table.* @andeplane
 src/MANYBODY/pair_atm.*             @sergeylishchuk
+src/MANYBODY/pair_nb3b_screened.*   @flodesani
 src/REPLICA/*_grem.*                @dstelter92
 src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
 src/EXTRA-COMPUTE/compute_born_matrix.* @Bibobu @athomps
@@ -135,6 +136,7 @@ src/timer.*               @akohlmey
 src/utils.*               @akohlmey @rbberger
 src/verlet.*              @sjplimp @stanmoore1
 src/math_eigen_impl.h     @jewettaij
+src/fix_press_langevin.*  @Bibobu
 
 # tools
 tools/coding_standard/* @akohlmey @rbberger
@@ -151,12 +153,12 @@ tools/vim/*           @hammondkd
 unittest/*            @akohlmey
 
 # cmake
-cmake/*               @rbberger
+cmake/*               @akohlmey
 cmake/Modules/LAMMPSInterfacePlugin.cmake @akohlmey
 cmake/Modules/MPI4WIN.cmake @akohlmey
 cmake/Modules/OpenCLLoader.cmake @akohlmey
-cmake/Modules/Packages/COLVARS.cmake @rbberger @giacomofiorin
+cmake/Modules/Packages/COLVARS.cmake @giacomofiorin
-cmake/Modules/Packages/KIM.cmake @rbberger @ellio167
+cmake/Modules/Packages/KIM.cmake @ellio167
 cmake/presets/*.cmake @akohlmey
 
 # python

.github/CONTRIBUTING.md

@@ -5,9 +5,9 @@ Thank you for considering to contribute to the LAMMPS software project.
 The following is a set of guidelines as well as explanations of policies and work flows for contributing to the LAMMPS molecular dynamics software project. These guidelines focus on submitting issues or pull requests on the LAMMPS GitHub project.
 
 Thus please also have a look at:
-* [The guide for submitting new features in the LAMMPS manual](https://www.lammps.org/doc/Modify_contribute.html)
+* [The guide for submitting new features in the LAMMPS manual](https://docs.lammps.org/Modify_contribute.html)
-* [The guide on programming style and requirement in the LAMMPS manual](https://www.lammps.org/doc/Modify_style.html)
+* [The guide on programming style and requirement in the LAMMPS manual](https://docs.lammps.org/Modify_requirements.html)
-* [The GitHub tutorial in the LAMMPS manual](http://lammps.sandia.gov/doc/Howto_github.html)
+* [The GitHub tutorial in the LAMMPS manual](http://docs.lammps.org/Howto_github.html)
 
 ## Table of Contents
 
@@ -27,17 +27,17 @@ __
 
 ## I don't want to read this whole thing I just have a question!
 
-> **Note:** Please do not file an issue to ask a general question about LAMMPS, its features, how to use specific commands, or how perform simulations or analysis in LAMMPS. Instead post your question to either the ['lammps-users' mailing list](https://lammps.sandia.gov/mail.html) or the [LAMMPS Material Science Discourse forum](https://matsci.org/lammps). You do not need to be subscribed to post to the list (but a mailing list subscription avoids having your post delayed until it is approved by a mailing list moderator). Most posts to the mailing list receive a response within less than 24 hours. Before posting to the mailing list, please read the [mailing list guidelines](https://lammps.sandia.gov/guidelines.html). Following those guidelines will help greatly to get a helpful response. Always mention which LAMMPS version you are using. The LAMMPS forum was recently created as part of a larger effort to build a materials science community and have discussions not just about using LAMMPS. Thus the forum may be also used for discussions that would be off-topic for the mailing list. Those will just have to be posted to a more general category.
+> **Note:** Please do not file an issue to ask a general question about LAMMPS, its features, how to use specific commands, or how perform simulations or analysis in LAMMPS. Instead post your question to the [LAMMPS Material Science Discourse forum](https://matsci.org/lammps). Before posting to the forum, please read the general [guidelines](https://www.lammps.org/guidelines.html) and the forum specific [suggestions](https://matsci.org/t/please-read-this-first-guidelines-and-suggestions-for-posting-lammps-questions/49913). Following those guidelines and suggestions will help greatly to get a helpful response.  *Always* mention which LAMMPS version you are using. The MatSci website may be also used for discussions that would be off-topic for the LAMMPS categories. Those will just have to be posted to a different category.
 
 ## How Can I Contribute?
 
 There are several ways how you can actively contribute to the LAMMPS project: you can discuss compiling and using LAMMPS, and solving LAMMPS related problems with other LAMMPS users on the lammps-users mailing list or the forum, you can report bugs or suggest enhancements by creating issues on GitHub (or posting them to the lammps-users mailing list or posting in the LAMMPS Materials Science Discourse forum), and you can contribute by submitting pull requests on GitHub or e-mail your code
-to one of the [LAMMPS core developers](https://lammps.sandia.gov/authors.html). As you may see from the aforementioned developer page, the LAMMPS software package includes the efforts of a very large number of contributors beyond the principal authors and maintainers.
+to one of the [LAMMPS core developers](https://www.lammps.org/authors.html). As you may see from the aforementioned developer page, the LAMMPS software package includes the efforts of a very large number of contributors beyond the principal authors and maintainers.
 
 ### Discussing How To Use LAMMPS
 
 The LAMMPS mailing list is hosted at SourceForge. The mailing list began in 2005, and now includes tens of thousands of messages in thousands of threads. LAMMPS developers try to respond to posted questions in a timely manner, but there are no guarantees. Please consider that people live in different timezone and may not have time to answer e-mails outside of their work hours.
-You can post to list by sending your email to lammps-users at lists.sourceforge.net (no subscription required), but before posting, please read the [mailing list guidelines](https://lammps.sandia.gov/guidelines.html) to maximize your chances to receive a helpful response.
+You can post to list by sending your email to lammps-users at lists.sourceforge.net (no subscription required), but before posting, please read the [mailing list guidelines](https://www.lammps.org/guidelines.html) to maximize your chances to receive a helpful response.
 
 Anyone can browse/search previous questions/answers in the archives. You do not have to subscribe to the list to post questions, receive answers (to your questions), or browse/search the archives. You **do** need to subscribe to the list if you want emails for **all** the posts (as individual messages or in digest form), or to answer questions yourself. Feel free to sign up and help us out! Answering questions from fellow LAMMPS users is a great way to pay back the community for providing you a useful tool for free, and to pass on the advice you have received yourself to others. It improves your karma and helps you understand your own research better.
 
@@ -47,7 +47,7 @@ The LAMMPS Materials Science Discourse forum was created recently to facilitate
 
 ### Reporting Bugs
 
-While developers writing code for LAMMPS are careful to test their code, LAMMPS is such a large and complex software, that it is impossible to test for all combinations of features under all normal and not so normal circumstances. Thus bugs do happen, and if you suspect, that you have encountered one, please try to document it and report it as an [Issue](https://github.com/lammps/lammps/issues) on the LAMMPS GitHub project web page. However, before reporting a bug, you need to check whether this is something that may have already been corrected. The [Latest Features and Bug Fixes in LAMMPS](https://lammps.sandia.gov/bug.html) web page lists all significant changes to LAMMPS over the years. It also tells you what the current latest development version of LAMMPS is, and you should test whether your issue still applies to that version.
+While developers writing code for LAMMPS are careful to test their code, LAMMPS is such a large and complex software, that it is impossible to test for all combinations of features under all normal and not so normal circumstances. Thus bugs do happen, and if you suspect, that you have encountered one, please try to document it and report it as an [Issue](https://github.com/lammps/lammps/issues) on the LAMMPS GitHub project web page. However, before reporting a bug, you need to check whether this is something that may have already been corrected. The [Latest Features and Bug Fixes in LAMMPS](https://www.lammps.org/bug.html) web page lists all significant changes to LAMMPS over the years. It also tells you what the current latest development version of LAMMPS is, and you should test whether your issue still applies to that version.
 
 When you click on the green "New Issue" button, you will be provided with a text field, where you can enter your message. That text field with contain a template with several headlines and some descriptions. Keep the headlines that are relevant to your reported potential bug and replace the descriptions with the information as suggested by the descriptions.
 You can also attach small text files (please add the file name extension `.txt` or it will be rejected), images, or small compressed text files (using gzip, do not use RAR or 7-ZIP or similar tools that are uncommon outside of Windows machines). In many cases, bugs are best illustrated by providing a small input deck (do **not** attach your entire production input, but remove everything that is not required to reproduce the issue, and scale down your system size, that the resulting calculation runs fast and can be run on small desktop quickly).
@@ -65,9 +65,9 @@ To be able to submit an issue on GitHub, you have to register for an account (fo
 
 We encourage users to submit new features or modifications for LAMMPS. Instructions, guidelines, requirements,
 and recommendations are in the following sections of the LAMMPS manual:
-* [The guide for submitting new features in the LAMMPS manual](https://lammps.sandia.gov/doc/Modify_contribute.html)
+* [The guide for submitting new features in the LAMMPS manual](https://docs.lammps.org/Modify_contribute.html)
-* [The guide on programming style and requirement in the LAMMPS manual](https://lammps.sandia.gov/doc/Modify_contribute.html)
+* [The guide on programming style and requirement in the LAMMPS manual](https://docs.lammps.org/Modify_requirements.html)
-* [The GitHub tutorial in the LAMMPS manual](http://lammps.sandia.gov/doc/Howto_github.html)
+* [The GitHub tutorial in the LAMMPS manual](http://docs.lammps.org/Howto_github.html)
 
 
 ## GitHub Workflows
@@ -85,7 +85,7 @@ For bug reports, the next step is that one of the core LAMMPS developers will se
 ### Pull Requests
 
 Pull requests are the **only** way that changes get made to the LAMMPS distribution.  So also the LAMMPS core developers will submit pull requests for their own changes and discuss them on GitHub.  Thus if you submit a pull request it will be treated in a similar fashion. When you submit a pull request you may opt to submit a "Draft" pull request.  That means your changes are visible and will be subject to testing, but reviewers will not be (auto-)assigned and comments will take into account that this is not complete. On the other hand, this is a perfect way to ask the LAMMPS developers for comments on non-obvious changes and get feedback and possible suggestions for improvements or recommendations about what to avoid.
-Immediately after the submission, the LAMMPS continuing integration server at ci.lammps.org will download your submitted branch and perform a number of tests: it will tests whether it compiles cleanly under various conditions, it will also do a check on whether your included documentation translates cleanly and run some unit tests and other checks. Whether these tests are successful or fail will be recorded.  If a test fails, please inspect the corresponding output on the CI server and take the necessary steps, if needed, so that the code can compile cleanly again.  The test will be re-run each time the pull request is updated with a push to the remote branch on GitHub.  If you are unsure about what you need to change, ask a question in the discussion area of the pull request.
+Immediately after the submission, the LAMMPS continuing integration server at https://ci.lammps.org will download your submitted branch and perform a number of tests: it will tests whether it compiles cleanly under various conditions, it will also do a check on whether your included documentation translates cleanly and run some unit tests and other checks. Whether these tests are successful or fail will be recorded.  If a test fails, please inspect the corresponding output on the CI server and take the necessary steps, if needed, so that the code can compile cleanly again.  The test will be re-run each time the pull request is updated with a push to the remote branch on GitHub.  If you are unsure about what you need to change, ask a question in the discussion area of the pull request.
 Next a LAMMPS core developer will self-assign and do an overall technical assessment of the submission.  If you submitted a draft pull request, this will not happen unless you mark it "ready for review".  If you are not yet invited as a LAMMPS collaborator, and your contribution seems significant, you may also receive an invitation for collaboration on the LAMMPS repository.  As part of the assessment, the pull request will be categorized with labels. There are two special labels: `needs_work` (indicates that work from the submitter of the pull request is needed) and `work_in_progress` (indicates, that the assigned LAMMPS developer will make changes, if not done by the contributor who made the submit). 
 You may also receive comments and suggestions on the overall submission or specific details and on occasion specific requests for changes as part of the review. If permitted, also additional changes may be pushed into your pull request branch or a pull request may be filed in your LAMMPS fork on GitHub to include those changes.
 The LAMMPS developer may then decide to assign the pull request to another developer (e.g. when that developer is more knowledgeable about the submitted feature or enhancement or has written the modified code). It may also happen, that additional developers are requested to provide a review and approve the changes. For submissions, that may change the general behavior of LAMMPS, or where a possibility of unwanted side effects exists, additional tests may be requested by the assigned developer.

.github/workflows/coverity.yml

@@ -59,16 +59,13 @@ jobs:
         -D BUILD_SHARED_LIBS=on \
         -D LAMMPS_SIZES=SMALLBIG \
         -D LAMMPS_EXCEPTIONS=off \
-        -D PKG_MESSAGE=on \
-        -D PKG_MPIIO=on \
         -D PKG_ATC=on \
         -D PKG_AWPMD=on \
-        -D PKG_BOCS=on \
-        -D PKG_EFF=on \
         -D PKG_H5MD=on \
         -D PKG_INTEL=on \
         -D PKG_LATBOLTZ=on \
         -D PKG_MANIFOLD=on \
+        -D PKG_MDI=on \
         -D PKG_MGPT=on \
         -D PKG_ML-PACE=on \
         -D PKG_ML-RANN=on \
@@ -77,7 +74,6 @@ jobs:
         -D PKG_PTM=on \
         -D PKG_QTB=on \
         -D PKG_SMTBQ=on \
-        -D PKG_TALLY=on \
         ../cmake
 
     - name: Run Coverity Scan

cmake/CMakeLists.txt

@@ -2,7 +2,6 @@
 ########################################
 # CMake build system
 # This file is part of LAMMPS
-# Created by Christoph Junghans and Richard Berger
 cmake_minimum_required(VERSION 3.16)
 ########################################
 # set policy to silence warnings about ignoring <PackageName>_ROOT but use it
@@ -106,7 +105,7 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
     if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
       set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
     else()
-      set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=2196")
+      set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=11074 -diag-disable=11076 -diag-disable=2196")
     endif()
   endif()
 endif()
@@ -159,17 +158,20 @@ endif()
 ########################################################################
 # User input options                                                   #
 ########################################################################
-# set path to python interpreter and thus enforcing python version when
+# backward compatibility with CMake before 3.12 and older LAMMPS documentation
-# in a virtual environment and PYTHON_EXECUTABLE is not set on command line
+if (PYTHON_EXECUTABLE)
-if(DEFINED ENV{VIRTUAL_ENV} AND NOT PYTHON_EXECUTABLE)
-  if(CMAKE_HOST_SYSTEM_NAME STREQUAL "Windows")
-    set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/Scripts/python.exe")
-  else()
-    set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/bin/python")
-  endif()
   set(Python_EXECUTABLE "${PYTHON_EXECUTABLE}")
+endif()
+# set path to python interpreter and thus enforcing python version when
+# in a virtual environment and Python_EXECUTABLE is not set on command line
+if(DEFINED ENV{VIRTUAL_ENV} AND NOT Python_EXECUTABLE)
+  if(CMAKE_HOST_SYSTEM_NAME STREQUAL "Windows")
+    set(Python_EXECUTABLE "$ENV{VIRTUAL_ENV}/Scripts/python.exe")
+  else()
+    set(Python_EXECUTABLE "$ENV{VIRTUAL_ENV}/bin/python")
+  endif()
   message(STATUS "Running in virtual environment: $ENV{VIRTUAL_ENV}\n"
-    "   Setting Python interpreter to: ${PYTHON_EXECUTABLE}")
+    "   Setting Python interpreter to: ${Python_EXECUTABLE}")
 endif()
 
 set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically")
@@ -425,6 +427,18 @@ if(BUILD_OMP)
   target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX)
 endif()
 
+# lower C++ standard for fmtlib sources when using Intel classic compiler
+if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_STANDARD GREATER_EQUAL 17)
+    AND (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 2021.10))
+  message(STATUS "Lowering C++ standard for compiling fmtlib sources with Intel Classic compiler")
+  get_filename_component(LMP_UTILS_SRC "${LAMMPS_SOURCE_DIR}/utils.cpp" ABSOLUTE)
+  get_filename_component(LMP_VARIABLE_SRC "${LAMMPS_SOURCE_DIR}/variable.cpp" ABSOLUTE)
+  get_filename_component(FMT_FORMAT_SRC "${LAMMPS_SOURCE_DIR}/fmtlib_format.cpp" ABSOLUTE)
+  get_filename_component(FMT_OS_SRC "${LAMMPS_SOURCE_DIR}/fmtlib_os.cpp" ABSOLUTE)
+  set_source_files_properties("${FMT_FORMAT_SRC}" "${FMT_OS_SRC}" "${LMP_VARIABLE_SRC}" "${LMP_UTILS_SRC}"
+          PROPERTIES COMPILE_OPTIONS "-std=c++14")
+endif()
+
 if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_TOOLS)
   enable_language(C)
   if (NOT USE_INTERNAL_LINALG)
@@ -794,9 +808,6 @@ install(
 ###############################################################################
 if(BUILD_SHARED_LIBS)
   # backward compatibility
-  if(PYTHON_EXECUTABLE)
-    set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
-  endif()
   find_package(Python COMPONENTS Interpreter)
   if(BUILD_IS_MULTI_CONFIG)
     set(MY_BUILD_DIR ${CMAKE_BINARY_DIR}/$<CONFIG>)

cmake/Modules/LAMMPSUtils.cmake

@@ -83,12 +83,12 @@ function(check_for_autogen_files source_dir)
     file(GLOB SRC_AUTOGEN_FILES CONFIGURE_DEPENDS ${source_dir}/style_*.h)
     file(GLOB SRC_AUTOGEN_PACKAGES CONFIGURE_DEPENDS ${source_dir}/packages_*.h)
     list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/lmpinstalledpkgs.h ${source_dir}/lmpgitversion.h)
-    list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/mliap_model_python_couple.h ${source_dir}/mliap_model_python_couple.cpp)
+    list(APPEND SRC_AUTOGEN_FILES ${source_dir}/mliap_model_python_couple.h ${source_dir}/mliap_model_python_couple.cpp)
     foreach(_SRC ${SRC_AUTOGEN_FILES})
       get_filename_component(FILENAME "${_SRC}" NAME)
       if(EXISTS ${source_dir}/${FILENAME})
         message(FATAL_ERROR "\n########################################################################\n"
-                              "Found header file(s) generated by the make-based build system\n"
+                            "Found header file ${source_dir}/${FILENAME} generated by the make-based build system\n"
                             "\n"
                             "Please run\n"
                             "make -C ${source_dir} purge\n"

cmake/Modules/Packages/KOKKOS.cmake

@@ -50,8 +50,8 @@ if(DOWNLOAD_KOKKOS)
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
   include(ExternalProject)
-  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.1.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.2.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "a5f096bd8ad01b97fdc7a32583b17a33" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  set(KOKKOS_MD5 "731647b61a4233f568d583702e9cd6d1" CACHE STRING "MD5 checksum of KOKKOS tarball")
   mark_as_advanced(KOKKOS_URL)
   mark_as_advanced(KOKKOS_MD5)
   GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@@ -76,7 +76,7 @@ if(DOWNLOAD_KOKKOS)
   add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
   add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 4.1.00 REQUIRED CONFIG)
+  find_package(Kokkos 4.2.00 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
 else()
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)

cmake/Modules/Packages/ML-PACE.cmake

@@ -1,6 +1,6 @@
-set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.01.3.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.10.04.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
 
-set(PACELIB_MD5 "4f0b3b5b14456fe9a73b447de3765caa" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
+set(PACELIB_MD5 "70ff79f4e59af175e55d24f3243ad1ff" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
 mark_as_advanced(PACELIB_URL)
 mark_as_advanced(PACELIB_MD5)
 GetFallbackURL(PACELIB_URL PACELIB_FALLBACK)

cmake/Modules/Packages/PYTHON.cmake

@@ -1,6 +1,6 @@
 
 if(NOT Python_INTERPRETER)
-  # backward compatibility
+  # backward compatibility with CMake before 3.12 and older LAMMPS documentation
   if(PYTHON_EXECUTABLE)
     set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
   endif()

cmake/packaging/build_windows_vs.cmake

@@ -21,6 +21,13 @@ file(WRITE qtdeploy.bat "@ECHO OFF\r\nset VSCMD_DEBUG=0\r\nCALL ${VC_INIT} x64\r
 execute_process(COMMAND cmd.exe /c qtdeploy.bat COMMAND_ECHO STDERR)
 file(REMOVE qtdeploy.bat)
 
+# download and uncompress static FFMpeg and gzip binaries
+file(DOWNLOAD "https://download.lammps.org/thirdparty/ffmpeg-gzip.zip" ffmpeg-gzip.zip)
+file(WRITE unpackzip.ps1 "Expand-Archive -Path ffmpeg-gzip.zip -DestinationPath LAMMPS_GUI")
+execute_process(COMMAND powershell -ExecutionPolicy Bypass -File unpackzip.ps1)
+file(REMOVE unpackzip.ps1)
+file(REMOVE ffmpeg-gzip.zip)
+
 # create zip archive
 file(WRITE makearchive.ps1 "Compress-Archive -Path LAMMPS_GUI -CompressionLevel Optimal -DestinationPath LAMMPS_GUI-Win10-amd64.zip")
 execute_process(COMMAND powershell -ExecutionPolicy Bypass -File makearchive.ps1)

cmake/presets/kokkos-cuda.cmake

@@ -6,6 +6,8 @@ set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_CUDA   ON CACHE BOOL "" FORCE)
 set(Kokkos_ARCH_PASCAL60 ON CACHE BOOL "" FORCE)
 set(BUILD_OMP ON CACHE BOOL "" FORCE)
+get_filename_component(NVCC_WRAPPER_CMD ${CMAKE_CURRENT_SOURCE_DIR}/../lib/kokkos/bin/nvcc_wrapper ABSOLUTE)
+set(CMAKE_CXX_COMPILER ${NVCC_WRAPPER_CMD} CACHE FILEPATH "" FORCE)
 
 # hide deprecation warnings temporarily for stable release
 set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)

cmake/presets/macos-multiarch.cmake

@@ -10,5 +10,3 @@ set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
 set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
 
 set(BUILD_MPI FALSE CACHE BOOL "" FORCE)
-set(BUILD_SHARED_LIBS FALSE CACHE BOOL "" FORCE)
-set(LAMMPS_EXCEPTIONS TRUE CACHE BOOL "" FORCE)

doc/Makefile

@@ -63,6 +63,7 @@ help:
 	@echo "  anchor_check  scan for duplicate anchor labels"
 	@echo "  style_check   check for complete and consistent style lists"
 	@echo "  package_check check for complete and consistent package lists"
+	@echo "  role_check    check for misformatted role keywords"
 	@echo "  spelling      spell-check the manual"
 
 # ------------------------------------------
@@ -98,6 +99,7 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
+		env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
 		$(PYTHON) $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
@@ -179,6 +181,7 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
+		env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
 		$(PYTHON) utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
@@ -227,6 +230,7 @@ char_check :
 role_check :
 	@( env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst && exit 1 || : )
 	@( env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst && exit 1 || : )
+	@( env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst && exit 1 || : )
 
 link_check : $(VENV) html
 	@(\

doc/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "2 August 2023" "2023-08-2"
+.TH LAMMPS "1" "21 November 2023" "2023-11-21"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 2 August 2023
+\- Molecular Dynamics Simulator.  Version 21 November 2023
 
 .SH SYNOPSIS
 .B lmp

doc/src/Build_cmake.rst

@@ -177,13 +177,13 @@ configuration is selected with the *-C* flag:
 
    ctest -C Debug
 
-The CMake scripts in LAMMPS have basic support for being compiled using a
+The CMake scripts in LAMMPS have basic support for being compiled using
-multi-config build system, but not all of it has been ported.  This is in
+a multi-config build system, but not all of it has been ported.  This is
-particular applicable to compiling packages that require additional libraries
+in particular applicable to compiling packages that require additional
-that would be downloaded and compiled by CMake.  The "windows" preset file
+libraries that would be downloaded and compiled by CMake.  The
-tries to keep track of which packages can be compiled natively with the
+``windows.cmake`` preset file tries to keep track of which packages can
-MSVC compilers out-of-the box.  Not all of those external libraries are
+be compiled natively with the MSVC compilers out-of-the box.  Not all of
-portable to Windows, either.
+the external libraries are portable to Windows, either.
 
 
 Installing CMake

doc/src/Build_extras.rst

@@ -626,22 +626,22 @@ They must be specified in uppercase.
    *  - HOPPER90
       - GPU
       - NVIDIA Hopper generation CC 9.0 GPU
-   *  - VEGA900
+   *  - AMD_GFX906
       - GPU
-      - AMD GPU MI25 GFX900
+      - AMD GPU MI50/MI60
-   *  - VEGA906
+   *  - AMD_GFX908
       - GPU
-      - AMD GPU MI50/MI60 GFX906
+      - AMD GPU MI100
-   *  - VEGA908
+   *  - AMD_GFX90A
       - GPU
-      - AMD GPU MI100 GFX908
+      - AMD GPU MI200
-   *  - VEGA90A
+   *  - AMD_GFX942
       - GPU
-      - AMD GPU MI200 GFX90A
+      - AMD GPU MI300
-   *  - NAVI1030
+   *  - AMD_GFX1030
       - GPU
       - AMD GPU V620/W6800
-   *  - NAVI1100
+   *  - AMD_GFX1100
       - GPU
       - AMD GPU RX7900XTX
    *  - INTEL_GEN
@@ -666,7 +666,7 @@ They must be specified in uppercase.
       - GPU
       - Intel GPU Ponte Vecchio
 
-This list was last updated for version 4.0.1 of the Kokkos library.
+This list was last updated for version 4.2 of the Kokkos library.
 
 .. tabs::
 
@@ -722,9 +722,10 @@ This list was last updated for version 4.0.1 of the Kokkos library.
       ``cmake/presets`` folder, ``kokkos-serial.cmake``,
       ``kokkos-openmp.cmake``, ``kokkos-cuda.cmake``,
       ``kokkos-hip.cmake``, and ``kokkos-sycl.cmake``.  They will enable
-      the KOKKOS package and enable some hardware choice.  So to compile
+      the KOKKOS package and enable some hardware choices.  For GPU
-      with CUDA device parallelization (for GPUs with CC 5.0 and up)
+      support those preset files must be customized to match the
-      with some common packages enabled, you can do the following:
+      hardware used. So to compile with CUDA device parallelization with
+      some common packages enabled, you can do the following:
 
       .. code-block:: bash
 
@@ -1055,12 +1056,12 @@ additional details.
 
       .. code-block:: bash
 
-         -D PYTHON_EXECUTABLE=path   # path to Python executable to use
+         -D Python_EXECUTABLE=path   # path to Python executable to use
 
       Without this setting, CMake will guess the default Python version
       on your system.  To use a different Python version, you can either
       create a virtualenv, activate it and then run cmake.  Or you can
-      set the PYTHON_EXECUTABLE variable to specify which Python
+      set the Python_EXECUTABLE variable to specify which Python
       interpreter should be used.  Note note that you will also need to
       have the development headers installed for this version,
       e.g. python2-devel.

doc/src/Build_package.rst

@@ -182,6 +182,7 @@ make a copy of one of them and modify it to suit your needs.
     cmake -C ../cmake/presets/all_on.cmake   [OPTIONS] ../cmake  # enable all packages
     cmake -C ../cmake/presets/all_off.cmake  [OPTIONS] ../cmake  # disable all packages
     mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake  #  compile with MinGW cross-compilers
+    cmake -C ../cmake/presets/macos-multiarch.cmake [OPTIONS] ../cmake # compile serial multi-arch binaries on macOS
 
 Presets that have names starting with "windows" are specifically for
 compiling LAMMPS :doc:`natively on Windows <Build_windows>` and

doc/src/Commands_fix.rst

@@ -69,7 +69,7 @@ OPT.
    * :doc:`drude/transform/inverse <fix_drude_transform>`
    * :doc:`dt/reset (k) <fix_dt_reset>`
    * :doc:`edpd/source <fix_dpd_source>`
-   * :doc:`efield <fix_efield>`
+   * :doc:`efield (k) <fix_efield>`
    * :doc:`efield/tip4p <fix_efield>`
    * :doc:`ehex <fix_ehex>`
    * :doc:`electrode/conp (i) <fix_electrode>`
@@ -181,6 +181,7 @@ OPT.
    * :doc:`pour <fix_pour>`
    * :doc:`precession/spin <fix_precession_spin>`
    * :doc:`press/berendsen <fix_press_berendsen>`
+   * :doc:`press/langevin <fix_press_langevin>`
    * :doc:`print <fix_print>`
    * :doc:`propel/self <fix_propel_self>`
    * :doc:`property/atom (k) <fix_property_atom>`
@@ -232,7 +233,7 @@ OPT.
    * :doc:`spring <fix_spring>`
    * :doc:`spring/chunk <fix_spring_chunk>`
    * :doc:`spring/rg <fix_spring_rg>`
-   * :doc:`spring/self <fix_spring_self>`
+   * :doc:`spring/self (k) <fix_spring_self>`
    * :doc:`srd <fix_srd>`
    * :doc:`store/force <fix_store_force>`
    * :doc:`store/state <fix_store_state>`

doc/src/Commands_pair.rst

@@ -220,7 +220,8 @@ OPT.
    * :doc:`morse/soft <pair_fep_soft>`
    * :doc:`multi/lucy <pair_multi_lucy>`
    * :doc:`multi/lucy/rx (k) <pair_multi_lucy_rx>`
-   * :doc:`nb3b/harmonic <pair_nb3b_harmonic>`
+   * :doc:`nb3b/harmonic <pair_nb3b>`
+   * :doc:`nb3b/screened <pair_nb3b>`
    * :doc:`nm/cut (o) <pair_nm>`
    * :doc:`nm/cut/coul/cut (o) <pair_nm>`
    * :doc:`nm/cut/coul/long (o) <pair_nm>`
@@ -265,7 +266,7 @@ OPT.
    * :doc:`smd/tri_surface <pair_smd_triangulated_surface>`
    * :doc:`smd/ulsph <pair_smd_ulsph>`
    * :doc:`smtbq <pair_smtbq>`
-   * :doc:`snap (k) <pair_snap>`
+   * :doc:`snap (ik) <pair_snap>`
    * :doc:`soft (go) <pair_soft>`
    * :doc:`sph/heatconduction <pair_sph_heatconduction>`
    * :doc:`sph/idealgas <pair_sph_idealgas>`
@@ -305,5 +306,5 @@ OPT.
    * :doc:`wf/cut <pair_wf_cut>`
    * :doc:`ylz <pair_ylz>`
    * :doc:`yukawa (gko) <pair_yukawa>`
-   * :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
+   * :doc:`yukawa/colloid (gko) <pair_yukawa_colloid>`
    * :doc:`zbl (gko) <pair_zbl>`

doc/src/Commands_removed.rst

@@ -88,7 +88,7 @@ The same functionality is available through
 MPIIO package
 -------------
 
-.. deprecated:: TBD
+.. deprecated:: 21Nov2023
 
 The MPIIO package has been removed from LAMMPS since it was unmaintained
 for many years and thus not updated to incorporate required changes that
@@ -107,7 +107,7 @@ see :doc:`restart <restart>`, :doc:`read_restart <read_restart>`,
 MSCG package
 ------------
 
-.. deprecated:: TBD
+.. deprecated:: 21Nov2023
 
 The MSCG package has been removed from LAMMPS since it was unmaintained
 for many years and instead superseded by the `OpenMSCG software

doc/src/Developer_unittest.rst

@@ -180,19 +180,11 @@ discarded but by setting the verbose flag (via setting the ``TEST_ARGS``
 environment variable, ``TEST_ARGS=-v``) it can be printed and used to
 understand why tests fail unexpectedly.
 
-Another complexity of these tests stems from the need to capture
+The specifics of so-called "death tests", i.e. conditions where LAMMPS
-situations where LAMMPS will stop with an error, i.e. handle so-called
+should fail and throw an exception, are implemented in the
-"death tests".  Here the LAMMPS code will operate differently depending
+``TEST_FAILURE()`` macro. These tests operate by capturing the screen
-on whether it was configured to throw C++ exceptions on errors or call
+output when executing the failing command and then comparing that with a
-either ``exit()`` or ``MPI_Abort()``.  In the latter case, the test code
+provided regular expression string pattern.  Example:
-also needs to detect whether LAMMPS was compiled with the OpenMPI
-library, as OpenMPI is **only** compatible the death test options of the
-GoogleTest library when C++ exceptions are enabled; otherwise those
-"death tests" must be skipped to avoid reporting bogus failures.  The
-specifics of this step are implemented in the ``TEST_FAILURE()``
-macro. These tests operate by capturing the screen output when executing
-the failing command and then comparing that with a provided regular
-expression string pattern.  Example:
 
 .. code-block:: c++
 

doc/src/Fortran.rst

@@ -3038,14 +3038,6 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    This function can be used to query if an error inside of LAMMPS
    has thrown a :ref:`C++ exception <exceptions>`.
 
-   .. note::
-
-      This function will always report "no error" when the LAMMPS library
-      has been compiled without ``-DLAMMPS_EXCEPTIONS``, which turns fatal
-      errors aborting LAMMPS into C++ exceptions. You can use the library
-      function :cpp:func:`lammps_config_has_exceptions` to check if this is
-      the case.
-
    :to: :cpp:func:`lammps_has_error`
    :r has_error: ``.TRUE.`` if there is an error.
    :rtype has_error: logical
@@ -3068,13 +3060,6 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    would happen only in a single MPI rank and thus may not be recoverable, as
    other MPI ranks may be waiting on the failing MPI rank(s) to send messages.
 
-   .. note::
-
-      This function will do nothing when the LAMMPS library has been
-      compiled without ``-DLAMMPS_EXCEPTIONS``, which turns errors aborting
-      LAMMPS into C++ exceptions.  You can use the function
-      :f:func:`config_has_exceptions` to check whether this is the case.
-
    :p character(len=\*) buffer: string buffer to copy the error message into
    :o integer(c_int) status [optional]: 1 when all ranks had the error,
     2 on a single-rank error.

doc/src/Howto_body.rst

@@ -170,9 +170,9 @@ with this body style to compute body/body and body/non-body interactions.
 The *rounded/polygon* body style represents body particles as a 2d
 polygon with a variable number of N vertices.  This style can only be
 used for 2d models; see the :doc:`boundary <boundary>` command.  See the
-"pair_style body/rounded/polygon" page for a diagram of two
+:doc:`pair_style body/rounded/polygon <pair_body_rounded_polygon>` page for
-squares with rounded circles at the vertices.  Special cases for N = 1
+a diagram of two squares with rounded circles at the vertices.  Special cases
-(circle) and N = 2 (rod with rounded ends) can also be specified.
+for N = 1 (circle) and N = 2 (rod with rounded ends) can also be specified.
 
 One use of this body style is for 2d discrete element models, as
 described in :ref:`Fraige <body-Fraige>`.

doc/src/Howto_lammps_gui.rst

@@ -5,48 +5,61 @@ This document describes **LAMMPS GUI version 1.5**.
 
 -----
 
-LAMMPS GUI is a simple graphical text editor that is linked to the
+LAMMPS GUI is a graphical text editor customized for editing LAMMPS
-:ref:`LAMMPS library <lammps_c_api>` and thus can run LAMMPS directly
+input files that is linked to the :ref:`LAMMPS library <lammps_c_api>`
-using the contents of the editor's text buffer as input.  It can
+and thus can run LAMMPS directly using the contents of the editor's text
-retrieve and display information from LAMMPS while it is running and is
+buffer as input.  It can retrieve and display information from LAMMPS
-adapted in multiple ways specifically for editing LAMMPS input files.
+while it is running, display visualizations created with the :doc:`dump
+image command <dump_image>`, and is adapted specifically for editing
+LAMMPS input files through text completion and reformatting, and linking
+to the online LAMMPS documentation for known LAMMPS commands and styles.
 
 .. note::
 
    Pre-compiled, ready-to-use LAMMPS GUI executables for Linux (Ubuntu
    20.04LTS or later and compatible), macOS (version 11 aka Big Sur or
    later), and Windows (version 10 or later) :ref:`are available
-   <lammps-gui-install>` for download.  The executables are linked to
+   <lammps_gui_install>` for download.  They may be linked to a
-   a current version of LAMMPS as well.  The source code for the
+   development version of LAMMPS in case they need features not yet
-   LAMMPS GUI is included in the ``tools/lammps-gui`` folder of the
+   available in a released version. Serial LAMMPS executables of the
-   LAMMPS distribution and it can be compiled alongside LAMMPS with
+   same LAMMPS version are included as well.  The source code for the
-   CMake.
+   LAMMPS GUI is included in the LAMMPS source code and can be found in
+   the ``tools/lammps-gui`` folder.  It can be compiled alongside LAMMPS
+   when :doc:`compiling with CMake <Build_cmake>`.
 
-LAMMPS GUI tries to be similar to what people traditionally would do
+LAMMPS GUI tries to provide an experience similar to what people
-to run LAMMPS using a command line window: editing inputs with a text
+traditionally would do to run LAMMPS using a command line window:
-editor, run LAMMPS on the input with selected command line flags, and
-then extract data from the created files and view them.  That
-procedure is quite effective and often required when running LAMMPS on
-high-performance computing facilities, or for people proficient in
-using the command line, as that allows them to use tools for the
-individual steps which they are most comfortable with.
 
-The main benefit of a GUI application is that many basic tasks can be
+- editing inputs with a text editor
-done directly from the GUI without switching to a text console or
+- run LAMMPS on the input with selected command line flags
-requiring external programs, let alone scripts to extract data from
+- and then use or extract data from the created files and visualize it
-the generated output.  It also integrates well with graphical desktop
+
-environments.
+That procedure is quite effective for people proficient in using the
+command line, as that allows them to use tools for the individual steps
+which they are most comfortable with.  It is often required when running
+LAMMPS on high-performance computing facilities.
+
+The main benefit of using the LAMMPS GUI application instead is that
+many basic tasks can be done directly from the GUI without switching to
+a text console window or using external programs, let alone writing
+scripts to extract data from the generated output.  It also integrates
+well with graphical desktop environments.
 
 LAMMPS GUI thus makes it easier for beginners to get started running
-simple LAMMPS simulations.  It is very suitable for tutorials on
+simple LAMMPS simulations.  It is very suitable for tutorials on LAMMPS
-LAMMPS since you only need to learn how to use a single program.  It
+since you only need to learn how to use a single program for most tasks
-is also designed to keep the barrier low when you decide to switch to
+and thus time can be saved and people can focus on learning LAMMPS.  It
-a full featured, standalone programming editor and more sophisticated
+is also designed to keep the barrier low when you decide to switch to a
+full featured, standalone programming editor and more sophisticated
 visualization and analysis tools and run LAMMPS from a command line.
 
 The following text provides a detailed tour of the features and
 functionality of the LAMMPS GUI.
 
+Suggestions for new features and reports of bugs are always welcome.
+You can use the :doc:`the same channels as for LAMMPS itself
+<Errors_bugs>` for that purpose.
+
 -----
 
 Main window
@@ -86,9 +99,9 @@ save them.
 Running LAMMPS
 ^^^^^^^^^^^^^^
 
-From within the LAMMPS GUI main window LAMMPS can be started either
+From within the LAMMPS GUI main window LAMMPS can be started either from
-from the ``Run`` menu using the ``Run LAMMPS from Editor Buffer``
+the ``Run`` menu using the ``Run LAMMPS from Editor Buffer`` entry, by
-entry, by the hotkey `Ctrl-Enter` (`Command-Enter` on macOS), or by
+the keyboard shortcut `Ctrl-Enter` (`Command-Enter` on macOS), or by
 clicking on the green "Run" button in the status bar.  All of these
 operations will cause LAMMPS to process the entire input script, which
 may contain multiple :doc:`run <run>` or :doc:`minimize <minimize>`
@@ -147,10 +160,10 @@ More information on those windows and how to adjust their behavior and
 contents is given below.
 
 An active LAMMPS run can be stopped cleanly by using either the ``Stop
-LAMMPS`` entry in the ``Run`` menu, the hotkey `Ctrl-/` (`Command-/`
+LAMMPS`` entry in the ``Run`` menu, the keyboard shortcut `Ctrl-/`
-on macOS), or by clicking on the red button in the status bar.  This
+(`Command-/` on macOS), or by clicking on the red button in the status
-will cause the running LAMMPS process to complete the current timestep
+bar.  This will cause the running LAMMPS process to complete the current
-(or iteration for energy minimization) and then complete the
+timestep (or iteration for energy minimization) and then complete the
 processing of the buffer while skipping all run or minimize commands.
 This is equivalent to the input script command :doc:`timer timeout 0
 <timer>` and is implemented by calling the
@@ -172,17 +185,20 @@ be seen in the command line window, as shown below.
 LAMMPS GUI captures the screen output as it is generated and updates
 the log window regularly during a run.
 
-By default, there will be a new window for each run, so that it is
+By default, the log window will be replaced each time a run is started.
-possible to visually compare outputs from different runs.  It is also
+The runs are counted and the run number for the current run is displayed
-possible to change the behavior of LAMMPS GUI in the preferences dialog
+in the window title.  It is possible to change the behavior of LAMMPS
-to *replace* an existing log window for a new run or to not show the log
+GUI in the preferences dialog to create a *new* log window for every run
-window by default.  It is also possible to show or hide the current log
+or to not show the current log window.  It is also possible to show or
-window from the ``View`` menu.
+hide the *current* log window from the ``View`` menu.
 
 The text in the log window is read-only and cannot be modified, but
-editor commands to select and copy all or parts of the text can be used.
+keyboard shortcuts to select and copy all or parts of the text can be
-The "Select All" and "Copy" functions are also available via a context
+used to transfer text to another program. Also, the keyboard shortcut
-menu by clicking with the right mouse button.
+`Ctrl-S` (`Command-S` on macOS) is available to save the log buffer to a
+file.  The "Select All" and "Copy" functions, as well as a "Save Log to
+File" option are also available from a context menu by clicking with the
+right mouse button into the log window text area.
 
 Chart Window
 ------------
@@ -199,10 +215,16 @@ The drop down menu on the top right allows selection of different
 properties that are computed and written to thermo output.  Only one
 property can be shown at a time.  The plots will be updated with new
 data as the run progresses, so they can be used to visually monitor the
-evolution of available properties.  From the ``File`` menu on the top
+evolution of available properties.  The window title will show the
-left, it is possible to save an image of the currently displayed plot or
+current run number that this chart window corresponds to.  Same as
-export the data in either plain text columns (for use by plotting tools
+explained for the log window above, by default, the chart window will
-like `gnuplot <http://www.gnuplot.info/>`_ or `grace
+be replaced on each new run, but the behavior can be changed in the
+preferences dialog.
+
+From the ``File`` menu on the top left, it is possible to save an image
+of the currently displayed plot or export the data in either plain text
+columns (for use by plotting tools like `gnuplot
+<http://www.gnuplot.info/>`_ or `grace
 <https://plasma-gate.weizmann.ac.il/Grace/>`_), or as CSV data which can
 be imported for further processing with Microsoft Excel or `pandas
 <https://pandas.pydata.org/>`_
@@ -225,19 +247,20 @@ displays the images created by LAMMPS as they are written.
    :align: center
    :scale: 50%
 
-The various buttons at the bottom right of the window allow either
+The various buttons at the bottom right of the window allow single
-single stepping through the sequence of images or playing an animation
+stepping through the sequence of images or playing an animation (as a
-(as a continuous loop or once from first to last).  It is also possible
+continuous loop or once from first to last).  It is also possible to
-to zoom in or zoom out of the displayed images.  The slide show window
+zoom in or zoom out of the displayed images, and to export the slide
-will be closed when a new file is loaded.
+show animation to a movie file, if `ffmpeg <https://ffmpeg.org/>`_ is
+installed.
 
 Variable Info
 -------------
 
-During a run, it may be of interest to monitor the value of input
+During a run, it may be of interest to monitor the value of input script
-script variables, for example to monitor the progress of loops.  This
+variables, for example to monitor the progress of loops.  This can be
-can be done by enabling the "Variables Window" in the ``View`` menu or
+done by enabling the "Variables Window" in the ``View`` menu or by using
-by using the `Ctrl-Shift-W` hotkey.  This will show info similar to
+the `Ctrl-Shift-W` keyboard shortcut.  This will show info similar to
 the :doc:`info variables <info>` command in a separate window as shown
 below.
 
@@ -250,16 +273,27 @@ during a run.  It will show "(none)" if there are no variables
 defined.  Note that it is also possible to *set* :doc:`index style
 variables <variable>`, that would normally be set via command line
 flags, via the "Set Variables..." dialog from the ``Run`` menu.
+LAMMPS GUI will automatically set the variable "gui_run" to the
+current value of the run counter.  That way it would be possible
+to automatically record a log for each run attempt by using the
+command
+
+.. code-block:: LAMMPS
+
+   log logfile-${gui_run}.txt
+
+at the beginning of an input file. That would record logs to files
+``logfile-1.txt``, ``logfile-2.txt``, and so on for successive runs.
 
 Viewing Snapshot Images
 -----------------------
 
 By selecting the ``Create Image`` entry in the ``Run`` menu, or by
-hitting the `Ctrl-I` (`Command-I` on macOS) hotkey, or by clicking on
+hitting the `Ctrl-I` (`Command-I` on macOS) keyboard shortcut, or by
-the "palette" button in the status bar, LAMMPS GUI will send a custom
+clicking on the "palette" button in the status bar, LAMMPS GUI will send
-:doc:`write_dump image <dump_image>` command to LAMMPS and read the
+a custom :doc:`write_dump image <dump_image>` command to LAMMPS and read
-resulting snapshot image with the current state of the system into an
+the resulting snapshot image with the current state of the system into
-image viewer window.  This functionality is not available *during* an
+an image viewer window.  This functionality is not available *during* an
 ongoing run.  When LAMMPS is not yet initialized, LAMMPS GUI will try to
 identify the line with the first run or minimize command and execute all
 command up to that line from the input buffer and then add a "run 0"
@@ -306,34 +340,41 @@ contents to a file.
 Context Specific Word Completion
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-By default, LAMMPS GUI will display a small popup frame with possible
+By default, LAMMPS GUI will display a small pop-up frame with possible
-completions for LAMMPS input script commands or styles after 2
+choices for LAMMPS input script commands or styles after 2 characters of
-characters of a word have been typed. The word can then be completed
+a word have been typed.
-through selecting an entry by scrolling down with the cursor keys and
+
-selecting with the 'Enter' key or by clicking on the entry with the
+.. image:: JPG/lammps-gui-complete.png
-mouse.  The automatic completion popup can be disabled in the
+   :align: center
-``Preferences`` dialog, but the completion can still be requested
+   :scale: 75%
-manually by either hitting the 'Shift-TAB' key or by right-clicking with
+
-the mouse and selecting the option from the context menu.  Most of the
+The word can then be completed through selecting an entry by scrolling
-completion information is taken from the LAMMPS instance and thus it
+up and down with the cursor keys and selecting with the 'Enter' key or
-will be adjusted to only show options available that have been enabled
+by clicking on the entry with the mouse.  The automatic completion
-while compiling LAMMPS, however that excludes accelerated styles and
+pop-up can be disabled in the ``Preferences`` dialog, but the completion
-commands, only non-suffix versions are shown.
+can still be requested manually by either hitting the 'Shift-TAB' key or
+by right-clicking with the mouse and selecting the option from the
+context menu.  Most of the completion information is taken from the
+LAMMPS instance and thus it will be adjusted to only show available
+options that have been enabled while compiling LAMMPS. That, however,
+excludes accelerated styles and commands; for improved clarity, only the
+non-suffix version of styles are shown.
 
 Line Reformatting
 ^^^^^^^^^^^^^^^^^
 
-The editor supports reformatting lines according to the syntax in
+The editor supports reformatting lines according to the syntax in order
-order to have consistently aligned lines.  This primarily means adding
+to have consistently aligned lines.  This primarily means adding
-space padding to commands, type specifiers, IDs and names.  This
+whitespace padding to commands, type specifiers, IDs and names.  This
 reformatting is performed by default when hitting the 'Enter' key to
-start a new line.  This feature can be turned off in the
+start a new line.  This feature can be turned on or off in the
 ``Preferences`` dialog, but it can still be manually performed by
-hitting the 'TAB' key.
+hitting the 'TAB' key.  The amount of padding can also be changed in the
+``Preferences`` dialog.
 
 Internally this functionality is achieved by splitting the line into
 "words" and then putting it back together with padding added where the
-context can be detected; otherwise a single space is used.
+context can be detected; otherwise a single space is used between words.
 
 Context Specific Help
 ^^^^^^^^^^^^^^^^^^^^^
@@ -343,23 +384,23 @@ Context Specific Help
    :scale: 50%
 
 A unique feature of the LAMMPS GUI is the option to look up the
-documentation for the command in the current line.  This can be done
+documentation for the command in the current line.  This can be done by
-by either clicking the right mouse button or by using the `Ctrl-?`
+either clicking the right mouse button or by using the `Ctrl-?` keyboard
-hotkey.  When clicking the mouse there are additional entries in the
+shortcut.  When clicking the mouse there are additional entries in the
-context menu that will open the corresponding documentation page in
+context menu that will open the corresponding documentation page in the
-the online LAMMPS documentation.  When using the hotkey, the first of
+online LAMMPS documentation.  When using the keyboard, the first of
 those entries will be chosen directly.
 
 Menu
 ----
 
 The menu bar has entries ``File``, ``Edit``, ``Run``, ``View``, and
-``About``.  Instead of using the mouse to click on them, the
+``About``.  Instead of using the mouse to click on them, the individual
-individual menus can also be activated by hitting the `Alt` key
+menus can also be activated by hitting the `Alt` key together with the
-together with the corresponding underlined letter, that is `Alt-F`
+corresponding underlined letter, that is `Alt-F` will activate the
-will activate the ``File`` menu.  For the corresponding activated
+``File`` menu.  For the corresponding activated sub-menus, the key
-sub-menus, the underlined letter together with the `Alt` key can again
+corresponding the underlined letters can again be used to select entries
-be used to select entries instead of using the mouse.
+instead of using the mouse.
 
 File
 ^^^^
@@ -385,8 +426,8 @@ Edit
 
 The ``Edit`` menu offers the usual editor functions like ``Undo``,
 ``Redo``, ``Cut``, ``Copy``, ``Paste``.  It can also open a
-``Preferences`` dialog (hotkey `Ctrl-P`) and allows deletion of all
+``Preferences`` dialog (keyboard shortcut `Ctrl-P`) and allows deletion
-stored preferences so they will be reset to default values.
+of all stored preferences so they will be reset to default values.
 
 Run
 ^^^
@@ -516,7 +557,7 @@ General Settings:
 - *Replace image window on new render:* when checked, an existing
   chart window will be replaced when a new snapshot image is requested,
   otherwise each command will create a new image window.
-- *Path to LAMMPS Shared Library File:* this options is only available
+- *Path to LAMMPS Shared Library File:* this option is only visible
   when LAMMPS GUI was compiled to load the LAMMPS library at run time
   instead of being linked to it directly.  With the ``Browse..`` button
   or by changing the text, a different shared library file with a
@@ -574,26 +615,26 @@ the range between 1 and 32.
 
 The two settings which follow enable or disable the automatic
 reformatting when hitting the 'Enter' key and the automatic display of
-the completion popup window.
+the completion pop-up window.
 
 -----------
 
-Hotkeys
+Keyboard Shortcuts
--------
+------------------
 
-Almost all functionality is accessible from the menu or via hotkeys.
+Almost all functionality is accessible from the menu of the editor
-The following hotkeys are available (On macOS use the Command key
+window or through keyboard shortcuts.  The following shortcuts are
-instead of Ctrl/Control).
+available (On macOS use the Command key instead of Ctrl/Control).
 
 .. list-table::
    :header-rows: 1
    :widths: auto
 
-   * - Hotkey
+   * - Shortcut
      - Function
-     - Hotkey
+     - Shortcut
      - Function
-     - Hotkey
+     - Shortcut
      - Function
    * - Ctrl+N
      - New File
@@ -620,7 +661,7 @@ instead of Ctrl/Control).
      - Ctrl+I
      - Snapshot Image
    * - Ctrl+Q
-     - Quit
+     - Quit Application
      - Ctrl+V
      - Paste text
      - Ctrl+L
@@ -653,3 +694,7 @@ instead of Ctrl/Control).
 Further editing keybindings `are documented with the Qt documentation
 <https://doc.qt.io/qt-5/qplaintextedit.html#editing-key-bindings>`_.  In
 case of conflicts the list above takes precedence.
+
+All other windows only support a subset of keyboard shortcuts listed
+above.  Typically, the shortcuts `Ctrl-/` (Stop Run), `Ctrl-W` (Close
+Window), and `Ctrl-Q` (Quit Application) are supported.

doc/src/Howto_output.rst

@@ -1,7 +1,7 @@
 Output from LAMMPS (thermo, dumps, computes, fixes, variables)
 ==============================================================
 
-There are four basic kinds of LAMMPS output:
+There are four basic forms of LAMMPS output:
 
 * :doc:`Thermodynamic output <thermo_style>`, which is a list of
   quantities printed every few timesteps to the screen and logfile.
@@ -20,18 +20,17 @@ output files, depending on what :doc:`dump <dump>` and :doc:`fix <fix>`
 commands you specify.
 
 As discussed below, LAMMPS gives you a variety of ways to determine
-what quantities are computed and printed when the thermodynamics,
+what quantities are calculated and printed when the thermodynamics,
 dump, or fix commands listed above perform output.  Throughout this
 discussion, note that users can also :doc:`add their own computes and
-fixes to LAMMPS <Modify>` which can then generate values that can then
+fixes to LAMMPS <Modify>` which can generate values that can then be
-be output with these commands.
+output with these commands.
 
 The following subsections discuss different LAMMPS commands related
 to output and the kind of data they operate on and produce:
 
 * :ref:`Global/per-atom/local/per-grid data <global>`
 * :ref:`Scalar/vector/array data <scalar>`
-* :ref:`Per-grid data <grid>`
 * :ref:`Disambiguation <disambiguation>`
 * :ref:`Thermodynamic output <thermo>`
 * :ref:`Dump file output <dump>`
@@ -48,34 +47,65 @@ to output and the kind of data they operate on and produce:
 Global/per-atom/local/per-grid data
 -----------------------------------
 
-Various output-related commands work with four different styles of
+Various output-related commands work with four different "styles" of
 data: global, per-atom, local, and per-grid.  A global datum is one or
 more system-wide values, e.g. the temperature of the system.  A
 per-atom datum is one or more values per atom, e.g. the kinetic energy
 of each atom.  Local datums are calculated by each processor based on
-the atoms it owns, but there may be zero or more per atom, e.g. a list
+the atoms it owns, and there may be zero or more per atom, e.g. a list
 of bond distances.
 
 A per-grid datum is one or more values per grid cell, for a grid which
-overlays the simulation domain.  The grid cells and the data they
+overlays the simulation domain.  Similar to atoms and per-atom data,
-store are distributed across processors; each processor owns the grid
+the grid cells and the data they store are distributed across
-cells whose center point falls within its subdomain.
+processors; each processor owns the grid cells whose center points
+fall within its subdomain.
 
 .. _scalar:
 
 Scalar/vector/array data
 ------------------------
 
-Global, per-atom, and local datums can come in three kinds: a single
+Global, per-atom, local, and per-grid datums can come in three
-scalar value, a vector of values, or a 2d array of values.  The doc
+"kinds": a single scalar value, a vector of values, or a 2d array of
-page for a "compute" or "fix" or "variable" that generates data will
+values.  More specifically these are the valid kinds for each style:
-specify both the style and kind of data it produces, e.g. a per-atom
-vector.
 
-When a quantity is accessed, as in many of the output commands
+* global scalar
-discussed below, it can be referenced via the following bracket
+* global vector
-notation, where ID in this case is the ID of a compute.  The leading
+* global array
-"c\_" would be replaced by "f\_" for a fix, or "v\_" for a variable:
+* per-atom vector
+* per-atom array
+* local vector
+* local array
+* per-grid vector
+* per-grid array
+
+A per-atom vector means a single value per atom; the "vector" is the
+length of the number of atoms.  A per-atom array means multiple values
+per atom.  Similarly a local vector or array means one or multiple
+values per entity (e.g. per bond in the system).  And a per-grid
+vector or array means one or multiple values per grid cell.
+
+The doc page for a compute or fix or variable that generates data will
+specify both the styles and kinds of data it produces, e.g. a per-atom
+vector.  Note that a compute or fix may generate multiple styles and
+kinds of output.  However, for per-atom data only a vector or array is
+output, never both.  Likewise for per-local and per-grid data.  An
+example of a fix which generates multiple styles and kinds of data is
+the :doc:`fix mdi/qm <fix_mdi_qm>` command.  It outputs a global
+scalar, global vector, and per-atom array for the quantum mechanical
+energy and virial of the system and forces on each atom.
+
+By contrast, different variable styles generate only a single kind of
+data: a global scalar for an equal-style variable, global vector for a
+vector-style variable, and a per-atom vector for an atom-style
+variable.
+
+When data is accessed by another command, as in many of the output
+commands discussed below, it can be referenced via the following
+bracket notation, where ID in this case is the ID of a compute.  The
+leading "c\_" would be replaced by "f\_" for a fix, or "v\_" for a
+variable (and ID would be the name of the variable):
 
 +-------------+--------------------------------------------+
 | c_ID        | entire scalar, vector, or array            |
@@ -85,40 +115,56 @@ notation, where ID in this case is the ID of a compute.  The leading
 | c_ID[I][J]  | one element of array                       |
 +-------------+--------------------------------------------+
 
-In other words, using one bracket reduces the dimension of the data
+Note that using one bracket reduces the dimension of the data once
-once (vector -> scalar, array -> vector).  Using two brackets reduces
+(vector -> scalar, array -> vector).  Using two brackets reduces the
-the dimension twice (array -> scalar).  Thus a command that uses
+dimension twice (array -> scalar).  Thus a command that uses scalar
-scalar values as input can typically also process elements of a vector
+values as input can also conceptually operate on an element of a
-or array.
+vector or array.
 
-.. _grid:
+Per-grid vectors or arrays are accessed similarly, except that the ID
-
+for the compute or fix includes a grid name and a data name.  This is
-Per-grid data
+because a fix or compute can create multiple grids (of different
-------------------------
+sizes) and multiple sets of data (for each grid).  The fix or compute
-
+defines names for each grid and for each data set, so that all of them
-Per-grid data can come in two kinds: a vector of values (one per grid
+can be accessed by other commands.  See the :doc:`Howto grid
-cekk), or a 2d array of values (multiple values per grid ckk).  The
+<Howto_grid>` doc page for more details.
-doc page for a "compute" or "fix" that generates data will specify
-names for both the grid(s) and datum(s) it produces, e.g. per-grid
-vectors or arrays, which can be referenced by other commands.  See the
-:doc:`Howto grid <Howto_grid>` doc page for more details.
 
 .. _disambiguation:
 
 Disambiguation
 --------------
 
-Some computes and fixes produce data in multiple styles, e.g. a global
+When a compute or fix produces data in multiple styles, e.g. global
-scalar and a per-atom vector. Usually the context in which the input
+and per-atom, a reference to the data can sometimes be ambiguous.
-script references the data determines which style is meant. Example:
+Usually the context in which the input script references the data
-if a compute provides both a global scalar and a per-atom vector, the
+determines which style is meant.
-former will be accessed by using ``c_ID`` in an equal-style variable,
+
-while the latter will be accessed by using ``c_ID`` in an atom-style
+For example, if a compute outputs a global vector and a per-atom
-variable.  Note that atom-style variable formulas can also access
+array, an element of the global vector will be accessed by using
-global scalars, but in this case it is not possible to do this
+``c_ID[I]`` in :doc:`thermodynamic output <thermo_style>`, while a
-directly because of the ambiguity.  Instead, an equal-style variable
+column of the per-atom array will be accessed by using ``c_ID[I]`` in
-can be defined which accesses the global scalar, and that variable can
+a :doc:`dump custom <dump>` command.
-be used in the atom-style variable formula in place of ``c_ID``.
+
+However, if a :doc:`atom-style variable <variable>` references
+``c_ID[I]``, then it could be intended to refer to a single element of
+the global vector or a column of the per-atom array.  The doc page for
+any command that has a potential ambiguity (variables are the most
+common) will explain how to resolve the ambiguity.
+
+In this case, an atom-style variables references per-atom data if it
+exists.  If access to an element of a global vector is needed (as in
+this example), an equal-style variable which references the value can
+be defined and used in the atom-style variable formula instead.
+
+Similarly, :doc:`thermodynamic output <thermo_style>` can only
+reference global data from a compute or fix.  But you can indirectly
+access per-atom data as follows.  The reference ``c_ID[245][2]`` for
+the ID of a :doc:`compute displace/atom <compute_displace_atom>`
+command, refers to the y-component of displacement for the atom with
+ID 245.  While you cannot use that reference directly in the
+:doc:`thermo_style <thermo_style>` command, you can use it an
+equal-style variable formula, and then reference the variable in
+thermodynamic output.
 
 .. _thermo:
 
@@ -389,7 +435,7 @@ output and input data types must match, e.g. global/per-atom/local
 data and scalar/vector/array data.
 
 Also note that, as described above, when a command takes a scalar as
-input, that could be an element of a vector or array.  Likewise a
+input, that could also be an element of a vector or array.  Likewise a
 vector input could be a column of an array.
 
 +--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+

doc/src/Howto_pylammps.rst

@@ -133,7 +133,7 @@ to the location in the virtual environment with:
 
 .. code-block:: bash
 
-   cmake . -DPYTHON_EXECUTABLE=$(which python)
+   cmake . -DPython_EXECUTABLE=$(which python)
 
    # install LAMMPS package in virtualenv
    (testing) make install-python

doc/src/Howto_structured_data.rst

@@ -119,6 +119,45 @@ for example :doc:`dump yaml <dump>` or :doc:`fix ave/time <fix_ave_time>`
 Depending on the kind of data being written, organization of the data
 or the specific syntax used may change, but the principles are very
 similar and all files should be readable with a suitable YAML parser.
+A simple example for this is given below:
+
+.. code-block:: python
+
+   import yaml
+   try:
+       from yaml import CSafeLoader as YamlLoader
+   except ImportError:
+       from yaml import SafeLoader as YamlLoader
+
+   timesteps = []
+   with open("dump.yaml", "r") as f:
+       data = yaml.load_all(f, Loader=YamlLoader)
+
+       for d in data:
+           print('Processing timestep %d' % d['timestep'])
+           timesteps.append(d)
+
+   print('Read %d timesteps from yaml dump' % len(timesteps))
+   print('Second timestep: ', timesteps[1]['timestep'])
+   print('Box info: x: ' , timesteps[1]['box'][0], ' y:', timesteps[1]['box'][1], ' z:',timesteps[1]['box'][2])
+   print('First 5 per-atom columns: ', timesteps[1]['keywords'][0:5])
+   print('Corresponding 10th atom data: ', timesteps[1]['data'][9][0:5])
+
+The corresponding output for a YAML dump command added to the "melt" example is:
+
+.. parsed-literal::
+
+   Processing timestep 0
+   Processing timestep 50
+   Processing timestep 100
+   Processing timestep 150
+   Processing timestep 200
+   Processing timestep 250
+   Read 6 timesteps from yaml dump
+   Second timestep:  50
+   Box info: x:  [0, 16.795961913825074]  y: [0, 16.795961913825074]  z: [0, 16.795961913825074]
+   First 5 per-atom columns:  ['id', 'type', 'x', 'y', 'z']
+   Corresponding 10th atom data:  [10, 1, 4.43828, 0.968481, 0.108555]
 
 Processing scalar data with Python
 ----------------------------------

doc/src/Howto_triclinic.rst

@@ -12,7 +12,8 @@ is created, e.g. by the :doc:`create_box <create_box>` or
 :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
 commands.  Additionally, LAMMPS defines box size parameters lx,ly,lz
 where lx = xhi-xlo, and similarly in the y and z dimensions.  The 6
-parameters, as well as lx,ly,lz, can be output via the :doc:`thermo_style custom <thermo_style>` command.
+parameters, as well as lx,ly,lz, can be output via the
+:doc:`thermo_style custom <thermo_style>` command.
 
 LAMMPS also allows simulations to be performed in triclinic
 (non-orthogonal) simulation boxes shaped as a parallelepiped with

doc/src/Intro_nonfeatures.rst

@@ -5,7 +5,7 @@ LAMMPS is designed to be a fast, parallel engine for molecular
 dynamics (MD) simulations.  It provides only a modest amount of
 functionality for setting up simulations and analyzing their output.
 
-Specifically, LAMMPS was not conceived and designed for:
+Originally, LAMMPS was not conceived and designed for:
 
 * being run through a GUI
 * building molecular systems, or building molecular topologies
@@ -14,9 +14,10 @@ Specifically, LAMMPS was not conceived and designed for:
 * visualize your MD simulation interactively
 * plot your output data
 
-Over the years some of these limitations have been reduced or
+Over the years many of these limitations have been reduced or
-removed, through features added to LAMMPS or external tools
+removed. In part through features added to LAMMPS and in part
-that either closely interface with LAMMPS or extend LAMMPS.
+through external tools that either closely interface with LAMMPS
+or extend LAMMPS.
 
 Here are suggestions on how to perform these tasks:
 
@@ -24,8 +25,9 @@ Here are suggestions on how to perform these tasks:
   wraps the library interface is provided.  Thus, GUI interfaces can be
   written in Python or C/C++ that run LAMMPS and visualize or plot its
   output.  Examples of this are provided in the python directory and
-  described on the :doc:`Python <Python_head>` doc page.  Also, there
+  described on the :doc:`Python <Python_head>` doc page.  As of version
-  are several external wrappers or GUI front ends.
+  2 August 2023 :ref:`a GUI tool <lammps_gui>` is included in LAMMPS.
+  Also, there are several external wrappers or GUI front ends.
 * **Builder:** Several pre-processing tools are packaged with LAMMPS.
   Some of them convert input files in formats produced by other MD codes
   such as CHARMM, AMBER, or Insight into LAMMPS input formats.  Some of

doc/src/Library.rst

@@ -80,13 +80,15 @@ run LAMMPS in serial mode.
    :class: note
 
    If the LAMMPS executable encounters an error condition, it will abort
-   after printing an error message. For a library interface this is
+   after printing an error message.  It does so by catching the
-   usually not desirable.  Thus LAMMPS can be compiled to to :ref:`throw
+   exceptions that LAMMPS could throw.  For a C library interface this
-   a C++ exception <exceptions>` instead.  If enabled, the library
+   is usually not desirable since the calling code might lack the
-   functions will catch those exceptions and return.  The error status
+   ability to catch such exceptions.  Thus, the library functions will
-   :cpp:func:`can be queried <lammps_has_error>` and an :cpp:func:`error
+   catch those exceptions and return from the affected functions.  The
-   message retrieved <lammps_get_last_error_message>`.  We thus
+   error status :cpp:func:`can be queried <lammps_has_error>` and an
-   recommend enabling C++ exceptions when using the library interface,
+   :cpp:func:`error message retrieved <lammps_get_last_error_message>`.
+   This is, for example used by the :doc:`LAMMPS python module
+   <Python_module>` and then a suitable Python exception is thrown.
 
 .. admonition:: Using the C library interface as a plugin
    :class: note

doc/src/Python_error.rst

@@ -15,9 +15,7 @@ Python exception handling mechanism.
 
    try:
       # LAMMPS will normally terminate itself and the running process if an error
-      # occurs. This would kill the Python interpreter. To avoid this, make sure to
+      # occurs. This would kill the Python interpreter.  The library wrapper will
-      # compile with LAMMPS_EXCEPTIONS enabled. This ensures the library API calls
-      # will not terminate the parent process. Instead, the library wrapper will
       # detect that an error has occured and throw a Python exception
 
       lmp.command('unknown')

doc/src/Python_install.rst

@@ -5,8 +5,7 @@ The LAMMPS Python module enables calling the :ref:`LAMMPS C library API
 <lammps_c_api>` from Python by dynamically loading functions in the
 LAMMPS shared library through the Python `ctypes <ctypes_>`_
 module.  Because of the dynamic loading, it is required that LAMMPS is
-compiled in :ref:`"shared" mode <exe>`.  It is also recommended to
+compiled in :ref:`"shared" mode <exe>`.
-compile LAMMPS with :ref:`C++ exceptions <exceptions>` enabled.
 
 Two components are necessary for Python to be able to invoke LAMMPS code:
 

doc/src/Tools.rst

@@ -645,9 +645,14 @@ LAMMPS GUI
 Overview
 ^^^^^^^^
 
-LAMMPS GUI is a simple graphical text editor that is linked to the
+LAMMPS GUI is a graphical text editor customized for editing LAMMPS
-:ref:`LAMMPS C-library interface <lammps_c_api>` and thus can run LAMMPS
+input files that is linked to the :ref:`LAMMPS C-library <lammps_c_api>`
-directly using the contents of the editor's text buffer as input.
+and thus can run LAMMPS directly using the contents of the editor's text
+buffer as input.  It can retrieve and display information from LAMMPS
+while it is running, display visualizations created with the :doc:`dump
+image command <dump_image>`, and is adapted specifically for editing
+LAMMPS input files through text completion and reformatting, and linking
+to the online LAMMPS documentation for known LAMMPS commands and styles.
 
 This is similar to what people traditionally would do to run LAMMPS:
 using a regular text editor to edit the input and run the necessary
@@ -656,9 +661,9 @@ terminal window.  This similarity is a design goal. While making it easy
 for beginners to start with LAMMPS, it is also the intention to simplify
 the transition to workflows like most experienced LAMMPS users do.
 
-All features have been extensively exposed to hotkeys, so that there is
+All features have been extensively exposed to keyboard shortcuts, so
-also appeal for experienced LAMMPS users, too, especially for
+that there is also appeal for experienced LAMMPS users for prototyping
-prototyping and testing simulations setups.
+and testing simulations setups.
 
 Features
 ^^^^^^^^
@@ -697,22 +702,26 @@ Prerequisites and portability
 LAMMPS GUI is programmed in C++ based on the C++11 standard and using
 the `Qt GUI framework <https://www.qt.io/product/framework>`_.
 Currently, Qt version 5.12 or later is required; Qt 5.15LTS is
-recommended; Qt 6.x not (yet) supported.  Building LAMMPS with CMake is
+recommended; support for Qt version 6.x is under active development and
-required.  The LAMMPS GUI has been successfully compiled and tested on:
+thus far only tested with Qt 6.5LTS on Linux.  Building LAMMPS with
+CMake is required.
+
+The LAMMPS GUI has been successfully compiled and tested on:
 
 - Ubuntu Linux 20.04LTS x86_64 using GCC 9, Qt version 5.12
 - Fedora Linux 38 x86\_64 using GCC 13 and Clang 16, Qt version 5.15LTS
+- Fedora Linux 38 x86\_64 using GCC 13, Qt version 6.5LTS
 - Apple macOS 12 (Monterey) and macOS 13 (Ventura) with Xcode on arm64 and x86\_64, Qt version 5.15LTS
 - Windows 10 and 11 x86_64 with Visual Studio 2022 and Visual C++ 14.36, Qt version 5.15LTS
 - Windows 10 and 11 x86_64 with MinGW / GCC 10.0 cross-compiler on Fedora 38, Qt version 5.15LTS
 
-.. _lammps-gui-install:
+.. _lammps_gui_install:
 
 
 Pre-compiled executables
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
-Pre-compiled LAMMPS executables including the GUI are currently
+Pre-compiled LAMMPS executable packages that include the GUI are currently
 available from https://download.lammps.org/static or
 https://github.com/lammps/lammps/releases.  You can unpack the archives
 (or mount the macOS disk image) and run the GUI directly in place. The
@@ -737,7 +746,10 @@ stored in a location where CMake can find them without additional help.
 Otherwise, the location of the Qt library installation must be indicated
 by setting ``-D Qt5_DIR=/path/to/qt5/lib/cmake/Qt5``, which is a path to
 a folder inside the Qt installation that contains the file
-``Qt5Config.cmake``.
+``Qt5Config.cmake``. Similarly, for Qt6 the location of the Qt library
+installation can be indicated by setting ``-D Qt6_DIR=/path/to/qt6/lib/cmake/Qt6``,
+if necessary.  When both, Qt5 and Qt6 are available, Qt6 will be preferred
+unless ``-D LAMMPS_GUI_USE_QT5=yes`` is set.
 
 It should be possible to build the LAMMPS GUI as a standalone
 compilation (e.g. when LAMMPS has been compiled with traditional make),

doc/src/atom_modify.rst

@@ -65,6 +65,11 @@ switch.  This is described on the :doc:`Build_settings <Build_settings>`
 doc page.  If atom IDs are not used, they must be specified as 0 for
 all atoms, e.g. in a data or restart file.
 
+.. note::
+
+   If a :doc:`triclinic simulation box <Howto_triclinic>` is used,
+   atom IDs are required, due to how neighbor lists are built.
+
 The *map* keyword determines how atoms with specific IDs are found
 when required.  An example are the bond (angle, etc) methods which
 need to find the local index of an atom with a specific global ID

doc/src/compute.rst

@@ -27,58 +27,62 @@ Examples
 Description
 """""""""""
 
-Define a computation that will be performed on a group of atoms.
+Define a diagnostic computation that will be performed on a group of
-Quantities calculated by a compute are instantaneous values, meaning
+atoms.  Quantities calculated by a compute are instantaneous values,
-they are calculated from information about atoms on the current
+meaning they are calculated from information about atoms on the
-timestep or iteration, though a compute may internally store some
+current timestep or iteration, though internally a compute may store
-information about a previous state of the system.  Defining a compute
+some information about a previous state of the system.  Defining a
-does not perform a computation.  Instead computes are invoked by other
+compute does not perform the computation.  Instead computes are
-LAMMPS commands as needed (e.g., to calculate a temperature needed for
+invoked by other LAMMPS commands as needed (e.g., to calculate a
-a thermostat fix or to generate thermodynamic or dump file output).
+temperature needed for a thermostat fix or to generate thermodynamic
-See the :doc:`Howto output <Howto_output>` page for a summary of
+or dump file output).  See the :doc:`Howto output <Howto_output>` page
-various LAMMPS output options, many of which involve computes.
+for a summary of various LAMMPS output options, many of which involve
+computes.
 
 The ID of a compute can only contain alphanumeric characters and
 underscores.
 
 ----------
 
-Computes calculate one or more of four styles of quantities: global,
+Computes calculate and store any of four *styles* of quantities:
-per-atom, local, or per-atom.  A global quantity is one or more
+global, per-atom, local, or per-grid.
-system-wide values, e.g. the temperature of the system.  A per-atom
-quantity is one or more values per atom, e.g. the kinetic energy of
-each atom.  Per-atom values are set to 0.0 for atoms not in the
-specified compute group.  Local quantities are calculated by each
-processor based on the atoms it owns, but there may be zero or more
-per atom, e.g. a list of bond distances.  Per-grid quantities are
-calculated on a regular 2d or 3d grid which overlays a 2d or 3d
-simulation domain.  The grid points and the data they store are
-distributed across processors; each processor owns the grid points
-which fall within its subdomain.
 
-Computes that produce per-atom quantities have the word "atom" at the
+A global quantity is one or more system-wide values, e.g. the
-end of their style, e.g. *ke/atom*\ .  Computes that produce local
+temperature of the system.  A per-atom quantity is one or more values
-quantities have the word "local" at the end of their style,
+per atom, e.g. the kinetic energy of each atom.  Per-atom values are
-e.g. *bond/local*\ .  Computes that produce per-grid quantities have
+set to 0.0 for atoms not in the specified compute group.  Local
-the word "grid" at the end of their style, e.g. *property/grid*\ .
+quantities are calculated by each processor based on the atoms it
-Styles with neither "atom" or "local" or "grid" at the end of their
+owns, but there may be zero or more per atom, e.g. a list of bond
-style name produce global quantities.
+distances.  Per-grid quantities are calculated on a regular 2d or 3d
+grid which overlays a 2d or 3d simulation domain.  The grid points and
+the data they store are distributed across processors; each processor
+owns the grid points which fall within its subdomain.
 
-Note that a single compute typically produces either global or
+As a general rule of thumb, computes that produce per-atom quantities
-per-atom or local or per-grid values.  It does not compute both global
+have the word "atom" at the end of their style, e.g. *ke/atom*\ .
-and per-atom values.  It can produce local values or per-grid values
+Computes that produce local quantities have the word "local" at the
-in tandem with global or per-atom quantities.  The compute doc page
+end of their style, e.g. *bond/local*\ .  Computes that produce
-will explain the details.
+per-grid quantities have the word "grid" at the end of their style,
+e.g. *property/grid*\ .  And styles with neither "atom" or "local" or
+"grid" at the end of their style name produce global quantities.
 
-Global, per-atom, local, and per-grid quantities come in three kinds:
+Global, per-atom, local, and per-grid quantities can also be of three
-a single scalar value, a vector of values, or a 2d array of values.
+*kinds*: a single scalar value (global only), a vector of values, or a
-The doc page for each compute describes the style and kind of values
+2d array of values.  For per-atom, local, and per-grid quantities, a
-it produces, e.g. a per-atom vector.  Some computes produce more than
+"vector" means a single value for each atom, each local entity
-one kind of a single style, e.g. a global scalar and a global vector.
+(e.g. bond), or grid cell.  Likewise an "array", means multiple values
+for each atom, each local entity, or each grid cell.
 
-When a compute quantity is accessed, as in many of the output commands
+Note that a single compute can produce any combination of global,
-discussed below, it can be referenced via the following bracket
+per-atom, local, or per-grid values.  Likewise it can produce any
-notation, where ID is the ID of the compute:
+combination of scalar, vector, or array output for each style.  The
+exception is that for per-atom, local, and per-grid output, either a
+vector or array can be produced, but not both.  The doc page for each
+compute explains the values it produces.
+
+When a compute output is accessed by another input script command it
+is referenced via the following bracket notation, where ID is the ID
+of the compute:
 
 +-------------+--------------------------------------------+
 | c_ID        | entire scalar, vector, or array            |
@@ -89,17 +93,23 @@ notation, where ID is the ID of the compute:
 +-------------+--------------------------------------------+
 
 In other words, using one bracket reduces the dimension of the
-quantity once (vector :math:`\to` scalar, array :math:`\to` vector).  Using two
+quantity once (vector :math:`\to` scalar, array :math:`\to` vector).
-brackets reduces the dimension twice (array :math:`\to` scalar).  Thus a
+Using two brackets reduces the dimension twice (array :math:`\to`
-command that uses scalar compute values as input can also process elements of a
+scalar).  Thus, for example, a command that uses global scalar compute
-vector or array.
+values as input can also process elements of a vector or array.
+Depending on the command, this can either be done directly using the
+syntax in the table, or by first defining a :doc:`variable <variable>`
+of the appropriate style to store the quantity, then using the
+variable as an input to the command.
 
-Note that commands and :doc:`variables <variable>` which use compute
+Note that commands and :doc:`variables <variable>` which take compute
-quantities typically do not allow for all kinds (e.g., a command may
+outputs as input typically do not allow for all styles and kinds of
-require a vector of values, not a scalar).  This means there is no
+data (e.g., a command may require global but not per-atom values, or
-ambiguity about referring to a compute quantity as c_ID even if it
+it may require a vector of values, not a scalar).  This means there is
-produces, for example, both a scalar and vector.  The doc pages for
+typically no ambiguity about referring to a compute output as c_ID
-various commands explain the details.
+even if it produces, for example, both a scalar and vector.  The doc
+pages for various commands explain the details, including how any
+ambiguities are resolved.
 
 ----------
 

doc/src/compute_composition_atom.rst

@@ -36,7 +36,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 21Nov2023
 
 Define a computation that calculates a local composition vector for each
 atom. For a central atom with :math:`M` neighbors within the neighbor cutoff sphere,

doc/src/compute_property_atom.rst

@@ -128,9 +128,9 @@ Attributes *i_name*, *d_name*, *i2_name*, *d2_name* refer to custom
 per-atom integer and floating-point vectors or arrays that have been
 added via the :doc:`fix property/atom <fix_property_atom>` command.
 When that command is used specific names are given to each attribute
-which are the "name" portion of these attributes.  For arrays *i2_name*
+which are the "name" portion of these attributes.  For arrays
-and *d2_name*, the column of the array must also be included following
+*i2_name* and *d2_name*, the column of the array must also be included
-the name in brackets (e.g., d2_xyz[2] or i2_mySpin[3]).
+following the name in brackets (e.g., d2_xyz[2] or i2_mySpin[3]).
 
 The additional quantities only accessible via this command, and not
 directly via the :doc:`dump custom <dump>` command, are as follows.

doc/src/compute_property_grid.rst

@@ -61,7 +61,7 @@ varying fastest, then Y, then Z slowest.  For 2d grids (in 2d
 simulations), the grid IDs range from 1 to Nx*Ny, with X varying
 fastest and Y slowest.
 
-.. versionadded:: TBD
+.. versionadded:: 21Nov2023
 
 The *proc* attribute is the ID of the processor which owns the grid
 cell.  Processor IDs range from 0 to Nprocs - 1, where Nprocs is the

doc/src/compute_reduce.rst

@@ -37,13 +37,16 @@ Syntax
        v_name = per-atom vector calculated by an atom-style variable with name
 
 * zero or more keyword/args pairs may be appended
-* keyword = *replace*
+* keyword = *replace* or *inputs*
 
   .. parsed-literal::
 
        *replace* args = vec1 vec2
          vec1 = reduced value from this input vector will be replaced
          vec2 = replace it with vec1[N] where N is index of max/min value from vec2
+       *inputs* arg = peratom or local
+         peratom = all inputs are per-atom quantities (default)
+         local = all input are local quantities
 
 Examples
 """"""""
@@ -60,38 +63,44 @@ Description
 """""""""""
 
 Define a calculation that "reduces" one or more vector inputs into
-scalar values, one per listed input.  The inputs can be per-atom or
+scalar values, one per listed input.  For the compute reduce command,
-local quantities; they cannot be global quantities.  Atom attributes
+the inputs can be either per-atom or local quantities and must all be
-are per-atom quantities, :doc:`computes <compute>` and :doc:`fixes <fix>`
+of the same kind (per-atom or local); see discussion of the optional
-may generate any of the three kinds of quantities, and :doc:`atom-style variables <variable>` generate per-atom quantities.  See the
+*inputs* keyword below.  The compute reduce/region command can only be
-:doc:`variable <variable>` command and its special functions which can
+used with per-atom inputs.
-perform the same operations as the compute reduce command on global
+
-vectors.
+Atom attributes are per-atom quantities, :doc:`computes <compute>` and
+:doc:`fixes <fix>` can generate either per-atom or local quantities,
+and :doc:`atom-style variables <variable>` generate per-atom
+quantities.  See the :doc:`variable <variable>` command and its
+special functions which can perform the same reduction operations as
+the compute reduce command on global vectors.
 
 The reduction operation is specified by the *mode* setting.  The *sum*
 option adds the values in the vector into a global total.  The *min*
 or *max* options find the minimum or maximum value across all vector
 values.  The *minabs* or *maxabs* options find the minimum or maximum
 value across all absolute vector values.  The *ave* setting adds the
-vector values into a global total, then divides by the number of values
+vector values into a global total, then divides by the number of
-in the vector.  The *sumsq* option sums the square of the values in the
+values in the vector.  The *sumsq* option sums the square of the
-vector into a global total.  The *avesq* setting does the same as *sumsq*,
+values in the vector into a global total.  The *avesq* setting does
-then divides the sum of squares by the number of values.  The last two options
+the same as *sumsq*, then divides the sum of squares by the number of
-can be useful for calculating the variance of some quantity (e.g., variance =
+values.  The last two options can be useful for calculating the
-sumsq :math:`-` ave\ :math:`^2`).  The *sumabs* option sums the absolute
+variance of some quantity (e.g., variance = sumsq :math:`-` ave\
-values in the vector into a global total.  The *aveabs* setting does the same
+:math:`^2`).  The *sumabs* option sums the absolute values in the
-as *sumabs*, then divides the sum of absolute values by the number of
+vector into a global total.  The *aveabs* setting does the same as
+*sumabs*, then divides the sum of absolute values by the number of
 values.
 
 Each listed input is operated on independently.  For per-atom inputs,
 the group specified with this command means only atoms within the
-group contribute to the result.  For per-atom inputs, if the compute
+group contribute to the result.  Likewise for per-atom inputs, if the
-reduce/region command is used, the atoms must also currently be within
+compute reduce/region command is used, the atoms must also currently
-the region.  Note that an input that produces per-atom quantities may
+be within the region.  Note that an input that produces per-atom
-define its own group which affects the quantities it returns.  For
+quantities may define its own group which affects the quantities it
-example, if a compute is used as an input which generates a per-atom
+returns.  For example, if a compute is used as an input which
-vector, it will generate values of 0.0 for atoms that are not in the
+generates a per-atom vector, it will generate values of 0.0 for atoms
-group specified for that compute.
+that are not in the group specified for that compute.
 
 Each listed input can be an atom attribute (position, velocity, force
 component) or can be the result of a :doc:`compute <compute>` or
@@ -123,52 +132,54 @@ array with six columns:
 
 ----------
 
-The atom attribute values (*x*, *y*, *z*, *vx*, *vy*, *vz*, *fx*, *fy*, and
+The atom attribute values (*x*, *y*, *z*, *vx*, *vy*, *vz*, *fx*,
-*fz*) are self-explanatory.  Note that other atom attributes can be used as
+*fy*, and *fz*) are self-explanatory.  Note that other atom attributes
-inputs to this fix by using the
+can be used as inputs to this fix by using the :doc:`compute
-:doc:`compute property/atom <compute_property_atom>` command and then specifying
+property/atom <compute_property_atom>` command and then specifying an
-an input value from that compute.
+input value from that compute.
 
 If a value begins with "c\_", a compute ID must follow which has been
-previously defined in the input script.  Computes can generate
+previously defined in the input script.  Valid computes can generate
-per-atom or local quantities.  See the individual
+per-atom or local quantities.  See the individual :doc:`compute
-:doc:`compute <compute>` page for details.  If no bracketed integer
+<compute>` page for details.  If no bracketed integer is appended, the
-is appended, the vector calculated by the compute is used.  If a
+vector calculated by the compute is used.  If a bracketed integer is
-bracketed integer is appended, the Ith column of the array calculated
+appended, the Ith column of the array calculated by the compute is
-by the compute is used.  Users can also write code for their own
+used.  Users can also write code for their own compute styles and
-compute styles and :doc:`add them to LAMMPS <Modify>`.  See the
+:doc:`add them to LAMMPS <Modify>`.  See the discussion above for how
-discussion above for how :math:`I` can be specified with a wildcard asterisk
+:math:`I` can be specified with a wildcard asterisk to effectively
-to effectively specify multiple values.
+specify multiple values.
 
 If a value begins with "f\_", a fix ID must follow which has been
-previously defined in the input script.  Fixes can generate per-atom
+previously defined in the input script.  Valid fixes can generate
-or local quantities.  See the individual :doc:`fix <fix>` page for
+per-atom or local quantities.  See the individual :doc:`fix <fix>`
-details.  Note that some fixes only produce their values on certain
+page for details.  Note that some fixes only produce their values on
-timesteps, which must be compatible with when compute reduce
+certain timesteps, which must be compatible with when compute reduce
 references the values, else an error results.  If no bracketed integer
 is appended, the vector calculated by the fix is used.  If a bracketed
 integer is appended, the Ith column of the array calculated by the fix
 is used.  Users can also write code for their own fix style and
 :doc:`add them to LAMMPS <Modify>`.  See the discussion above for how
-:math:`I` can be specified with a wildcard asterisk to effectively specify
+:math:`I` can be specified with a wildcard asterisk to effectively
-multiple values.
+specify multiple values.
 
 If a value begins with "v\_", a variable name must follow which has
 been previously defined in the input script.  It must be an
 :doc:`atom-style variable <variable>`.  Atom-style variables can
 reference thermodynamic keywords and various per-atom attributes, or
 invoke other computes, fixes, or variables when they are evaluated, so
-this is a very general means of generating per-atom quantities to reduce.
+this is a very general means of generating per-atom quantities to
+reduce.
 
 ----------
 
 If the *replace* keyword is used, two indices *vec1* and *vec2* are
-specified, where each index ranges from 1 to the number of input values.
+specified, where each index ranges from 1 to the number of input
-The replace keyword can only be used if the *mode* is *min* or *max*\ .
+values.  The replace keyword can only be used if the *mode* is *min*
-It works as follows.  A min/max is computed as usual on the *vec2*
+or *max*\ .  It works as follows.  A min/max is computed as usual on
-input vector.  The index :math:`N` of that value within *vec2* is also stored.
+the *vec2* input vector.  The index :math:`N` of that value within
-Then, instead of performing a min/max on the *vec1* input vector, the
+*vec2* is also stored.  Then, instead of performing a min/max on the
-stored index is used to select the :math:`N`\ th element of the *vec1* vector.
+*vec1* input vector, the stored index is used to select the :math:`N`\
+th element of the *vec1* vector.
 
 Thus, for example, if you wish to use this compute to find the bond
 with maximum stretch, you can do it as follows:
@@ -190,6 +201,16 @@ information in this context, the *replace* keywords will extract the
 atom IDs for the two atoms in the bond of maximum stretch.  These atom
 IDs and the bond stretch will be printed with thermodynamic output.
 
+.. versionadded:: 21Nov2023
+
+The *inputs* keyword allows selection of whether all the inputs are
+per-atom or local quantities.  As noted above, all the inputs must be
+the same kind (per-atom or local).  Per-atom is the default setting.
+If a compute or fix is specified as an input, it must produce per-atom
+or local data to match this setting.  If it produces both, e.g. for
+the :doc:`compute voronoi/atom <compute_voronoi_atom>` command, then
+this keyword selects between them.
+
 ----------
 
 If a single input is specified this compute produces a global scalar
@@ -197,38 +218,41 @@ value.  If multiple inputs are specified, this compute produces a
 global vector of values, the length of which is equal to the number of
 inputs specified.
 
-As discussed below, for the *sum*, *sumabs*, and *sumsq* modes, the value(s)
+As discussed below, for the *sum*, *sumabs*, and *sumsq* modes, the
-produced by this compute are all "extensive", meaning their value
+value(s) produced by this compute are all "extensive", meaning their
-scales linearly with the number of atoms involved.  If normalized
+value scales linearly with the number of atoms involved.  If
-values are desired, this compute can be accessed by the
+normalized values are desired, this compute can be accessed by the
 :doc:`thermo_style custom <thermo_style>` command with
-:doc:`thermo_modify norm yes <thermo_modify>` set as an option.
+:doc:`thermo_modify norm yes <thermo_modify>` set as an option.  Or it
-Or it can be accessed by a
+can be accessed by a :doc:`variable <variable>` that divides by the
-:doc:`variable <variable>` that divides by the appropriate atom count.
+appropriate atom count.
 
 ----------
 
 Output info
 """""""""""
 
-This compute calculates a global scalar if a single input value is specified
+This compute calculates a global scalar if a single input value is
-or a global vector of length :math:`N`, where :math:`N` is the number of
+specified or a global vector of length :math:`N`, where :math:`N` is
-inputs, and which can be accessed by indices 1 to :math:`N`.  These values can
+the number of inputs, and which can be accessed by indices 1 to
-be used by any command that uses global scalar or vector values from a
+:math:`N`.  These values can be used by any command that uses global
-compute as input.  See the :doc:`Howto output <Howto_output>` doc page
+scalar or vector values from a compute as input.  See the :doc:`Howto
-for an overview of LAMMPS output options.
+output <Howto_output>` doc page for an overview of LAMMPS output
+options.
 
 All the scalar or vector values calculated by this compute are
 "intensive", except when the *sum*, *sumabs*, or *sumsq* modes are used on
 per-atom or local vectors, in which case the calculated values are
 "extensive".
 
-The scalar or vector values will be in whatever :doc:`units <units>` the
+The scalar or vector values will be in whatever :doc:`units <units>`
-quantities being reduced are in.
+the quantities being reduced are in.
 
 Restrictions
 """"""""""""
- none
+
+As noted above, the compute reduce/region command can only be used
+with per-atom inputs.
 
 Related commands
 """"""""""""""""
@@ -238,4 +262,4 @@ Related commands
 Default
 """""""
 
-none
+The default value for the *inputs* keyword is peratom.

doc/src/compute_voronoi_atom.rst

@@ -13,7 +13,7 @@ Syntax
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * voronoi/atom = style name of this compute command
 * zero or more keyword/value pairs may be appended
-* keyword = *only_group* or *occupation* or *surface* or *radius* or *edge_histo* or *edge_threshold* or *face_threshold* or *neighbors* or *peratom*
+* keyword = *only_group* or *occupation* or *surface* or *radius* or *edge_histo* or *edge_threshold* or *face_threshold* or *neighbors*
 
   .. parsed-literal::
 
@@ -31,7 +31,6 @@ Syntax
        *face_threshold* arg = minarea
          minarea = minimum area for a face to be counted
        *neighbors* value = *yes* or *no* = store list of all neighbors or no
-       *peratom* value = *yes* or *no* = per-atom quantities accessible or no
 
 Examples
 """"""""
@@ -53,14 +52,12 @@ atoms in the simulation box.  The tessellation is calculated using all
 atoms in the simulation, but non-zero values are only stored for atoms
 in the group.
 
-By default two per-atom quantities are calculated by this compute.
+Two per-atom quantities are calculated by this compute.  The first is
-The first is the volume of the Voronoi cell around each atom.  Any
+the volume of the Voronoi cell around each atom.  Any point in an
-point in an atom's Voronoi cell is closer to that atom than any other.
+atom's Voronoi cell is closer to that atom than any other.  The second
-The second is the number of faces of the Voronoi cell. This is
+is the number of faces of the Voronoi cell. This is equal to the
-equal to the number of nearest neighbors of the central atom,
+number of nearest neighbors of the central atom, plus any exterior
-plus any exterior faces (see note below). If the *peratom* keyword
+faces (see note below).
-is set to "no", the per-atom quantities are still calculated,
-but they are not accessible.
 
 ----------
 
@@ -97,13 +94,13 @@ present in atom_style sphere for granular models.
 
 The *edge_histo* keyword activates the compilation of a histogram of
 number of edges on the faces of the Voronoi cells in the compute
-group. The argument *maxedge* of the this keyword is the largest number
+group. The argument *maxedge* of the this keyword is the largest
-of edges on a single Voronoi cell face expected to occur in the
+number of edges on a single Voronoi cell face expected to occur in the
-sample. This keyword adds the generation of a global vector with
+sample. This keyword generates output of a global vector by this
-*maxedge*\ +1 entries. The last entry in the vector contains the number of
+compute with *maxedge*\ +1 entries. The last entry in the vector
-faces with more than *maxedge* edges. Since the polygon with the
+contains the number of faces with more than *maxedge* edges. Since the
-smallest amount of edges is a triangle, entries 1 and 2 of the vector
+polygon with the smallest amount of edges is a triangle, entries 1 and
-will always be zero.
+2 of the vector will always be zero.
 
 The *edge_threshold* and *face_threshold* keywords allow the
 suppression of edges below a given minimum length and faces below a
@@ -127,8 +124,8 @@ to locate vacancies (the coordinates are given by the atom coordinates
 at the time step when the compute was first invoked), while column two
 data can be used to identify interstitial atoms.
 
-If the *neighbors* value is set to yes, then this compute creates a
+If the *neighbors* value is set to yes, then this compute also creates
-local array with 3 columns. There is one row for each face of each
+a local array with 3 columns. There is one row for each face of each
 Voronoi cell. The 3 columns are the atom ID of the atom that owns the
 cell, the atom ID of the atom in the neighboring cell (or zero if the
 face is external), and the area of the face.  The array can be
@@ -143,8 +140,8 @@ containing all the Voronoi neighbors in a system:
    compute 6 all voronoi/atom neighbors yes
    dump d2 all local 1 dump.neighbors index c_6[1] c_6[2] c_6[3]
 
-If the *face_threshold* keyword is used, then only faces
+If the *face_threshold* keyword is used, then only faces with areas
-with areas greater than the threshold are stored.
+greater than the threshold are stored.
 
 ----------
 
@@ -158,48 +155,52 @@ Voro++ software in the src/VORONOI/README file.
 
 .. note::
 
-   The calculation of Voronoi volumes is performed by each processor for
+   The calculation of Voronoi volumes is performed by each processor
-   the atoms it owns, and includes the effect of ghost atoms stored by
+   for the atoms it owns, and includes the effect of ghost atoms
-   the processor.  This assumes that the Voronoi cells of owned atoms
+   stored by the processor.  This assumes that the Voronoi cells of
-   are not affected by atoms beyond the ghost atom cut-off distance.
+   owned atoms are not affected by atoms beyond the ghost atom cut-off
-   This is usually a good assumption for liquid and solid systems, but
+   distance.  This is usually a good assumption for liquid and solid
-   may lead to underestimation of Voronoi volumes in low density
+   systems, but may lead to underestimation of Voronoi volumes in low
-   systems.  By default, the set of ghost atoms stored by each processor
+   density systems.  By default, the set of ghost atoms stored by each
-   is determined by the cutoff used for :doc:`pair_style <pair_style>`
+   processor is determined by the cutoff used for :doc:`pair_style
-   interactions.  The cutoff can be set explicitly via the
+   <pair_style>` interactions.  The cutoff can be set explicitly via
-   :doc:`comm_modify cutoff <comm_modify>` command.  The Voronoi cells
+   the :doc:`comm_modify cutoff <comm_modify>` command.  The Voronoi
-   for atoms adjacent to empty regions will extend into those regions up
+   cells for atoms adjacent to empty regions will extend into those
-   to the communication cutoff in :math:`x`, :math:`y`, or :math:`z`.
+   regions up to the communication cutoff in :math:`x`, :math:`y`, or
-   In that situation, an exterior face is created at the cutoff distance
+   :math:`z`.  In that situation, an exterior face is created at the
-   normal to the :math:`x`, :math:`y`, or :math:`z` direction.  For
+   cutoff distance normal to the :math:`x`, :math:`y`, or :math:`z`
-   triclinic systems, the exterior face is parallel to the corresponding
+   direction.  For triclinic systems, the exterior face is parallel to
-   reciprocal lattice vector.
+   the corresponding reciprocal lattice vector.
 
 .. note::
 
-   The Voro++ package performs its calculation in 3d.  This will
+   The Voro++ package performs its calculation in 3d.  This will still
-   still work for a 2d LAMMPS simulation, provided all the atoms have the
+   work for a 2d LAMMPS simulation, provided all the atoms have the
-   same :math:`z`-coordinate. The Voronoi cell of each atom will be a columnar
+   same :math:`z`-coordinate. The Voronoi cell of each atom will be a
-   polyhedron with constant cross-sectional area along the :math:`z`-direction
+   columnar polyhedron with constant cross-sectional area along the
-   and two exterior faces at the top and bottom of the simulation box. If
+   :math:`z`-direction and two exterior faces at the top and bottom of
-   the atoms do not all have the same :math:`z`-coordinate, then the columnar
+   the simulation box. If the atoms do not all have the same
-   cells will be accordingly distorted. The cross-sectional area of each
+   :math:`z`-coordinate, then the columnar cells will be accordingly
-   Voronoi cell can be obtained by dividing its volume by the :math:`z` extent
+   distorted. The cross-sectional area of each Voronoi cell can be
-   of the simulation box.  Note that you define the :math:`z` extent of the
+   obtained by dividing its volume by the :math:`z` extent of the
-   simulation box for 2d simulations when using the
+   simulation box.  Note that you define the :math:`z` extent of the
-   :doc:`create_box <create_box>` or :doc:`read_data <read_data>` commands.
+   simulation box for 2d simulations when using the :doc:`create_box
+   <create_box>` or :doc:`read_data <read_data>` commands.
 
 Output info
 """""""""""
 
-By default, this compute calculates a per-atom array with two
+.. deprecated:: 21Nov2023
-columns. In regular dynamic tessellation mode the first column is the
+
-Voronoi volume, the second is the neighbor count, as described above
+   The *peratom* keyword was removed as it is no longer required.
-(read above for the output data in case the *occupation* keyword is
+
-specified).  These values can be accessed by any command that uses
+This compute calculates a per-atom array with two columns. In regular
-per-atom values from a compute as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
+dynamic tessellation mode the first column is the Voronoi volume, the
-options. If the *peratom* keyword is set to "no", the per-atom array
+second is the neighbor count, as described above (read above for the
-is still created, but it is not accessible.
+output data in case the *occupation* keyword is specified).  These
+values can be accessed by any command that uses per-atom values from a
+compute as input.  See the :doc:`Howto output <Howto_output>` page for
+an overview of LAMMPS output options.
 
 If the *edge_histo* keyword is used, then this compute generates a
 global vector of length *maxedge*\ +1, containing a histogram of the
@@ -209,17 +210,6 @@ If the *neighbors* value is set to *yes*, then this compute calculates a
 local array with three columns. There is one row for each face of each
 Voronoi cell.
 
-.. note::
-
-   Some LAMMPS commands such as the :doc:`compute reduce <compute_reduce>`
-   command can accept either a per-atom or local quantity. If this compute
-   produces both quantities, the command
-   may access the per-atom quantity, even if you want to access the local
-   quantity.  This effect can be eliminated by using the *peratom*
-   keyword to turn off the production of the per-atom quantities.  For
-   the default value *yes* both quantities are produced.  For the value
-   *no*, only the local array is produced.
-
 The Voronoi cell volume will be in distance :doc:`units <units>` cubed.
 The Voronoi face area will be in distance :doc:`units <units>` squared.
 
@@ -227,7 +217,8 @@ Restrictions
 """"""""""""
 
 This compute is part of the VORONOI package.  It is only enabled if
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
 
 It also requires you have a copy of the Voro++ library built and
 installed on your system.  See instructions on obtaining and
@@ -241,5 +232,4 @@ Related commands
 Default
 """""""
 
-*neighbors* no, *peratom* yes
+The default for the neighbors keyword is no.
-

doc/src/dump.rst

@@ -613,7 +613,7 @@ when running on large numbers of processors.
 Note that using the "\*" and "%" characters together can produce a
 large number of small dump files!
 
-.. deprecated:: TBD
+.. deprecated:: 21Nov2023
 
 The MPIIO package and the the corresponding "/mpiio" dump styles, except
 for the unrelated "netcdf/mpiio" style were removed from LAMMPS.
@@ -805,16 +805,16 @@ computes, fixes, or variables when they are evaluated, so this is a very
 general means of creating quantities to output to a dump file.
 
 The *i_name*, *d_name*, *i2_name*, *d2_name* attributes refer to
-per-atom integer and floating-point vectors or arrays that have been
+custom per-atom integer and floating-point vectors or arrays that have
-added via the :doc:`fix property/atom <fix_property_atom>` command.
+been added via the :doc:`fix property/atom <fix_property_atom>`
-When that command is used specific names are given to each attribute
+command.  When that command is used specific names are given to each
-which are the "name" portion of these keywords.  For arrays *i2_name*
+attribute which are the "name" portion of these keywords.  For arrays
-and *d2_name*, the column of the array must also be included following
+*i2_name* and *d2_name*, the column of the array must also be included
-the name in brackets (e.g., d2_xyz[i], i2_mySpin[i], where :math:`i` is
+following the name in brackets (e.g., d2_xyz[i], i2_mySpin[i], where
-in the range from 1 to :math:`M`, where :math:`M` is the number of
+:math:`i` is in the range from 1 to :math:`M`, where :math:`M` is the
-columns in the custom array). See the discussion above for how :math:`i`
+number of columns in the custom array).  See the discussion above for
-can be specified with a wildcard asterisk to effectively specify
+how :math:`i` can be specified with a wildcard asterisk to effectively
-multiple values.
+specify multiple values.
 
 See the :doc:`Modify <Modify>` page for information on how to add
 new compute and fix styles to LAMMPS to calculate per-atom quantities

doc/src/dump_image.rst

@@ -599,7 +599,7 @@ image will appear.  The *sfactor* value must be a value 0.0 <=
 *sfactor* <= 1.0, where *sfactor* = 1 is a highly reflective surface
 and *sfactor* = 0 is a rough non-shiny surface.
 
-.. versionadded:: TBD
+.. versionadded:: 21Nov2023
 
 The *fsaa* keyword can be used with the dump image command to improve
 the image quality by enabling full scene anti-aliasing.  Internally the

doc/src/fix.rst

@@ -77,35 +77,44 @@ for individual fixes for info on which ones can be restarted.
 
 ----------
 
-Some fixes calculate one or more of four styles of quantities: global,
+Some fixes calculate and store any of four *styles* of quantities:
-per-atom, local, or per-grid, which can be used by other commands or
+global, per-atom, local, or per-grid.
-output as described below.  A global quantity is one or more
-system-wide values, e.g. the energy of a wall interacting with
-particles.  A per-atom quantity is one or more values per atom,
-e.g. the displacement vector for each atom since time 0.  Per-atom
-values are set to 0.0 for atoms not in the specified fix group.  Local
-quantities are calculated by each processor based on the atoms it
-owns, but there may be zero or more per atoms.  Per-grid quantities
-are calculated on a regular 2d or 3d grid which overlays a 2d or 3d
-simulation domain.  The grid points and the data they store are
-distributed across processors; each processor owns the grid points
-which fall within its subdomain.
 
-Note that a single fix typically produces either global or per-atom or
+A global quantity is one or more system-wide values, e.g. the energy
-local or per-grid values (or none at all).  It does not produce both
+of a wall interacting with particles.  A per-atom quantity is one or
-global and per-atom.  It can produce local or per-grid values in
+more values per atom, e.g. the original coordinates of each atom at
-tandem with global or per-atom values.  The fix doc page will explain
+time 0.  Per-atom values are set to 0.0 for atoms not in the specified
-the details.
+fix group.  Local quantities are calculated by each processor based on
+the atoms it owns, but there may be zero or more per atom, e.g. values
+for each bond.  Per-grid quantities are calculated on a regular 2d or
+3d grid which overlays a 2d or 3d simulation domain.  The grid points
+and the data they store are distributed across processors; each
+processor owns the grid points which fall within its subdomain.
 
-Global, per-atom, local, and per-grid quantities come in three kinds:
+As a general rule of thumb, fixes that produce per-atom quantities
-a single scalar value, a vector of values, or a 2d array of values.
+have the word "atom" at the end of their style, e.g. *ave/atom*\ .
-The doc page for each fix describes the style and kind of values it
+Fixes that produce local quantities have the word "local" at the end
-produces, e.g. a per-atom vector.  Some fixes produce more than one
+of their style, e.g. *store/local*\ .  Fixes that produce per-grid
-kind of a single style, e.g. a global scalar and a global vector.
+quantities have the word "grid" at the end of their style,
+e.g. *ave/grid*\ .
 
-When a fix quantity is accessed, as in many of the output commands
+Global, per-atom, local, and per-grid quantities can also be of three
-discussed below, it can be referenced via the following bracket
+*kinds*: a single scalar value (global only), a vector of values, or a
-notation, where ID is the ID of the fix:
+2d array of values.  For per-atom, local, and per-grid quantities, a
+"vector" means a single value for each atom, each local entity
+(e.g. bond), or grid cell.  Likewise an "array", means multiple values
+for each atom, each local entity, or each grid cell.
+
+Note that a single fix can produce any combination of global,
+per-atom, local, or per-grid values.  Likewise it can produce any
+combination of scalar, vector, or array output for each style.  The
+exception is that for per-atom, local, and per-grid output, either a
+vector or array can be produced, but not both.  The doc page for each
+fix explains the values it produces, if any.
+
+When a fix output is accessed by another input script command it is
+referenced via the following bracket notation, where ID is the ID of
+the fix:
 
 +-------------+--------------------------------------------+
 | f_ID        | entire scalar, vector, or array            |
@@ -116,19 +125,23 @@ notation, where ID is the ID of the fix:
 +-------------+--------------------------------------------+
 
 In other words, using one bracket reduces the dimension of the
-quantity once (vector :math:`\to` scalar, array :math:`\to` vector).  Using two
+quantity once (vector :math:`\to` scalar, array :math:`\to` vector).
-brackets reduces the dimension twice (array :math:`\to` scalar).  Thus, a
+Using two brackets reduces the dimension twice (array :math:`\to`
-command that uses scalar fix values as input can also process elements of a
+scalar).  Thus, for example, a command that uses global scalar fix
-vector or array.
+values as input can also process elements of a vector or array.
+Depending on the command, this can either be done directly using the
+syntax in the table, or by first defining a :doc:`variable <variable>`
+of the appropriate style to store the quantity, then using the
+variable as an input to the command.
 
-Note that commands and :doc:`variables <variable>` that use fix
+Note that commands and :doc:`variables <variable>` which take fix
-quantities typically do not allow for all kinds (e.g., a command may
+outputs as input typically do not allow for all styles and kinds of
-require a vector of values, not a scalar), and even if they do, the context
+data (e.g., a command may require global but not per-atom values, or
-in which they are called can be used to resolve which output is being
+it may require a vector of values, not a scalar).  This means there is
-requested.  This means there is no
+typically no ambiguity about referring to a fix output as c_ID even if
-ambiguity about referring to a fix quantity as f_ID even if it
+it produces, for example, both a scalar and vector.  The doc pages for
-produces, for example, both a scalar and vector.  The doc pages for
+various commands explain the details, including how any ambiguities
-various commands explain the details.
+are resolved.
 
 ----------
 
@@ -333,6 +346,7 @@ accelerated styles exist.
 * :doc:`pour <fix_pour>` - pour new atoms/molecules into a granular simulation domain
 * :doc:`precession/spin <fix_precession_spin>` - apply a precession torque to each magnetic spin
 * :doc:`press/berendsen <fix_press_berendsen>` - pressure control by Berendsen barostat
+* :doc:`press/langevin <fix_press_langevin>` - pressure control by Langevin barostat
 * :doc:`print <fix_print>` - print text and variables during a simulation
 * :doc:`propel/self <fix_propel_self>` - model self-propelled particles
 * :doc:`property/atom <fix_property_atom>` - add customized per-atom values

doc/src/fix_adapt_fep.rst

@@ -307,7 +307,9 @@ the :doc:`run <run>` command.  This fix is not invoked during
 
 Restrictions
 """"""""""""
- none
+
+The keyword "scale yes" is not supported for scaling per-atom parameters
+diameter and change. You can use :doc:`fix adapt <fix_adapt>` for those.
 
 Related commands
 """"""""""""""""

doc/src/fix_atom_swap.rst

@@ -181,6 +181,12 @@ This fix is part of the MC package.  It is only enabled if LAMMPS was
 built with that package.  See the :doc:`Build package <Build_package>`
 doc page for more info.
 
+This fix cannot be used with systems that do not have per-type masses
+(e.g. atom style sphere) since the implemented algorithm pre-computes
+velocity rescaling factors from per-type masses and ignores any per-atom
+masses, if present.  In case both, per-type and per-atom masses are
+present, a warning is printed.
+
 Related commands
 """"""""""""""""
 

doc/src/fix_ave_chunk.rst

@@ -541,10 +541,10 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`, `fix
+:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`,
-:doc:ave/histo <fix_ave_histo>`, :doc:`fix ave/time <fix_ave_time>`,
+:doc:`fix ave/histo <fix_ave_histo>`, :doc:`fix ave/time <fix_ave_time>`,
-:doc:`variable <variable>`, :doc:`fix ave/correlate
+:doc:`variable <variable>`, :doc:`fix ave/correlate <fix_ave_correlate>`,
-:doc:<fix_ave_correlate>`, `fix ave/atogrid <fix_ave_grid>`
+:doc:`fix ave/grid <fix_ave_grid>`
 
 
 Default

doc/src/fix_ave_histo.rst

@@ -79,9 +79,10 @@ Description
 
 Use one or more values as inputs every few timesteps to create a
 single histogram.  The histogram can then be averaged over longer
-timescales.  The resulting histogram can be used by other :doc:`output commands <Howto_output>`, and can also be written to a file.  The
+timescales.  The resulting histogram can be used by other :doc:`output
-fix ave/histo/weight command has identical syntax to fix ave/histo,
+commands <Howto_output>`, and can also be written to a file.  The fix
-except that exactly two values must be specified.  See details below.
+ave/histo/weight command has identical syntax to fix ave/histo, except
+that exactly two values must be specified.  See details below.
 
 The group specified with this command is ignored for global and local
 input values.  For per-atom input values, only atoms in the group
@@ -96,14 +97,18 @@ different ways; see the discussion of the *beyond* keyword below.
 
 Each input value can be an atom attribute (position, velocity, force
 component) or can be the result of a :doc:`compute <compute>` or
-:doc:`fix <fix>` or the evaluation of an equal-style or vector-style or
+:doc:`fix <fix>` or the evaluation of an equal-style or vector-style
-atom-style :doc:`variable <variable>`.  The set of input values can be
+or atom-style :doc:`variable <variable>`.  The set of input values can
-either all global, all per-atom, or all local quantities.  Inputs of
+be either all global, all per-atom, or all local quantities.  Inputs
-different kinds (e.g. global and per-atom) cannot be mixed.  Atom
+of different kinds (e.g. global and per-atom) cannot be mixed.  Atom
-attributes are per-atom vector values.  See the page for
+attributes are per-atom vector values.  See the page for individual
-individual "compute" and "fix" commands to see what kinds of
+"compute" and "fix" commands to see what kinds of quantities they
-quantities they generate.  See the optional *kind* keyword below for
+generate.
-how to force the fix ave/histo command to disambiguate if necessary.
+
+Note that a compute or fix can produce multiple kinds of data (global,
+per-atom, local).  If LAMMPS cannot unambiguously determine which kind
+of data to use, the optional *kind* keyword discussed below can force
+the desired disambiguation.
 
 Note that the output of this command is a single histogram for all
 input values combined together, not one histogram per input value.
@@ -258,13 +263,14 @@ keyword is set to *vector*, then all input values must be global or
 per-atom or local vectors, or columns of global or per-atom or local
 arrays.
 
-The *kind* keyword only needs to be set if a compute or fix produces
+The *kind* keyword only needs to be used if any of the specified input
-more than one kind of output (global, per-atom, local).  If this is
+computes or fixes produce more than one kind of output (global,
-not the case, then LAMMPS will determine what kind of input is
+per-atom, local).  If not, LAMMPS will determine the kind of data all
-provided and whether all the input arguments are consistent.  If a
+the inputs produce and verify it is all the same kind.  If not, an
-compute or fix produces more than one kind of output, the *kind*
+error will be triggered.  If a compute or fix produces more than one
-keyword should be used to specify which output will be used.  The
+kind of output, the *kind* keyword should be used to specify which
-remaining input arguments must still be consistent.
+output will be used.  The other input arguments must still be
+consistent.
 
 The *beyond* keyword determines how input values that fall outside the
 *lo* to *hi* bounds are treated.  Values such that *lo* :math:`\le` value

doc/src/fix_deposit.rst

@@ -17,12 +17,16 @@ Syntax
 * M = insert a single atom or molecule every M steps
 * seed = random # seed (positive integer)
 * one or more keyword/value pairs may be appended to args
-* keyword = *region* or *id* or *global* or *local* or *near* or *gaussian* or *attempt* or *rate* or *vx* or *vy* or *vz* or *target* or *mol* or *molfrac* or *rigid* or *shake* or *orient* or *units*
+* keyword = *region* or *var* or *set* or *id* or *global* or *local* or *near* or *gaussian* or *attempt* or *rate* or *vx* or *vy* or *vz* or *target* or *mol* or *molfrac* or *rigid* or *shake* or *orient* or *units*
 
   .. parsed-literal::
 
        *region* value = region-ID
          region-ID = ID of region to use as insertion volume
+       *var* value = name = variable name to evaluate for test of atom creation
+       *set* values = dim name
+         dim = *x* or *y* or *z*
+         name = name of variable to set with x, y, or z atom position
        *id* value = *max* or *next*
          max = atom ID for new atom(s) is max ID of all current atoms plus one
          next = atom ID for new atom(s) increments by one for every deposition
@@ -193,17 +197,19 @@ simulation that is "nearby" the chosen x,y position.  In this context,
 particles is less than the *delta* setting.
 
 Once a trial x,y,z position has been selected, the insertion is only
-performed if no current atom in the simulation is within a distance R
+performed if both the *near* and *var* keywords are satisfied (see below).
-of any atom in the new particle, including the effect of periodic
+If either the *near* or the *var* keyword is not satisfied, a new random
-boundary conditions if applicable.  R is defined by the *near*
+position within the insertion volume is chosen and another trial is made.
-keyword.  Note that the default value for R is 0.0, which will allow
+Up to Q attempts are made.  If one or more particle insertions are not
-atoms to strongly overlap if you are inserting where other atoms are
+successful, LAMMPS prints a warning message.
-present.  This distance test is performed independently for each atom
+
-in an inserted molecule, based on the randomly rotated configuration
+The *near* keyword ensures that no current atom in the simulation is within
-of the molecule.  If this test fails, a new random position within the
+a distance R of any atom in the new particle, including the effect of
-insertion volume is chosen and another trial is made.  Up to Q
+periodic boundary conditions if applicable.  Note that the default value
-attempts are made.  If the particle is not successfully inserted,
+for R is 0.0, which will allow atoms to strongly overlap if you are
-LAMMPS prints a warning message.
+inserting where other atoms are present.  This distance test is performed
+independently for each atom in an inserted molecule, based on the randomly
+rotated configuration of the molecule.
 
 .. note::
 
@@ -214,6 +220,26 @@ LAMMPS prints a warning message.
    existing particle.  LAMMPS will issue a warning if R is smaller than
    this value, based on the radii of existing and inserted particles.
 
+.. versionadded:: 21Nov2023
+
+The *var* and *set* keywords can be used together to provide a criterion
+for accepting or rejecting the addition of an individual atom, based on its
+coordinates.  The *name* specified for the *var* keyword is the name of an
+:doc:`equal-style variable <variable>` that should evaluate to a zero or
+non-zero value based on one or two or three variables that will store the
+*x*, *y*, or *z* coordinates of an atom (one variable per coordinate).  If
+used, these other variables must be :doc:`internal-style variables
+<variable>` defined in the input script; their initial numeric value can be
+anything. They must be internal-style variables, because this command
+resets their values directly.  The *set* keyword is used to identify the
+names of these other variables, one variable for the *x*-coordinate of a
+created atom, one for *y*, and one for *z*.  When an atom is created, its
+:math:`(x,y,z)` coordinates become the values for any *set* variable that
+is defined.  The *var* variable is then evaluated.  If the returned value
+is 0.0, the atom is not created.  If it is non-zero, the atom is created.
+For an example of how to use these keywords, see the
+:doc:`create_atoms <create_atoms>` command.
+
 The *rate* option moves the insertion volume in the z direction (3d)
 or y direction (2d).  This enables particles to be inserted from a
 successively higher height over time.  Note that this parameter is
@@ -289,10 +315,11 @@ operation of the fix continues in an uninterrupted fashion.
    The fix will try to detect it and stop with an error.
 
 None of the :doc:`fix_modify <fix_modify>` options are relevant to this
-fix.  No global or per-atom quantities are stored by this fix for
+fix.  This fix computes a global scalar, which can be accessed by various
-access by various :doc:`output commands <Howto_output>`.  No parameter
+output commands.  The scalar is the cumulative number of insertions.  The
-of this fix can be used with the *start/stop* keywords of the
+scalar value calculated by this fix is "intensive".  No parameter of this
-:doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+fix can be used with the *start/stop* keywords of the :doc:`run <run>`
+command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""

doc/src/fix_efield.rst

@@ -1,4 +1,5 @@
 .. index:: fix efield
+.. index:: fix efield/kk
 .. index:: fix efield/tip4p
 
 fix efield command
@@ -210,6 +211,12 @@ the iteration count during the minimization.
    system (the quantity being minimized), you MUST enable the
    :doc:`fix_modify <fix_modify>` *energy* option for this fix.
 
+----------
+
+.. include:: accel_styles.rst
+
+----------
+
 Restrictions
 """"""""""""
 

doc/src/fix_pimd.rst

@@ -31,7 +31,7 @@ Syntax
 
   .. parsed-literal::
        *keywords* = *method* or *integrator* or *ensemble* or *fmmode* or *fmass* or *scale* or *temp* or *thermostat* or *tau* or *iso* or *aniso* or *barostat* or *taup* or *fixcom* or *lj*
-       *method* value = *nmpimd*
+       *method* value = *nmpimd* (default) or *pimd*
        *integrator* value = *obabo* or *baoab*
        *fmmode* value = *physical* or *normal*
        *fmass* value = scaling factor on mass
@@ -137,8 +137,6 @@ normal-mode PIMD.  A value of *cmd* is for centroid molecular dynamics
    the real particle.
 
 .. note::
-   Fix pimd/langevin only supports *method* value *nmpimd*. This should be enough
-   for most PIMD applications for quantum thermodynamics purpose.
 
    Motion of the centroid can be effectively uncoupled from the other
    normal modes by scaling the fictitious masses to achieve a partial
@@ -151,6 +149,16 @@ normal-mode PIMD.  A value of *cmd* is for centroid molecular dynamics
    only the k > 0 modes are thermostatted, not the centroid degrees of
    freedom.
 
+.. versionadded:: 21Nov2023
+
+   Mode *pimd* added to fix pimd/langevin.
+
+Fix pimd/langevin supports the *method* values *nmpimd* and *pimd*. The default value is *nmpimd*.
+If *method* is *nmpimd*, the normal mode representation is used to integrate the equations of motion.
+The exact solution of harmonic oscillator is used to propagate the free ring polymer part of the Hamiltonian.
+If *method* is *pimd*, the Cartesian representation is used to integrate the equations of motion.
+The harmonic force is added to the total force of the system, and the numerical integrator is used to propagate the Hamiltonian.
+
 The keyword *integrator* specifies the Trotter splitting method used by *fix pimd/langevin*.
 See :ref:`(Liu) <Liu>` for a discussion on the OBABO and BAOAB splitting schemes. Typically
 either of the two should work fine.
@@ -207,6 +215,7 @@ The keyword *thermostat* reads *style* and *seed* of thermostat for fix style *p
 be *PILE_L* (path integral Langevin equation local thermostat, as described in :ref:`Ceriotti <Ceriotti2>`), and *seed* should a positive integer number, which serves as the seed of the pseudo random number generator.
 
 .. note::
+
    The fix style *pimd/langevin* uses the stochastic PILE_L thermostat to control temperature. This thermostat works on the normal modes
    of the ring polymer. The *tau* parameter controls the centroid mode, and the *scale* parameter controls the non-centroid modes.
 
@@ -269,6 +278,7 @@ related tasks for each of the partitions, e.g.
    read_restart system_${ibead}.restart2
 
 .. note::
+
    Fix *pimd/langevin* dumps the Cartesian coordinates, but dumps the velocities and
    forces in the normal mode representation. If the Cartesian velocities and forces are
    needed, it is easy to perform the transformation when doing post-processing.

doc/src/fix_pour.rst

@@ -245,8 +245,9 @@ produce the same behavior if you adjust the fix pour parameters
 appropriately.
 
 None of the :doc:`fix_modify <fix_modify>` options are relevant to this
-fix.  No global or per-atom quantities are stored by this fix for
+fix.  This fix computes a global scalar, which can be accessed by various
-access by various :doc:`output commands <Howto_output>`.  No parameter
+output commands.  The scalar is the cumulative number of insertions.  The
+scalar value calculated by this fix is "intensive".  No parameter
 of this fix can be used with the *start/stop* keywords of the
 :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
 

doc/src/fix_press_langevin.rst

@@ -0,0 +1,301 @@
+.. index:: fix press/langevin
+
+fix press/langevin command
+===========================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix ID group-ID press/langevin keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* press/langevin = style name of this fix command
+
+  .. parsed-literal::
+
+     one or more keyword value pairs may be appended
+     keyword = *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *xz* or *yz* or *couple* or *dilate* or *modulus* or *temp* or *flip*
+       *iso* or *aniso* or *tri* values = Pstart Pstop Pdamp
+         Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
+         Pdamp = pressure damping parameter (time units)
+       *x* or *y* or *z* or *xy* or *xz* or *yz* values = Pstart Pstop Pdamp
+         Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
+         Pdamp = pressure damping parameter
+       *flip* value = *yes* or *no* = allow or disallow box flips when it becomes highly skewed
+       *couple* = *none* or *xyz* or *xy* or *yz* or *xz*
+       *friction* value = Friction coefficient for the barostat (time units)
+       *temp* values = Tstart, Tstop, seed
+       Tstart, Tstop = target temperature used for the barostat at start/end of run
+       seed = seed of the random number generator
+       *dilate* value = *all* or *partial*
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 1 all press/langevin iso 0.0 0.0 1000.0 temp 300 300 487374
+   fix 2 all press/langevin aniso 0.0 0.0 1000.0 temp 100 300 238 dilate partial
+
+Description
+"""""""""""
+
+Adjust the pressure of the system by using a Langevin stochastic barostat
+:ref:`(Gronbech) <Gronbech>`, which rescales the system volume and
+(optionally) the atoms coordinates within the simulation box every
+timestep.
+
+The Langevin barostat couple each direction *L* with a pseudo-particle that obeys
+the Langevin equation such as:
+
+.. math::
+
+   f_P = & \frac{N k_B T_{target}}{V} + \frac{1}{V d}\sum_{i=1}^{N} \vec r_i \cdot \vec f_i - P_{target} \\
+   Q\ddot{L} + \alpha{}\dot{L} = & f_P + \beta(t)\\
+   L^{n+1} = & L^{n} + bdt\dot{L}^{n} \frac{bdt^{2}}{2Q} \\
+   \dot{L}^{n+1} = & \alpha\dot{L}^{n} + \frac{dt}{2Q}\left(a f^{n}_{P} + f^{n+1}_{P}\right) + \frac{b}{Q}\beta^{n+1} \\
+   a = & \frac{1-\frac{\alpha{}dt}{2Q}}{1+\frac{\alpha{}dt}{2Q}} \\
+   b = & \frac{1}{1+\frac{\alpha{}dt}{2Q}} \\
+   \left< \beta(t)\beta(t') \right> = & 2\alpha k_B Tdt
+
+Where :math:`dt` is the timestep :math:`\dot{L}` and :math:`\ddot{L}` the first
+and second derivatives of the coupled direction with regard to time,
+:math:`\alpha` is a friction coefficient, :math:`\beta` is a random gaussian
+variable and :math:`Q` the effective mass of the coupled pseudoparticle. The
+two first terms on the right-hand side of the first equation are the virial
+expression of the canonical pressure. It is to be noted that the temperature
+used to compute the pressure is not based on the atom velocities but rather on
+the canonical
+target temperature directly. This temperature is specified using the *temp*
+keyword parameter and should be close to the expected target temperature of the
+system.
+
+Regardless of what atoms are in the fix group, a global pressure is
+computed for all atoms. Similarly, when the size of the simulation
+box is changed, all atoms are re-scaled to new positions, unless the
+keyword *dilate* is specified with a value of *partial*, in which case
+only the atoms in the fix group are re-scaled. The latter can be
+useful for leaving the coordinates of atoms in a solid substrate
+unchanged and controlling the pressure of a surrounding fluid.
+
+.. note::
+
+   Unlike the :doc:`fix npt <fix_nh>` or :doc:`fix nph <fix_nh>` commands which
+   perform Nose-Hoover barostatting AND time integration, this fix does NOT
+   perform time integration of the atoms but only of the barostat coupled
+   coordinate. It then only modifies the box size and atom coordinates to
+   effect barostatting. Thus you must use a separate time integration fix,
+   like :doc:`fix nve <fix_nve>` or :doc:`fix nvt <fix_nh>` to actually update
+   the positions and velocities of atoms.  This fix can be used in conjunction
+   with thermostatting fixes to control the temperature, such as :doc:`fix nvt
+   <fix_nh>` or :doc:`fix langevin <fix_langevin>` or :doc:`fix temp/berendsen
+   <fix_temp_berendsen>`.
+
+See the :doc:`Howto barostat <Howto_barostat>` page for a
+discussion of different ways to perform barostatting.
+
+----------
+
+The barostat is specified using one or more of the *iso*, *aniso*, *tri* *x*,
+*y*, *z*, *xy*, *xz*, *yz*, and *couple* keywords.  These keywords give you the
+ability to specify the 3 diagonal components of an external stress tensor, and
+to couple various of these components together so that the dimensions they
+represent are varied together during a constant-pressure simulation.
+
+The target pressures for each of the 6 diagonal components of the stress tensor
+can be specified independently via the *x*, *y*, *z*, keywords, which
+correspond to the 3 simulation box dimensions, and the *xy*, *xz* and *yz*
+keywords which corresponds to the 3 simulation box tilt factors. For each
+component, the external pressure or tensor component at each timestep is a
+ramped value during the run from *Pstart* to *Pstop*\ . If a target pressure is
+specified for a component, then the corresponding box dimension will change
+during a simulation.  For example, if the *y* keyword is used, the y-box length
+will change.  A box dimension will not change if that component is not
+specified, although you have the option to change that dimension via the
+:doc:`fix deform <fix_deform>` command.
+
+The *Pdamp* parameter can be seen in the same way as a Nose-Hoover parameter as
+it is used to compute the mass of the fictitious particle. Without friction,
+the barostat can be compared to a single particle Nose-Hoover barostat and
+should follow a similar decay in time. The mass of the barostat is
+linked to *Pdamp* by the relation
+:math:`Q=(N_{at}+1)\cdot{}k_BT_{target}\cdot{}P_{damp}^2`. Note that *Pdamp*
+should be expressed in time units.
+
+.. note::
+
+   As for Berendsen barostat, a Langevin barostat will not work well for
+   arbitrary values of *Pdamp*\ .  If *Pdamp* is too small, the pressure and
+   volume can fluctuate wildly; if it is too large, the pressure will take a
+   very long time to equilibrate.  A good choice for many models is a *Pdamp*
+   of around 1000 timesteps.  However, note that *Pdamp* is specified in time
+   units, and that timesteps are NOT the same as time units for most
+   :doc:`units <units>` settings.
+
+----------
+
+The *temp* keyword sets the temperature to use in the equation of motion of the
+barostat. This value is used to compute the value of the force :math:`f_P` in
+the equation of motion. It is important to note that this value is not the
+instantaneous temperature but a target temperature that ramps from *Tstart* to
+*Tstop*. Also the required argument *seed* sets the seed for the random
+number generator used in the generation of the random forces.
+
+----------
+
+The *couple* keyword allows two or three of the diagonal components of
+the pressure tensor to be "coupled" together.  The value specified
+with the keyword determines which are coupled.  For example, *xz*
+means the *Pxx* and *Pzz* components of the stress tensor are coupled.
+*Xyz* means all 3 diagonal components are coupled.  Coupling means two
+things: the instantaneous stress will be computed as an average of the
+corresponding diagonal components, and the coupled box dimensions will
+be changed together in lockstep, meaning coupled dimensions will be
+dilated or contracted by the same percentage every timestep.  The
+*Pstart*, *Pstop*, *Pdamp* parameters for any coupled dimensions must
+be identical.  *Couple xyz* can be used for a 2d simulation; the *z*
+dimension is simply ignored.
+
+----------
+
+The *iso*, *aniso* and *tri* keywords are simply shortcuts that are
+equivalent to specifying several other keywords together.
+
+The keyword *iso* means couple all 3 diagonal components together when
+pressure is computed (hydrostatic pressure), and dilate/contract the
+dimensions together.  Using "iso Pstart Pstop Pdamp" is the same as
+specifying these 4 keywords:
+
+.. parsed-literal::
+
+   x Pstart Pstop Pdamp
+   y Pstart Pstop Pdamp
+   z Pstart Pstop Pdamp
+   couple xyz
+
+The keyword *aniso* means *x*, *y*, and *z* dimensions are controlled
+independently using the *Pxx*, *Pyy*, and *Pzz* components of the
+stress tensor as the driving forces, and the specified scalar external
+pressure.  Using "aniso Pstart Pstop Pdamp" is the same as specifying
+these 4 keywords:
+
+.. parsed-literal::
+
+   x Pstart Pstop Pdamp
+   y Pstart Pstop Pdamp
+   z Pstart Pstop Pdamp
+   couple none
+
+The keyword *tri* is the same as *aniso* but also adds the control on the
+shear pressure coupled with the tilt factors.
+
+.. parsed-literal::
+
+   x Pstart Pstop Pdamp
+   y Pstart Pstop Pdamp
+   z Pstart Pstop Pdamp
+   xy Pstart Pstop Pdamp
+   xz Pstart Pstop Pdamp
+   yz Pstart Pstop Pdamp
+   couple none
+
+----------
+
+The *flip* keyword allows the tilt factors for a triclinic box to
+exceed half the distance of the parallel box length, as discussed
+below.  If the *flip* value is set to *yes*, the bound is enforced by
+flipping the box when it is exceeded.  If the *flip* value is set to
+*no*, the tilt will continue to change without flipping.  Note that if
+applied stress induces large deformations (e.g. in a liquid), this
+means the box shape can tilt dramatically and LAMMPS will run less
+efficiently, due to the large volume of communication needed to
+acquire ghost atoms around a processor's irregular-shaped subdomain.
+For extreme values of tilt, LAMMPS may also lose atoms and generate an
+error.
+
+----------
+
+The *friction* keyword sets the friction parameter :math:`\alpha` in the
+equations of motion of the barostat. For each barostat direction, the value of
+:math:`\alpha` depends on both *Pdamp* and *friction*. The value given as a
+parameter is the Langevin characteristic time
+:math:`\tau_{L}=\frac{Q}{\alpha}` in time units. The langevin time can be understood as a
+decorrelation time for the pressure. A long Langevin time value will make the
+barostat act as an underdamped oscillator while a short value will make it
+act as an overdamped oscillator. The ideal configuration would be to find
+the critical parameter of the barostat. Empirically this is observed to
+occur for :math:`\tau_{L}\approx{}P_{damp}`.  For this reason, if the *friction*
+keyword is not used, the default value *Pdamp* is used for each barostat direction.
+
+----------
+
+This fix computes pressure each timestep. To do
+this, the fix creates its own computes of style "pressure",
+as if this command had been issued:
+
+.. code-block:: LAMMPS
+
+   compute fix-ID_press group-ID pressure NULL virial
+
+The kinetic contribution to the pressure is taken as the ensemble value
+:math:`\frac{Nk_bT}{V}` and computed by the fix itself.
+
+See the :doc:`compute pressure <compute_pressure>` command for details.  Note
+that the IDs of the new compute is the fix-ID + underscore + "press" and the
+group for the new computes is the same as the fix group.
+
+Note that this is NOT the compute used by thermodynamic output (see the
+:doc:`thermo_style <thermo_style>` command) with ID = *thermo_press*. This
+means you can change the attributes of this fix's pressure via the
+:doc:`compute_modify <compute_modify>` command or print this temperature or
+pressure during thermodynamic output via the :doc:`thermo_style custom
+<thermo_style>` command using the appropriate compute-ID. It also means that
+changing attributes of *thermo_temp* or *thermo_press* will have no effect on
+this fix.
+
+Restart, fix_modify, output, run start/stop, minimize info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+
+The :doc:`fix_modify <fix_modify>` *press* option is
+supported by this fix.  You can use it to assign a
+:doc:`compute <compute>` you have defined to this fix which will be used
+in its pressure calculations.
+
+No global or per-atom quantities are stored by this fix for access by
+various :doc:`output commands <Howto_output>`.
+
+This fix can ramp its target pressure and temperature over multiple runs, using
+the *start* and *stop* keywords of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this. It is recommended that
+the ramped temperature is the same as the effective temperature of the
+thermostatted system. That is, if the system's temperature is ramped by other
+commands, it is recommended to do the same with this pressure control.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+Any dimension being adjusted by this fix must be periodic.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix press/berendsen <fix_press_berendsen>`,
+:doc:`fix nve <fix_nve>`, :doc:`fix nph <fix_nh>`, :doc:`fix npt <fix_nh>`, :doc:`fix langevin <fix_langevin>`,
+:doc:`fix_modify <fix_modify>`
+
+Default
+"""""""
+
+The keyword defaults are *dilate* = all, *flip* = yes, and *friction* = *Pdamp*.
+
+----------
+
+.. _Gronbech:
+
+**(Gronbech)** Gronbech-Jensen, Farago, J Chem Phys, 141, 194108 (2014).

doc/src/fix_rigid.rst

@@ -843,7 +843,7 @@ stress/atom <compute_stress_atom>` commands.  The former can be
 accessed by :doc:`thermodynamic output <thermo_style>`.  The default
 setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
 
-All of the *rigid* styles (not the *rigid/small* styles) compute a
+All of the *rigid* styles (but not the *rigid/small* styles) compute a
 global array of values which can be accessed by various :doc:`output
 commands <Howto_output>`.  Similar information about the bodies
 defined by the *rigid/small* styles can be accessed via the
@@ -887,7 +887,8 @@ Restrictions
 """"""""""""
 
 These fixes are all part of the RIGID package.  It is only enabled if
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
 
 Assigning a temperature via the :doc:`velocity create <velocity>`
 command to a system with :doc:`rigid bodies <fix_rigid>` may not have

doc/src/fix_spring_self.rst

@@ -1,4 +1,5 @@
 .. index:: fix spring/self
+.. index:: fix spring/self/kk
 
 fix spring/self command
 =======================
@@ -80,6 +81,12 @@ invoked by the :doc:`minimize <minimize>` command.
    you MUST enable the :doc:`fix_modify <fix_modify>` *energy* option for
    this fix.
 
+----------
+
+.. include:: accel_styles.rst
+
+----------
+
 Restrictions
 """"""""""""
  none

doc/src/fix_srd.rst

@@ -61,24 +61,30 @@ Description
 Treat a group of particles as stochastic rotation dynamics (SRD)
 particles that serve as a background solvent when interacting with big
 (colloidal) particles in groupbig-ID.  The SRD formalism is described
-in :ref:`(Hecht) <Hecht>`.  The key idea behind using SRD particles as a
+in :ref:`(Hecht) <Hecht>`.  The same methodology is also called
-cheap coarse-grained solvent is that SRD particles do not interact
+multi-particle collision dynamics (MPCD) in the literature.
-with each other, but only with the solute particles, which in LAMMPS
-can be spheroids, ellipsoids, or line segments, or triangles, or rigid
-bodies containing multiple spheroids or ellipsoids or line segments
-or triangles.  The collision and rotation properties of the model
-imbue the SRD particles with fluid-like properties, including an
-effective viscosity.  Thus simulations with large solute particles can
-be run more quickly, to measure solute properties like diffusivity
-and viscosity in a background fluid.  The usual LAMMPS fixes for such
-simulations, such as :doc:`fix deform <fix_deform>`, :doc:`fix viscosity <fix_viscosity>`, and :doc:`fix nvt/sllod <fix_nvt_sllod>`,
-can be used in conjunction with the SRD model.
 
-For more details on how the SRD model is implemented in LAMMPS, :ref:`this paper <Petersen1>` describes the implementation and usage of pure SRD
+The key idea behind using SRD particles as a cheap coarse-grained
-fluids.  :ref:`This paper <Lechman>`, which is nearly complete, describes
+solvent is that SRD particles do not interact with each other, but
-the implementation and usage of mixture systems (solute particles in
+only with the solute particles, which in LAMMPS can be spheroids,
-an SRD fluid).  See the examples/srd directory for sample input
+ellipsoids, or line segments, or triangles, or rigid bodies containing
-scripts using SRD particles in both settings.
+multiple spheroids or ellipsoids or line segments or triangles.  The
+collision and rotation properties of the model imbue the SRD particles
+with fluid-like properties, including an effective viscosity.  Thus
+simulations with large solute particles can be run more quickly, to
+measure solute properties like diffusivity and viscosity in a
+background fluid.  The usual LAMMPS fixes for such simulations, such
+as :doc:`fix deform <fix_deform>`, :doc:`fix viscosity
+<fix_viscosity>`, and :doc:`fix nvt/sllod <fix_nvt_sllod>`, can be
+used in conjunction with the SRD model.
+
+These 3 papers give more details on how the SRD model is implemented
+in LAMMPS.  :ref:`(Petersen) <Petersen1>` describes pure SRD fluid
+systems.  :ref:`(Bolintineanu1) <Bolintineanu1>` describes models
+where pure SRD fluids interact with boundary walls.
+:ref:`(Bolintineanu2) <Bolintineanu2>` describes mixture models where
+large colloidal particles are solvated by an SRD fluid.  See the
+``examples/srd`` directory for sample input scripts.
 
 This fix does two things:
 
@@ -357,28 +363,28 @@ These are the 12 quantities.  All are values for the current timestep,
 except for quantity 5 and the last three, each of which are
 cumulative quantities since the beginning of the run.
 
-* (1) # of SRD/big collision checks performed
+(1) # of SRD/big collision checks performed
-* (2) # of SRDs which had a collision
+(2) # of SRDs which had a collision
-* (3) # of SRD/big collisions (including multiple bounces)
+(3) # of SRD/big collisions (including multiple bounces)
-* (4) # of SRD particles inside a big particle
+(4) # of SRD particles inside a big particle
-* (5) # of SRD particles whose velocity was rescaled to be < Vmax
+(5) # of SRD particles whose velocity was rescaled to be < Vmax
-* (6) # of bins for collision searching
+(6) # of bins for collision searching
-* (7) # of bins for SRD velocity rotation
+(7) # of bins for SRD velocity rotation
-* (8) # of bins in which SRD temperature was computed
+(8) # of bins in which SRD temperature was computed
-* (9) SRD temperature
+(9) SRD temperature
-* (10) # of SRD particles which have undergone max # of bounces
+(10) # of SRD particles which have undergone max # of bounces
-* (11) max # of bounces any SRD particle has had in a single step
+(11) max # of bounces any SRD particle has had in a single step
-* (12) # of reneighborings due to SRD particles moving too far
+(12) # of reneighborings due to SRD particles moving too far
 
 No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""
 
-This command can only be used if LAMMPS was built with the SRD
+This command can only be used if LAMMPS was built with the SRD package.
-package.  See the :doc:`Build package <Build_package>` doc
+See the :doc:`Build package <Build_package>` doc page for more info.
-page for more info.
 
 Related commands
 """"""""""""""""
@@ -404,6 +410,12 @@ no, and rescale = yes.
 **(Petersen)** Petersen, Lechman, Plimpton, Grest, in' t Veld, Schunk, J
 Chem Phys, 132, 174106 (2010).
 
-.. _Lechman:
+.. _Bolintineanu1:
 
-**(Lechman)** Lechman, et al, in preparation (2010).
+**(Bolintineanu1)**
+Bolintineanu, Lechman, Plimpton, Grest, Phys Rev E, 86, 066703 (2012).
+
+.. _Bolintineanu2:
+
+**(Bolintineanu2)** Bolintineanu, Grest, Lechman, Pierce, Plimpton,
+Schunk, Comp Particle Mechanics, 1, 321-356 (2014).

doc/src/improper_amoeba.rst

@@ -68,8 +68,8 @@ for more info.
 Related commands
 """"""""""""""""
 
-:doc:`improper_coeff <improper_coeff>`, `improper_harmonic
+:doc:`improper_coeff <improper_coeff>`,
-:doc:<improper_harmonic>`
+:doc:`improper_harmonic <improper_harmonic>`
 
 Default
 """""""

doc/src/pair_body_rounded_polyhedron.rst

@@ -40,7 +40,7 @@ rounded/polyhedron particles.
 This pairwise interaction between the rounded polyhedra is described
 in :ref:`Wang <pair-Wang>`, where a polyhedron does not have sharp corners
 and edges, but is rounded at its vertices and edges by spheres
-centered on each vertex with a specified diameter.  The edges if the
+centered on each vertex with a specified diameter.  The edges of the
 polyhedron are defined between pairs of adjacent vertices.  Its faces
 are defined by a loop of edges.  The sphere diameter for each polygon
 is specified in the data file read by the :doc:`read data <read_data>`

doc/src/pair_ilp_tmd.rst

@@ -22,12 +22,12 @@ Examples
 .. code-block:: LAMMPS
 
    pair_style  hybrid/overlay ilp/tmd 16.0 1
-   pair_coeff  * * ilp/tmd  TMD.ILP Mo S S
+   pair_coeff  * * ilp/tmd  MoS2.ILP Mo S S
 
    pair_style  hybrid/overlay sw/mod sw/mod ilp/tmd 16.0
    pair_coeff  * * sw/mod 1  tmd.sw.mod Mo S S NULL NULL NULL
    pair_coeff  * * sw/mod 2  tmd.sw.mod NULL NULL NULL Mo S S
-   pair_coeff  * * ilp/tmd   TMD.ILP    Mo S S Mo S S
+   pair_coeff  * * ilp/tmd   MoS2.ILP   Mo S S Mo S S
 
 Description
 """""""""""
@@ -69,7 +69,7 @@ calculating the normals.
    each atom `i`, its six nearest neighboring atoms belonging to the same
    sub-layer are chosen to define the normal vector `{\bf n}_i`.
 
-The parameter file (e.g. TMD.ILP), is intended for use with *metal*
+The parameter file (e.g. MoS2.ILP), is intended for use with *metal*
 :doc:`units <units>`, with energies in meV. Two additional parameters,
 *S*, and *rcut* are included in the parameter file. *S* is designed to
 facilitate scaling of energies. *rcut* is designed to build the neighbor
@@ -77,7 +77,7 @@ list for calculating the normals for each atom pair.
 
 .. note::
 
-   The parameters presented in the parameter file (e.g. TMD.ILP),
+   The parameters presented in the parameter file (e.g. MoS2.ILP),
    are fitted with taper function by setting the cutoff equal to 16.0
    Angstrom.  Using different cutoff or taper function should be careful.
    These parameters provide a good description in both short- and long-range
@@ -133,10 +133,10 @@ if LAMMPS was built with that package.  See the :doc:`Build package
 This pair style requires the newton setting to be *on* for pair
 interactions.
 
-The TMD.ILP potential file provided with LAMMPS (see the potentials
+The MoS2.ILP potential file provided with LAMMPS (see the potentials
 directory) are parameterized for *metal* units.  You can use this
 potential with any LAMMPS units, but you would need to create your own
-custom TMD.ILP potential file with coefficients listed in the appropriate
+custom MoS2.ILP potential file with coefficients listed in the appropriate
 units, if your simulation does not use *metal* units.
 
 Related commands

doc/src/pair_nb3b.rst

@@ -1,14 +1,20 @@
 .. index:: pair_style nb3b/harmonic
+.. index:: pair_style nb3b/screened
 
 pair_style nb3b/harmonic command
 ================================
 
+pair_style nb3b/screened command
+================================
+
 Syntax
 """"""
 
 .. code-block:: LAMMPS
 
-   pair_style nb3b/harmonic
+   pair_style style
+
+* style = *nb3b/harmonic* or *nb3b/screened*
 
 Examples
 """"""""
@@ -18,10 +24,14 @@ Examples
    pair_style nb3b/harmonic
    pair_coeff * * MgOH.nb3bharmonic Mg O H
 
+   pair_style nb3b/screened
+   pair_coeff * * PO.nb3b.screened P NULL O
+   pair_coeff * * SiOH.nb3b.screened Si O H
+
 Description
 """""""""""
 
-This pair style computes a non-bonded 3-body harmonic potential for the
+The pair style *nb3b/harmonic* computes a non-bonded 3-body harmonic potential for the
 energy E of a system of atoms as
 
 .. math::
@@ -33,7 +43,17 @@ prefactor. Note that the usual 1/2 factor is included in *K*\ . The form
 of the potential is identical to that used in angle_style *harmonic*,
 but in this case, the atoms do not need to be explicitly bonded.
 
-Only a single pair_coeff command is used with this style which
+Style *nb3b/screened* adds an additional exponentially decaying factor to
+the harmonic term, given by
+
+.. math::
+
+   E = K (\theta - \theta_0)^2 \exp \left(- \frac{r_{ij}}{\rho_{ij}} - \frac{r_{ik}}{\rho_{ik}} \right)
+
+where :math:`\rho_ij` and :math:`\rho_ik` are the screening factors along
+the two bonds. Note that the usual 1/2 factor is included in *K*.
+
+Only a single pair_coeff command is used with these styles which
 specifies a potential file with parameters for specified elements.
 These are mapped to LAMMPS atom types by specifying N additional
 arguments after the filename in the pair_coeff command, where N is the
@@ -61,8 +81,8 @@ type 4 to the C element in the potential file.  If a mapping value is
 specified as NULL, the mapping is not performed.  This can be used
 when the potential is used as part of the *hybrid* pair style.  The
 NULL values are placeholders for atom types that will be used with
-other potentials. An example of a pair_coeff command for use with the
+other potentials. Two examples of pair_coeff command for use with the
-*hybrid* pair style is:
+*hybrid* pair style are:
 
 .. code-block:: LAMMPS
 

doc/src/pair_reaxff.rst

@@ -43,18 +43,18 @@ Examples
 Description
 """""""""""
 
-Style *reaxff* computes the ReaxFF potential of van Duin, Goddard and
+Pair style *reaxff* computes the ReaxFF potential of van Duin, Goddard
-co-workers.  ReaxFF uses distance-dependent bond-order functions to
+and co-workers.  ReaxFF uses distance-dependent bond-order functions to
 represent the contributions of chemical bonding to the potential
 energy.  There is more than one version of ReaxFF.  The version
 implemented in LAMMPS uses the functional forms documented in the
 supplemental information of the following paper:
-:ref:`(Chenoweth et al., 2008) <Chenoweth_20082>`.  The version integrated
+:ref:`(Chenoweth et al., 2008) <Chenoweth_20082>` and matches the
-into LAMMPS matches the version of ReaxFF From Summer 2010.  For more
+version of the reference ReaxFF implementation from Summer 2010.  For
-technical details about the pair reaxff implementation of ReaxFF, see
+more technical details about the implementation of ReaxFF in pair style
-the :ref:`(Aktulga) <Aktulga>` paper. The *reaxff* style was initially
+*reaxff*, see the :ref:`(Aktulga) <Aktulga>` paper. The *reaxff* style
-implemented as a stand-alone C code and is now converted to C++ and
+was initially implemented as a stand-alone C code and is now converted
-integrated into LAMMPS as a package.
+to C++ and integrated into LAMMPS as a package.
 
 The *reaxff/kk* style is a Kokkos version of the ReaxFF potential that
 is derived from the *reaxff* style.  The Kokkos version can run on GPUs
@@ -72,8 +72,7 @@ from LAMMPS after the 12 December 2018 version.
 
 LAMMPS provides several different versions of ffield.reax in its
 potentials dir, each called potentials/ffield.reax.label.  These are
-documented in potentials/README.reax.  The default ffield.reax
+documented in potentials/README.reax.
-contains parameterizations for the following elements: C, H, O, N.
 
 The format of these files is identical to that used originally by van
 Duin.  We have tested the accuracy of *pair_style reaxff* potential
@@ -110,12 +109,14 @@ control variable.  The format of the control file is described below.
    not agree.
 
 Examples using *pair_style reaxff* are provided in the examples/reax
-subdirectory.
+directory and its subdirectories.
 
-Use of this pair style requires that a charge be defined for every
+Use of this pair style requires using an :doc:`atom_style <atom_style>`
-atom.  See the :doc:`atom_style <atom_style>` and
+that includes a per-atom charge property *or* using
-:doc:`read_data <read_data>` commands for details on how to specify
+:doc:`fix property/atom q <fix_property_atom>`.  Charges can be set
-charges.
+via :doc:`read_data <read_data>` or :doc:`set <set>`.  Using an initial
+charge that is close to the result of charge equilibration will speed
+up that process.
 
 The ReaxFF parameter files provided were created using a charge
 equilibration (QEq) model for handling the electrostatic interactions.

doc/src/pair_snap.rst

@@ -1,10 +1,11 @@
 .. index:: pair_style snap
+.. index:: pair_style snap/intel
 .. index:: pair_style snap/kk
 
 pair_style snap command
 =======================
 
-Accelerator Variants: *snap/kk*
+Accelerator Variants: *snap/intel*, *snap/kk*
 
 Syntax
 """"""
@@ -260,6 +261,14 @@ This style is part of the ML-SNAP package.  It is only enabled if LAMMPS
 was built with that package.  See the :doc:`Build package
 <Build_package>` page for more info.
 
+The *snap/intel* accelerator variant will *only* be available if LAMMPS
+is built with Intel *compilers* and for CPUs with AVX-512 support.
+While the INTEL package in general allows multiple floating point
+precision modes to be selected, *snap/intel* will currently always use
+full double precision regardless of the precision mode selected.
+Additionally, the *intel* variant of snap will **NOT** use multiple
+threads with OpenMP.
+
 Related commands
 """"""""""""""""
 

doc/src/pair_style.rst

@@ -297,7 +297,8 @@ accelerated styles exist.
 * :doc:`morse/soft <pair_morse>` - Morse potential with a soft core
 * :doc:`multi/lucy <pair_multi_lucy>` - DPD potential with density-dependent force
 * :doc:`multi/lucy/rx <pair_multi_lucy_rx>` - reactive DPD potential with density-dependent force
-* :doc:`nb3b/harmonic <pair_nb3b_harmonic>` - non-bonded 3-body harmonic potential
+* :doc:`nb3b/harmonic <pair_nb3b>` - non-bonded 3-body harmonic potential
+* :doc:`nb3b/screened <pair_nb3b>` - non-bonded 3-body screened harmonic potential
 * :doc:`nm/cut <pair_nm>` - N-M potential
 * :doc:`nm/cut/coul/cut <pair_nm>` - N-M potential with cutoff Coulomb
 * :doc:`nm/cut/coul/long <pair_nm>` - N-M potential with long-range Coulomb

doc/src/pair_yukawa_colloid.rst

@@ -1,11 +1,12 @@
 .. index:: pair_style yukawa/colloid
 .. index:: pair_style yukawa/colloid/gpu
+.. index:: pair_style yukawa/colloid/kk
 .. index:: pair_style yukawa/colloid/omp
 
 pair_style yukawa/colloid command
 =================================
 
-Accelerator Variants: *yukawa/colloid/gpu*, *yukawa/colloid/omp*
+Accelerator Variants: *yukawa/colloid/gpu*, *yukawa/colloid/kk*, *yukawa/colloid/omp*
 
 Syntax
 """"""
@@ -131,6 +132,12 @@ per-type polydispersity is allowed.  This means all particles of the
 same type must have the same diameter.  Each type can have a different
 diameter.
 
+----------
+
+.. include:: accel_styles.rst
+
+----------
+
 Related commands
 """"""""""""""""
 

doc/src/region.rst

@@ -24,6 +24,7 @@ Syntax
          c1,c2 = coords of cone axis in other 2 dimensions (distance units)
          radlo,radhi = cone radii at lo and hi end (distance units)
          lo,hi = bounds of cone in dim (distance units)
+         c1,c2,radlo,radhi,lo,hi can be a variable (see below)
        *cylinder* args = dim c1 c2 radius lo hi
          dim = *x* or *y* or *z* = axis of cylinder
          c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
@@ -206,7 +207,8 @@ equal-style :doc:`variable <variable>`.  Likewise, for style *sphere*
 and *ellipsoid* the x-, y-, and z- coordinates of the center of the
 sphere/ellipsoid can be specified as an equal-style variable.  And for
 style *cylinder* the two center positions c1 and c2 for the location
-of the cylinder axes can be specified as a equal-style variable.
+of the cylinder axes can be specified as a equal-style variable. For style *cone*
+all properties can be defined via equal-style variables.
 
 If the value is a variable, it should be specified as v_name, where
 name is the variable name.  In this case, the variable will be

doc/src/thermo_style.rst

@@ -385,19 +385,20 @@ creates a global vector with 6 values.
 The *c_ID* and *c_ID[I]* and *c_ID[I][J]* keywords allow global values
 calculated by a compute to be output.  As discussed on the
 :doc:`compute <compute>` doc page, computes can calculate global,
-per-atom, or local values.  Only global values can be referenced by
+per-atom, local, and per-grid values.  Only global values can be
-this command.  However, per-atom compute values for an individual atom
+referenced by this command.  However, per-atom compute values for an
-can be referenced in a :doc:`variable <variable>` and the variable
+individual atom can be referenced in a :doc:`equal-style variable
-referenced by thermo_style custom, as discussed below.  See the
+<variable>` and the variable referenced by thermo_style custom, as
-discussion above for how the I in *c_ID[I]* can be specified with a
+discussed below.  See the discussion above for how the I in *c_ID[I]*
-wildcard asterisk to effectively specify multiple values from a global
+can be specified with a wildcard asterisk to effectively specify
-compute vector.
+multiple values from a global compute vector.
 
 The ID in the keyword should be replaced by the actual ID of a compute
 that has been defined elsewhere in the input script.  See the
-:doc:`compute <compute>` command for details.  If the compute calculates
+:doc:`compute <compute>` command for details.  If the compute
-a global scalar, vector, or array, then the keyword formats with 0, 1,
+calculates a global scalar, vector, or array, then the keyword formats
-or 2 brackets will reference a scalar value from the compute.
+with 0, 1, or 2 brackets will reference a scalar value from the
+compute.
 
 Note that some computes calculate "intensive" global quantities like
 temperature; others calculate "extensive" global quantities like
@@ -410,13 +411,14 @@ norm <thermo_modify>` option being used.
 
 The *f_ID* and *f_ID[I]* and *f_ID[I][J]* keywords allow global values
 calculated by a fix to be output.  As discussed on the :doc:`fix
-<fix>` doc page, fixes can calculate global, per-atom, or local
+<fix>` doc page, fixes can calculate global, per-atom, local, and
-values.  Only global values can be referenced by this command.
+per-grid values.  Only global values can be referenced by this
-However, per-atom fix values can be referenced for an individual atom
+command.  However, per-atom fix values can be referenced for an
-in a :doc:`variable <variable>` and the variable referenced by
+individual atom in a :doc:`equal-style variable <variable>` and the
-thermo_style custom, as discussed below.  See the discussion above for
+variable referenced by thermo_style custom, as discussed below.  See
-how the I in *f_ID[I]* can be specified with a wildcard asterisk to
+the discussion above for how the I in *f_ID[I]* can be specified with
-effectively specify multiple values from a global fix vector.
+a wildcard asterisk to effectively specify multiple values from a
+global fix vector.
 
 The ID in the keyword should be replaced by the actual ID of a fix
 that has been defined elsewhere in the input script.  See the
@@ -438,14 +440,15 @@ output.  The name in the keyword should be replaced by the variable
 name that has been defined elsewhere in the input script.  Only
 equal-style and vector-style variables can be referenced; the latter
 requires a bracketed term to specify the Ith element of the vector
-calculated by the variable.  However, an atom-style variable can be
+calculated by the variable.  However, an equal-style variable can use
-referenced for an individual atom by an equal-style variable and that
+an atom-style variable in its formula indexed by the ID of an
-variable referenced.  See the :doc:`variable <variable>` command for
+individual atom.  This is a way to output a specific atom's per-atom
-details.  Variables of style *equal* and *vector* and *atom* define a
+coordinates or other per-atom properties in thermo output.  See the
-formula which can reference per-atom properties or thermodynamic
+:doc:`variable <variable>` command for details.  Note that variables
-keywords, or they can invoke other computes, fixes, or variables when
+of style *equal* and *vector* and *atom* define a formula which can
-evaluated, so this is a very general means of creating thermodynamic
+reference per-atom properties or thermodynamic keywords, or they can
-output.
+invoke other computes, fixes, or variables when evaluated, so this is
+a very general means of creating thermodynamic output.
 
 Note that equal-style and vector-style variables are assumed to
 produce "intensive" global quantities, which are thus printed as-is,

doc/src/variable.rst

@@ -53,7 +53,7 @@ Syntax
                           x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x \|\| y, x \|\^ y, !x
          math functions = sqrt(x), exp(x), ln(x), log(x), abs(x),
                           sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x),
-                          random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x)
+                          random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ternary(x,y,z),
                           ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z),
                           logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c),
                           vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
@@ -71,6 +71,7 @@ Syntax
          feature functions = is_available(category,feature), is_active(category,feature), is_defined(category,id)
          atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
          atom vector = id, mass, type, mol, radius, q, x, y, z, vx, vy, vz, fx, fy, fz
+         custom atom property = i_name, d_name, i_name[i], d_name[i], i2_name[i], d2_name[i], i2_name[i][j], d_name[i][j]
          compute references = c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i]
          fix references = f_ID, f_ID[i], f_ID[i][j], F_ID, F_ID[i]
          variable references = v_name, v_name[i]
@@ -514,48 +515,49 @@ is a valid (though strange) variable formula:
 Specifically, a formula can contain numbers, constants, thermo
 keywords, math operators, math functions, group functions, region
 functions, special functions, feature functions, atom values, atom
-vectors, compute references, fix references, and references to other
+vectors, custom atom properties, compute references, fix references, and references to other
 variables.
 
-+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
++------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Number                 | 0.2, 100, 1.0e20, -15.4, etc                                                                                                                                                                                                                                                                                                                      |
-+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
++------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Constant               | PI, version, on, off, true, false, yes, no                                                                                                                                                                                                                                                                                                        |
-+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
++------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Thermo keywords        | vol, pe, ebond, etc                                                                                                                                                                                                                                                                                                                               |
-+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
++------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Math operators         | (), -x, x+y, x-y, x\*y, x/y, x\^y, x%y, x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x \|\| y, x \|\^ y, !x                                                                                                                                                                                                                              |
-+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
++------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| Math functions     | sqrt(x), exp(x), ln(x), log(x), abs(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)   |
+| Math functions         | sqrt(x), exp(x), ln(x), log(x), abs(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ternary(x,y,z), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)  |
-+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
++------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Group functions        | count(ID), mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), fcm(ID,dim), bound(ID,dir), gyration(ID), ke(ID), angmom(ID,dim), torque(ID,dim), inertia(ID,dimdim), omega(ID,dim)                                                                                                                                                                    |
-+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
++------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Region functions       | count(ID,IDR), mass(ID,IDR), charge(ID,IDR), xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), angmom(ID,dim,IDR), torque(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR)                                                                                                                |
-+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
++------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Special functions      | sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label)                                                                                                                                                  |
-+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
++------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Feature functions      | is_available(category,feature), is_active(category,feature), is_defined(category,id)                                                                                                                                                                                                                                                              |
-+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
++------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Atom values            | id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]                                                                                                                                                                                                                                                 |
-+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
++------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Atom vectors           | id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q                                                                                                                                                                                                                                                                                           |
-+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
++------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| Custom atom properties | i_name, d_name, i_name[i], d_name[i], i2_name[i], d2_name[i], i2_name[i][j], d_name[i][j]                                                                                                                                                                                                                                                         |
++------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Compute references     | c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i]                                                                                                                                                                                                                                                                                                          |
-+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
++------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Fix references         | f_ID, f_ID[i], f_ID[i][j], F_ID, F_ID[i]                                                                                                                                                                                                                                                                                                          |
-+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
++------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Other variables        | v_name, v_name[i]                                                                                                                                                                                                                                                                                                                                 |
-+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
++------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 
 Most of the formula elements produce a scalar value.  Some produce a
 global or per-atom vector of values.  Global vectors can be produced
 by computes or fixes or by other vector-style variables.  Per-atom
-vectors are produced by atom vectors, compute references that
+vectors are produced by atom vectors, computes or fixes which output a
-represent a per-atom vector, fix references that represent a per-atom
+per-atom vector or array, and variables that are atom-style variables.
-vector, and variables that are atom-style variables.  Math functions
+Math functions that operate on scalar values produce a scalar value;
-that operate on scalar values produce a scalar value; math function
+math function that operate on global or per-atom vectors do so
-that operate on global or per-atom vectors do so element-by-element
+element-by-element and produce a global or per-atom vector.
-and produce a global or per-atom vector.
 
 A formula for equal-style variables cannot use any formula element
 that produces a global or per-atom vector.  A formula for a
@@ -564,12 +566,13 @@ scalar value or a global vector value, but cannot use a formula
 element that produces a per-atom vector.  A formula for an atom-style
 variable can use formula elements that produce either a scalar value
 or a per-atom vector, but not one that produces a global vector.
+
 Atom-style variables are evaluated by other commands that define a
-:doc:`group <group>` on which they operate, e.g. a :doc:`dump <dump>` or
+:doc:`group <group>` on which they operate, e.g. a :doc:`dump <dump>`
-:doc:`compute <compute>` or :doc:`fix <fix>` command.  When they invoke
+or :doc:`compute <compute>` or :doc:`fix <fix>` command.  When they
-the atom-style variable, only atoms in the group are included in the
+invoke the atom-style variable, only atoms in the group are included
-formula evaluation.  The variable evaluates to 0.0 for atoms not in
+in the formula evaluation.  The variable evaluates to 0.0 for atoms
-the group.
+not in the group.
 
 ----------
 
@@ -703,6 +706,13 @@ library.  Ceil() is the smallest integer not less than its argument.
 Floor() if the largest integer not greater than its argument.  Round()
 is the nearest integer to its argument.
 
+.. versionadded:: TBD
+
+The ternary(x,y,z) function is the equivalent of the ternary operator
+(? and :) in C or C++.  It takes 3 arguments.  The first argument is a
+conditional.  The result of the function is y if x evaluates to true
+(non-zero).  The result is z if x evaluates to false (zero).
+
 The ramp(x,y) function uses the current timestep to generate a value
 linearly interpolated between the specified x,y values over the course
 of a run, according to this formula:
@@ -1034,10 +1044,9 @@ to built-in commands.  For all of these styles except *command*,
 appending of active suffixes is also tried before reporting failure.
 
 The *feature* category checks the availability of the following
-compile-time enabled features: GZIP support, PNG support, JPEG
+compile-time enabled features: GZIP support, PNG support, JPEG support,
-support, FFMPEG support, and C++ exceptions for error
+FFMPEG support, and C++ exceptions for error handling. Corresponding
-handling. Corresponding names are *gzip*, *png*, *jpeg*, *ffmpeg* and
+names are *gzip*, *png*, *jpeg*, *ffmpeg* and *exceptions*\ .
-*exceptions*\ .
 
 Example: Only dump in a given format if the compiled binary supports it.
 
@@ -1138,69 +1147,111 @@ only defined if an :doc:`atom_style <atom_style>` is being used that
 defines molecule IDs.
 
 Note that many other atom attributes can be used as inputs to a
-variable by using the :doc:`compute property/atom <compute_property_atom>` command and then specifying
+variable by using the :doc:`compute property/atom
-a quantity from that compute.
+<compute_property_atom>` command and then referencing that compute.
+
+----------
+
+Custom atom properties
+----------------------
+
+.. versionadded:: TBD
+
+Custom atom properties refer to per-atom integer and floating point
+vectors or arrays that have been added via the :doc:`fix property/atom
+<fix_property_atom>` command.  When that command is used specific
+names are given to each attribute which are the "name" portion of
+these references.  References beginning with *i* and *d* refer to
+integer and floating point properties respectively.  Per-atom vectors
+are referenced by *i_name* and *d_name*; per-atom arrays are
+referenced by *i2_name* and *d2_name*.
+
+The various allowed references to integer custom atom properties in
+the variable formulas for equal-, vector-, and atom-style variables
+are listed in the following table.  References to floating point
+custom atom properties are the same; just replace the leading "i" with
+"d".
+
++--------+---------------+------------------------------------------+
+| equal  | i_name[I]     | element of per-atom vector (I = atom ID) |
+| equal  | i2_name[I][J] | element of per-atom array (I = atom ID)  |
++--------+---------------+------------------------------------------+
+| vector | i_name[I]     | element of per-atom vector (I = atom ID) |
+| vector | i2_name[I][J] | element of per-atom array (I = atom ID)  |
++--------+---------------+------------------------------------------+
+| atom   | i_name        | per-atom vector                          |
+| atom   | i2_name[I]    | column of per-atom array                 |
++--------+---------------+------------------------------------------+
+
+The I and J indices in these custom atom property references can be
+integers or can be a variable name, specified as v_name, where name is
+the name of the variable.  The rules for this syntax are the same as
+for indices in the "Atom Values and Vectors" discussion above.
 
 ----------
 
 Compute References
 ------------------
 
-Compute references access quantities calculated by a
+Compute references access quantities calculated by a :doc:`compute
-:doc:`compute <compute>`.  The ID in the reference should be replaced by
+<compute>`.  The ID in the reference should be replaced by the ID of a
-the ID of a compute defined elsewhere in the input script.  As
+compute defined elsewhere in the input script.
-discussed in the page for the :doc:`compute <compute>` command,
-computes can produce global, per-atom, or local values.  Only global
-and per-atom values can be used in a variable.  Computes can also
-produce a scalar, vector, or array.
 
-An equal-style variable can only use scalar values, which means a
+As discussed on the page for the :doc:`compute <compute>` command,
-global scalar, or an element of a global or per-atom vector or array.
+computes can produce global, per-atom, local, and per-grid values.
-A vector-style variable can use scalar values or a global vector of
+Only global and per-atom values can be used in a variable.  Computes
-values, or a column of a global array of values.  Atom-style variables
+can also produce scalars (global only), vectors, and arrays.  See the
-can use global scalar values.  They can also use per-atom vector
+doc pages for individual computes to see what different kinds of data
-values, or a column of a per-atom array.  See the doc pages for
+they produce.
-individual computes to see what kind of values they produce.
 
-Examples of different kinds of compute references are as follows.
+An equal-style variable can only use scalar values, either from global
-There is typically no ambiguity (see exception below) as to what a
+or per-atom data.  In the case of per-atom data, this would be a value
-reference means, since computes only produce either global or per-atom
+for a specific atom.
-quantities, never both.
 
-+-------------+-------------------------------------------------------------------------------------------------------+
+A vector-style variable can use scalar values (same as for equal-style
-| c_ID       | global scalar, or per-atom vector                                                                      |
+variables), or global vectors of values.  The latter can also be a
-+-------------+-------------------------------------------------------------------------------------------------------+
+column of a global array.
-| c_ID[I]    | Ith element of global vector, or atom I's value in per-atom vector, or Ith column from per-atom array  |
-+-------------+-------------------------------------------------------------------------------------------------------+
-| c_ID[I][J] | I,J element of global array, or atom I's Jth value in per-atom array                                   |
-+-------------+-------------------------------------------------------------------------------------------------------+
 
-For I and J indices, integers can be specified or a variable name,
+Atom-style variables can use scalar values (same as for equal-style
-specified as v_name, where name is the name of the variable.  The
+variables), or per-atom vectors of values.  The latter can also be a
-rules for this syntax are the same as for the "Atom Values and
+column of a per-atom array.
-Vectors" discussion above.
 
-One source of ambiguity for compute references is when a vector-style
+The various allowed compute references in the variable formulas for
-variable refers to a compute that produces both a global scalar and a
+equal-, vector-, and atom-style variables are listed in the following
-global vector.  Consider a compute with ID "foo" that does this,
+table:
-referenced as follows by variable "a", where "myVec" is another
-vector-style variable:
 
-.. code-block:: LAMMPS
++--------+------------+------------------------------------------+
+| equal  | c_ID       | global scalar                            |
+| equal  | c_ID[I]    | element of global vector                 |
+| equal  | c_ID[I][J] | element of global array                  |
+| equal  | C_ID[I]    | element of per-atom vector (I = atom ID) |
+| equal  | C_ID[I][J] | element of per-atom array (I = atom ID)  |
++--------+------------+------------------------------------------+
+| vector | c_ID       | global vector                            |
+| vector | c_ID[I]    | column of global array                   |
++--------+------------+------------------------------------------+
+| atom   | c_ID       | per-atom vector                          |
+| atom   | c_ID[I]    | column of per-atom array                 |
++--------+------------+------------------------------------------+
 
-   variable a vector c_foo*v_myVec
+Note that if an equal-style variable formula wishes to access per-atom
+data from a compute, it must use capital "C" as the ID prefix and not
+lower-case "c".
 
-The reference "c_foo" could refer to either the global scalar or
+Also note that if a vector- or atom-style variable formula needs to
-global vector produced by compute "foo".  In this case, "c_foo" will
+access a scalar value from a compute (i.e. the 5 kinds of values in
-always refer to the global scalar, and "C_foo" can be used to
+the first 5 lines of the table), it can not do so directly.  Instead,
-reference the global vector.  Similarly if the compute produces both a
+it can use a reference to an equal-style variable which stores the
-global vector and global array, then "c_foo[I]" will always refer to
+scalar value from the compute.
-an element of the global vector, and "C_foo[I]" can be used to
-reference the Ith column of the global array.
 
-Note that if a variable containing a compute is evaluated directly in
+The I and J indices in these compute references can be integers or can
-an input script (not during a run), then the values accessed by the
+be a variable name, specified as v_name, where name is the name of the
-compute must be current.  See the discussion below about "Variable
+variable.  The rules for this syntax are the same as for indices in
+the "Atom Values and Vectors" discussion above.
+
+If a variable containing a compute is evaluated directly in an input
+script (not during a run), then the values accessed by the compute
+should be current.  See the discussion below about "Variable
 Accuracy".
 
 ----------
@@ -1208,51 +1259,59 @@ Accuracy".
 Fix References
 --------------
 
-Fix references access quantities calculated by a :doc:`fix <compute>`.
+Fix references access quantities calculated by a :doc:`fix <fix>`.
 The ID in the reference should be replaced by the ID of a fix defined
-elsewhere in the input script.  As discussed in the page for the
+elsewhere in the input script.
-:doc:`fix <fix>` command, fixes can produce global, per-atom, or local
-values.  Only global and per-atom values can be used in a variable.
-Fixes can also produce a scalar, vector, or array.  An equal-style
-variable can only use scalar values, which means a global scalar, or
-an element of a global or per-atom vector or array.  Atom-style
-variables can use the same scalar values.  They can also use per-atom
-vector values.  A vector value can be a per-atom vector itself, or a
-column of an per-atom array.  See the doc pages for individual fixes
-to see what kind of values they produce.
 
-The different kinds of fix references are exactly the same as the
+As discussed on the page for the :doc:`fix <fix>` command, fixes can
-compute references listed in the above table, where "c\_" is replaced
+produce global, per-atom, local, and per-grid values.  Only global and
-by "f\_".  Again, there is typically no ambiguity (see exception below)
+per-atom values can be used in a variable.  Fixes can also produce
-as to what a reference means, since fixes only produce either global
+scalars (global only), vectors, and arrays.  See the doc pages for
-or per-atom quantities, never both.
+individual fixes to see what different kinds of data they produce.
 
-+-------------+-------------------------------------------------------------------------------------------------------+
+An equal-style variable can only use scalar values, either from global
-| f_ID       | global scalar, or per-atom vector                                                                      |
+or per-atom data.  In the case of per-atom data, this would be a value
-+-------------+-------------------------------------------------------------------------------------------------------+
+for a specific atom.
-| f_ID[I]    | Ith element of global vector, or atom I's value in per-atom vector, or Ith column from per-atom array  |
-+-------------+-------------------------------------------------------------------------------------------------------+
-| f_ID[I][J] | I,J element of global array, or atom I's Jth value in per-atom array                                   |
-+-------------+-------------------------------------------------------------------------------------------------------+
 
-For I and J indices, integers can be specified or a variable name,
+A vector-style variable can use scalar values (same as for equal-style
-specified as v_name, where name is the name of the variable.  The
+variables), or global vectors of values.  The latter can also be a
-rules for this syntax are the same as for the "Atom Values and
+column of a global array.
-Vectors" discussion above.
 
-One source of ambiguity for fix references is the same ambiguity
+Atom-style variables can use scalar values (same as for equal-style
-discussed for compute references above.  Namely when a vector-style
+variables), or per-atom vectors of values.  The latter can also be a
-variable refers to a fix that produces both a global scalar and a
+column of a per-atom array.
-global vector.  The solution is the same as for compute references.
-For a fix with ID "foo", "f_foo" will always refer to the global
-scalar, and "F_foo" can be used to reference the global vector.  And
-similarly for distinguishing between a fix's global vector versus
-global array with "f_foo[I]" versus "F_foo[I]".
 
-Note that if a variable containing a fix is evaluated directly in an
+The allowed fix references in variable formulas for equal-, vector-,
-input script (not during a run), then the values accessed by the fix
+and atom-style variables are listed in the following table:
-should be current.  See the discussion below about "Variable
+
-Accuracy".
++--------+------------+------------------------------------------+
+| equal  | f_ID       | global scalar                            |
+| equal  | f_ID[I]    | element of global vector                 |
+| equal  | f_ID[I][J] | element of global array                  |
+| equal  | F_ID[I]    | element of per-atom vector (I = atom ID) |
+| equal  | F_ID[I][J] | element of per-atom array (I = atom ID)  |
++--------+------------+------------------------------------------+
+| vector | f_ID       | global vector                            |
+| vector | f_ID[I]    | column of global array                   |
++--------+------------+------------------------------------------+
+| atom   | f_ID       | per-atom vector                          |
+| atom   | f_ID[I]    | column of per-atom array                 |
++--------+------------+------------------------------------------+
+
+Note that if an equal-style variable formula wishes to access per-atom
+data from a fix, it must use capital "F" as the ID prefix and not
+lower-case "f".
+
+Also note that if a vector- or atom-style variable formula needs to
+access a scalar value from a fix (i.e. the 5 kinds of values in the
+first 5 lines of the table), it can not do so directly.  Instead, it
+can use a reference to an equal-style variable which stores the scalar
+value from the fix.
+
+The I and J indices in these fix references can be integers or can be
+a variable name, specified as v_name, where name is the name of the
+variable.  The rules for this syntax are the same as for indices in
+the "Atom Values and Vectors" discussion above.
 
 Note that some fixes only generate quantities on certain timesteps.
 If a variable attempts to access the fix on non-allowed timesteps, an
@@ -1260,6 +1319,10 @@ error is generated.  For example, the :doc:`fix ave/time <fix_ave_time>`
 command may only generate averaged quantities every 100 steps.  See
 the doc pages for individual fix commands for details.
 
+If a variable containing a fix is evaluated directly in an input
+script (not during a run), then the values accessed by the fix should
+be current.  See the discussion below about "Variable Accuracy".
+
 ----------
 
 Variable References
@@ -1294,26 +1357,32 @@ including other atom-style or atomfile-style variables.  If it uses a
 vector-style variable, a subscript must be used to access a single
 value from the vector-style variable.
 
-Examples of different kinds of variable references are as follows.
+The allowed variable references in variable formulas for equal-,
-There is no ambiguity as to what a reference means, since variables
+vector-, and atom-style variables are listed in the following table.
-produce only a global scalar or global vector or per-atom vector.
+Note that there is no ambiguity as to what a reference means, since
+referenced variables produce only a global scalar or global vector or
+per-atom vector.
 
-+------------+----------------------------------------------------------------------+
++--------+-----------+-----------------------------------------------------------------------------------+
-| v_name    | global scalar from equal-style variable                               |
+| equal  | v_name    | global scalar from an equal-style variable                                        |
-+------------+----------------------------------------------------------------------+
+| equal  | v_name[I] | element of global vector from a vector-style variable                             |
-| v_name    | global vector from vector-style variable                              |
+| equal  | v_name[I] | element of per-atom vector (I = atom ID) from an atom- or atomfile-style variable |
-+------------+----------------------------------------------------------------------+
++--------+-----------+-----------------------------------------------------------------------------------+
-| v_name    | per-atom vector from atom-style or atomfile-style variable            |
+| vector | v_name    | global scalar from an equal-style variable                                        |
-+------------+----------------------------------------------------------------------+
+| vector | v_name    | global vector from a vector-style variable                                        |
-| v_name[I] | Ith element of a global vector from vector-style variable             |
+| vector | v_name[I] | element of global vector from a vector-style variable                             |
-+------------+----------------------------------------------------------------------+
+| vector | v_name[I] | element of per-atom vector (I = atom ID) from an atom- or atomfile-style variable |
-| v_name[I] | value of atom with ID = I from atom-style or atomfile-style variable  |
++--------+-----------+-----------------------------------------------------------------------------------+
-+------------+----------------------------------------------------------------------+
+| atom   | v_name    | global scalar from an equal-style variable                                        |
+| atom   | v_name    | per-atom vector from an atom-style or atomfile-style variable                     |
+| atom   | v_name[I] | element of global vector from a vector-style variable                             |
+| atom   | v_name[I] | element of per-atom vector (I = atom ID) from an atom- or atomfile-style variable |
++--------+-----------+-----------------------------------------------------------------------------------+
 
 For the I index, an integer can be specified or a variable name,
 specified as v_name, where name is the name of the variable.  The
-rules for this syntax are the same as for the "Atom Values and
+rules for this syntax are the same as for indices in the "Atom Values
-Vectors" discussion above.
+and Vectors" discussion above.
 
 ----------
 

doc/utils/sphinx-config/LAMMPSLexer.py

@@ -76,12 +76,12 @@ class LAMMPSLexer(RegexLexer):
             include('conditionals'),
             include('keywords'),
             (r'#.*?\n', Comment),
-            ('"', String, 'string'),
+            (r'"', String, 'string'),
-            ('\'', String, 'single_quote_string'),
+            (r'\'', String, 'single_quote_string'),
             (r'[0-9]+:[0-9]+(:[0-9]+)?', Number),
             (r'[0-9]+(\.[0-9]+)?([eE]\-?[0-9]+)?', Number),
-            ('\$?\(', Name.Variable, 'expression'),
+            (r'\$?\(', Name.Variable, 'expression'),
-            ('\$\{', Name.Variable, 'variable'),
+            (r'\$\{', Name.Variable, 'variable'),
             (r'[\w_\.\[\]]+', Name),
             (r'\$[\w_]+', Name.Variable),
             (r'\s+', Whitespace),
@@ -97,21 +97,21 @@ class LAMMPSLexer(RegexLexer):
         ]
         ,
         'variable' : [
-            ('[^\}]+', Name.Variable),
+            (r'[^\}]+', Name.Variable),
-            ('\}', Name.Variable, '#pop'),
+            (r'\}', Name.Variable, '#pop'),
         ],
         'string' : [
-            ('[^"]+', String),
+            (r'[^"]+', String),
-            ('"', String, '#pop'),
+            (r'"', String, '#pop'),
         ],
         'single_quote_string' : [
-            ('[^\']+', String),
+            (r'[^\']+', String),
-            ('\'', String, '#pop'),
+            (r'\'', String, '#pop'),
         ],
         'expression' : [
-            ('[^\(\)]+', Name.Variable),
+            (r'[^\(\)]+', Name.Variable),
-            ('\(', Name.Variable, 'expression'),
+            (r'\(', Name.Variable, 'expression'),
-            ('\)', Name.Variable, '#pop'),
+            (r'\)', Name.Variable, '#pop'),
         ],
         'modify_cmd' : [
             (r'[\w_\-\.\[\]]+', Name.Variable.Identifier),

doc/utils/sphinx-config/false_positives.txt

@@ -2892,6 +2892,7 @@ pscrozi
 pseudocode
 Pseudocode
 pseudodynamics
+pseudoparticle
 pseudopotential
 psllod
 pSp
@@ -3755,6 +3756,7 @@ uncomment
 uncommented
 uncompress
 uncompute
+underdamped
 underprediction
 undump
 uniaxial

examples/PACKAGES/pimd/langevin_metal_units/in.langevin.metal

@@ -0,0 +1,28 @@
+variable ibead uloop 99 pad
+
+units metal
+atom_style atomic
+atom_modify map yes
+boundary p p p
+pair_style lj/cut 9.5251
+read_data data.metalnpt${ibead}
+
+pair_coeff    * * 0.00965188 3.4
+pair_modify shift yes
+
+mass 1 39.948
+
+timestep 0.001
+
+velocity all create 0.0 ${ibead}
+
+fix 1 all pimd/langevin method nmpimd ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
+
+thermo_style custom step temp f_1[*] vol press
+thermo 100
+thermo_modify norm no
+
+# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz
+# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
+
+run 1000

examples/PACKAGES/pimd/langevin_metal_units/in.pimd-langevin.metal

@@ -16,7 +16,7 @@ timestep 0.001
 
 velocity all create 0.0 ${ibead}
 
-fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
+fix 1 all pimd/langevin method pimd ensemble nvt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 taup 1.0 fixcom no
 
 thermo_style custom step temp f_1[*] vol press
 thermo 100

examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++

@@ -1,2 +1,2 @@
-LAMMPS (28 Mar 2023)
+LAMMPS (3 Aug 2023)
 Running on 4 partitions of processors

examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++.0

@@ -1,5 +1,6 @@
-LAMMPS (28 Mar 2023)
+LAMMPS (3 Aug 2023)
 Processor partition = 0
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
   using 1 OpenMP thread(s) per MPI task
 variable ibead uloop 99 pad
 
@@ -29,7 +30,7 @@ timestep 0.001
 velocity all create 0.0 ${ibead}
 velocity all create 0.0 01
 
-fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
+fix 1 all pimd/langevin method nmpimd ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
 
 Initializing PIMD BZP barostat...
   The barostat mass is W = 2.3401256650800001e+01
@@ -43,7 +44,6 @@ thermo_modify norm no
 
 run 1000
 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
-
 Initializing PI Langevin equation thermostat...
   Bead ID    |    omega    |    tau    |    c1    |    c2
       0     0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02
@@ -66,31 +66,31 @@ Neighbor list info ...
       bin: standard
 Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
    Step          Temp          f_1[1]         f_1[2]         f_1[3]         f_1[4]         f_1[5]         f_1[6]         f_1[7]         f_1[8]         f_1[9]        f_1[10]        f_1[11]        f_1[12]        f_1[13]        f_1[14]        f_1[15]         Volume         Press     
-         0   0              0              0             -7.3046601      4.3005229     -21.877018     -8.7249482      2.9571502     -1743.5332     -698.49808     -172.07477      0              0              0.033460054   -0.37064378     4.216227       13402.228     -164.47373    
+         0   0              0              0             -7.3046601      4.3005229      3.3062167     -8.7249482      2.9571502     -1743.5332     -698.49808     -172.07477      0              0              0.033460054   -0.37064378     4.216227       13402.228     -164.47373    
-       100   149.95804      3.8573359      0             -7.7921375      42.886648     -23.396327     -1.980193       2.954003      -1888.0547     -1648.7118     -332.0298      -0.099139345    0.11500091     0.033044702   -0.3701566      42.83112       13235.861     -101.30374    
+       100   149.95804      3.8573359      0             -7.7921375      42.886648      2.9263894     -1.980193       2.954003      -1888.0547     -1648.7118     -332.0298      -0.099139345    0.11500091     0.033044702   -0.3701566      42.83112       13235.861     -101.30374    
-       200   245.00113      6.3021074      0             -8.2639651      41.690123     -22.521598     -4.273021       2.9600599     -1906.2904     -1609.02       -265.94404     -0.20527926     0.49305948     0.031504957   -0.36829556     41.729191      12619.125      112.22426    
+       200   245.00113      6.3021074      0             -8.2639651      41.690123      3.1450717     -4.273021       2.9600599     -1906.2904     -1609.02       -265.94404     -0.20527926     0.49305948     0.031504957   -0.36829556     41.729191      12619.125      112.22426    
-       300   300.57486      7.7316177      0             -8.2986331      43.180131     -21.755813     -7.7032433      2.9714114     -1968.7685      290.49656      251.72564     -0.21935745     0.56300721     0.029467915   -0.36568855     43.236828      11803.2        814.45889    
+       300   300.57486      7.7316177      0             -8.2986331      43.180131      3.336518      -7.7032433      2.9714114     -1968.7685      290.49656      251.72564     -0.21935745     0.56300721     0.029467915   -0.36568855     43.236828      11803.2        814.45889    
-       400   368.08438      9.4681493      0             -8.4800193      49.109699     -24.824142      2.9744597      2.9794185     -2335.993       1368.7398      570.03286     -0.028366234    0.0094148316   0.028338146   -0.36416383     49.028096      11350.678      1202.0398    
+       400   368.08438      9.4681493      0             -8.4800193      49.109699      2.5694358      2.9744597      2.9794185     -2335.993       1368.7398      570.03286     -0.028366234    0.0094148316   0.028338146   -0.36416383     49.028096      11350.678      1202.0398    
-       500   419.32066      10.786088      0             -8.640773       45.427771     -22.825143      16.22356       2.9684828     -2113.91       -272.84753      185.53392      0.091614289    0.098205455    0.028793585   -0.36478567     45.368325      11533.101      952.59748    
+       500   419.32066      10.786088      0             -8.640773       45.427771      3.0691855      16.22356       2.9684828     -2113.91       -272.84753      185.53392      0.091614289    0.098205455    0.028793585   -0.36478567     45.368325      11533.101      952.59748    
-       600   385.4127       9.9138817      0             -8.4356035      47.783726     -22.456104      6.837575       2.967236      -2023.8117     -918.27943     -2.4106994      0.093360761    0.10198539     0.029589188   -0.36584873     47.725157      11851.775      676.62913    
+       600   385.4127       9.9138817      0             -8.4356035      47.783726      3.1614452      6.837575       2.967236      -2023.8117     -918.27943     -2.4106994      0.093360761    0.10198539     0.029589188   -0.36584873     47.725157      11851.775      676.62913    
-       700   360.14242      9.2638601      0             -8.2900275      42.626187     -20.571698     -5.7252564      2.9560528     -1806.9448     -1418.2247     -148.41657      0.075011202    0.065835696    0.030359455   -0.36685105     42.558523      12160.301      456.91446    
+       700   360.14242      9.2638601      0             -8.2900275      42.626187      3.6325468     -5.7252564      2.9560528     -1806.9448     -1418.2247     -148.41657      0.075011202    0.065835696    0.030359455   -0.36685105     42.558523      12160.301      456.91446    
-       800   346.92167      8.923786       0             -8.0694169      45.160336     -21.885719     -6.7745694      2.9575472     -1894.3641     -1329.3179     -136.42193      0.011114896    0.0014455064   0.030808183   -0.3674233      45.076543      12340.037      454.60123    
+       800   346.92167      8.923786       0             -8.0694169      45.160336      3.3040415     -6.7745694      2.9575472     -1894.3641     -1329.3179     -136.42193      0.011114896    0.0014455064   0.030808183   -0.3674233      45.076543      12340.037      454.60123    
-       900   364.39442      9.3732334      0             -8.0415668      45.604542     -21.816625      5.586068       2.9578604     -1890.4653     -1271.1107     -111.89061     -0.020285587    0.0048148677   0.030774258   -0.36738033     45.521594      12326.448      499.75868    
+       900   364.39442      9.3732334      0             -8.0415668      45.604542      3.321315       5.586068       2.9578604     -1890.4653     -1271.1107     -111.89061     -0.020285587    0.0048148677   0.030774258   -0.36738033     45.521594      12326.448      499.75868    
-      1000   390.77042      10.051697      0             -8.1948009      45.264242     -22.833545      6.9260573      2.960122      -2007.6188     -1179.7125     -70.907567     -0.062733519    0.046047757    0.030329191   -0.36681215     45.191633      12148.179      572.98799    
+      1000   390.77042      10.051697      0             -8.1948009      45.264242      3.0670849      6.9260573      2.960122      -2007.6188     -1179.7125     -70.907567     -0.062733519    0.046047757    0.030329191   -0.36681215     45.191633      12148.179      572.98799    
-Loop time of 0.248186 on 1 procs for 1000 steps with 200 atoms
+Loop time of 0.218442 on 1 procs for 1000 steps with 200 atoms
 
-Performance: 348.126 ns/day, 0.069 hours/ns, 4029.238 timesteps/s, 805.848 katom-step/s
+Performance: 395.527 ns/day, 0.061 hours/ns, 4577.865 timesteps/s, 915.573 katom-step/s
-99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.14541    | 0.14541    | 0.14541    |   0.0 | 58.59
+Pair    | 0.11918    | 0.11918    | 0.11918    |   0.0 | 54.56
-Neigh   | 0.00099082 | 0.00099082 | 0.00099082 |   0.0 |  0.40
+Neigh   | 0.0010314  | 0.0010314  | 0.0010314  |   0.0 |  0.47
-Comm    | 0.0039966  | 0.0039966  | 0.0039966  |   0.0 |  1.61
+Comm    | 0.0046197  | 0.0046197  | 0.0046197  |   0.0 |  2.11
-Output  | 0.00016346 | 0.00016346 | 0.00016346 |   0.0 |  0.07
+Output  | 0.0001329  | 0.0001329  | 0.0001329  |   0.0 |  0.06
-Modify  | 0.096205   | 0.096205   | 0.096205   |   0.0 | 38.76
+Modify  | 0.092616   | 0.092616   | 0.092616   |   0.0 | 42.40
-Other   |            | 0.001425   |            |       |  0.57
+Other   |            | 0.0008616  |            |       |  0.39
 
 Nlocal:            200 ave         200 max         200 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++.1

@@ -1,5 +1,6 @@
-LAMMPS (28 Mar 2023)
+LAMMPS (3 Aug 2023)
 Processor partition = 1
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
   using 1 OpenMP thread(s) per MPI task
 variable ibead uloop 99 pad
 
@@ -17,7 +18,7 @@ Reading data file ...
   200 atoms
   reading velocities ...
   200 velocities
-  read_data CPU = 0.001 seconds
+  read_data CPU = 0.002 seconds
 
 pair_coeff    * * 0.00965188 3.4
 pair_modify shift yes
@@ -29,10 +30,7 @@ timestep 0.001
 velocity all create 0.0 ${ibead}
 velocity all create 0.0 02
 
-fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
+fix 1 all pimd/langevin method nmpimd ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
-
-Initializing PIMD BZP barostat...
-The barostat mass is W = 2.3401256650800001e+01
 
 thermo_style custom step temp f_1[*] vol press
 thermo 100
@@ -43,15 +41,6 @@ thermo_modify norm no
 
 run 1000
 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
-
-Initializing PI Langevin equation thermostat...
-Bead ID    |    omega    |    tau    |    c1    |    c2
-    0     0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02
-    1     8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
-    2     1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01
-    3     8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
-PILE_L thermostat successfully initialized!
-
 Neighbor list info ...
   update: every = 1 steps, delay = 0 steps, check = yes
   max neighbors/atom: 2000, page size: 100000
@@ -66,31 +55,31 @@ Neighbor list info ...
       bin: standard
 Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
    Step          Temp          f_1[1]         f_1[2]         f_1[3]         f_1[4]         f_1[5]         f_1[6]         f_1[7]         f_1[8]         f_1[9]        f_1[10]        f_1[11]        f_1[12]        f_1[13]        f_1[14]        f_1[15]         Volume         Press     
-         0   0              0              11.920908     -7.3063682      4.3005229     -21.877018     -8.7249482      2.9571502     -1743.5332     -698.49808     -172.07477      0              0              0.033460054   -0.37064378     4.216227       13402.228     -167.65544    
+         0   0              0              11.920908     -7.3063682      4.3005229      3.3062167     -8.7249482      2.9571502     -1743.5332     -698.49808     -172.07477      0              0              0.033460054   -0.37064378     4.216227       13402.228     -167.65544    
-       100   483.61933      12.440028      11.405863     -7.7749671      42.886648     -23.396327     -1.980193       2.954003      -1888.0547     -1648.7118     -332.0298      -0.099139345    0.11500091     0.033044702   -0.3701566      42.83112       13235.861      606.14668    
+       100   483.61933      12.440028      11.405863     -7.7749671      42.886648      2.9263894     -1.980193       2.954003      -1888.0547     -1648.7118     -332.0298      -0.099139345    0.11500091     0.033044702   -0.3701566      42.83112       13235.861      606.14668    
-       200   452.03836      11.627678      11.47094      -8.2534927      41.690123     -22.521598     -4.273021       2.9600599     -1906.2904     -1609.02       -265.94404     -0.20527926     0.49305948     0.031504957   -0.36829556     41.729191      12619.125      583.5476     
+       200   452.03836      11.627678      11.47094      -8.2534927      41.690123      3.1450717     -4.273021       2.9600599     -1906.2904     -1609.02       -265.94404     -0.20527926     0.49305948     0.031504957   -0.36829556     41.729191      12619.125      583.5476     
-       300   470.25997      12.096389      11.739306     -8.3750153      43.180131     -21.755813     -7.7032433      2.9714114     -1968.7685      290.49656      251.72564     -0.21935745     0.56300721     0.029467915   -0.36568855     43.236828      11803.2        1152.6851    
+       300   470.25997      12.096389      11.739306     -8.3750153      43.180131      3.336518      -7.7032433      2.9714114     -1968.7685      290.49656      251.72564     -0.21935745     0.56300721     0.029467915   -0.36568855     43.236828      11803.2        1152.6851    
-       400   459.46597      11.818737      12.502421     -8.5240576      49.109699     -24.824142      2.9744597      2.9794185     -2335.993       1368.7398      570.03286     -0.028366234    0.0094148316   0.028338146   -0.36416383     49.028096      11350.678      1381.0251    
+       400   459.46597      11.818737      12.502421     -8.5240576      49.109699      2.5694358      2.9744597      2.9794185     -2335.993       1368.7398      570.03286     -0.028366234    0.0094148316   0.028338146   -0.36416383     49.028096      11350.678      1381.0251    
-       500   442.73121      11.388273      11.19396      -8.6488583      45.427771     -22.825143      16.22356       2.9684828     -2113.91       -272.84753      185.53392      0.091614289    0.098205455    0.028793585   -0.36478567     45.368325      11533.101      1000.6119    
+       500   442.73121      11.388273      11.19396      -8.6488583      45.427771      3.0691855      16.22356       2.9684828     -2113.91       -272.84753      185.53392      0.091614289    0.098205455    0.028793585   -0.36478567     45.368325      11533.101      1000.6119    
-       600   493.47034      12.693424      11.91335      -8.4625706      47.783726     -22.456104      6.837575       2.967236      -2023.8117     -918.27943     -2.4106994      0.093360761    0.10198539     0.029589188   -0.36584873     47.725157      11851.775      904.52944    
+       600   493.47034      12.693424      11.91335      -8.4625706      47.783726      3.1614452      6.837575       2.967236      -2023.8117     -918.27943     -2.4106994      0.093360761    0.10198539     0.029589188   -0.36584873     47.725157      11851.775      904.52944    
-       700   470.04548      12.090871      10.348757     -8.278182       42.626187     -20.571698     -5.7252564      2.9560528     -1806.9448     -1418.2247     -148.41657      0.075011202    0.065835696    0.030359455   -0.36685105     42.558523      12160.301      715.22796    
+       700   470.04548      12.090871      10.348757     -8.278182       42.626187      3.6325468     -5.7252564      2.9560528     -1806.9448     -1418.2247     -148.41657      0.075011202    0.065835696    0.030359455   -0.36685105     42.558523      12160.301      715.22796    
-       800   458.04928      11.782296      11.152029     -8.0926613      45.160336     -21.885719     -6.7745694      2.9575472     -1894.3641     -1329.3179     -136.42193      0.011114896    0.0014455064   0.030808183   -0.3674233      45.076543      12340.037      678.21261    
+       800   458.04928      11.782296      11.152029     -8.0926613      45.160336      3.3040415     -6.7745694      2.9575472     -1894.3641     -1329.3179     -136.42193      0.011114896    0.0014455064   0.030808183   -0.3674233      45.076543      12340.037      678.21261    
-       900   468.60547      12.05383       10.937315     -8.0319335      45.604542     -21.816625      5.586068       2.9578604     -1890.4653     -1271.1107     -111.89061     -0.020285587    0.0048148677   0.030774258   -0.36738033     45.521594      12326.448      735.24377    
+       900   468.60547      12.05383       10.937315     -8.0319335      45.604542      3.321315       5.586068       2.9578604     -1890.4653     -1271.1107     -111.89061     -0.020285587    0.0048148677   0.030774258   -0.36738033     45.521594      12326.448      735.24377    
-      1000   427.44192      10.99499       11.916587     -8.2229199      45.264242     -22.833545      6.9260573      2.960122      -2007.6188     -1179.7125     -70.907567     -0.062733519    0.046047757    0.030329191   -0.36681215     45.191633      12148.179      637.98311    
+      1000   427.44192      10.99499       11.916587     -8.2229199      45.264242      3.0670849      6.9260573      2.960122      -2007.6188     -1179.7125     -70.907567     -0.062733519    0.046047757    0.030329191   -0.36681215     45.191633      12148.179      637.98311    
-Loop time of 0.248186 on 1 procs for 1000 steps with 200 atoms
+Loop time of 0.218435 on 1 procs for 1000 steps with 200 atoms
 
-Performance: 348.126 ns/day, 0.069 hours/ns, 4029.238 timesteps/s, 805.848 katom-step/s
+Performance: 395.541 ns/day, 0.061 hours/ns, 4578.021 timesteps/s, 915.604 katom-step/s
-99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.14654    | 0.14654    | 0.14654    |   0.0 | 59.04
+Pair    | 0.11791    | 0.11791    | 0.11791    |   0.0 | 53.98
-Neigh   | 0.00099986 | 0.00099986 | 0.00099986 |   0.0 |  0.40
+Neigh   | 0.0010247  | 0.0010247  | 0.0010247  |   0.0 |  0.47
-Comm    | 0.0041628  | 0.0041628  | 0.0041628  |   0.0 |  1.68
+Comm    | 0.0035577  | 0.0035577  | 0.0035577  |   0.0 |  1.63
-Output  | 0.00018019 | 0.00018019 | 0.00018019 |   0.0 |  0.07
+Output  | 0.00011003 | 0.00011003 | 0.00011003 |   0.0 |  0.05
-Modify  | 0.094878   | 0.094878   | 0.094878   |   0.0 | 38.23
+Modify  | 0.09496    | 0.09496    | 0.09496    |   0.0 | 43.47
-Other   |            | 0.001424   |            |       |  0.57
+Other   |            | 0.0008711  |            |       |  0.40
 
 Nlocal:            200 ave         200 max         200 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++.2

@@ -1,5 +1,6 @@
-LAMMPS (28 Mar 2023)
+LAMMPS (3 Aug 2023)
 Processor partition = 2
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
   using 1 OpenMP thread(s) per MPI task
 variable ibead uloop 99 pad
 
@@ -17,7 +18,7 @@ Reading data file ...
   200 atoms
   reading velocities ...
   200 velocities
-  read_data CPU = 0.001 seconds
+  read_data CPU = 0.002 seconds
 
 pair_coeff    * * 0.00965188 3.4
 pair_modify shift yes
@@ -29,10 +30,7 @@ timestep 0.001
 velocity all create 0.0 ${ibead}
 velocity all create 0.0 03
 
-fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
+fix 1 all pimd/langevin method nmpimd ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
-
-Initializing PIMD BZP barostat...
-The barostat mass is W = 2.3401256650800001e+01
 
 thermo_style custom step temp f_1[*] vol press
 thermo 100
@@ -43,15 +41,6 @@ thermo_modify norm no
 
 run 1000
 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
-
-Initializing PI Langevin equation thermostat...
-Bead ID    |    omega    |    tau    |    c1    |    c2
-    0     0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02
-    1     8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
-    2     1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01
-    3     8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
-PILE_L thermostat successfully initialized!
-
 Neighbor list info ...
   update: every = 1 steps, delay = 0 steps, check = yes
   max neighbors/atom: 2000, page size: 100000
@@ -66,31 +55,31 @@ Neighbor list info ...
       bin: standard
 Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
    Step          Temp          f_1[1]         f_1[2]         f_1[3]         f_1[4]         f_1[5]         f_1[6]         f_1[7]         f_1[8]         f_1[9]        f_1[10]        f_1[11]        f_1[12]        f_1[13]        f_1[14]        f_1[15]         Volume         Press     
-         0   0              0              10.862314     -7.320388       4.3005229     -21.877018     -8.7249482      2.9571502     -1743.5332     -698.49808     -172.07477      0              0              0.033460054   -0.37064378     4.216227       13402.228     -175.34503    
+         0   0              0              10.862314     -7.320388       4.3005229      3.3062167     -8.7249482      2.9571502     -1743.5332     -698.49808     -172.07477      0              0              0.033460054   -0.37064378     4.216227       13402.228     -175.34503    
-       100   455.18121      11.708521      11.48472      -7.8033686      42.886648     -23.396327     -1.980193       2.954003      -1888.0547     -1648.7118     -332.0298      -0.099139345    0.11500091     0.033044702   -0.3701566      42.83112       13235.861      526.41632    
+       100   455.18121      11.708521      11.48472      -7.8033686      42.886648      2.9263894     -1.980193       2.954003      -1888.0547     -1648.7118     -332.0298      -0.099139345    0.11500091     0.033044702   -0.3701566      42.83112       13235.861      526.41632    
-       200   460.81997      11.853566      10.817157     -8.2276485      41.690123     -22.521598     -4.273021       2.9600599     -1906.2904     -1609.02       -265.94404     -0.20527926     0.49305948     0.031504957   -0.36829556     41.729191      12619.125      615.80924    
+       200   460.81997      11.853566      10.817157     -8.2276485      41.690123      3.1450717     -4.273021       2.9600599     -1906.2904     -1609.02       -265.94404     -0.20527926     0.49305948     0.031504957   -0.36829556     41.729191      12619.125      615.80924    
-       300   481.48652      12.385166      10.035423     -8.3866916      43.180131     -21.755813     -7.7032433      2.9714114     -1968.7685      290.49656      251.72564     -0.21935745     0.56300721     0.029467915   -0.36568855     43.236828      11803.2        1169.2917    
+       300   481.48652      12.385166      10.035423     -8.3866916      43.180131      3.336518      -7.7032433      2.9714114     -1968.7685      290.49656      251.72564     -0.21935745     0.56300721     0.029467915   -0.36568855     43.236828      11803.2        1169.2917    
-       400   487.3584       12.536208      11.766522     -8.3643382      49.109699     -24.824142      2.9744597      2.9794185     -2335.993       1368.7398      570.03286     -0.028366234    0.0094148316   0.028338146   -0.36416383     49.028096      11350.678      1574.1427    
+       400   487.3584       12.536208      11.766522     -8.3643382      49.109699      2.5694358      2.9744597      2.9794185     -2335.993       1368.7398      570.03286     -0.028366234    0.0094148316   0.028338146   -0.36416383     49.028096      11350.678      1574.1427    
-       500   446.36019      11.48162       12.144202     -8.680266       45.427771     -22.825143      16.22356       2.9684828     -2113.91       -272.84753      185.53392      0.091614289    0.098205455    0.028793585   -0.36478567     45.368325      11533.101      979.68395    
+       500   446.36019      11.48162       12.144202     -8.680266       45.427771      3.0691855      16.22356       2.9684828     -2113.91       -272.84753      185.53392      0.091614289    0.098205455    0.028793585   -0.36478567     45.368325      11533.101      979.68395    
-       600   500.3783       12.871115      11.075008     -8.47833        47.783726     -22.456104      6.837575       2.967236      -2023.8117     -918.27943     -2.4106994      0.093360761    0.10198539     0.029589188   -0.36584873     47.725157      11851.775      912.39361    
+       600   500.3783       12.871115      11.075008     -8.47833        47.783726      3.1614452      6.837575       2.967236      -2023.8117     -918.27943     -2.4106994      0.093360761    0.10198539     0.029589188   -0.36584873     47.725157      11851.775      912.39361    
-       700   435.40634      11.199857      10.923558     -8.3090105      42.626187     -20.571698     -5.7252564      2.9560528     -1806.9448     -1418.2247     -148.41657      0.075011202    0.065835696    0.030359455   -0.36685105     42.558523      12160.301      617.20857    
+       700   435.40634      11.199857      10.923558     -8.3090105      42.626187      3.6325468     -5.7252564      2.9560528     -1806.9448     -1418.2247     -148.41657      0.075011202    0.065835696    0.030359455   -0.36685105     42.558523      12160.301      617.20857    
-       800   446.82793      11.493652      11.599712     -8.0900498      45.160336     -21.885719     -6.7745694      2.9575472     -1894.3641     -1329.3179     -136.42193      0.011114896    0.0014455064   0.030808183   -0.3674233      45.076543      12340.037      652.13243    
+       800   446.82793      11.493652      11.599712     -8.0900498      45.160336      3.3040415     -6.7745694      2.9575472     -1894.3641     -1329.3179     -136.42193      0.011114896    0.0014455064   0.030808183   -0.3674233      45.076543      12340.037      652.13243    
-       900   448.28506      11.531133      12.130739     -8.0810557      45.604542     -21.816625      5.586068       2.9578604     -1890.4653     -1271.1107     -111.89061     -0.020285587    0.0048148677   0.030774258   -0.36738033     45.521594      12326.448      674.68073    
+       900   448.28506      11.531133      12.130739     -8.0810557      45.604542      3.321315       5.586068       2.9578604     -1890.4653     -1271.1107     -111.89061     -0.020285587    0.0048148677   0.030774258   -0.36738033     45.521594      12326.448      674.68073    
-      1000   440.94913      11.342433      10.765654     -8.1419484      45.264242     -22.833545      6.9260573      2.960122      -2007.6188     -1179.7125     -70.907567     -0.062733519    0.046047757    0.030329191   -0.36681215     45.191633      12148.179      730.67128    
+      1000   440.94913      11.342433      10.765654     -8.1419484      45.264242      3.0670849      6.9260573      2.960122      -2007.6188     -1179.7125     -70.907567     -0.062733519    0.046047757    0.030329191   -0.36681215     45.191633      12148.179      730.67128    
-Loop time of 0.248185 on 1 procs for 1000 steps with 200 atoms
+Loop time of 0.218435 on 1 procs for 1000 steps with 200 atoms
 
-Performance: 348.128 ns/day, 0.069 hours/ns, 4029.259 timesteps/s, 805.852 katom-step/s
+Performance: 395.541 ns/day, 0.061 hours/ns, 4578.019 timesteps/s, 915.604 katom-step/s
-97.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.14702    | 0.14702    | 0.14702    |   0.0 | 59.24
+Pair    | 0.12079    | 0.12079    | 0.12079    |   0.0 | 55.30
-Neigh   | 0.0010003  | 0.0010003  | 0.0010003  |   0.0 |  0.40
+Neigh   | 0.0010224  | 0.0010224  | 0.0010224  |   0.0 |  0.47
-Comm    | 0.0039821  | 0.0039821  | 0.0039821  |   0.0 |  1.60
+Comm    | 0.0035478  | 0.0035478  | 0.0035478  |   0.0 |  1.62
-Output  | 0.00023527 | 0.00023527 | 0.00023527 |   0.0 |  0.09
+Output  | 0.00010889 | 0.00010889 | 0.00010889 |   0.0 |  0.05
-Modify  | 0.094519   | 0.094519   | 0.094519   |   0.0 | 38.08
+Modify  | 0.092098   | 0.092098   | 0.092098   |   0.0 | 42.16
-Other   |            | 0.001427   |            |       |  0.58
+Other   |            | 0.0008684  |            |       |  0.40
 
 Nlocal:            200 ave         200 max         200 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++.3

@@ -1,5 +1,6 @@
-LAMMPS (28 Mar 2023)
+LAMMPS (3 Aug 2023)
 Processor partition = 3
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
   using 1 OpenMP thread(s) per MPI task
 variable ibead uloop 99 pad
 
@@ -29,10 +30,7 @@ timestep 0.001
 velocity all create 0.0 ${ibead}
 velocity all create 0.0 04
 
-fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
+fix 1 all pimd/langevin method nmpimd ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
-
-Initializing PIMD BZP barostat...
-The barostat mass is W = 2.3401256650800001e+01
 
 thermo_style custom step temp f_1[*] vol press
 thermo 100
@@ -43,15 +41,6 @@ thermo_modify norm no
 
 run 1000
 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
-
-Initializing PI Langevin equation thermostat...
-Bead ID    |    omega    |    tau    |    c1    |    c2
-    0     0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02
-    1     8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
-    2     1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01
-    3     8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
-PILE_L thermostat successfully initialized!
-
 Neighbor list info ...
   update: every = 1 steps, delay = 0 steps, check = yes
   max neighbors/atom: 2000, page size: 100000
@@ -66,31 +55,31 @@ Neighbor list info ...
       bin: standard
 Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
    Step          Temp          f_1[1]         f_1[2]         f_1[3]         f_1[4]         f_1[5]         f_1[6]         f_1[7]         f_1[8]         f_1[9]        f_1[10]        f_1[11]        f_1[12]        f_1[13]        f_1[14]        f_1[15]         Volume         Press     
-         0   0              0              10.794425     -7.3457072      4.3005229     -21.877018     -8.7249482      2.9571502     -1743.5332     -698.49808     -172.07477      0              0              0.033460054   -0.37064378     4.216227       13402.228     -191.02389    
+         0   0              0              10.794425     -7.3457072      4.3005229      3.3062167     -8.7249482      2.9571502     -1743.5332     -698.49808     -172.07477      0              0              0.033460054   -0.37064378     4.216227       13402.228     -191.02389    
-       100   426.01705      10.958338      12.206372     -7.8040582      42.886648     -23.396327     -1.980193       2.954003      -1888.0547     -1648.7118     -332.0298      -0.099139345    0.11500091     0.033044702   -0.3701566      42.83112       13235.861      464.39271    
+       100   426.01705      10.958338      12.206372     -7.8040582      42.886648      2.9263894     -1.980193       2.954003      -1888.0547     -1648.7118     -332.0298      -0.099139345    0.11500091     0.033044702   -0.3701566      42.83112       13235.861      464.39271    
-       200   414.52703      10.662783      11.934129     -8.2331312      41.690123     -22.521598     -4.273021       2.9600599     -1906.2904     -1609.02       -265.94404     -0.20527926     0.49305948     0.031504957   -0.36829556     41.729191      12619.125      502.87052    
+       200   414.52703      10.662783      11.934129     -8.2331312      41.690123      3.1450717     -4.273021       2.9600599     -1906.2904     -1609.02       -265.94404     -0.20527926     0.49305948     0.031504957   -0.36829556     41.729191      12619.125      502.87052    
-       300   424.85622      10.928478      11.681713     -8.357621       43.180131     -21.755813     -7.7032433      2.9714114     -1968.7685      290.49656      251.72564     -0.21935745     0.56300721     0.029467915   -0.36568855     43.236828      11803.2        1058.1162    
+       300   424.85622      10.928478      11.681713     -8.357621       43.180131      3.336518      -7.7032433      2.9714114     -1968.7685      290.49656      251.72564     -0.21935745     0.56300721     0.029467915   -0.36568855     43.236828      11803.2        1058.1162    
-       400   485.80103      12.496148      12.255827     -8.3658975      49.109699     -24.824142      2.9744597      2.9794185     -2335.993       1368.7398      570.03286     -0.028366234    0.0094148316   0.028338146   -0.36416383     49.028096      11350.678      1570.2486    
+       400   485.80103      12.496148      12.255827     -8.3658975      49.109699      2.5694358      2.9744597      2.9794185     -2335.993       1368.7398      570.03286     -0.028366234    0.0094148316   0.028338146   -0.36416383     49.028096      11350.678      1570.2486    
-       500   462.99006      11.909386      11.187609     -8.6934698      45.427771     -22.825143      16.22356       2.9684828     -2113.91       -272.84753      185.53392      0.091614289    0.098205455    0.028793585   -0.36478567     45.368325      11533.101      1014.2134    
+       500   462.99006      11.909386      11.187609     -8.6934698      45.427771      3.0691855      16.22356       2.9684828     -2113.91       -272.84753      185.53392      0.091614289    0.098205455    0.028793585   -0.36478567     45.368325      11533.101      1014.2134    
-       600   465.24407      11.967366      11.168375     -8.4422887      47.783726     -22.456104      6.837575       2.967236      -2023.8117     -918.27943     -2.4106994      0.093360761    0.10198539     0.029589188   -0.36584873     47.725157      11851.775      864.12413    
+       600   465.24407      11.967366      11.168375     -8.4422887      47.783726      3.1614452      6.837575       2.967236      -2023.8117     -918.27943     -2.4106994      0.093360761    0.10198539     0.029589188   -0.36584873     47.725157      11851.775      864.12413    
-       700   426.16111      10.962044      11.000011     -8.2855512      42.626187     -20.571698     -5.7252564      2.9560528     -1806.9448     -1418.2247     -148.41657      0.075011202    0.065835696    0.030359455   -0.36685105     42.558523      12160.301      614.76939    
+       700   426.16111      10.962044      11.000011     -8.2855512      42.626187      3.6325468     -5.7252564      2.9560528     -1806.9448     -1418.2247     -148.41657      0.075011202    0.065835696    0.030359455   -0.36685105     42.558523      12160.301      614.76939    
-       800   454.53159      11.691811      10.834606     -8.0654281      45.160336     -21.885719     -6.7745694      2.9575472     -1894.3641     -1329.3179     -136.42193      0.011114896    0.0014455064   0.030808183   -0.3674233      45.076543      12340.037      684.85907    
+       800   454.53159      11.691811      10.834606     -8.0654281      45.160336      3.3040415     -6.7745694      2.9575472     -1894.3641     -1329.3179     -136.42193      0.011114896    0.0014455064   0.030808183   -0.3674233      45.076543      12340.037      684.85907    
-       900   441.72064      11.362278      10.4492       -8.0786302      45.604542     -21.816625      5.586068       2.9578604     -1890.4653     -1271.1107     -111.89061     -0.020285587    0.0048148677   0.030774258   -0.36738033     45.521594      12326.448      659.68525    
+       900   441.72064      11.362278      10.4492       -8.0786302      45.604542      3.321315       5.586068       2.9578604     -1890.4653     -1271.1107     -111.89061     -0.020285587    0.0048148677   0.030774258   -0.36738033     45.521594      12326.448      659.68525    
-      1000   429.90929      11.058457      11.851933     -8.1578394      45.264242     -22.833545      6.9260573      2.960122      -2007.6188     -1179.7125     -70.907567     -0.062733519    0.046047757    0.030329191   -0.36681215     45.191633      12148.179      698.73278    
+      1000   429.90929      11.058457      11.851933     -8.1578394      45.264242      3.0670849      6.9260573      2.960122      -2007.6188     -1179.7125     -70.907567     -0.062733519    0.046047757    0.030329191   -0.36681215     45.191633      12148.179      698.73278    
-Loop time of 0.248175 on 1 procs for 1000 steps with 200 atoms
+Loop time of 0.218441 on 1 procs for 1000 steps with 200 atoms
 
-Performance: 348.141 ns/day, 0.069 hours/ns, 4029.409 timesteps/s, 805.882 katom-step/s
+Performance: 395.530 ns/day, 0.061 hours/ns, 4577.899 timesteps/s, 915.580 katom-step/s
-98.1% CPU use with 1 MPI tasks x 1 OpenMP threads
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.14919    | 0.14919    | 0.14919    |   0.0 | 60.12
+Pair    | 0.11655    | 0.11655    | 0.11655    |   0.0 | 53.35
-Neigh   | 0.00099112 | 0.00099112 | 0.00099112 |   0.0 |  0.40
+Neigh   | 0.0010236  | 0.0010236  | 0.0010236  |   0.0 |  0.47
-Comm    | 0.0040992  | 0.0040992  | 0.0040992  |   0.0 |  1.65
+Comm    | 0.0035622  | 0.0035622  | 0.0035622  |   0.0 |  1.63
-Output  | 0.0001723  | 0.0001723  | 0.0001723  |   0.0 |  0.07
+Output  | 0.0001071  | 0.0001071  | 0.0001071  |   0.0 |  0.05
-Modify  | 0.092299   | 0.092299   | 0.092299   |   0.0 | 37.19
+Modify  | 0.096348   | 0.096348   | 0.096348   |   0.0 | 44.11
-Other   |            | 0.00142    |            |       |  0.57
+Other   |            | 0.0008537  |            |       |  0.39
 
 Nlocal:            200 ave         200 max         200 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++

@@ -0,0 +1,2 @@
+LAMMPS (3 Aug 2023)
+Running on 4 partitions of processors

examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++.0

@@ -0,0 +1,103 @@
+LAMMPS (3 Aug 2023)
+Processor partition = 0
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 99 pad
+
+units metal
+atom_style atomic
+atom_modify map yes
+boundary p p p
+pair_style lj/cut 9.5251
+read_data data.metalnpt${ibead}
+read_data data.metalnpt01
+Reading data file ...
+  orthogonal box = (-11.876697 -11.876697 -11.876697) to (11.876697 11.876697 11.876697)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  200 atoms
+  reading velocities ...
+  200 velocities
+  read_data CPU = 0.001 seconds
+
+pair_coeff    * * 0.00965188 3.4
+pair_modify shift yes
+
+mass 1 39.948
+
+timestep 0.001
+
+velocity all create 0.0 ${ibead}
+velocity all create 0.0 01
+
+fix 1 all pimd/langevin method pimd ensemble nvt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 taup 1.0 fixcom no
+
+thermo_style custom step temp f_1[*] vol press
+thermo 100
+thermo_modify norm no
+
+# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz
+# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
+
+run 1000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Initializing PI Langevin equation thermostat...
+  Bead ID    |    omega    |    tau    |    c1    |    c2
+      0     5.92546167e+01 1.00000000e+00 9.99500125e-01 3.16148726e-02
+      1     5.92546167e+01 1.00000000e+00 9.99500125e-01 3.16148726e-02
+      2     5.92546167e+01 1.00000000e+00 9.99500125e-01 3.16148726e-02
+      3     5.92546167e+01 1.00000000e+00 9.99500125e-01 3.16148726e-02
+  PILE_L thermostat successfully initialized!
+
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 11.5251
+  ghost atom cutoff = 11.5251
+  binsize = 5.76255, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
+   Step          Temp          f_1[1]         f_1[2]         f_1[3]         f_1[4]         f_1[5]         f_1[6]         f_1[7]         f_1[8]         f_1[9]        f_1[10]         Volume         Press     
+         0   0              0              8.8893303     -7.3046601      4.3005229      3.3062167      0              0             -1743.5332      0              0              13402.228     -164.47373    
+       100   248.24141      6.3854564      4.1458616     -7.7546467      9.6829291      3.3062167      0              0             -1743.5332      0.00061164884  127.22547      13402.228      26.894568    
+       200   346.2569       8.9066861      2.6427185     -7.8943744      14.016847      3.3062167      0              0             -1743.5332      0.00088274242  177.45909      13402.228      91.225638    
+       300   217.65314      5.5986414      7.0223362     -7.788449       18.162833      3.3062167      0              0             -1743.5332      0.00054181173  111.54876      13402.228     -125.00786    
+       400   266.83825      6.8638187      6.2507813     -7.7241546      21.628032      3.3062167      0              0             -1743.5332      0.0007209203   136.75648      13402.228      21.104834    
+       500   342.40379      8.8075736      5.1959052     -7.7020799      25.668758      3.3062167      0              0             -1743.5332      0.00087137898  175.48435      13402.228      208.60351    
+       600   280.37754      7.2120867      8.0025846     -7.5954127      28.570788      3.3062167      0              0             -1743.5332      0.00072432598  143.69546      13402.228      162.09838    
+       700   377.11625      9.700474       6.0049074     -7.5861377      30.034627      3.3062167      0              0             -1743.5332      0.00092377441  193.27472      13402.228      389.35575    
+       800   378.36221      9.7325237      6.1704761     -7.6170017      31.447502      3.3062167      0              0             -1743.5332      0.00097254954  193.91329      13402.228      387.71781    
+       900   271.99864      6.9965581      9.037081      -7.4781664      32.906719      3.3062167      0              0             -1743.5332      0.00074024142  139.40121      13402.228      266.3664     
+      1000   362.4753       9.3238683      8.0266514     -7.4835536      34.914285      3.3062167      0              0             -1743.5332      0.00088800624  185.77114      13402.228      433.67079    
+Loop time of 0.166656 on 1 procs for 1000 steps with 200 atoms
+
+Performance: 518.435 ns/day, 0.046 hours/ns, 6000.401 timesteps/s, 1.200 Matom-step/s
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.10478    | 0.10478    | 0.10478    |   0.0 | 62.87
+Neigh   | 0.00096007 | 0.00096007 | 0.00096007 |   0.0 |  0.58
+Comm    | 0.0035065  | 0.0035065  | 0.0035065  |   0.0 |  2.10
+Output  | 0.0001037  | 0.0001037  | 0.0001037  |   0.0 |  0.06
+Modify  | 0.056454   | 0.056454   | 0.056454   |   0.0 | 33.87
+Other   |            | 0.0008515  |            |       |  0.51
+
+Nlocal:            200 ave         200 max         200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           1360 ave        1360 max        1360 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:           9544 ave        9544 max        9544 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 9544
+Ave neighs/atom = 47.72
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++.1

@@ -0,0 +1,95 @@
+LAMMPS (3 Aug 2023)
+Processor partition = 1
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 99 pad
+
+units metal
+atom_style atomic
+atom_modify map yes
+boundary p p p
+pair_style lj/cut 9.5251
+read_data data.metalnpt${ibead}
+read_data data.metalnpt02
+Reading data file ...
+  orthogonal box = (-11.876697 -11.876697 -11.876697) to (11.876697 11.876697 11.876697)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  200 atoms
+  reading velocities ...
+  200 velocities
+  read_data CPU = 0.001 seconds
+
+pair_coeff    * * 0.00965188 3.4
+pair_modify shift yes
+
+mass 1 39.948
+
+timestep 0.001
+
+velocity all create 0.0 ${ibead}
+velocity all create 0.0 02
+
+fix 1 all pimd/langevin method pimd ensemble nvt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 taup 1.0 fixcom no
+
+thermo_style custom step temp f_1[*] vol press
+thermo 100
+thermo_modify norm no
+
+# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz
+# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
+
+run 1000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 11.5251
+  ghost atom cutoff = 11.5251
+  binsize = 5.76255, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
+   Step          Temp          f_1[1]         f_1[2]         f_1[3]         f_1[4]         f_1[5]         f_1[6]         f_1[7]         f_1[8]         f_1[9]        f_1[10]         Volume         Press     
+         0   0              0              8.4854554     -7.3063682      4.3005229      3.3062167      0              0             -1743.5332      0              0              13402.228     -167.65544    
+       100   231.55472      5.9562285      3.9188988     -7.7552569      9.6829291      3.3062167      0              0             -1743.5332      0.00061164884  127.22547      13402.228     -9.7693407    
+       200   366.33366      9.423116       2.3606144     -7.8893287      14.016847      3.3062167      0              0             -1743.5332      0.00088274242  177.45909      13402.228      131.05061    
+       300   213.74457      5.4981021      6.4391043     -7.7947526      18.162833      3.3062167      0              0             -1743.5332      0.00054181173  111.54876      13402.228     -136.92734    
+       400   273.60832      7.0379636      5.6777233     -7.7709858      21.628032      3.3062167      0              0             -1743.5332      0.0007209203   136.75648      13402.228     -0.14681392   
+       500   338.99655      8.7199299      5.4335645     -7.7194465      25.668758      3.3062167      0              0             -1743.5332      0.00087137898  175.48435      13402.228      190.1705     
+       600   298.58126      7.6803369      7.2512164     -7.5741948      28.570788      3.3062167      0              0             -1743.5332      0.00072432598  143.69546      13402.228      226.78095    
+       700   352.53291      9.0681226      5.4845895     -7.5875298      30.034627      3.3062167      0              0             -1743.5332      0.00092377441  193.27472      13402.228      335.39327    
+       800   389.70585      10.024313      5.143907      -7.6218106      31.447502      3.3062167      0              0             -1743.5332      0.00097254954  193.91329      13402.228      409.36108    
+       900   285.3019       7.3387547      7.6228894     -7.5140003      32.906719      3.3062167      0              0             -1743.5332      0.00074024142  139.40121      13402.228      266.93105    
+      1000   345.35667      8.8835299      6.9652602     -7.5180013      34.914285      3.3062167      0              0             -1743.5332      0.00088800624  185.77114      13402.228      368.83819    
+Loop time of 0.16666 on 1 procs for 1000 steps with 200 atoms
+
+Performance: 518.420 ns/day, 0.046 hours/ns, 6000.230 timesteps/s, 1.200 Matom-step/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.10798    | 0.10798    | 0.10798    |   0.0 | 64.79
+Neigh   | 0.00097784 | 0.00097784 | 0.00097784 |   0.0 |  0.59
+Comm    | 0.0035304  | 0.0035304  | 0.0035304  |   0.0 |  2.12
+Output  | 8.5625e-05 | 8.5625e-05 | 8.5625e-05 |   0.0 |  0.05
+Modify  | 0.05322    | 0.05322    | 0.05322    |   0.0 | 31.93
+Other   |            | 0.0008694  |            |       |  0.52
+
+Nlocal:            200 ave         200 max         200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           1360 ave        1360 max        1360 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:           9552 ave        9552 max        9552 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 9552
+Ave neighs/atom = 47.76
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++.2

@@ -0,0 +1,95 @@
+LAMMPS (3 Aug 2023)
+Processor partition = 2
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 99 pad
+
+units metal
+atom_style atomic
+atom_modify map yes
+boundary p p p
+pair_style lj/cut 9.5251
+read_data data.metalnpt${ibead}
+read_data data.metalnpt03
+Reading data file ...
+  orthogonal box = (-11.876697 -11.876697 -11.876697) to (11.876697 11.876697 11.876697)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  200 atoms
+  reading velocities ...
+  200 velocities
+  read_data CPU = 0.001 seconds
+
+pair_coeff    * * 0.00965188 3.4
+pair_modify shift yes
+
+mass 1 39.948
+
+timestep 0.001
+
+velocity all create 0.0 ${ibead}
+velocity all create 0.0 03
+
+fix 1 all pimd/langevin method pimd ensemble nvt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 taup 1.0 fixcom no
+
+thermo_style custom step temp f_1[*] vol press
+thermo 100
+thermo_modify norm no
+
+# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz
+# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
+
+run 1000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 11.5251
+  ghost atom cutoff = 11.5251
+  binsize = 5.76255, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
+   Step          Temp          f_1[1]         f_1[2]         f_1[3]         f_1[4]         f_1[5]         f_1[6]         f_1[7]         f_1[8]         f_1[9]        f_1[10]         Volume         Press     
+         0   0              0              8.4016332     -7.320388       4.3005229      3.3062167      0              0             -1743.5332      0              0              13402.228     -175.34503    
+       100   235.06814      6.0466034      4.1185166     -7.7660023      9.6829291      3.3062167      0              0             -1743.5332      0.00061164884  127.22547      13402.228     -7.6578222    
+       200   341.9927       8.7969992      2.7767151     -7.9109058      14.016847      3.3062167      0              0             -1743.5332      0.00088274242  177.45909      13402.228      69.587081    
+       300   206.29873      5.3065745      7.3388955     -7.7440046      18.162833      3.3062167      0              0             -1743.5332      0.00054181173  111.54876      13402.228     -118.3143     
+       400   305.56268      7.8599181      5.7681208     -7.7110516      21.628032      3.3062167      0              0             -1743.5332      0.0007209203   136.75648      13402.228      107.63706    
+       500   313.47536      8.0634543      5.5086382     -7.7030371      25.668758      3.3062167      0              0             -1743.5332      0.00087137898  175.48435      13402.228      145.14899    
+       600   258.53638      6.6502715      8.1299001     -7.6530176      28.570788      3.3062167      0              0             -1743.5332      0.00072432598  143.69546      13402.228      92.36234     
+       700   357.63679      9.1994085      6.539048      -7.6186515      30.034627      3.3062167      0              0             -1743.5332      0.00092377441  193.27472      13402.228      329.17147    
+       800   391.32883      10.066061      5.7809035     -7.6148923      31.447502      3.3062167      0              0             -1743.5332      0.00097254954  193.91329      13402.228      415.13205    
+       900   308.61185      7.9383512      8.9544585     -7.4803275      32.906719      3.3062167      0              0             -1743.5332      0.00074024142  139.40121      13402.228      341.46691    
+      1000   317.70376      8.1722204      7.3013798     -7.4667312      34.914285      3.3062167      0              0             -1743.5332      0.00088800624  185.77114      13402.228      352.92253    
+Loop time of 0.16666 on 1 procs for 1000 steps with 200 atoms
+
+Performance: 518.420 ns/day, 0.046 hours/ns, 6000.235 timesteps/s, 1.200 Matom-step/s
+98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.10509    | 0.10509    | 0.10509    |   0.0 | 63.06
+Neigh   | 0.00096379 | 0.00096379 | 0.00096379 |   0.0 |  0.58
+Comm    | 0.0035557  | 0.0035557  | 0.0035557  |   0.0 |  2.13
+Output  | 7.8072e-05 | 7.8072e-05 | 7.8072e-05 |   0.0 |  0.05
+Modify  | 0.05611    | 0.05611    | 0.05611    |   0.0 | 33.67
+Other   |            | 0.0008601  |            |       |  0.52
+
+Nlocal:            200 ave         200 max         200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           1364 ave        1364 max        1364 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:           9545 ave        9545 max        9545 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 9545
+Ave neighs/atom = 47.725
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++.3

@@ -0,0 +1,95 @@
+LAMMPS (3 Aug 2023)
+Processor partition = 3
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 99 pad
+
+units metal
+atom_style atomic
+atom_modify map yes
+boundary p p p
+pair_style lj/cut 9.5251
+read_data data.metalnpt${ibead}
+read_data data.metalnpt04
+Reading data file ...
+  orthogonal box = (-11.876697 -11.876697 -11.876697) to (11.876697 11.876697 11.876697)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  200 atoms
+  reading velocities ...
+  200 velocities
+  read_data CPU = 0.001 seconds
+
+pair_coeff    * * 0.00965188 3.4
+pair_modify shift yes
+
+mass 1 39.948
+
+timestep 0.001
+
+velocity all create 0.0 ${ibead}
+velocity all create 0.0 04
+
+fix 1 all pimd/langevin method pimd ensemble nvt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 taup 1.0 fixcom no
+
+thermo_style custom step temp f_1[*] vol press
+thermo 100
+thermo_modify norm no
+
+# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz
+# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
+
+run 1000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 11.5251
+  ghost atom cutoff = 11.5251
+  binsize = 5.76255, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
+   Step          Temp          f_1[1]         f_1[2]         f_1[3]         f_1[4]         f_1[5]         f_1[6]         f_1[7]         f_1[8]         f_1[9]        f_1[10]         Volume         Press     
+         0   0              0              7.8012276     -7.3457072      4.3005229      3.3062167      0              0             -1743.5332      0              0              13402.228     -191.02389    
+       100   241.19035      6.2040835      3.9473764     -7.7641902      9.6829291      3.3062167      0              0             -1743.5332      0.00061164884  127.22547      13402.228      3.5720518    
+       200   325.21166      8.3653443      2.3529831     -7.9137212      14.016847      3.3062167      0              0             -1743.5332      0.00088274242  177.45909      13402.228      33.184125    
+       300   209.19735      5.381135       6.7063061     -7.801056       18.162833      3.3062167      0              0             -1743.5332      0.00054181173  111.54876      13402.228     -154.10632    
+       400   280.84513      7.2241142      5.8838331     -7.7320495      21.628032      3.3062167      0              0             -1743.5332      0.0007209203   136.75648      13402.228      45.624285    
+       500   367.15726      9.4443014      5.2842629     -7.6643085      25.668758      3.3062167      0              0             -1743.5332      0.00087137898  175.48435      13402.228      283.59979    
+       600   294.68254      7.5800508      6.5104311     -7.6234652      28.570788      3.3062167      0              0             -1743.5332      0.00072432598  143.69546      13402.228      183.09906    
+       700   356.64514      9.1739005      5.2769462     -7.6204507      30.034627      3.3062167      0              0             -1743.5332      0.00092377441  193.27472      13402.228      334.31754    
+       800   360.77353      9.2800941      5.7976264     -7.6946985      31.447502      3.3062167      0              0             -1743.5332      0.00097254954  193.91329      13402.228      299.62001    
+       900   291.14241      7.4889889      7.5124196     -7.5102882      32.906719      3.3062167      0              0             -1743.5332      0.00074024142  139.40121      13402.228      277.94834    
+      1000   362.48694      9.3241677      6.8711151     -7.4856221      34.914285      3.3062167      0              0             -1743.5332      0.00088800624  185.77114      13402.228      428.98682    
+Loop time of 0.166662 on 1 procs for 1000 steps with 200 atoms
+
+Performance: 518.414 ns/day, 0.046 hours/ns, 6000.167 timesteps/s, 1.200 Matom-step/s
+98.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.10817    | 0.10817    | 0.10817    |   0.0 | 64.90
+Neigh   | 0.00096402 | 0.00096402 | 0.00096402 |   0.0 |  0.58
+Comm    | 0.0044991  | 0.0044991  | 0.0044991  |   0.0 |  2.70
+Output  | 8.5449e-05 | 8.5449e-05 | 8.5449e-05 |   0.0 |  0.05
+Modify  | 0.052066   | 0.052066   | 0.052066   |   0.0 | 31.24
+Other   |            | 0.00088    |            |       |  0.53
+
+Nlocal:            200 ave         200 max         200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           1368 ave        1368 max        1368 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:           9541 ave        9541 max        9541 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 9541
+Ave neighs/atom = 47.705
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/PACKAGES/pimd/langevin_metal_units/run.sh

@@ -1 +1,3 @@
-mpirun -np 4 $LMP -in in.lmp -p 4x1 -log log -screen screen
+mpirun -np 4 $LMP -in in.langevin.metal -p 4x1 -log log.langevin.metal -screen screen
+mpirun -np 4 $LMP -in in.pimd-langevin.metal -p 4x1 -log log.pimd-langevin.metal -screen screen
+

examples/balance/in.balance

@@ -50,5 +50,6 @@ fix             10 all balance 50 0.9 rcb
 
 thermo_style    custom step temp epair press f_10[3] f_10
 thermo          100
+timestep        0.001
 
 run             10000

examples/balance/in.balance.bond.fast

@@ -59,5 +59,6 @@ fix             10 all balance 50 0.9 rcb
 
 thermo_style    custom step temp epair press f_10[3] f_10
 thermo          100
+timestep        0.001
 
 run             10000

examples/balance/in.balance.bond.slow

@@ -58,5 +58,6 @@ fix             10 all balance 50 0.9 rcb
 
 thermo_style    custom step temp epair press f_10[3] f_10
 thermo          100
+timestep        0.001
 
 run             40000

examples/balance/log.27Nov18.balance.bond.fast.g++.2

@@ -1,242 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# 2d circle of particles inside a box with LJ walls
-
-variable        b index 0
-
-variable	x index 50
-variable	y index 20
-variable	d index 20
-variable	v index 5
-variable	w index 2
-
-units		lj
-dimension       2
-atom_style	bond
-boundary        f f p
-
-lattice		hex 0.85
-Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
-region		box block 0 $x 0 $y -0.5 0.5
-region		box block 0 50 0 $y -0.5 0.5
-region		box block 0 50 0 20 -0.5 0.5
-create_box	1 box bond/types 1 extra/bond/per/atom 6
-Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
-  2 by 1 by 1 MPI processor grid
-region		circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
-region		circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
-region		circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
-region		circle sphere 11 6.7735026918962581988 0.0 10
-create_atoms	1 region circle
-Created 361 atoms
-  Time spent = 0.000778913 secs
-mass		1 1.0
-
-velocity	all create 0.5 87287 loop geom
-velocity        all set $v $w 0 sum yes
-velocity        all set 5 $w 0 sum yes
-velocity        all set 5 2 0 sum yes
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 10.0 1.0 2.5
-
-bond_style      harmonic
-bond_coeff      1 10.0 1.2
-
-# need to preserve 1-3, 1-4 pairwise interactions during hard collisions
-
-special_bonds   lj/coul 0 1 1
-  0 = max # of 1-2 neighbors
-  1 = max # of special neighbors
-create_bonds    many all all 1 1.0 1.5
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 2.8
-  ghost atom cutoff = 2.8
-  binsize = 1.4, bins = 42 29 1
-  2 neighbor lists, perpetual/occasional/extra = 1 1 0
-  (1) command create_bonds, occasional
-      attributes: full, newton on
-      pair build: full/bin
-      stencil: full/bin/2d
-      bin: standard
-  (2) pair lj/cut, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/2d/newton
-      bin: standard
-Added 1014 bonds, new total = 1014
-  6 = max # of 1-2 neighbors
-  6 = max # of special neighbors
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix		1 all nve
-
-fix             2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
-fix             2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
-fix             3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
-fix             3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
-
-comm_style      tiled
-comm_modify     cutoff 10.0   # because bonds stretch a long ways
-fix             10 all balance 50 0.9 rcb
-
-#compute         1 all property/atom proc
-#variable        p atom (c_1%10)+1
-#dump            2 all custom 50 tmp.dump id v_p x y z
-
-#dump            3 all image 50 image.*.jpg v_p type bond atom 0.25 #                adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
-#variable        colors string #                "red green blue yellow white #                purple pink orange lime gray"
-#dump_modify     3 pad 5 amap 0 10 sa 1 10 ${colors}
-
-thermo_style    custom step temp epair press f_10[3] f_10
-thermo          100
-
-run		10000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 2.8
-  ghost atom cutoff = 10
-  binsize = 1.4, bins = 42 29 1
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/cut, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/2d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 5.156 | 5.167 | 5.177 Mbytes
-Step Temp E_pair Press f_10[3] f_10 
-       0    25.701528   -2.2032569    3.1039469            2    1.0193906 
-     100    27.623422    -6.228166    2.6542136    1.0803324    1.0027701 
-     200     33.35302   -15.746749    3.2018248    1.1246537    1.0027701 
-     300     39.17734     -24.1557    4.9116986    1.1468144    1.0027701 
-     400    41.660701   -27.615203    8.6214678    1.2077562    1.0027701 
-     500    37.154935   -24.096954    3.2656298    1.2243767    1.0083102 
-     600    35.062196   -21.527799    2.3688444    1.1800554    1.0027701 
-     700    36.962955   -22.265373    3.0233424    1.1800554    1.0083102 
-     800    38.514356   -24.625735    5.2876402    1.2077562    1.0027701 
-     900    37.840168   -24.069158     4.443617    1.2022161    1.0083102 
-    1000    36.429396   -23.978878    7.2603394    1.1966759    1.0027701 
-    1100     34.75827   -22.743232    6.6304628    1.1745152    1.0083102 
-    1200    31.057199    -21.46544    3.7869701    1.1634349    1.0083102 
-    1300    33.127345   -22.426161     5.824726    1.0858726    1.0027701 
-    1400    31.678654   -21.604473    3.2219261    1.0360111    1.0083102 
-    1500    28.345212   -18.030807   0.93335223    1.1191136    1.0027701 
-    1600    26.031412   -15.389052   0.82549542    1.1080332    1.0027701 
-    1700    25.082832    -13.48625    1.0006592    1.0858726    1.0027701 
-    1800    25.673875   -13.965883   0.54607043    1.0692521    1.0027701 
-    1900    26.530842   -13.979318    2.0285449    1.1024931    1.0027701 
-    2000    25.910771   -14.244515    1.9592232    1.1191136    1.0027701 
-    2100    28.505636   -16.220559    1.7154775    1.1191136    1.0027701 
-    2200    28.142753   -15.564302    2.9946076    1.1135734    1.0027701 
-    2300    26.606225   -13.734442    1.4589278    1.0083102    1.0083102 
-    2400    25.664988   -12.389759    1.3450183    1.0360111    1.0027701 
-    2500    25.145328   -11.815173   0.48162788    1.0360111    1.0027701 
-    2600    26.654868   -13.916929    2.8361012    1.0581717    1.0083102 
-    2700      27.3758   -15.495452    4.1206412    1.0360111    1.0027701 
-    2800     23.60864   -14.520038    1.8948923    1.0193906    1.0027701 
-    2900    20.604557   -12.901121   0.17526991    1.0138504    1.0027701 
-    3000    20.852473   -12.756946  -0.44987285    1.0360111    1.0027701 
-    3100    21.934986   -12.797691   0.76186765    1.0415512    1.0027701 
-    3200    23.293263   -12.368233  0.021937309    1.0526316    1.0027701 
-    3300    22.091492    -10.88605  0.013006632    1.0415512    1.0083102 
-    3400    23.535429   -10.937804    2.0738989    1.0360111    1.0027701 
-    3500    24.503573   -12.202994     1.126785    1.0581717    1.0027701 
-    3600     23.54503   -12.745709   0.39022194    1.0858726    1.0027701 
-    3700    22.658187   -10.986188  -0.18869692    1.0692521    1.0027701 
-    3800    21.282045   -9.7879088 -0.061253454    1.0193906    1.0027701 
-    3900    20.571754   -9.1157993   -1.0178917    1.0526316    1.0027701 
-    4000    23.779702   -10.230328    1.0778525    1.0581717    1.0083102 
-    4100    23.675854    -10.63724   0.59402249    1.0415512    1.0027701 
-    4200    24.058963    -11.89505    0.3866378    1.0526316    1.0027701 
-    4300    22.683721   -11.358978    1.8269036    1.0470914    1.0083102 
-    4400    23.002345   -11.081443    0.4529456    1.0415512    1.0027701 
-    4500    21.984542   -10.233276  -0.60718244    1.0415512    1.0083102 
-    4600    22.079237    -9.979061   0.53013572    1.0415512    1.0027701 
-    4700    22.336961   -10.323583  -0.37512832    1.0249307    1.0027701 
-    4800    23.351699   -10.143724   0.95694397    1.0470914    1.0027701 
-    4900    23.643954   -10.687354    1.6062522    1.0858726    1.0083102 
-    5000    25.158132   -11.532398    1.3083639    1.0914127    1.0027701 
-    5100    23.755521   -10.978548   0.60587307    1.0470914    1.0027701 
-    5200    21.842692   -10.443216  -0.41185899    1.0637119    1.0027701 
-    5300    22.828066   -10.871114    1.1754353    1.0470914    1.0027701 
-    5400    24.883977    -12.39165   0.65101173    1.0470914    1.0027701 
-    5500    22.908286   -11.419431    1.4712698    1.0637119    1.0027701 
-    5600    22.718634   -12.083974    1.5706808    1.0526316    1.0027701 
-    5700    23.080763   -11.464882    1.2979578    1.0304709    1.0083102 
-    5800    21.877026   -11.483185     0.279772    1.0360111    1.0027701 
-    5900    22.526809   -10.868636   0.37121786    1.0637119    1.0083102 
-    6000    22.908857   -10.311118   0.58244569    1.0526316    1.0083102 
-    6100    22.399847   -10.222706   0.87875674    1.0858726    1.0027701 
-    6200    22.623463   -10.035541  -0.25811274    1.0304709    1.0027701 
-    6300    21.518006   -10.017552  -0.98187611    1.0470914    1.0083102 
-    6400    21.269816   -11.297716   0.20058535    1.0138504    1.0027701 
-    6500    23.362834   -11.263306   0.47670072    1.0692521    1.0027701 
-    6600    23.705236   -12.358492  -0.63286237    1.0027701    1.0027701 
-    6700    22.410623   -10.849516   0.57027834    1.0581717    1.0083102 
-    6800    21.661639   -9.3981379   0.38726515    1.0470914    1.0027701 
-    6900    21.856521   -8.8451751  0.053822789    1.0304709    1.0027701 
-    7000    21.069495   -8.6443387  -0.10412144    1.0193906    1.0027701 
-    7100    22.305494   -10.098469  -0.22662961    1.0581717    1.0027701 
-    7200     23.52884   -11.055929 -0.099869868    1.0692521    1.0027701 
-    7300    24.042008   -11.411758    2.0528788    1.0415512    1.0027701 
-    7400    22.870777   -12.408763   0.33346225    1.0249307    1.0027701 
-    7500    21.290152   -10.963058   0.26940112    1.0083102    1.0027701 
-    7600    21.702686    -10.36214   0.84057004    1.0083102    1.0027701 
-    7700    22.478034   -10.832724  -0.70855164    1.0747922    1.0027701 
-    7800    22.856853   -11.161008  -0.88354803    1.0083102    1.0083102 
-    7900    22.579842   -10.789899   0.40865274    1.0360111    1.0027701 
-    8000    24.364281   -12.116023  -0.44788445    1.0249307    1.0083102 
-    8100    22.993409   -10.261331   0.44712215    1.0193906    1.0027701 
-    8200    23.006207   -10.723372    1.2357091    1.0415512    1.0083102 
-    8300    23.292233   -10.041314     2.143692    1.0581717    1.0027701 
-    8400    21.658087   -10.089378  -0.25838681    1.0083102    1.0027701 
-    8500    23.268456   -10.356603  0.089787317    1.0526316    1.0083102 
-    8600    22.572019    -10.32801   0.12320758    1.0526316    1.0027701 
-    8700    22.970465   -10.662456   0.57027398    1.0581717    1.0083102 
-    8800    23.515552   -10.415842    1.0048598    1.0138504    1.0083102 
-    8900    22.733961   -10.343495   0.19917627    1.0360111    1.0083102 
-    9000    21.835458   -9.8740971   -1.0653164    1.0193906    1.0027701 
-    9100    22.062821   -9.2303832   0.21428267    1.0415512    1.0083102 
-    9200    23.020404   -10.321542  -0.48757848    1.0193906    1.0083102 
-    9300    22.529362   -9.2916938   0.57056277    1.0415512    1.0027701 
-    9400    23.301911   -10.538876   0.80637627    1.0138504    1.0027701 
-    9500    21.984286   -9.4754676  -0.19048233    1.0193906    1.0027701 
-    9600    23.710224   -10.274983   0.72268146    1.0249307    1.0027701 
-    9700    22.317038   -9.3509008  -0.45727658    1.0360111    1.0027701 
-    9800     23.41615   -10.026331  -0.45909049    1.0415512    1.0027701 
-    9900    22.130299    -11.18528  -0.15359132    1.0747922    1.0027701 
-   10000    23.273859   -11.337403    0.4036321    1.0304709    1.0083102 
-Loop time of 1.18289 on 2 procs for 10000 steps with 361 atoms
-
-Performance: 3652073.393 tau/day, 8453.874 timesteps/s
-97.0% CPU use with 2 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.25191    | 0.25685    | 0.2618     |   1.0 | 21.71
-Bond    | 0.097655   | 0.098332   | 0.099009   |   0.2 |  8.31
-Neigh   | 0.53258    | 0.53993    | 0.54728    |   1.0 | 45.65
-Comm    | 0.13457    | 0.15372    | 0.17288    |   4.9 | 13.00
-Output  | 0.0013587  | 0.0016007  | 0.0018427  |   0.6 |  0.14
-Modify  | 0.074109   | 0.074314   | 0.074518   |   0.1 |  6.28
-Other   |            | 0.05813    |            |       |  4.91
-
-Nlocal:    180.5 ave 182 max 179 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost:    172.5 ave 175 max 170 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs:    1421 ave 1488 max 1354 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-
-Total # of neighbors = 2842
-Ave neighs/atom = 7.87258
-Ave special neighs/atom = 5.61773
-Neighbor list builds = 4884
-Dangerous builds = 0
-Total wall time: 0:00:01

examples/balance/log.27Nov18.balance.bond.fast.g++.4

@@ -1,242 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# 2d circle of particles inside a box with LJ walls
-
-variable        b index 0
-
-variable	x index 50
-variable	y index 20
-variable	d index 20
-variable	v index 5
-variable	w index 2
-
-units		lj
-dimension       2
-atom_style	bond
-boundary        f f p
-
-lattice		hex 0.85
-Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
-region		box block 0 $x 0 $y -0.5 0.5
-region		box block 0 50 0 $y -0.5 0.5
-region		box block 0 50 0 20 -0.5 0.5
-create_box	1 box bond/types 1 extra/bond/per/atom 6
-Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
-  2 by 2 by 1 MPI processor grid
-region		circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
-region		circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
-region		circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
-region		circle sphere 11 6.7735026918962581988 0.0 10
-create_atoms	1 region circle
-Created 361 atoms
-  Time spent = 0.00067687 secs
-mass		1 1.0
-
-velocity	all create 0.5 87287 loop geom
-velocity        all set $v $w 0 sum yes
-velocity        all set 5 $w 0 sum yes
-velocity        all set 5 2 0 sum yes
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 10.0 1.0 2.5
-
-bond_style      harmonic
-bond_coeff      1 10.0 1.2
-
-# need to preserve 1-3, 1-4 pairwise interactions during hard collisions
-
-special_bonds   lj/coul 0 1 1
-  0 = max # of 1-2 neighbors
-  1 = max # of special neighbors
-create_bonds    many all all 1 1.0 1.5
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 2.8
-  ghost atom cutoff = 2.8
-  binsize = 1.4, bins = 42 29 1
-  2 neighbor lists, perpetual/occasional/extra = 1 1 0
-  (1) command create_bonds, occasional
-      attributes: full, newton on
-      pair build: full/bin
-      stencil: full/bin/2d
-      bin: standard
-  (2) pair lj/cut, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/2d/newton
-      bin: standard
-Added 1014 bonds, new total = 1014
-  6 = max # of 1-2 neighbors
-  6 = max # of special neighbors
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix		1 all nve
-
-fix             2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
-fix             2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
-fix             3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
-fix             3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
-
-comm_style      tiled
-comm_modify     cutoff 10.0   # because bonds stretch a long ways
-fix             10 all balance 50 0.9 rcb
-
-#compute         1 all property/atom proc
-#variable        p atom (c_1%10)+1
-#dump            2 all custom 50 tmp.dump id v_p x y z
-
-#dump            3 all image 50 image.*.jpg v_p type bond atom 0.25 #                adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
-#variable        colors string #                "red green blue yellow white #                purple pink orange lime gray"
-#dump_modify     3 pad 5 amap 0 10 sa 1 10 ${colors}
-
-thermo_style    custom step temp epair press f_10[3] f_10
-thermo          100
-
-run		10000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 2.8
-  ghost atom cutoff = 10
-  binsize = 1.4, bins = 42 29 1
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/cut, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/2d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 5.122 | 5.141 | 5.174 Mbytes
-Step Temp E_pair Press f_10[3] f_10 
-       0    25.701528   -2.2032569    3.1039469    3.2354571    1.0526316 
-     100    27.623422    -6.228166    2.6542136    1.2631579    1.0083102 
-     200     33.35302   -15.746749    3.2018248    1.2963989    1.0193906 
-     300     39.17734     -24.1557    4.9116986    1.2963989    1.0193906 
-     400    41.660701   -27.615203    8.6214679    1.3518006    1.0083102 
-     500    37.154928   -24.096946    3.2656177    1.3296399    1.0304709 
-     600    35.059873   -21.524223    2.3729526    1.3296399    1.0083102 
-     700    36.735117   -22.012675     3.266197    1.3296399    1.0083102 
-     800    39.218223   -25.076176    4.7162461    1.4182825    1.0193906 
-     900    38.003628   -24.598176    3.4651756    1.4958449    1.0083102 
-    1000    37.599298   -25.117714    4.6714491    1.2963989    1.0193906 
-    1100    35.587211   -24.476201    4.8766816    1.2077562    1.0083102 
-    1200     33.05745   -21.457847    4.7304313    1.2188366    1.0193906 
-    1300    35.505899   -20.103017    7.0543469    1.1523546    1.0193906 
-    1400    32.687958   -18.411286    2.8022421    1.1523546    1.0083102 
-    1500    30.681103   -13.979491    1.5780815    1.1523546    1.0083102 
-    1600    28.134276   -12.408217    1.4370834    1.2188366    1.0193906 
-    1700    29.150676   -12.486223    1.7118526    1.1745152    1.0083102 
-    1800    29.456937   -11.386522    2.0484739    1.1966759    1.0193906 
-    1900    28.029998   -11.168436   0.38519481    1.1080332    1.0193906 
-    2000    29.476997   -12.337678    1.8878345    1.1523546    1.0083102 
-    2100    30.113294   -12.201714    2.8003366    1.1634349    1.0193906 
-    2200    31.599067   -13.710787    2.5654923    1.2188366    1.0083102 
-    2300    31.333799   -12.269386    1.9573739    1.1412742    1.0193906 
-    2400    28.587094    -10.98229     2.090581    1.1745152    1.0083102 
-    2500    28.012332   -11.416553    2.3293146    1.1855956    1.0083102 
-    2600    28.703189    -13.33369    2.7247345    1.1080332    1.0083102 
-    2700    26.933934   -13.546384   0.71447362    1.0415512    1.0304709 
-    2800    24.556936   -12.231427  0.012081842    1.0526316    1.0193906 
-    2900    24.362943   -10.921093   -0.6063159    1.0858726    1.0193906 
-    3000    24.583358   -10.025143   0.35975315    1.0637119    1.0083102 
-    3100    26.119046   -10.124317   0.75140102    1.0415512    1.0193906 
-    3200    27.665317   -11.418452   0.39942176    1.1301939    1.0083102 
-    3300    27.771434   -9.9777413   0.94693011    1.1080332    1.0083102 
-    3400    25.692188   -9.9016885    2.2582772    1.0415512    1.0083102 
-    3500    27.009276   -10.504438   0.98279258    1.1301939    1.0083102 
-    3600    26.082843   -9.4359595 -0.030819747    1.1301939    1.0083102 
-    3700    23.956851   -8.4601884  -0.45748969    1.0858726    1.0304709 
-    3800     24.92141   -8.3315871  -0.19512647    1.0969529    1.0083102 
-    3900    26.048044   -9.6299934   0.40522014    1.0858726    1.0083102 
-    4000    26.558961   -10.032084   0.56213613    1.1745152    1.0083102 
-    4100    26.949686   -10.133598    1.0140825    1.0747922    1.0083102 
-    4200    25.868196   -9.3971859    1.2758465    1.0969529    1.0083102 
-    4300    24.563369   -9.5992996   0.17389949    1.1191136    1.0193906 
-    4400    24.032818   -10.002668   0.10233743    1.0969529    1.0083102 
-    4500    25.281577    -9.948799    0.7590423    1.1523546    1.0083102 
-    4600    25.010901   -10.195479  -0.24424931    1.0747922    1.0193906 
-    4700    25.062368   -9.2973021    1.1755931    1.0858726    1.0193906 
-    4800     25.70912    -8.890895    1.0780397    1.1080332    1.0193906 
-    4900    26.027757   -10.205469    1.0644859    1.1080332    1.0083102 
-    5000    25.845739   -9.8511049   0.49059257    1.1301939    1.0193906 
-    5100    25.614064   -9.0396911   0.40825814    1.0526316    1.0304709 
-    5200    25.548135    -9.000613   0.81571441    1.1080332    1.0083102 
-    5300    26.592601   -9.2385129    1.4983434    1.0637119    1.0193906 
-    5400    26.230779   -9.8226036    1.0072462    1.0858726    1.0083102 
-    5500    26.809887   -9.9569954    1.4074968    1.0415512    1.0083102 
-    5600    25.722206   -10.240487   -0.5216434    1.0747922    1.0193906 
-    5700    24.973866   -9.0820997   0.92104357    1.0193906    1.0083102 
-    5800    24.257134   -9.5439897  -0.75290789    1.0858726    1.0083102 
-    5900    25.524917   -8.9920216    1.2049479    1.1191136    1.0083102 
-    6000    24.816532   -9.5865764  -0.66634446    1.0637119    1.0193906 
-    6100    27.034385   -9.4017037    1.0769494    1.0969529    1.0083102 
-    6200     24.19144   -8.2292864   0.97913204    1.0415512    1.0193906 
-    6300    26.112877   -9.1531212   0.77578963    1.0526316    1.0193906 
-    6400    25.820541   -9.9662231 -0.092724413    1.0969529    1.0193906 
-    6500    26.181404   -9.5875764  -0.30106405    1.1634349    1.0083102 
-    6600    27.770851   -8.8366116   0.94545206    1.0304709    1.0193906 
-    6700    26.065489   -9.8223382   0.24640067    1.0526316    1.0193906 
-    6800    27.468165   -10.160923    2.7263738    1.0747922    1.0304709 
-    6900    27.317955   -10.356911     1.131609    1.0526316    1.0304709 
-    7000    26.343789   -9.9153453    1.0385354    1.0858726    1.0193906 
-    7100    24.366577   -8.9243936   0.37685043    1.0526316    1.0193906 
-    7200    25.570042   -8.9195237   0.44206575    1.0637119    1.0193906 
-    7300    24.635046   -8.4524117  -0.20581694    1.0193906    1.0193906 
-    7400    27.161863   -7.9885934    1.1323072    1.0858726    1.0193906 
-    7500      26.8044   -9.5703931   0.69476535    1.0858726    1.0193906 
-    7600    27.381006   -10.702178  -0.20230101    1.0526316    1.0083102 
-    7700    26.507406    -9.828117   0.50115907    1.0415512    1.0193906 
-    7800    25.945271   -8.9912842   0.89121191    1.0747922    1.0083102 
-    7900    24.498681   -7.7193231  -0.63874494    1.0858726    1.0083102 
-    8000    24.517408   -7.6046107  -0.91642337    1.0415512    1.0083102 
-    8100    26.388387   -8.1883906  0.093136981    1.1080332    1.0193906 
-    8200    26.261054   -8.7223732 -0.086859057    1.0747922    1.0083102 
-    8300    26.287026   -9.2583895   0.79506804    1.0858726    1.0083102 
-    8400    24.691375   -9.0701909  -0.40058151    1.0637119    1.0193906 
-    8500    25.390612   -7.9499801   0.59874113    1.1412742    1.0193906 
-    8600     26.84383   -8.5520984   0.37618599    1.0637119    1.0083102 
-    8700    25.685137    -7.688836  0.035978149    1.0415512    1.0193906 
-    8800    26.614591   -9.0444146   0.20671465    1.0193906    1.0083102 
-    8900    25.782718   -8.2594705   0.54378816    1.0747922    1.0304709 
-    9000    26.026886   -8.6777252   0.25418163    1.1191136    1.0083102 
-    9100    27.246916   -9.0307861     1.211131    1.0526316    1.0193906 
-    9200    27.282948    -9.180029 -0.0056269613    1.0747922    1.0083102 
-    9300    27.029692   -8.7791461   0.35971649    1.0304709    1.0083102 
-    9400    26.549013   -7.5083174   0.77607249    1.0969529    1.0193906 
-    9500    25.533731   -9.2763668   0.28360762    1.0969529    1.0083102 
-    9600    27.997538   -9.2766769    1.6968428    1.0637119    1.0083102 
-    9700    26.977436     -9.21372    1.8007256    1.0637119    1.0083102 
-    9800    25.547091   -9.1024445  -0.29158273    1.0969529    1.0193906 
-    9900    26.378841   -8.7645665    1.0385835    1.1080332    1.0083102 
-   10000    26.699368   -8.5450739   0.19591452    1.0526316    1.0193906 
-Loop time of 0.916576 on 4 procs for 10000 steps with 361 atoms
-
-Performance: 4713193.307 tau/day, 10910.170 timesteps/s
-92.2% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.10915    | 0.12374    | 0.14167    |   3.5 | 13.50
-Bond    | 0.047075   | 0.049849   | 0.054161   |   1.2 |  5.44
-Neigh   | 0.31176    | 0.3246     | 0.3384     |   1.7 | 35.41
-Comm    | 0.24271    | 0.26717    | 0.30549    |   4.9 | 29.15
-Output  | 0.0017068  | 0.0021075  | 0.0031145  |   1.3 |  0.23
-Modify  | 0.064639   | 0.065705   | 0.067641   |   0.5 |  7.17
-Other   |            | 0.08341    |            |       |  9.10
-
-Nlocal:    90.25 ave 92 max 89 min
-Histogram: 1 0 0 2 0 0 0 0 0 1
-Nghost:    248.25 ave 264 max 230 min
-Histogram: 1 0 0 0 0 2 0 0 0 1
-Neighs:    569.5 ave 657 max 519 min
-Histogram: 2 0 0 0 1 0 0 0 0 1
-
-Total # of neighbors = 2278
-Ave neighs/atom = 6.31025
-Ave special neighs/atom = 5.61773
-Neighbor list builds = 4964
-Dangerous builds = 14
-Total wall time: 0:00:00

examples/balance/log.27Nov18.balance.bond.slow.g++.2

@@ -1,541 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# 2d circle of particles inside a box with LJ walls
-
-variable        b index 0
-
-variable	x index 50
-variable	y index 20
-variable	d index 20
-
-# careful not to slam into wall too hard
-
-variable	v index 0.3
-variable	w index 0.08
-
-units		lj
-dimension       2
-atom_style	bond
-boundary        f f p
-
-lattice		hex 0.85
-Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
-region		box block 0 $x 0 $y -0.5 0.5
-region		box block 0 50 0 $y -0.5 0.5
-region		box block 0 50 0 20 -0.5 0.5
-create_box	1 box bond/types 1 extra/bond/per/atom 6
-Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
-  2 by 1 by 1 MPI processor grid
-region		circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
-region		circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
-region		circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
-region		circle sphere 11 6.7735026918962581988 0.0 10
-create_atoms	1 region circle
-Created 361 atoms
-  Time spent = 0.000762701 secs
-mass		1 1.0
-
-velocity	all create 0.5 87287 loop geom
-velocity        all set $v $w 0 sum yes
-velocity        all set 0.3 $w 0 sum yes
-velocity        all set 0.3 0.08 0 sum yes
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 10.0 1.0 2.5
-
-bond_style      harmonic
-bond_coeff      1 10.0 1.2
-
-create_bonds    many all all 1 1.0 1.5
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 2.8
-  ghost atom cutoff = 2.8
-  binsize = 1.4, bins = 42 29 1
-  2 neighbor lists, perpetual/occasional/extra = 1 1 0
-  (1) command create_bonds, occasional
-      attributes: full, newton on
-      pair build: full/bin
-      stencil: full/bin/2d
-      bin: standard
-  (2) pair lj/cut, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/2d/newton
-      bin: standard
-Added 1014 bonds, new total = 1014
-  6 = max # of 1-2 neighbors
-  30 = max # of 1-3 neighbors
-  180 = max # of 1-4 neighbors
-  36 = max # of special neighbors
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix		1 all nve
-
-fix             2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
-fix             2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
-fix             3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
-fix             3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
-
-comm_style      tiled
-fix             10 all balance 50 0.9 rcb
-
-#compute         1 all property/atom proc
-#variable        p atom (c_1%10)+1
-#dump            2 all custom 50 tmp.dump id v_p x y z
-
-#dump            3 all image 200 image.*.jpg v_p type bond atom 0.25 #                adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
-#variable        colors string #                "red green blue yellow white #                purple pink orange lime gray"
-#dump_modify     3 pad 5 amap 0 10 sa 1 10 ${colors}
-
-thermo_style    custom step temp epair press f_10[3] f_10
-thermo          100
-
-run		40000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 2.8
-  ghost atom cutoff = 2.8
-  binsize = 1.4, bins = 42 29 1
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/cut, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/2d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.079 | 7.108 | 7.137 Mbytes
-Step Temp E_pair Press f_10[3] f_10 
-       0   0.57437856            0   0.26099453            2    1.0193906 
-     100   0.29756515            0   0.10149401    1.0027701    1.0027701 
-     200   0.35394813            0  0.075159099    1.0027701    1.0083102 
-     300   0.39245849            0  0.033002384    1.0027701    1.0027701 
-     400   0.34078347            0 -0.020825841    1.0083102    1.0027701 
-     500   0.35201095            0 -0.062637506    1.0027701    1.0027701 
-     600   0.34014717            0  -0.11122965    1.0249307    1.0027701 
-     700    0.3323524            0  -0.11598015    1.0083102    1.0027701 
-     800   0.35116047            0 -0.096162395    1.0138504    1.0027701 
-     900   0.35695352            0  -0.01385176    1.0249307    1.0027701 
-    1000   0.36986539            0  0.056772858    1.0027701    1.0027701 
-    1100   0.34584644            0  0.084941323    1.0138504    1.0027701 
-    1200   0.31921435            0   0.10545078    1.0138504    1.0027701 
-    1300   0.32952819            0     0.124902    1.0027701    1.0027701 
-    1400   0.34497365            0   0.12662081    1.0138504    1.0027701 
-    1500   0.33429243            0  0.096230972    1.0193906    1.0027701 
-    1600   0.33765387            0  0.025800542    1.0193906    1.0027701 
-    1700   0.35134464            0  -0.04422593    1.0083102    1.0027701 
-    1800   0.35003859            0 -0.096745576    1.0083102    1.0083102 
-    1900   0.33839618            0 -0.095465943    1.0027701    1.0027701 
-    2000   0.33732078            0 -0.094652802    1.0027701    1.0027701 
-    2100   0.34552238            0 -0.076729261    1.0083102    1.0027701 
-    2200   0.34893142            0 -0.036853228    1.0083102    1.0083102 
-    2300   0.35379341            0  0.021124847    1.0193906    1.0027701 
-    2400   0.34829744            0   0.09230184    1.0027701    1.0027701 
-    2500   0.33038141            0    0.1399855    1.0027701    1.0083102 
-    2600   0.30983019            0   0.12754742    1.0083102    1.0027701 
-    2700   0.32992561            0   0.10485138    1.0193906    1.0027701 
-    2800   0.34604747            0  0.066174138    1.0083102    1.0027701 
-    2900    0.3444791            0  0.036590652    1.0083102    1.0083102 
-    3000   0.34721342            0 -0.023793368    1.0138504    1.0027701 
-    3100   0.33404314            0  -0.08374223    1.0083102    1.0027701 
-    3200   0.33019355            0  -0.12715599    1.0083102    1.0027701 
-    3300   0.33515177            0  -0.12217394    1.0083102    1.0027701 
-    3400   0.33628481            0 -0.070877624    1.0083102    1.0027701 
-    3500   0.34257038            0 -0.021612062    1.0027701    1.0027701 
-    3600   0.32838009            0  0.030131228    1.0027701    1.0027701 
-    3700   0.34462142            0  0.074586378    1.0138504    1.0027701 
-    3800   0.30891825            0   0.10605673    1.0138504    1.0027701 
-    3900   0.33847951            0   0.13956139    1.0027701    1.0027701 
-    4000   0.32952079            0   0.12688129    1.0027701    1.0027701 
-    4100   0.32646772            0  0.081089042    1.0083102    1.0027701 
-    4200   0.35399503            0  0.013422873    1.0027701    1.0027701 
-    4300   0.33154914            0 -0.050919508    1.0027701    1.0083102 
-    4400   0.34113556            0    -0.083171    1.0249307    1.0027701 
-    4500   0.32651708            0   -0.1063133    1.0193906    1.0027701 
-    4600   0.34359609            0   -0.1076395    1.0027701    1.0027701 
-    4700   0.34973537            0 -0.088231606    1.0138504    1.0027701 
-    4800   0.35198515            0 -0.020901044    1.0027701    1.0027701 
-    4900   0.35187284            0  0.043645941    1.0193906    1.0027701 
-    5000   0.34887336            0  0.095698609    1.0027701    1.0027701 
-    5100   0.30308163            0   0.11649328    1.0138504    1.0027701 
-    5200   0.32401285            0   0.12072411    1.0083102    1.0083102 
-    5300   0.33025072            0   0.10933161    1.0138504    1.0027701 
-    5400   0.33288012            0  0.078356448    1.0083102    1.0027701 
-    5500   0.35142492            0  0.036958063    1.0027701    1.0027701 
-    5600   0.35125368            0 -0.041371343    1.0193906    1.0027701 
-    5700   0.34547744            0 -0.096450846    1.0193906    1.0027701 
-    5800   0.30939887            0  -0.12356656    1.0027701    1.0083102 
-    5900   0.32315628            0  -0.11338676    1.0083102    1.0027701 
-    6000   0.34117485            0 -0.066198961    1.0027701    1.0027701 
-    6100   0.35298043            0 -0.016172816    1.0138504    1.0027701 
-    6200   0.35130653            0  0.027660468    1.0027701    1.0027701 
-    6300   0.35398766            0  0.087221238    1.0027701    1.0027701 
-    6400   0.30963379            0   0.11990957    1.0138504    1.0027701 
-    6500    0.3174541            0   0.14103528    1.0083102    1.0083102 
-    6600   0.31989791            0   0.11575506    1.0083102    1.0083102 
-    6700   0.33811477            0  0.060747353    1.0083102    1.0083102 
-    6800    0.3424043            0  0.010357152    1.0083102    1.0027701 
-    6900   0.34804319            0 -0.042621786    1.0083102    1.0027701 
-    7000   0.35357865            0 -0.067248959    1.0027701    1.0027701 
-    7100   0.33556885            0  -0.10983726    1.0083102    1.0027701 
-    7200   0.33531101            0    -0.112179    1.0027701    1.0027701 
-    7300   0.35742607            0 -0.078405267    1.0083102    1.0027701 
-    7400   0.34577559            0  -0.01985432    1.0027701    1.0083102 
-    7500    0.3498641            0  0.052289439    1.0027701    1.0027701 
-    7600   0.33773715            0  0.092939035    1.0027701    1.0027701 
-    7700   0.33093497            0   0.11924405    1.0083102    1.0027701 
-    7800   0.31435814            0   0.12701724    1.0027701    1.0027701 
-    7900   0.33132217            0   0.10793075    1.0083102    1.0027701 
-    8000   0.33451798            0  0.077993125    1.0027701    1.0027701 
-    8100   0.35188371            0  0.019929977    1.0083102    1.0083102 
-    8200   0.33645742            0 -0.039302079    1.0027701    1.0027701 
-    8300    0.3415632            0 -0.098067982    1.0138504    1.0027701 
-    8400   0.30619282            0  -0.12952879    1.0138504    1.0027701 
-    8500   0.34446484            0 -0.098084709    1.0027701    1.0027701 
-    8600   0.33761673            0  -0.07069818    1.0027701    1.0027701 
-    8700   0.34495452            0 -0.022458056    1.0083102    1.0027701 
-    8800   0.33502983            0  0.027742411    1.0027701    1.0027701 
-    8900   0.35418591            0  0.092390134    1.0083102    1.0083102 
-    9000   0.31648387            0   0.12467398    1.0083102    1.0027701 
-    9100   0.33994825            0   0.14460327    1.0138504    1.0027701 
-    9200   0.33822571            0   0.11273284    1.0027701    1.0027701 
-    9300   0.33260773            0  0.060063671    1.0083102    1.0083102 
-    9400   0.36140305            0  0.021427642    1.0138504    1.0027701 
-    9500   0.34273562            0 -0.034064202    1.0083102    1.0027701 
-    9600   0.33867054            0 -0.089076906    1.0138504    1.0027701 
-    9700   0.32088235            0  -0.12027075    1.0138504    1.0083102 
-    9800    0.3320823            0  -0.11602794    1.0138504    1.0027701 
-    9900   0.33916442            0 -0.080281044    1.0083102    1.0027701 
-   10000   0.34852268            0  -0.01000914    1.0083102    1.0083102 
-   10100   0.32955942            0   0.04258493    1.0027701    1.0083102 
-   10200   0.34487898            0  0.086971308    1.0083102    1.0027701 
-   10300   0.32325593            0   0.11558149    1.0138504    1.0027701 
-   10400   0.30927871            0   0.12239437    1.0027701    1.0027701 
-   10500   0.33176799            0   0.12285937    1.0138504    1.0083102 
-   10600   0.35120027            0  0.084897432    1.0027701    1.0027701 
-   10700   0.33129697            0 0.0053089279    1.0138504    1.0027701 
-   10800   0.36028769            0  -0.04280715    1.0083102    1.0027701 
-   10900   0.35552287            0 -0.084955999    1.0138504    1.0027701 
-   11000    0.3406024            0 -0.096554577    1.0027701    1.0027701 
-   11100   0.33041202            0  -0.10703492    1.0138504    1.0027701 
-   11200   0.32442686            0 -0.084328121    1.0193906    1.0027701 
-   11300   0.35952468            0 -0.020191965    1.0083102    1.0027701 
-   11400   0.34610624            0   0.03440148    1.0138504    1.0027701 
-   11500    0.3415612            0    0.1041929    1.0027701    1.0027701 
-   11600   0.34040042            0   0.13215705    1.0138504    1.0027701 
-   11700   0.33555094            0   0.12738686    1.0193906    1.0027701 
-   11800    0.3458647            0   0.10963398    1.0027701    1.0083102 
-   11900   0.33836678            0  0.067253864    1.0138504    1.0027701 
-   12000   0.34853314            0   0.03201448    1.0027701    1.0027701 
-   12100   0.34600048            0 -0.034833402    1.0083102    1.0027701 
-   12200   0.33145631            0  -0.09865675    1.0083102    1.0027701 
-   12300   0.32848884            0   -0.1248489    1.0083102    1.0027701 
-   12400    0.3321344            0  -0.11266575    1.0027701    1.0083102 
-   12500   0.32622305            0 -0.061634993    1.0083102    1.0083102 
-   12600   0.36213537            0 -0.0090593315    1.0138504    1.0027701 
-   12700   0.34673866            0  0.036734645    1.0138504    1.0027701 
-   12800   0.34606618            0  0.086267678    1.0138504    1.0027701 
-   12900   0.34271431            0   0.12415522    1.0027701    1.0027701 
-   13000   0.31993287            0   0.13879926    1.0027701    1.0083102 
-   13100    0.3422918            0   0.11978905    1.0083102    1.0027701 
-   13200   0.33055236            0  0.062620483    1.0083102    1.0027701 
-   13300   0.34652207            0 0.0043833459    1.0138504    1.0027701 
-   13400   0.33574661            0  -0.04691024    1.0027701    1.0027701 
-   13500   0.33940837            0 -0.074241604    1.0027701    1.0083102 
-   13600   0.32093414            0   -0.1078027    1.0138504    1.0083102 
-   13700   0.34336597            0  -0.10544097    1.0027701    1.0027701 
-   13800   0.35806461            0 -0.072531559    1.0027701    1.0027701 
-   13900   0.35209713            0 -0.018851408    1.0083102    1.0083102 
-   14000   0.35702629            0  0.061046366    1.0027701    1.0027701 
-   14100   0.33234093            0  0.094086465    1.0027701    1.0027701 
-   14200    0.3459466            0   0.12186656    1.0027701    1.0027701 
-   14300    0.3327428            0   0.11396572    1.0027701    1.0027701 
-   14400   0.32409443            0   0.10658903    1.0083102    1.0083102 
-   14500   0.35022184            0  0.083558031    1.0083102    1.0083102 
-   14600   0.34823843            0  0.024605569    1.0083102    1.0083102 
-   14700   0.35298973            0 -0.040418888    1.0027701    1.0027701 
-   14800   0.33679845            0  -0.10067728    1.0027701    1.0027701 
-   14900   0.32790966            0  -0.10925568    1.0083102    1.0027701 
-   15000   0.34208495            0  -0.09568004    1.0193906    1.0027701 
-   15100   0.33647529            0 -0.055652929    1.0027701    1.0027701 
-   15200   0.35328398            0 -0.020236536    1.0083102    1.0027701 
-   15300   0.34252669            0  0.026434179    1.0083102    1.0027701 
-   15400   0.34409435            0  0.094410599    1.0027701    1.0027701 
-   15500   0.32288994            0   0.12034455    1.0083102    1.0027701 
-   15600   0.32109689            0   0.13645185    1.0083102    1.0027701 
-   15700   0.33681572            0  0.098607746    1.0083102    1.0027701 
-   15800   0.33635195            0   0.05570715    1.0083102    1.0083102 
-   15900   0.34289757            0  0.013849092    1.0083102    1.0027701 
-   16000   0.34225547            0 -0.035597548    1.0193906    1.0027701 
-   16100   0.33660991            0 -0.076931881    1.0027701    1.0027701 
-   16200   0.32802152            0  -0.12765884    1.0083102    1.0027701 
-   16300    0.3469374            0  -0.10785455    1.0083102    1.0083102 
-   16400   0.34053641            0 -0.070259853    1.0027701    1.0027701 
-   16500   0.34610591            0 -0.014315306    1.0083102    1.0027701 
-   16600   0.35109001            0  0.041251169    1.0138504    1.0027701 
-   16700   0.34336905            0  0.077996627    1.0193906    1.0027701 
-   16800   0.33277414            0   0.11053634    1.0027701    1.0083102 
-   16900   0.32183338            0   0.11680626    1.0027701    1.0027701 
-   17000   0.34044352            0   0.10806555    1.0138504    1.0027701 
-   17100   0.32967873            0  0.067759786    1.0138504    1.0027701 
-   17200   0.36172278            0 -0.0048631904    1.0083102    1.0083102 
-   17300   0.35619435            0  -0.04215545    1.0027701    1.0027701 
-   17400   0.34540936            0 -0.093994174    1.0083102    1.0027701 
-   17500   0.33193585            0 -0.098831315    1.0083102    1.0027701 
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-   37900   0.33610448            0  0.036836828    1.0138504    1.0027701 
-   38000   0.32757228            0  0.020902031    1.0027701    1.0027701 
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-   38300   0.32509773            0   0.03610738    1.0138504    1.0027701 
-   38400   0.32111741            0  0.034474043    1.0083102    1.0083102 
-   38500   0.30590608            0  0.053461212    1.0083102    1.0027701 
-   38600   0.32322402            0  0.053453832    1.0138504    1.0083102 
-   38700   0.33843057            0  0.076264534    1.0027701    1.0027701 
-   38800   0.31350741            0  0.064733869    1.0083102    1.0027701 
-   38900   0.31943061            0  0.067836769    1.0083102    1.0027701 
-   39000   0.33775583            0    0.0788316    1.0083102    1.0083102 
-   39100   0.34256036            0  0.075874935    1.0027701    1.0027701 
-   39200   0.33128527            0  0.071610976    1.0193906    1.0027701 
-   39300   0.34519653            0  0.046257301    1.0083102    1.0083102 
-   39400   0.34351844            0  0.052422917    1.0027701    1.0027701 
-   39500   0.35716037            0  0.048916058    1.0083102    1.0027701 
-   39600   0.34000737            0  0.016149089    1.0083102    1.0027701 
-   39700   0.34587892            0  0.021619621    1.0083102    1.0083102 
-   39800   0.34878036            0 0.0092881327    1.0083102    1.0027701 
-   39900   0.35225411            0 -0.011341599    1.0083102    1.0027701 
-   40000   0.36309266            0 0.0050869295    1.0304709    1.0027701 
-Loop time of 1.30389 on 2 procs for 40000 steps with 361 atoms
-
-Performance: 13252650.572 tau/day, 30677.432 timesteps/s
-97.6% CPU use with 2 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.041365   | 0.041785   | 0.042204   |   0.2 |  3.20
-Bond    | 0.35501    | 0.37082    | 0.38664    |   2.6 | 28.44
-Neigh   | 0.30901    | 0.31013    | 0.31125    |   0.2 | 23.78
-Comm    | 0.12939    | 0.15871    | 0.18803    |   7.4 | 12.17
-Output  | 0.00489    | 0.005671   | 0.0064521  |   1.0 |  0.43
-Modify  | 0.28208    | 0.28362    | 0.28516    |   0.3 | 21.75
-Other   |            | 0.1332     |            |       | 10.21
-
-Nlocal:    180.5 ave 181 max 180 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost:    52.5 ave 53 max 52 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs:    0 ave 0 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 0
-Ave neighs/atom = 0
-Ave special neighs/atom = 31.0249
-Neighbor list builds = 3079
-Dangerous builds = 0
-Total wall time: 0:00:01

examples/balance/log.27Nov18.balance.bond.slow.g++.4

@@ -1,541 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# 2d circle of particles inside a box with LJ walls
-
-variable        b index 0
-
-variable	x index 50
-variable	y index 20
-variable	d index 20
-
-# careful not to slam into wall too hard
-
-variable	v index 0.3
-variable	w index 0.08
-
-units		lj
-dimension       2
-atom_style	bond
-boundary        f f p
-
-lattice		hex 0.85
-Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
-region		box block 0 $x 0 $y -0.5 0.5
-region		box block 0 50 0 $y -0.5 0.5
-region		box block 0 50 0 20 -0.5 0.5
-create_box	1 box bond/types 1 extra/bond/per/atom 6
-Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
-  2 by 2 by 1 MPI processor grid
-region		circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
-region		circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
-region		circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
-region		circle sphere 11 6.7735026918962581988 0.0 10
-create_atoms	1 region circle
-Created 361 atoms
-  Time spent = 0.000665188 secs
-mass		1 1.0
-
-velocity	all create 0.5 87287 loop geom
-velocity        all set $v $w 0 sum yes
-velocity        all set 0.3 $w 0 sum yes
-velocity        all set 0.3 0.08 0 sum yes
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 10.0 1.0 2.5
-
-bond_style      harmonic
-bond_coeff      1 10.0 1.2
-
-create_bonds    many all all 1 1.0 1.5
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 2.8
-  ghost atom cutoff = 2.8
-  binsize = 1.4, bins = 42 29 1
-  2 neighbor lists, perpetual/occasional/extra = 1 1 0
-  (1) command create_bonds, occasional
-      attributes: full, newton on
-      pair build: full/bin
-      stencil: full/bin/2d
-      bin: standard
-  (2) pair lj/cut, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/2d/newton
-      bin: standard
-Added 1014 bonds, new total = 1014
-  6 = max # of 1-2 neighbors
-  30 = max # of 1-3 neighbors
-  180 = max # of 1-4 neighbors
-  36 = max # of special neighbors
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix		1 all nve
-
-fix             2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
-fix             2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
-fix             3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
-fix             3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
-
-comm_style      tiled
-fix             10 all balance 50 0.9 rcb
-
-#compute         1 all property/atom proc
-#variable        p atom (c_1%10)+1
-#dump            2 all custom 50 tmp.dump id v_p x y z
-
-#dump            3 all image 200 image.*.jpg v_p type bond atom 0.25 #                adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
-#variable        colors string #                "red green blue yellow white #                purple pink orange lime gray"
-#dump_modify     3 pad 5 amap 0 10 sa 1 10 ${colors}
-
-thermo_style    custom step temp epair press f_10[3] f_10
-thermo          100
-
-run		40000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 2.8
-  ghost atom cutoff = 2.8
-  binsize = 1.4, bins = 42 29 1
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/cut, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/2d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.02 | 7.048 | 7.096 Mbytes
-Step Temp E_pair Press f_10[3] f_10 
-       0   0.57437856            0   0.26099453    3.2354571    1.0526316 
-     100   0.29756515            0   0.10149401    1.0193906    1.0083102 
-     200   0.35394813            0  0.075159099    1.0304709    1.0193906 
-     300   0.39245849            0  0.033002384    1.0083102    1.0193906 
-     400   0.34078347            0 -0.020825841    1.0304709    1.0083102 
-     500   0.35201095            0 -0.062637506    1.0193906    1.0083102 
-     600   0.34014717            0  -0.11122965    1.0415512    1.0083102 
-     700    0.3323524            0  -0.11598015    1.0193906    1.0083102 
-     800   0.35116047            0 -0.096162395    1.0193906    1.0193906 
-     900   0.35695352            0  -0.01385176    1.0526316    1.0193906 
-    1000   0.36986539            0  0.056772858    1.0083102    1.0083102 
-    1100   0.34584644            0  0.084941323    1.0304709    1.0083102 
-    1200   0.31921435            0   0.10545078    1.0415512    1.0083102 
-    1300   0.32952819            0     0.124902    1.0083102    1.0193906 
-    1400   0.34497365            0   0.12662081    1.0193906    1.0083102 
-    1500   0.33429243            0  0.096230972    1.0193906    1.0193906 
-    1600   0.33765387            0  0.025800542    1.0304709    1.0083102 
-    1700   0.35134464            0  -0.04422593    1.0415512    1.0083102 
-    1800   0.35003859            0 -0.096745576    1.0304709    1.0083102 
-    1900   0.33839618            0 -0.095465943    1.0193906    1.0083102 
-    2000   0.33732078            0 -0.094652802    1.0083102    1.0083102 
-    2100   0.34552238            0 -0.076729261    1.0304709    1.0083102 
-    2200   0.34893142            0 -0.036853228    1.0304709    1.0083102 
-    2300   0.35379341            0  0.021124847    1.0304709    1.0193906 
-    2400   0.34829744            0   0.09230184    1.0304709    1.0083102 
-    2500   0.33038141            0    0.1399855    1.0193906    1.0193906 
-    2600   0.30983019            0   0.12754742    1.0083102    1.0083102 
-    2700   0.32992561            0   0.10485138    1.0415512    1.0083102 
-    2800   0.34604747            0  0.066174138    1.0083102    1.0083102 
-    2900    0.3444791            0  0.036590652    1.0193906    1.0193906 
-    3000   0.34721342            0 -0.023793368    1.0193906    1.0193906 
-    3100   0.33404314            0  -0.08374223    1.0415512    1.0083102 
-    3200   0.33019355            0  -0.12715599    1.0083102    1.0304709 
-    3300   0.33515177            0  -0.12217394    1.0193906    1.0083102 
-    3400   0.33628481            0 -0.070877624    1.0193906    1.0083102 
-    3500   0.34257038            0 -0.021612062    1.0304709    1.0083102 
-    3600   0.32838009            0  0.030131228    1.0083102    1.0083102 
-    3700   0.34462142            0  0.074586378    1.0526316    1.0193906 
-    3800   0.30891825            0   0.10605673    1.0304709    1.0083102 
-    3900   0.33847951            0   0.13956139    1.0083102    1.0083102 
-    4000   0.32952079            0   0.12688129    1.0193906    1.0304709 
-    4100   0.32646772            0  0.081089042    1.0304709    1.0193906 
-    4200   0.35399503            0  0.013422873    1.0083102    1.0083102 
-    4300   0.33154914            0 -0.050919508    1.0193906    1.0193906 
-    4400   0.34113556            0    -0.083171    1.0304709    1.0083102 
-    4500   0.32651708            0   -0.1063133    1.0304709    1.0083102 
-    4600   0.34359609            0   -0.1076395    1.0083102    1.0083102 
-    4700   0.34973537            0 -0.088231606    1.0415512    1.0083102 
-    4800   0.35198515            0 -0.020901044    1.0415512    1.0083102 
-    4900   0.35187284            0  0.043645941    1.0415512    1.0083102 
-    5000   0.34887336            0  0.095698609    1.0193906    1.0083102 
-    5100   0.30308163            0   0.11649328    1.0193906    1.0083102 
-    5200   0.32401285            0   0.12072411    1.0193906    1.0083102 
-    5300   0.33025072            0   0.10933161    1.0193906    1.0083102 
-    5400   0.33288012            0  0.078356448    1.0083102    1.0193906 
-    5500   0.35142492            0  0.036958063    1.0193906    1.0083102 
-    5600   0.35125368            0 -0.041371343    1.0304709    1.0083102 
-    5700   0.34547744            0 -0.096450846    1.0637119    1.0083102 
-    5800   0.30939887            0  -0.12356656    1.0083102    1.0193906 
-    5900   0.32315628            0  -0.11338676    1.0193906    1.0193906 
-    6000   0.34117485            0 -0.066198961    1.0193906    1.0083102 
-    6100   0.35298043            0 -0.016172816    1.0304709    1.0193906 
-    6200   0.35130653            0  0.027660468    1.0415512    1.0083102 
-    6300   0.35398766            0  0.087221238    1.0083102    1.0083102 
-    6400   0.30963379            0   0.11990957    1.0415512    1.0083102 
-    6500    0.3174541            0   0.14103528    1.0193906    1.0193906 
-    6600   0.31989791            0   0.11575506    1.0304709    1.0193906 
-    6700   0.33811477            0  0.060747353    1.0415512    1.0193906 
-    6800    0.3424043            0  0.010357152    1.0193906    1.0083102 
-    6900   0.34804319            0 -0.042621786    1.0193906    1.0083102 
-    7000   0.35357865            0 -0.067248959    1.0083102    1.0083102 
-    7100   0.33556885            0  -0.10983726    1.0193906    1.0083102 
-    7200   0.33531101            0    -0.112179    1.0304709    1.0083102 
-    7300   0.35742607            0 -0.078405267    1.0304709    1.0193906 
-    7400   0.34577559            0  -0.01985432    1.0193906    1.0083102 
-    7500    0.3498641            0  0.052289439    1.0526316    1.0083102 
-    7600   0.33773715            0  0.092939035    1.0083102    1.0193906 
-    7700   0.33093497            0   0.11924405    1.0304709    1.0083102 
-    7800   0.31435814            0   0.12701724    1.0083102    1.0304709 
-    7900   0.33132217            0   0.10793075    1.0083102    1.0083102 
-    8000   0.33451798            0  0.077993125    1.0304709    1.0193906 
-    8100   0.35188371            0  0.019929977    1.0193906    1.0083102 
-    8200   0.33645742            0 -0.039302079    1.0193906    1.0193906 
-    8300    0.3415632            0 -0.098067982    1.0193906    1.0083102 
-    8400   0.30619282            0  -0.12952879    1.0304709    1.0193906 
-    8500   0.34446484            0 -0.098084709    1.0083102    1.0083102 
-    8600   0.33761673            0  -0.07069818    1.0193906    1.0083102 
-    8700   0.34495452            0 -0.022458056    1.0193906    1.0083102 
-    8800   0.33502983            0  0.027742411    1.0193906    1.0083102 
-    8900   0.35418591            0  0.092390134    1.0083102    1.0193906 
-    9000   0.31648387            0   0.12467398    1.0193906    1.0083102 
-    9100   0.33994825            0   0.14460327    1.0193906    1.0083102 
-    9200   0.33822571            0   0.11273284    1.0193906    1.0083102 
-    9300   0.33260773            0  0.060063671    1.0083102    1.0193906 
-    9400   0.36140305            0  0.021427642    1.0193906    1.0083102 
-    9500   0.34273562            0 -0.034064202    1.0193906    1.0083102 
-    9600   0.33867054            0 -0.089076906    1.0193906    1.0083102 
-    9700   0.32088235            0  -0.12027075    1.0193906    1.0083102 
-    9800    0.3320823            0  -0.11602794    1.0415512    1.0083102 
-    9900   0.33916442            0 -0.080281044    1.0083102    1.0083102 
-   10000   0.34852268            0  -0.01000914    1.0193906    1.0083102 
-   10100   0.32955942            0   0.04258493    1.0083102    1.0083102 
-   10200   0.34487898            0  0.086971308    1.0304709    1.0083102 
-   10300   0.32325593            0   0.11558149    1.0304709    1.0193906 
-   10400   0.30927871            0   0.12239437    1.0083102    1.0083102 
-   10500   0.33176799            0   0.12285937    1.0193906    1.0083102 
-   10600   0.35120027            0  0.084897432    1.0415512    1.0083102 
-   10700   0.33129697            0 0.0053089279    1.0193906    1.0193906 
-   10800   0.36028769            0  -0.04280715    1.0193906    1.0083102 
-   10900   0.35552287            0 -0.084955999    1.0193906    1.0193906 
-   11000    0.3406024            0 -0.096554577    1.0083102    1.0083102 
-   11100   0.33041202            0  -0.10703492    1.0304709    1.0193906 
-   11200   0.32442686            0 -0.084328121    1.0304709    1.0193906 
-   11300   0.35952468            0 -0.020191965    1.0304709    1.0083102 
-   11400   0.34610624            0   0.03440148    1.0193906    1.0193906 
-   11500    0.3415612            0    0.1041929    1.0193906    1.0083102 
-   11600   0.34040042            0   0.13215705    1.0304709    1.0083102 
-   11700   0.33555094            0   0.12738686    1.0415512    1.0193906 
-   11800    0.3458647            0   0.10963398    1.0083102    1.0193906 
-   11900   0.33836678            0  0.067253864    1.0193906    1.0193906 
-   12000   0.34853314            0   0.03201448    1.0193906    1.0083102 
-   12100   0.34600048            0 -0.034833402    1.0304709    1.0193906 
-   12200   0.33145631            0  -0.09865675    1.0193906    1.0193906 
-   12300   0.32848884            0   -0.1248489    1.0193906    1.0083102 
-   12400    0.3321344            0  -0.11266575    1.0083102    1.0083102 
-   12500   0.32622305            0 -0.061634993    1.0304709    1.0083102 
-   12600   0.36213537            0 -0.0090593315    1.0526316    1.0083102 
-   12700   0.34673866            0  0.036734645    1.0193906    1.0083102 
-   12800   0.34606618            0  0.086267678    1.0193906    1.0083102 
-   12900   0.34271431            0   0.12415522    1.0193906    1.0083102 
-   13000   0.31993287            0   0.13879926    1.0193906    1.0193906 
-   13100    0.3422918            0   0.11978905    1.0083102    1.0083102 
-   13200   0.33055236            0  0.062620483    1.0083102    1.0083102 
-   13300   0.34652207            0 0.0043833459    1.0304709    1.0083102 
-   13400   0.33574661            0  -0.04691024    1.0304709    1.0083102 
-   13500   0.33940837            0 -0.074241604    1.0304709    1.0083102 
-   13600   0.32093414            0   -0.1078027    1.0193906    1.0083102 
-   13700   0.34336597            0  -0.10544097    1.0193906    1.0083102 
-   13800   0.35806461            0 -0.072531559    1.0193906    1.0083102 
-   13900   0.35209713            0 -0.018851408    1.0193906    1.0083102 
-   14000   0.35702629            0  0.061046366    1.0083102    1.0083102 
-   14100   0.33234093            0  0.094086465    1.0083102    1.0083102 
-   14200    0.3459466            0   0.12186656    1.0193906    1.0193906 
-   14300    0.3327428            0   0.11396572    1.0193906    1.0083102 
-   14400   0.32409443            0   0.10658903    1.0193906    1.0193906 
-   14500   0.35022184            0  0.083558031    1.0083102    1.0083102 
-   14600   0.34823843            0  0.024605569    1.0083102    1.0193906 
-   14700   0.35298973            0 -0.040418888    1.0193906    1.0083102 
-   14800   0.33679845            0  -0.10067728    1.0193906    1.0083102 
-   14900   0.32790966            0  -0.10925568    1.0193906    1.0193906 
-   15000   0.34208495            0  -0.09568004    1.0193906    1.0083102 
-   15100   0.33647529            0 -0.055652929    1.0083102    1.0083102 
-   15200   0.35328398            0 -0.020236536    1.0415512    1.0193906 
-   15300   0.34252669            0  0.026434179    1.0304709    1.0083102 
-   15400   0.34409435            0  0.094410599    1.0304709    1.0083102 
-   15500   0.32288994            0   0.12034455    1.0304709    1.0193906 
-   15600   0.32109689            0   0.13645185    1.0193906    1.0083102 
-   15700   0.33681572            0  0.098607746    1.0415512    1.0193906 
-   15800   0.33635195            0   0.05570715    1.0193906    1.0083102 
-   15900   0.34289757            0  0.013849092    1.0304709    1.0083102 
-   16000   0.34225547            0 -0.035597548    1.0304709    1.0083102 
-   16100   0.33660991            0 -0.076931881    1.0193906    1.0193906 
-   16200   0.32802152            0  -0.12765884    1.0083102    1.0193906 
-   16300    0.3469374            0  -0.10785455    1.0083102    1.0083102 
-   16400   0.34053641            0 -0.070259853    1.0193906    1.0083102 
-   16500   0.34610591            0 -0.014315306    1.0193906    1.0193906 
-   16600   0.35109001            0  0.041251169    1.0304709    1.0083102 
-   16700   0.34336905            0  0.077996627    1.0193906    1.0083102 
-   16800   0.33277414            0   0.11053634    1.0083102    1.0083102 
-   16900   0.32183338            0   0.11680626    1.0193906    1.0083102 
-   17000   0.34044352            0   0.10806555    1.0193906    1.0083102 
-   17100   0.32967873            0  0.067759786    1.0193906    1.0193906 
-   17200   0.36172278            0 -0.0048631904    1.0304709    1.0083102 
-   17300   0.35619435            0  -0.04215545    1.0193906    1.0083102 
-   17400   0.34540936            0 -0.093994174    1.0193906    1.0083102 
-   17500   0.33193585            0 -0.098831315    1.0083102    1.0193906 
-   17600    0.3544756            0 -0.085660403    1.0193906    1.0083102 
-   17700   0.34505209            0 -0.069640515    1.0304709    1.0193906 
-   17800   0.36291124            0 -0.0063088133    1.0083102    1.0193906 
-   17900   0.34255705            0  0.046794555    1.0304709    1.0193906 
-   18000   0.34163238            0   0.11767705    1.0193906    1.0193906 
-   18100    0.3466445            0    0.1351712    1.0415512    1.0193906 
-   18200   0.33037668            0   0.12703659    1.0083102    1.0083102 
-   18300   0.33677404            0   0.10956306    1.0083102    1.0304709 
-   18400   0.34978954            0  0.087193072    1.0193906    1.0193906 
-   18500   0.33354363            0  0.051095814    1.0526316    1.0193906 
-   18600   0.34651729            0 0.0056245561    1.0304709    1.0193906 
-   18700   0.32622232            0 -0.047319269    1.0083102    1.0193906 
-   18800   0.32978847            0 -0.054929416    1.0304709    1.0193906 
-   18900   0.34192451            0 -0.037252471    1.0193906    1.0083102 
-   19000   0.34061294            0 -0.001167235    1.0083102    1.0083102 
-   19100   0.34194478            0  0.016945224    1.0526316    1.0193906 
-   19200   0.33321765            0  0.050665354    1.0526316    1.0083102 
-   19300   0.33197783            0  0.080470585    1.0193906    1.0083102 
-   19400   0.33284715            0   0.12423599    1.0304709    1.0304709 
-   19500   0.33867856            0   0.12689524    1.0083102    1.0083102 
-   19600   0.36092786            0   0.11417704    1.0193906    1.0083102 
-   19700   0.34270183            0  0.069038291    1.0415512    1.0083102 
-   19800   0.34880695            0  0.042483681    1.0193906    1.0083102 
-   19900   0.33903644            0  0.034788638    1.0083102    1.0193906 
-   20000   0.32590125            0  0.011383785    1.0193906    1.0083102 
-   20100   0.30358859            0 0.0030743554    1.0526316    1.0193906 
-   20200   0.31830224            0  0.017637826    1.0193906    1.0193906 
-   20300   0.34195438            0  0.072811099    1.0304709    1.0193906 
-   20400   0.31249563            0   0.10063541    1.0415512    1.0083102 
-   20500   0.31544938            0    0.1405794    1.0083102    1.0083102 
-   20600   0.30071644            0   0.12763486    1.0193906    1.0193906 
-   20700    0.2890265            0    0.1136651    1.0083102    1.0083102 
-   20800   0.28962296            0  0.094481978    1.0193906    1.0083102 
-   20900   0.29447212            0    0.0967165    1.0193906    1.0193906 
-   21000   0.31159961            0  0.067307231    1.0083102    1.0083102 
-   21100   0.30490648            0  0.017689358    1.0083102    1.0304709 
-   21200   0.30687262            0 -0.016055512    1.0193906    1.0193906 
-   21300   0.30083286            0 -0.0014988997    1.0193906    1.0083102 
-   21400   0.32070426            0  0.015960302    1.0083102    1.0083102 
-   21500   0.31439311            0  0.038170385    1.0304709    1.0083102 
-   21600   0.32617832            0  0.043263788    1.0083102    1.0083102 
-   21700   0.35151793            0  0.066302727    1.0193906    1.0083102 
-   21800   0.35912885            0  0.070099103    1.0193906    1.0083102 
-   21900   0.32451958            0  0.068935768    1.0304709    1.0193906 
-   22000   0.35219298            0  0.067161227    1.0193906    1.0193906 
-   22100   0.34857705            0  0.032731746    1.0193906    1.0083102 
-   22200   0.34750227            0 0.0056917695    1.0193906    1.0083102 
-   22300   0.34766017            0 -0.0027090483    1.0193906    1.0083102 
-   22400   0.33426062            0 -0.023196063    1.0304709    1.0083102 
-   22500   0.34174625            0 -0.025019717    1.0083102    1.0083102 
-   22600    0.3356145            0 -0.029707418    1.0304709    1.0193906 
-   22700    0.3362653            0 -0.035815733    1.0193906    1.0193906 
-   22800   0.33973405            0 -0.0024705835    1.0193906    1.0083102 
-   22900   0.33813085            0 0.0077527467    1.0083102    1.0193906 
-   23000   0.33339981            0  0.028340744    1.0193906    1.0083102 
-   23100   0.34079832            0  0.018521302    1.0415512    1.0193906 
-   23200   0.33074548            0  0.032378405    1.0193906    1.0083102 
-   23300   0.32965664            0  0.035989589    1.0193906    1.0083102 
-   23400   0.30927749            0  0.024581106    1.0193906    1.0083102 
-   23500   0.32890632            0   0.01092479    1.0304709    1.0193906 
-   23600   0.34137438            0 0.0094839745    1.0193906    1.0193906 
-   23700   0.34512638            0 -0.012392771    1.0304709    1.0193906 
-   23800   0.31781354            0 -0.012908449    1.0193906    1.0083102 
-   23900   0.32405513            0 -0.015018071    1.0415512    1.0193906 
-   24000   0.33549728            0 -0.012812915    1.0193906    1.0193906 
-   24100   0.31368736            0 -0.020818372    1.0083102    1.0083102 
-   24200   0.33533836            0 0.0056121057    1.0304709    1.0193906 
-   24300   0.32530627            0  0.018183931    1.0415512    1.0083102 
-   24400   0.31930662            0  0.027446878    1.0083102    1.0193906 
-   24500   0.33540302            0  0.040307455    1.0304709    1.0083102 
-   24600   0.34020431            0  0.027403921    1.0083102    1.0083102 
-   24700    0.3291814            0   0.01204865    1.0193906    1.0083102 
-   24800   0.31552604            0  0.019654111    1.0083102    1.0193906 
-   24900   0.34727253            0   0.01670543    1.0193906    1.0083102 
-   25000   0.35120105            0 0.0038617562    1.0193906    1.0083102 
-   25100   0.32706871            0 -0.021196623    1.0415512    1.0193906 
-   25200   0.32915282            0 -0.017146508    1.0083102    1.0193906 
-   25300   0.32577518            0  -0.01312495    1.0193906    1.0083102 
-   25400   0.33286855            0 0.0014726193    1.0415512    1.0193906 
-   25500   0.33002601            0 0.0080974022    1.0193906    1.0083102 
-   25600   0.34127655            0  0.014296091    1.0526316    1.0083102 
-   25700   0.34048065            0  0.022513032    1.0193906    1.0083102 
-   25800   0.33029079            0  0.038733531    1.0526316    1.0083102 
-   25900   0.33031324            0  0.026156982    1.0083102    1.0193906 
-   26000   0.32967371            0  0.028727383    1.0083102    1.0193906 
-   26100   0.33775718            0  0.015607478    1.0083102    1.0193906 
-   26200   0.35097144            0  0.012291703    1.0083102    1.0083102 
-   26300   0.34303792            0 0.00094823191    1.0083102    1.0193906 
-   26400   0.33632665            0 -0.0026904889    1.0193906    1.0193906 
-   26500   0.33580127            0 -0.0074168555    1.0193906    1.0193906 
-   26600   0.33063188            0 -0.020378601    1.0083102    1.0193906 
-   26700   0.33581846            0 -0.00084397268    1.0083102    1.0193906 
-   26800   0.32998532            0  0.015932208    1.0304709    1.0193906 
-   26900   0.33825444            0  0.010428603    1.0304709    1.0083102 
-   27000   0.32081518            0  0.019818223    1.0415512    1.0193906 
-   27100   0.31448098            0  0.020093416    1.0193906    1.0083102 
-   27200   0.32643684            0  0.021934917    1.0193906    1.0083102 
-   27300   0.33289466            0  0.023713072    1.0415512    1.0083102 
-   27400   0.32310744            0  0.024110945    1.0415512    1.0083102 
-   27500   0.33115619            0 0.0025776713    1.0304709    1.0193906 
-   27600   0.33295887            0 -0.010710764    1.0193906    1.0193906 
-   27700   0.32968876            0 -0.0064595905    1.0193906    1.0193906 
-   27800   0.34064581            0 -0.0086519116    1.0193906    1.0083102 
-   27900   0.33559187            0 -0.0055753593    1.0526316    1.0083102 
-   28000   0.32300727            0 -0.0004153384    1.0304709    1.0083102 
-   28100   0.32147461            0 -0.0058543412    1.0083102    1.0083102 
-   28200   0.35532383            0  0.013646951    1.0304709    1.0083102 
-   28300   0.31507942            0  0.026532255    1.0415512    1.0193906 
-   28400   0.32711006            0  0.033214981    1.0193906    1.0083102 
-   28500   0.34472462            0  0.028050837    1.0304709    1.0193906 
-   28600   0.33708059            0  0.019115676    1.0083102    1.0083102 
-   28700   0.34478087            0  0.023743689    1.0304709    1.0083102 
-   28800   0.34546686            0 0.0081772997    1.0304709    1.0083102 
-   28900   0.34004886            0  0.017771865    1.0415512    1.0193906 
-   29000   0.33604232            0 -0.010505671    1.0304709    1.0193906 
-   29100   0.33541374            0 -0.016273261    1.0083102    1.0083102 
-   29200   0.34347489            0 -0.010002306    1.0083102    1.0083102 
-   29300   0.34083904            0 0.0089701784    1.0193906    1.0193906 
-   29400   0.34846892            0  0.020765104    1.0083102    1.0083102 
-   29500    0.3416255            0  0.022650856    1.0304709    1.0083102 
-   29600   0.33725496            0  0.020693083    1.0193906    1.0193906 
-   29700   0.34480638            0  0.024317128    1.0304709    1.0083102 
-   29800   0.31459471            0  0.023097895    1.0083102    1.0083102 
-   29900   0.33014448            0   0.03114046    1.0193906    1.0083102 
-   30000   0.33741498            0  0.015624314    1.0083102    1.0193906 
-   30100   0.32598657            0 -0.0018860541    1.0415512    1.0193906 
-   30200   0.34855815            0 0.0017983372    1.0083102    1.0083102 
-   30300   0.33375921            0 0.0010991235    1.0083102    1.0193906 
-   30400   0.35008944            0 -0.0027316177    1.0193906    1.0083102 
-   30500   0.33279729            0 -0.0035788551    1.0193906    1.0193906 
-   30600   0.33868746            0 -0.0016249482    1.0083102    1.0193906 
-   30700   0.33597034            0 -0.0014524001    1.0193906    1.0193906 
-   30800    0.3227257            0  0.016353457    1.0193906    1.0193906 
-   30900   0.32676516            0  0.027396654    1.0193906    1.0083102 
-   31000   0.34083982            0  0.031606413    1.0415512    1.0193906 
-   31100   0.32165238            0  0.013583368    1.0083102    1.0083102 
-   31200    0.3428492            0  0.020486611    1.0304709    1.0083102 
-   31300   0.32372541            0   0.01215566    1.0083102    1.0083102 
-   31400   0.32734692            0  0.016229397    1.0083102    1.0083102 
-   31500   0.33089262            0 0.0060426618    1.0083102    1.0083102 
-   31600   0.34273493            0 -0.013456537    1.0083102    1.0193906 
-   31700   0.32723905            0 -0.019243766    1.0193906    1.0083102 
-   31800   0.33636488            0 0.0027814902    1.0083102    1.0083102 
-   31900   0.32834805            0   0.00706877    1.0083102    1.0193906 
-   32000   0.33995148            0 0.0018383309    1.0193906    1.0193906 
-   32100   0.33412282            0 0.0076455933    1.0083102    1.0083102 
-   32200   0.34334884            0  0.023586129    1.0083102    1.0083102 
-   32300   0.32778925            0  0.020564321    1.0193906    1.0083102 
-   32400   0.33163443            0  0.038878463    1.0193906    1.0083102 
-   32500   0.32290345            0  0.022247461    1.0193906    1.0083102 
-   32600   0.34113954            0  0.010966365    1.0304709    1.0193906 
-   32700   0.33390633            0 0.0037777555    1.0193906    1.0083102 
-   32800   0.34385341            0  0.010556575    1.0193906    1.0193906 
-   32900   0.32137047            0 0.00022027143    1.0304709    1.0193906 
-   33000   0.32079172            0 -0.017261272    1.0193906    1.0083102 
-   33100   0.33570882            0 -0.0051942206    1.0083102    1.0083102 
-   33200   0.34320894            0 -0.011515281    1.0193906    1.0083102 
-   33300   0.32794746            0 -0.0018153673    1.0083102    1.0193906 
-   33400   0.33060982            0  0.027118146    1.0193906    1.0083102 
-   33500   0.33641809            0   0.02143035    1.0083102    1.0193906 
-   33600   0.33643061            0  0.020833068    1.0304709    1.0083102 
-   33700    0.3485949            0  0.030918751    1.0193906    1.0083102 
-   33800    0.3283985            0   0.01947613    1.0193906    1.0083102 
-   33900   0.31959761            0  0.021128147    1.0083102    1.0304709 
-   34000   0.33897984            0  0.015270986    1.0193906    1.0083102 
-   34100   0.32392267            0 0.0020130852    1.0304709    1.0193906 
-   34200   0.33084514            0 -0.024316708    1.0193906    1.0193906 
-   34300    0.3342259            0 -0.0059047764    1.0193906    1.0304709 
-   34400   0.33385098            0 0.0063818721    1.0193906    1.0083102 
-   34500   0.33255603            0  -0.01023837    1.0083102    1.0304709 
-   34600   0.34766173            0 0.0056703013    1.0193906    1.0083102 
-   34700     0.339822            0 0.0061648559    1.0193906    1.0193906 
-   34800   0.33902329            0  0.030037037    1.0415512    1.0193906 
-   34900    0.3216153            0  0.027996689    1.0083102    1.0083102 
-   35000   0.32701056            0  0.024778517    1.0193906    1.0083102 
-   35100    0.3124942            0  0.011316548    1.0304709    1.0193906 
-   35200   0.34486416            0  0.011670127    1.0083102    1.0083102 
-   35300   0.33275353            0  0.020491246    1.0193906    1.0193906 
-   35400   0.33618763            0  0.014678874    1.0083102    1.0083102 
-   35500   0.32352282            0 -0.018568683    1.0193906    1.0193906 
-   35600   0.32617903            0 -0.012796912    1.0193906    1.0304709 
-   35700   0.32378048            0 -0.021318585    1.0193906    1.0193906 
-   35800    0.3371086            0 -0.0023678632    1.0193906    1.0193906 
-   35900   0.33818476            0  0.011197742    1.0193906    1.0083102 
-   36000   0.35142144            0  0.022520935    1.0083102    1.0193906 
-   36100   0.35147297            0  0.020277852    1.0193906    1.0083102 
-   36200   0.33489465            0  0.014564878    1.0415512    1.0193906 
-   36300   0.33841515            0  0.036439962    1.0193906    1.0083102 
-   36400   0.32301096            0  0.019966746    1.0304709    1.0083102 
-   36500   0.35612028            0  0.036509556    1.0083102    1.0083102 
-   36600   0.33841597            0 -0.0042180605    1.0193906    1.0193906 
-   36700   0.34477654            0 -0.0052770853    1.0193906    1.0083102 
-   36800   0.33804317            0 -0.013751733    1.0083102    1.0083102 
-   36900   0.35003816            0 -0.0021184393    1.0083102    1.0083102 
-   37000   0.32965041            0 -0.020900951    1.0193906    1.0083102 
-   37100   0.34653095            0 -0.013667977    1.0193906    1.0083102 
-   37200   0.35019871            0 -0.0071740923    1.0193906    1.0304709 
-   37300   0.34859745            0   0.02006041    1.0304709    1.0083102 
-   37400   0.35739859            0  0.020892822    1.0304709    1.0083102 
-   37500   0.34128859            0  0.041072111    1.0193906    1.0193906 
-   37600   0.33781905            0  0.023376738    1.0193906    1.0083102 
-   37700   0.32961874            0  0.030953741    1.0193906    1.0083102 
-   37800     0.343987            0  0.029579795    1.0083102    1.0083102 
-   37900   0.33610448            0  0.036836828    1.0415512    1.0304709 
-   38000   0.32757228            0  0.020902031    1.0193906    1.0193906 
-   38100   0.32735808            0  0.019544751    1.0193906    1.0083102 
-   38200   0.35646953            0  0.044607528    1.0083102    1.0304709 
-   38300   0.32509773            0   0.03610738    1.0193906    1.0083102 
-   38400   0.32111741            0  0.034474043    1.0193906    1.0193906 
-   38500   0.30590608            0  0.053461212    1.0304709    1.0083102 
-   38600   0.32322402            0  0.053453832    1.0193906    1.0304709 
-   38700   0.33843057            0  0.076264534    1.0083102    1.0193906 
-   38800   0.31350741            0  0.064733869    1.0415512    1.0083102 
-   38900   0.31943061            0  0.067836769    1.0304709    1.0193906 
-   39000   0.33775583            0    0.0788316    1.0193906    1.0193906 
-   39100   0.34256036            0  0.075874935    1.0083102    1.0193906 
-   39200   0.33128527            0  0.071610976    1.0193906    1.0083102 
-   39300   0.34519653            0  0.046257301    1.0193906    1.0083102 
-   39400   0.34351844            0  0.052422917    1.0304709    1.0304709 
-   39500   0.35716037            0  0.048916058    1.0304709    1.0083102 
-   39600   0.34000737            0  0.016149089    1.0304709    1.0083102 
-   39700   0.34587892            0  0.021619621    1.0526316    1.0083102 
-   39800   0.34878036            0 0.0092881327    1.0083102    1.0193906 
-   39900   0.35225411            0 -0.011341599    1.0083102    1.0193906 
-   40000   0.36309266            0 0.0050869295    1.0304709    1.0083102 
-Loop time of 1.12306 on 4 procs for 40000 steps with 361 atoms
-
-Performance: 15386559.518 tau/day, 35617.036 timesteps/s
-90.9% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.023094   | 0.023348   | 0.023582   |   0.1 |  2.08
-Bond    | 0.17827    | 0.19268    | 0.21984    |   3.7 | 17.16
-Neigh   | 0.18144    | 0.18231    | 0.18323    |   0.1 | 16.23
-Comm    | 0.23759    | 0.28095    | 0.30794    |   5.0 | 25.02
-Output  | 0.0062952  | 0.013342   | 0.034226   |  10.4 |  1.19
-Modify  | 0.2379     | 0.24327    | 0.25076    |   0.9 | 21.66
-Other   |            | 0.1871     |            |       | 16.66
-
-Nlocal:    90.25 ave 91 max 89 min
-Histogram: 1 0 0 0 0 1 0 0 0 2
-Nghost:    59.25 ave 61 max 56 min
-Histogram: 1 0 0 0 0 0 0 0 2 1
-Neighs:    0 ave 0 max 0 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 0
-Ave neighs/atom = 0
-Ave special neighs/atom = 31.0249
-Neighbor list builds = 3079
-Dangerous builds = 0
-Total wall time: 0:00:01

examples/balance/log.27Nov18.balance.clock.dynamic.g++.2

@@ -1,227 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# 3d Lennard-Jones melt
-
-units		lj
-atom_style	atomic
-processors      * 1 1
-
-lattice		fcc 0.8442
-Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
-region		box block 0 10 0 10 0 10
-create_box	3 box
-Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
-  2 by 1 by 1 MPI processor grid
-create_atoms	1 box
-Created 4000 atoms
-  Time spent = 0.000549078 secs
-mass		* 1.0
-
-region		long block 3 6 0 10 0 10
-set             region long type 2
-  1400 settings made for type
-
-velocity	all create 1.0 87287
-
-pair_style	lj/cut 2.5
-pair_coeff	* * 1.0 1.0 2.5
-pair_coeff      * 2 1.0 1.0 5.0
-
-neighbor	0.3 bin
-neigh_modify	every 2 delay 4 check yes
-fix		p all property/atom d_WEIGHT
-compute		p all property/atom d_WEIGHT
-fix		0 all balance 50 1.0 shift x 10 1.0                 weight time 1.0 weight store WEIGHT
-variable	maximb equal f_0[1]
-variable	iter   equal f_0[2]
-variable 	prev   equal f_0[3]
-variable	final  equal f_0
-
-#fix		3 all print 50 "${iter} ${prev} ${final} ${maximb}"
-
-fix		1 all nve
-
-#dump		id all atom 50 dump.melt
-#dump		id all custom 50 dump.lammpstrj id type x y z c_p
-
-#dump		2 all image 25 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30
-#dump_modify	2 pad 3
-
-#dump		3 all movie 25 movie.mpg type type #		axes yes 0.8 0.02 view 60 -30
-#dump_modify	3 pad 3
-
-thermo		50
-run		500
-Neighbor list info ...
-  update every 2 steps, delay 4 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 5.3
-  ghost atom cutoff = 5.3
-  binsize = 2.65, bins = 7 7 7
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/cut, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 4.562 | 4.753 | 4.944 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume 
-       0            1   -6.9453205            0   -5.4456955   -5.6812358    4738.2137 
-      50   0.49578514   -6.1929216            0   -5.4494298   -1.6668039    4738.2137 
-     100   0.53275389   -6.2475932            0   -5.4486622   -1.9063885    4738.2137 
-     150   0.53316457   -6.2483202            0   -5.4487733   -1.9476162    4738.2137 
-     200     0.536665   -6.2530113            0    -5.448215    -1.933468    4738.2137 
-     250   0.55006273     -6.27163            0   -5.4467422   -2.0438847    4738.2137 
-     300   0.55111476   -6.2727642            0   -5.4462987   -2.0384873    4738.2137 
-     350   0.55211503    -6.274054            0   -5.4460885   -2.0116976    4738.2137 
-     400   0.54638463   -6.2661715            0   -5.4467995    -1.992248    4738.2137 
-     450   0.55885307   -6.2852263            0   -5.4471563   -2.0669747    4738.2137 
-     500   0.54587069   -6.2662849            0   -5.4476836   -2.0078802    4738.2137 
-Loop time of 3.7099 on 2 procs for 500 steps with 4000 atoms
-
-Performance: 58222.644 tau/day, 134.775 timesteps/s
-99.2% CPU use with 2 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 2.5145     | 2.5951     | 2.6756     |   5.0 | 69.95
-Neigh   | 0.8388     | 0.88634    | 0.93387    |   5.0 | 23.89
-Comm    | 0.17027    | 0.20258    | 0.23489    |   7.2 |  5.46
-Output  | 0.00029612 | 0.00032723 | 0.00035834 |   0.0 |  0.01
-Modify  | 0.016136   | 0.017057   | 0.017979   |   0.7 |  0.46
-Other   |            | 0.008504   |            |       |  0.23
-
-Nlocal:    2000 ave 2157 max 1843 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost:    10465.5 ave 10840 max 10091 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs:    298070 ave 305706 max 290433 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-
-Total # of neighbors = 596139
-Ave neighs/atom = 149.035
-Neighbor list builds = 51
-Dangerous builds = 0
-run		500
-Per MPI rank memory allocation (min/avg/max) = 4.944 | 4.947 | 4.951 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume 
-     500   0.54587069   -6.2662849            0   -5.4476836   -2.0078802    4738.2137 
-     550   0.54137926   -6.2592773            0   -5.4474115   -1.9770236    4738.2137 
-     600   0.54022886   -6.2573307            0     -5.44719   -1.9619637    4738.2137 
-     650   0.54709009   -6.2678862            0   -5.4474562   -1.9958342    4738.2137 
-     700   0.54590044   -6.2656903            0   -5.4470444   -1.9957108    4738.2137 
-     750   0.55098488   -6.2724831            0   -5.4462124   -2.0287523    4738.2137 
-     800    0.5520987   -6.2739184            0   -5.4459774   -2.0084991    4738.2137 
-     850   0.54963958   -6.2702473            0    -5.445994   -1.9740031    4738.2137 
-     900   0.54390586   -6.2615476            0   -5.4458927   -1.9400871    4738.2137 
-     950   0.54741732   -6.2665755            0   -5.4456548   -1.9466417    4738.2137 
-    1000   0.54200867   -6.2591246            0   -5.4463148   -1.8881624    4738.2137 
-Loop time of 3.70634 on 2 procs for 500 steps with 4000 atoms
-
-Performance: 58278.514 tau/day, 134.904 timesteps/s
-99.0% CPU use with 2 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 2.5536     | 2.6173     | 2.6811     |   3.9 | 70.62
-Neigh   | 0.82942    | 0.88683    | 0.94424    |   6.1 | 23.93
-Comm    | 0.16927    | 0.17474    | 0.1802     |   1.3 |  4.71
-Output  | 0.00030422 | 0.00033307 | 0.00036192 |   0.0 |  0.01
-Modify  | 0.016714   | 0.017824   | 0.018933   |   0.8 |  0.48
-Other   |            | 0.009277   |            |       |  0.25
-
-Nlocal:    2000 ave 2136 max 1864 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost:    10413.5 ave 10877 max 9950 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs:    300836 ave 312313 max 289358 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-
-Total # of neighbors = 601671
-Ave neighs/atom = 150.418
-Neighbor list builds = 51
-Dangerous builds = 0
-fix		0 all balance 50 1.0 shift x 5 1.0                 weight neigh 0.5 weight time 0.66 weight store WEIGHT
-run             500
-Per MPI rank memory allocation (min/avg/max) = 4.951 | 5.142 | 5.334 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume 
-    1000   0.54200867   -6.2591246            0   -5.4463148   -1.8881624    4738.2137 
-    1050   0.54633412   -6.2656384            0   -5.4463421   -1.9012895    4738.2137 
-    1100   0.54325667   -6.2612166            0   -5.4465353   -1.8870463    4738.2137 
-    1150   0.55057583   -6.2719187            0   -5.4462614   -1.9575881    4738.2137 
-    1200   0.53728175    -6.251744            0   -5.4460228   -1.8124097    4738.2137 
-    1250   0.54077561   -6.2567544            0   -5.4457938   -1.8418133    4738.2137 
-    1300   0.54430333    -6.260995            0   -5.4447442    -1.856351    4738.2137 
-    1350   0.55097839   -6.2715909            0   -5.4453299   -1.9014337    4738.2137 
-    1400   0.53858139   -6.2526781            0    -5.445008   -1.7965773    4738.2137 
-    1450    0.5421844   -6.2574683            0    -5.444395   -1.7901189    4738.2137 
-    1500   0.54200617   -6.2571433            0   -5.4443373   -1.8000344    4738.2137 
-Loop time of 4.8272 on 2 procs for 500 steps with 4000 atoms
-
-Performance: 44746.478 tau/day, 103.580 timesteps/s
-98.5% CPU use with 2 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.9951     | 2.6814     | 3.3676     |  41.9 | 55.55
-Neigh   | 0.82826    | 0.90961    | 0.99095    |   8.5 | 18.84
-Comm    | 0.44043    | 1.2083     | 1.9762     |  69.9 | 25.03
-Output  | 0.00034881 | 0.0003655  | 0.00038218 |   0.0 |  0.01
-Modify  | 0.016762   | 0.01755    | 0.018337   |   0.6 |  0.36
-Other   |            | 0.01001    |            |       |  0.21
-
-Nlocal:    2000 ave 2564 max 1436 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost:    10334 ave 10752 max 9916 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs:    302958 ave 499873 max 106044 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-
-Total # of neighbors = 605917
-Ave neighs/atom = 151.479
-Neighbor list builds = 51
-Dangerous builds = 0
-run             500
-Per MPI rank memory allocation (min/avg/max) = 4.955 | 5.336 | 5.717 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume 
-    1500   0.54200617   -6.2571433            0   -5.4443373   -1.8000344    4738.2137 
-    1550   0.53713591   -6.2504068            0   -5.4449044   -1.7647087    4738.2137 
-    1600    0.5467956   -6.2646482            0   -5.4446599   -1.8115778    4738.2137 
-    1650   0.53806575   -6.2519004            0   -5.4450036   -1.7409135    4738.2137 
-    1700    0.5347949   -6.2468958            0    -5.444904   -1.7162322    4738.2137 
-    1750   0.53714528   -6.2506529            0   -5.4451365   -1.7340402    4738.2137 
-    1800    0.5274989   -6.2358675            0    -5.444817   -1.6874989    4738.2137 
-    1850   0.54585906   -6.2629475            0   -5.4443636   -1.7758918    4738.2137 
-    1900    0.5301071   -6.2387551            0   -5.4437932   -1.6381903    4738.2137 
-    1950   0.54288149   -6.2582818            0   -5.4441632   -1.7367819    4738.2137 
-    2000   0.52766162   -6.2348587            0   -5.4435642   -1.5589151    4738.2137 
-Loop time of 4.90351 on 2 procs for 500 steps with 4000 atoms
-
-Performance: 44050.062 tau/day, 101.968 timesteps/s
-98.1% CPU use with 2 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.9937     | 2.6502     | 3.3067     |  40.3 | 54.05
-Neigh   | 0.81645    | 0.88655    | 0.95664    |   7.4 | 18.08
-Comm    | 0.61197    | 1.3389     | 2.0659     |  62.8 | 27.31
-Output  | 0.00036287 | 0.0003773  | 0.00039172 |   0.0 |  0.01
-Modify  | 0.016585   | 0.017429   | 0.018274   |   0.6 |  0.36
-Other   |            | 0.01003    |            |       |  0.20
-
-Nlocal:    2000 ave 2564 max 1436 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost:    10256 ave 10620 max 9892 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs:    303988 ave 502064 max 105911 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-
-Total # of neighbors = 607975
-Ave neighs/atom = 151.994
-Neighbor list builds = 51
-Dangerous builds = 0
-Total wall time: 0:00:17

examples/balance/log.27Nov18.balance.clock.dynamic.g++.4

@@ -1,227 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# 3d Lennard-Jones melt
-
-units		lj
-atom_style	atomic
-processors      * 1 1
-
-lattice		fcc 0.8442
-Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
-region		box block 0 10 0 10 0 10
-create_box	3 box
-Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
-  4 by 1 by 1 MPI processor grid
-create_atoms	1 box
-Created 4000 atoms
-  Time spent = 0.000421762 secs
-mass		* 1.0
-
-region		long block 3 6 0 10 0 10
-set             region long type 2
-  1400 settings made for type
-
-velocity	all create 1.0 87287
-
-pair_style	lj/cut 2.5
-pair_coeff	* * 1.0 1.0 2.5
-pair_coeff      * 2 1.0 1.0 5.0
-
-neighbor	0.3 bin
-neigh_modify	every 2 delay 4 check yes
-fix		p all property/atom d_WEIGHT
-compute		p all property/atom d_WEIGHT
-fix		0 all balance 50 1.0 shift x 10 1.0                 weight time 1.0 weight store WEIGHT
-variable	maximb equal f_0[1]
-variable	iter   equal f_0[2]
-variable 	prev   equal f_0[3]
-variable	final  equal f_0
-
-#fix		3 all print 50 "${iter} ${prev} ${final} ${maximb}"
-
-fix		1 all nve
-
-#dump		id all atom 50 dump.melt
-#dump		id all custom 50 dump.lammpstrj id type x y z c_p
-
-#dump		2 all image 25 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30
-#dump_modify	2 pad 3
-
-#dump		3 all movie 25 movie.mpg type type #		axes yes 0.8 0.02 view 60 -30
-#dump_modify	3 pad 3
-
-thermo		50
-run		500
-Neighbor list info ...
-  update every 2 steps, delay 4 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 5.3
-  ghost atom cutoff = 5.3
-  binsize = 2.65, bins = 7 7 7
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/cut, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.691 | 4.072 | 4.454 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume 
-       0            1   -6.9453205            0   -5.4456955   -5.6812358    4738.2137 
-      50   0.48653399   -6.1788509            0   -5.4492324   -1.6017778    4738.2137 
-     100   0.53411175    -6.249885            0   -5.4489177   -1.9317606    4738.2137 
-     150   0.53646658   -6.2527206            0   -5.4482219   -1.9689568    4738.2137 
-     200   0.54551611   -6.2656326            0   -5.4475631   -2.0042104    4738.2137 
-     250   0.54677719   -6.2671162            0   -5.4471555   -2.0015995    4738.2137 
-     300    0.5477618   -6.2678071            0   -5.4463698    -1.997842    4738.2137 
-     350   0.55600296   -6.2801497            0   -5.4463538   -2.0394056    4738.2137 
-     400   0.53241503   -6.2453665            0   -5.4469436    -1.878594    4738.2137 
-     450    0.5439158      -6.2623            0   -5.4466302   -1.9744161    4738.2137 
-     500   0.55526241   -6.2793396            0   -5.4466542   -2.0595015    4738.2137 
-Loop time of 2.69458 on 4 procs for 500 steps with 4000 atoms
-
-Performance: 80160.913 tau/day, 185.558 timesteps/s
-94.2% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.0903     | 1.4509     | 1.7199     |  22.5 | 53.84
-Neigh   | 0.31688    | 0.47906    | 0.71852    |  24.2 | 17.78
-Comm    | 0.60463    | 0.72402    | 0.84257    |  12.7 | 26.87
-Output  | 0.00035119 | 0.00067121 | 0.0015202  |   0.0 |  0.02
-Modify  | 0.00811    | 0.010936   | 0.014029   |   2.7 |  0.41
-Other   |            | 0.02904    |            |       |  1.08
-
-Nlocal:    1000 ave 1504 max 634 min
-Histogram: 2 0 0 0 0 0 1 0 0 1
-Nghost:    8759.25 ave 9896 max 8021 min
-Histogram: 2 0 0 0 0 1 0 0 0 1
-Neighs:    149308 ave 179946 max 116419 min
-Histogram: 1 1 0 0 0 0 0 0 1 1
-
-Total # of neighbors = 597231
-Ave neighs/atom = 149.308
-Neighbor list builds = 50
-Dangerous builds = 0
-run		500
-Per MPI rank memory allocation (min/avg/max) = 4.097 | 4.288 | 4.475 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume 
-     500   0.55526241   -6.2793396            0   -5.4466542   -2.0595015    4738.2137 
-     550   0.53879347   -6.2554274            0   -5.4474393   -1.9756834    4738.2137 
-     600   0.54275982   -6.2616799            0   -5.4477437   -1.9939993    4738.2137 
-     650   0.54526651    -6.265098            0   -5.4474027   -2.0303672    4738.2137 
-     700   0.54369381    -6.263201            0   -5.4478642   -1.9921967    4738.2137 
-     750   0.54452777   -6.2640839            0   -5.4474964   -1.9658675    4738.2137 
-     800   0.55061744   -6.2725556            0   -5.4468359   -2.0100922    4738.2137 
-     850   0.55371614   -6.2763992            0   -5.4460326   -2.0065329    4738.2137 
-     900   0.54756622   -6.2668303            0   -5.4456863   -1.9796122    4738.2137 
-     950   0.54791593   -6.2673161            0   -5.4456477   -1.9598278    4738.2137 
-    1000   0.54173198   -6.2586101            0   -5.4462153   -1.9007466    4738.2137 
-Loop time of 2.64502 on 4 procs for 500 steps with 4000 atoms
-
-Performance: 81662.873 tau/day, 189.034 timesteps/s
-93.3% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.1279     | 1.4127     | 1.6268     |  18.0 | 53.41
-Neigh   | 0.32225    | 0.49572    | 0.76053    |  26.2 | 18.74
-Comm    | 0.64504    | 0.6974     | 0.75498    |   5.7 | 26.37
-Output  | 0.00035477 | 0.00062996 | 0.001343   |   0.0 |  0.02
-Modify  | 0.0077929  | 0.010538   | 0.013856   |   2.6 |  0.40
-Other   |            | 0.02803    |            |       |  1.06
-
-Nlocal:    1000 ave 1437 max 597 min
-Histogram: 1 1 0 0 0 0 0 1 0 1
-Nghost:    8674 ave 9370 max 8013 min
-Histogram: 1 0 1 0 0 0 0 1 0 1
-Neighs:    150170 ave 187030 max 102149 min
-Histogram: 1 0 0 0 0 1 0 1 0 1
-
-Total # of neighbors = 600678
-Ave neighs/atom = 150.169
-Neighbor list builds = 53
-Dangerous builds = 0
-fix		0 all balance 50 1.0 shift x 5 1.0                 weight neigh 0.5 weight time 0.66 weight store WEIGHT
-run             500
-Per MPI rank memory allocation (min/avg/max) = 4.08 | 4.269 | 4.458 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume 
-    1000   0.54173198   -6.2586101            0   -5.4462153   -1.9007466    4738.2137 
-    1050   0.54629742   -6.2657526            0   -5.4465113    -1.945821    4738.2137 
-    1100   0.55427881   -6.2781733            0    -5.446963   -2.0021027    4738.2137 
-    1150   0.54730654    -6.267257            0   -5.4465025   -1.9420678    4738.2137 
-    1200    0.5388281   -6.2547963            0   -5.4467562    -1.890178    4738.2137 
-    1250   0.54848768   -6.2694237            0   -5.4468979   -1.9636797    4738.2137 
-    1300   0.54134321   -6.2590728            0    -5.447261   -1.9170271    4738.2137 
-    1350   0.53564389   -6.2501521            0   -5.4468871   -1.8642306    4738.2137 
-    1400   0.53726924   -6.2518379            0   -5.4461355   -1.8544028    4738.2137 
-    1450   0.54525935   -6.2632653            0   -5.4455808   -1.9072158    4738.2137 
-    1500   0.54223346   -6.2591057            0   -5.4459588   -1.8866984    4738.2137 
-Loop time of 2.61342 on 4 procs for 500 steps with 4000 atoms
-
-Performance: 82650.254 tau/day, 191.320 timesteps/s
-93.1% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.222      | 1.4442     | 1.5812     |  12.3 | 55.26
-Neigh   | 0.29672    | 0.48201    | 0.73859    |  27.6 | 18.44
-Comm    | 0.59138    | 0.65738    | 0.70906    |   6.5 | 25.15
-Output  | 0.00036502 | 0.00091559 | 0.0020845  |   0.0 |  0.04
-Modify  | 0.0095406  | 0.012674   | 0.017643   |   2.8 |  0.48
-Other   |            | 0.01621    |            |       |  0.62
-
-Nlocal:    1000 ave 1446 max 670 min
-Histogram: 2 0 0 0 0 0 1 0 0 1
-Nghost:    8641 ave 9376 max 8019 min
-Histogram: 1 1 0 0 0 0 0 1 0 1
-Neighs:    150494 ave 184085 max 105390 min
-Histogram: 1 0 1 0 0 0 0 0 0 2
-
-Total # of neighbors = 601974
-Ave neighs/atom = 150.494
-Neighbor list builds = 51
-Dangerous builds = 0
-run             500
-Per MPI rank memory allocation (min/avg/max) = 4.08 | 4.269 | 4.458 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume 
-    1500   0.54223346   -6.2591057            0   -5.4459588   -1.8866984    4738.2137 
-    1550   0.55327018   -6.2750125            0   -5.4453148   -1.9506585    4738.2137 
-    1600    0.5441901   -6.2612622            0   -5.4451811   -1.8559436    4738.2137 
-    1650   0.54710046   -6.2661938            0   -5.4457483   -1.8882766    4738.2137 
-    1700    0.5366569   -6.2504957            0   -5.4457116   -1.8067998    4738.2137 
-    1750    0.5486468   -6.2681121            0   -5.4453476   -1.8662631    4738.2137 
-    1800   0.54476176   -6.2615037            0   -5.4445653   -1.8352743    4738.2137 
-    1850    0.5414305   -6.2555519            0   -5.4436091   -1.8005747    4738.2137 
-    1900   0.53992655   -6.2541344            0    -5.444447   -1.7768718    4738.2137 
-    1950   0.54666071   -6.2640943            0   -5.4443082   -1.7947052    4738.2137 
-    2000   0.54556196   -6.2625262            0   -5.4443879   -1.8071631    4738.2137 
-Loop time of 2.81593 on 4 procs for 500 steps with 4000 atoms
-
-Performance: 76706.532 tau/day, 177.561 timesteps/s
-90.7% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.2508     | 1.4839     | 1.6521     |  13.4 | 52.70
-Neigh   | 0.34188    | 0.54016    | 0.82358    |  27.6 | 19.18
-Comm    | 0.70575    | 0.75254    | 0.80167    |   4.6 | 26.72
-Output  | 0.00041604 | 0.001362   | 0.0041099  |   4.3 |  0.05
-Modify  | 0.010564   | 0.013653   | 0.018      |   2.7 |  0.48
-Other   |            | 0.02432    |            |       |  0.86
-
-Nlocal:    1000 ave 1555 max 569 min
-Histogram: 2 0 0 0 0 0 0 1 0 1
-Nghost:    8672.75 ave 9821 max 7993 min
-Histogram: 2 0 0 0 1 0 0 0 0 1
-Neighs:    151656 ave 164603 max 133455 min
-Histogram: 1 0 0 0 0 0 1 1 0 1
-
-Total # of neighbors = 606625
-Ave neighs/atom = 151.656
-Neighbor list builds = 56
-Dangerous builds = 0
-Total wall time: 0:00:10

examples/balance/log.27Nov18.balance.clock.static.g++.2

@@ -1,195 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# 3d Lennard-Jones melt
-
-units		lj
-atom_style	atomic
-processors      * 1 1
-
-variable	factor index 1.0
-
-lattice		fcc 0.8442
-Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
-region		box block 0 10 0 10 0 10
-create_box	3 box
-Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
-  2 by 1 by 1 MPI processor grid
-create_atoms	1 box
-Created 4000 atoms
-  Time spent = 0.000517368 secs
-mass		* 1.0
-
-region		long block 3 6 0 10 0 10
-set             region long type 2
-  1400 settings made for type
-
-velocity	all create 1.0 87287
-
-pair_style	lj/cut 2.5
-pair_coeff	* * 1.0 1.0 2.5
-pair_coeff      * 2 1.0 1.0 5.0
-
-neighbor	0.3 bin
-neigh_modify	every 2 delay 4 check yes
-
-group		fast type 1
-2600 atoms in group fast
-group		slow type 2
-1400 atoms in group slow
-balance		1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt
-Neighbor list info ...
-  update every 2 steps, delay 4 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 5.3
-  ghost atom cutoff = 5.3
-  binsize = 2.65, bins = 7 7 7
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/cut, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-  rebalancing time: 0.000522375 seconds
-  iteration count = 1
-  time weight factor: 1
-  initial/final max load/proc = 2000 2000
-  initial/final imbalance factor = 1 1
-  x cuts: 0 0.5 1
-  y cuts: 0 1
-  z cuts: 0 1
-
-fix		1 all nve
-
-#dump		id all atom 50 dump.melt
-
-#dump		2 all image 25 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30
-#dump_modify	2 pad 3
-
-#dump		3 all movie 25 movie.mpg type type #		axes yes 0.8 0.02 view 60 -30
-#dump_modify	3 pad 3
-
-thermo		50
-run		250
-Per MPI rank memory allocation (min/avg/max) = 4.297 | 4.488 | 4.678 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0            1   -6.9453205            0   -5.4456955   -5.6812358 
-      50   0.49578514   -6.1929216            0   -5.4494298   -1.6668039 
-     100   0.53275389   -6.2475932            0   -5.4486622   -1.9063885 
-     150   0.53316457   -6.2483202            0   -5.4487733   -1.9476162 
-     200     0.536665   -6.2530113            0    -5.448215    -1.933468 
-     250   0.55006273     -6.27163            0   -5.4467422   -2.0438847 
-Loop time of 1.96356 on 2 procs for 250 steps with 4000 atoms
-
-Performance: 55002.186 tau/day, 127.320 timesteps/s
-99.4% CPU use with 2 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.0024     | 1.243      | 1.4835     |  21.6 | 63.30
-Neigh   | 0.3963     | 0.41601    | 0.43572    |   3.1 | 21.19
-Comm    | 0.032948   | 0.29324    | 0.55353    |  48.1 | 14.93
-Output  | 0.00013924 | 0.00014722 | 0.00015521 |   0.0 |  0.01
-Modify  | 0.0072696  | 0.0073524  | 0.0074351  |   0.1 |  0.37
-Other   |            | 0.003842   |            |       |  0.20
-
-Nlocal:    2000 ave 2051 max 1949 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost:    10443 ave 10506 max 10380 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs:    298332 ave 363449 max 233215 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-
-Total # of neighbors = 596664
-Ave neighs/atom = 149.166
-Neighbor list builds = 24
-Dangerous builds = 0
-balance		1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt
-  rebalancing time: 0.000424623 seconds
-  iteration count = 3
-  time weight factor: 1
-  initial/final max load/proc = 1.91926 1.6972
-  initial/final imbalance factor = 1.15689 1.02304
-  x cuts: 0 0.4375 1
-  y cuts: 0 1
-  z cuts: 0 1
-run		250
-Per MPI rank memory allocation (min/avg/max) = 4.681 | 4.683 | 4.685 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-     250   0.55006273     -6.27163            0   -5.4467422   -2.0438847 
-     300   0.55111476   -6.2727642            0   -5.4462987   -2.0384873 
-     350   0.55211503    -6.274054            0   -5.4460885   -2.0116976 
-     400   0.54638463   -6.2661715            0   -5.4467995    -1.992248 
-     450   0.55885307   -6.2852263            0   -5.4471563   -2.0669747 
-     500   0.54587069   -6.2662849            0   -5.4476836   -2.0078802 
-Loop time of 1.84751 on 2 procs for 250 steps with 4000 atoms
-
-Performance: 58457.127 tau/day, 135.317 timesteps/s
-99.5% CPU use with 2 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.1214     | 1.2291     | 1.3368     |   9.7 | 66.53
-Neigh   | 0.37418    | 0.41926    | 0.46434    |   7.0 | 22.69
-Comm    | 0.033842   | 0.18738    | 0.34091    |  35.5 | 10.14
-Output  | 0.00016665 | 0.00018752 | 0.00020838 |   0.0 |  0.01
-Modify  | 0.0062993  | 0.0072798  | 0.0082603  |   1.1 |  0.39
-Other   |            | 0.00428    |            |       |  0.23
-
-Nlocal:    2000 ave 2284 max 1716 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost:    10450 ave 10742 max 10158 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs:    298063 ave 326003 max 270123 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-
-Total # of neighbors = 596126
-Ave neighs/atom = 149.031
-Neighbor list builds = 25
-Dangerous builds = 0
-balance		1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt
-  rebalancing time: 0.000502825 seconds
-  iteration count = 3
-  time weight factor: 1
-  initial/final max load/proc = 1.80118 1.79434
-  initial/final imbalance factor = 1.0927 1.08854
-  x cuts: 0 0.507812 1
-  y cuts: 0 1
-  z cuts: 0 1
-run 		250
-Per MPI rank memory allocation (min/avg/max) = 4.681 | 4.683 | 4.686 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-     500   0.54587069   -6.2662849            0   -5.4476836   -2.0078802 
-     550   0.54137926   -6.2592773            0   -5.4474115   -1.9770236 
-     600   0.54022886   -6.2573307            0     -5.44719   -1.9619637 
-     650   0.54709009   -6.2678862            0   -5.4474562   -1.9958342 
-     700   0.54590044   -6.2656903            0   -5.4470444   -1.9957108 
-     750   0.55098488   -6.2724831            0   -5.4462124   -2.0287523 
-Loop time of 2.03694 on 2 procs for 250 steps with 4000 atoms
-
-Performance: 53020.655 tau/day, 122.733 timesteps/s
-99.3% CPU use with 2 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.92132    | 1.2301     | 1.5389     |  27.8 | 60.39
-Neigh   | 0.3924     | 0.42313    | 0.45386    |   4.7 | 20.77
-Comm    | 0.032816   | 0.37246    | 0.71211    |  55.7 | 18.29
-Output  | 0.00013733 | 0.00014532 | 0.0001533  |   0.0 |  0.01
-Modify  | 0.0069692  | 0.0072372  | 0.0075052  |   0.3 |  0.36
-Other   |            | 0.003856   |            |       |  0.19
-
-Nlocal:    2000 ave 2097 max 1903 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost:    10439.5 ave 10561 max 10318 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs:    299628 ave 378859 max 220397 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-
-Total # of neighbors = 599256
-Ave neighs/atom = 149.814
-Neighbor list builds = 25
-Dangerous builds = 0
-Total wall time: 0:00:05