Merge pull request #3029 from akohlmey/maintenance-2021-09-29

Second round of maintenance fixes for the stable release

cmake/Modules/LAMMPSUtils.cmake

@@ -25,7 +25,7 @@ function(validate_option name values)
 endfunction(validate_option)
 
 function(get_lammps_version version_header variable)
-    file(READ ${version_header} line)
+    file(STRINGS ${version_header} line REGEX LAMMPS_VERSION)
     set(MONTHS x Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec)
     string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\1" day "${line}")
     string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\2" month "${line}")

cmake/Modules/Packages/GPU.cmake

@@ -306,12 +306,12 @@ elseif(GPU_API STREQUAL "HIP")
 
         if(HIP_COMPILER STREQUAL "clang")
           add_custom_command(OUTPUT ${CUBIN_FILE}
-            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
+            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
             DEPENDS ${CU_CPP_FILE}
             COMMENT "Generating ${CU_NAME}.cubin")
         else()
           add_custom_command(OUTPUT ${CUBIN_FILE}
-            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
+            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
             DEPENDS ${CU_CPP_FILE}
             COMMENT "Generating ${CU_NAME}.cubin")
         endif()

cmake/Modules/Packages/MACHDYN.cmake

@@ -7,8 +7,9 @@ endif()
 option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT})
 if(DOWNLOAD_EIGEN3)
   message(STATUS "Eigen3 download requested - we will build our own")
-  set(EIGEN3_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.9/eigen-3.3.9.tar.gz" CACHE STRING "URL for Eigen3 tarball")
-  set(EIGEN3_MD5 "609286804b0f79be622ccf7f9ff2b660" CACHE STRING "MD5 checksum of Eigen3 tarball")
+
+  set(EIGEN3_URL "https://download.lammps.org/thirdparty/eigen-3.4.0.tar.gz" CACHE STRING "URL for Eigen3 tarball")
+  set(EIGEN3_MD5 "4c527a9171d71a72a9d4186e65bea559" CACHE STRING "MD5 checksum of Eigen3 tarball")
   mark_as_advanced(EIGEN3_URL)
   mark_as_advanced(EIGEN3_MD5)
   include(ExternalProject)

doc/Makefile

@@ -230,7 +230,7 @@ $(VENV):
 	)
 
 $(MATHJAX):
-	@git clone -b 3.2.0 -c advice.detachedHead=0 --depth 1 git://github.com/mathjax/MathJax.git $@
+	@git clone -b 3.2.0 -c advice.detachedHead=0 --depth 1 https://github.com/mathjax/MathJax.git $@
 
 $(ANCHORCHECK): $(VENV)
 	@( \

doc/github-development-workflow.md

@@ -33,9 +33,9 @@ when necessary.
 ## Pull Requests
 
 ALL changes to the LAMMPS code and documentation, however trivial, MUST
-be submitted as a pull request to GitHub. All changes to the "master"
+be submitted as a pull request to GitHub. All changes to the "develop"
 branch must be made exclusively through merging pull requests. The
-"unstable" and "stable" branches, respectively are only to be updated
+"release" and "stable" branches, respectively are only to be updated
 upon patch or stable releases with fast-forward merges based on the
 associated tags. Pull requests may also be submitted to (long-running)
 feature branches created by LAMMPS developers inside the LAMMPS project,
@@ -123,16 +123,16 @@ and thus were this comment should be placed.
 
 LAMMPS uses a continuous release development model with incremental
 changes, i.e. significant effort is made - including automated pre-merge
-testing - that the code in the branch "master" does not get easily
+testing - that the code in the branch "develop" does not get easily
 broken.  These tests are run after every update to a pull request.  More
 extensive and time consuming tests (including regression testing) are
-performed after code is merged to the "master" branch. There are patch
+performed after code is merged to the "develop" branch. There are patch
 releases of LAMMPS every 3-5 weeks at a point, when the LAMMPS
 developers feel, that a sufficient amount of changes have happened, and
 the post-merge testing has been successful. These patch releases are
-marked with a `patch_<version date>` tag and the "unstable" branch
+marked with a `patch_<version date>` tag and the "release" branch
 follows only these versions (and thus is always supposed to be of
-production quality, unlike "master", which may be temporary broken, in
+production quality, unlike "develop", which may be temporary broken, in
 the case of larger change sets or unexpected incompatibilities or side
 effects.
 

doc/src/Build_diskspace.rst

@@ -14,7 +14,7 @@ environments with restricted disk space capacity it may be needed to
 reduce the storage requirements. Here are some suggestions:
 
 - Create a so-called shallow repository by cloning only the last commit
-  instead of the full project history by using ``git clone git@github.com:lammps/lammps --depth=1 --branch=master``.
+  instead of the full project history by using ``git clone git@github.com:lammps/lammps --depth=1 --branch=develop``.
   This reduces the downloaded size to about half.  With ``--depth=1`` it is not possible to check out different
   versions/branches of LAMMPS, using ``--depth=1000`` will make multiple recent versions available at little
   extra storage needs (the entire git history had nearly 30,000 commits in fall 2021).

doc/src/Build_manual.rst

@@ -33,12 +33,15 @@ various tools and files.  Some of them have to be installed (see below).  For
 the rest the build process will attempt to download and install them into
 a python virtual environment and local folders.
 
-A current version of the manual (latest patch release, aka unstable
-branch) is is available online at:
-`https://docs.lammps.org/Manual.html <https://docs.lammps.org/Manual.html>`_.
-A version of the manual corresponding to the ongoing development (aka master branch)
-is available online at: `https://docs.lammps.org/latest/
-<https://docs.lammps.org/latest/>`_
+A current version of the manual (latest patch release, that is the state
+of the *release* branch) is is available online at:
+`https://docs.lammps.org/ <https://docs.lammps.org/>`_.
+A version of the manual corresponding to the ongoing development (that is
+the state of the *develop* branch) is available online at:
+`https://docs.lammps.org/latest/ <https://docs.lammps.org/latest/>`_
+A version of the manual corresponding to the latest stable LAMMPS release
+(that is the state of the *stable* branch) is available online at:
+`https://docs.lammps.org/stable/ <https://docs.lammps.org/stable/>`_
 
 Build using GNU make
 --------------------

doc/src/Developer_write.rst

@@ -53,7 +53,7 @@ of each timestep. First of all, implement a constructor:
      if (narg < 4)
        error->all(FLERR,"Illegal fix print/vel command");
 
-     nevery = force->inumeric(FLERR,arg[3]);
+     nevery = utils::inumeric(FLERR,arg[3],false,lmp);
      if (nevery <= 0)
        error->all(FLERR,"Illegal fix print/vel command");
    }

doc/src/Howto_github.rst

@@ -7,11 +7,11 @@ LAMMPS GitHub tutorial
 
 This document describes the process of how to use GitHub to integrate
 changes or additions you have made to LAMMPS into the official LAMMPS
-distribution.  It uses the process of updating this very tutorial as
-an example to describe the individual steps and options.  You need to
-be familiar with git and you may want to have a look at the
-`git book <http://git-scm.com/book/>`_ to reacquaint yourself with some
-of the more advanced git features used below.
+distribution.  It uses the process of updating this very tutorial as an
+example to describe the individual steps and options.  You need to be
+familiar with git and you may want to have a look at the `git book
+<http://git-scm.com/book/>`_ to familiarize yourself with some of the
+more advanced git features used below.
 
 As of fall 2016, submitting contributions to LAMMPS via pull requests
 on GitHub is the preferred option for integrating contributed features
@@ -37,15 +37,15 @@ username or e-mail address and password.
 **Forking the repository**
 
 To get changes into LAMMPS, you need to first fork the `lammps/lammps`
-repository on GitHub. At the time of writing, *master* is the preferred
+repository on GitHub. At the time of writing, *develop* is the preferred
 target branch. Thus go to `LAMMPS on GitHub <https://github.com/lammps/lammps>`_
-and make sure branch is set to "master", as shown in the figure below.
+and make sure branch is set to "develop", as shown in the figure below.
 
 .. image:: JPG/tutorial_branch.png
    :align: center
 
-If it is not, use the button to change it to *master*\ . Once it is, use the
-fork button to create a fork.
+If it is not, use the button to change it to *develop*. Once it is, use
+the fork button to create a fork.
 
 .. image:: JPG/tutorial_fork.png
    :align: center
@@ -64,11 +64,12 @@ LAMMPS development.
 **Adding changes to your own fork**
 
 Additions to the upstream version of LAMMPS are handled using *feature
-branches*\ .  For every new feature, a so-called feature branch is
+branches*.  For every new feature, a so-called feature branch is
 created, which contains only those modification relevant to one specific
 feature. For example, adding a single fix would consist of creating a
 branch with only the fix header and source file and nothing else.  It is
-explained in more detail here: `feature branch workflow <https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow>`_.
+explained in more detail here: `feature branch workflow
+<https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow>`_.
 
 **Feature branches**
 
@@ -94,8 +95,8 @@ The above command copies ("clones") the git repository to your local
 machine to a directory with the name you chose. If none is given, it will
 default to "lammps". Typical names are "mylammps" or something similar.
 
-You can use this local clone to make changes and
-test them without interfering with the repository on GitHub.
+You can use this local clone to make changes and test them without
+interfering with the repository on GitHub.
 
 To pull changes from upstream into this copy, you can go to the directory
 and use git pull:
@@ -103,28 +104,46 @@ and use git pull:
 .. code-block:: bash
 
      $ cd mylammps
-     $ git checkout master
-     $ git pull https://github.com/lammps/lammps
+     $ git checkout develop
+     $ git pull https://github.com/lammps/lammps develop
 
 You can also add this URL as a remote:
 
 .. code-block:: bash
 
-     $ git remote add lammps_upstream https://www.github.com/lammps/lammps
+     $ git remote add upstream https://www.github.com/lammps/lammps
 
-At this point, you typically make a feature branch from the updated master
+From then on you can update your upstream branches with:
+
+.. code-block:: bash
+
+     $ git fetch upstream
+
+and then refer to the upstream repository branches with
+`upstream/develop` or `upstream/release` and so on.
+
+At this point, you typically make a feature branch from the updated
 branch for the feature you want to work on. This tutorial contains the
 workflow that updated this tutorial, and hence we will call the branch
 "github-tutorial-update":
 
 .. code-block:: bash
 
-    $ git checkout -b github-tutorial-update master
+    $ git fetch upstream
+    $ git checkout -b github-tutorial-update upstream/develop
 
 Now that we have changed branches, we can make our changes to our local
 repository. Just remember that if you want to start working on another,
 unrelated feature, you should switch branches!
 
+.. note::
+
+   Committing changes to the *develop*, *release*, or *stable* branches
+   is strongly discouraged.  While it may be convenient initially, it
+   will create more work in the long run.  Various texts and tutorials
+   on using git effectively discuss the motivation for using feature
+   branches instead.
+
 **After changes are made**
 
 After everything is done, add the files to the branch and commit them:
@@ -287,28 +306,32 @@ After each push, the automated checks are run again.
 
 LAMMPS developers may add labels to your pull request to assign it to
 categories (mostly for bookkeeping purposes), but a few of them are
-important: needs_work, work_in_progress, test-for-regression, and
-full-regression-test. The first two indicate, that your pull request
-is not considered to be complete. With "needs_work" the burden is on
-exclusively on you; while "work_in_progress" can also mean, that a
-LAMMPS developer may want to add changes. Please watch the comments
-to the pull requests. The two "test" labels are used to trigger
-extended tests before the code is merged. This is sometimes done by
-LAMMPS developers, if they suspect that there may be some subtle
-side effects from your changes. It is not done by default, because
-those tests are very time consuming.
+important: *needs_work*, *work_in_progress*, *run_tests*,
+*test_for_regression*, and *ready_for_merge*.  The first two indicate,
+that your pull request is not considered to be complete. With
+"needs_work" the burden is on exclusively on you; while
+"work_in_progress" can also mean, that a LAMMPS developer may want to
+add changes. Please watch the comments to the pull requests. The two
+"test" labels are used to trigger extended tests before the code is
+merged. This is sometimes done by LAMMPS developers, if they suspect
+that there may be some subtle side effects from your changes. It is not
+done by default, because those tests are very time consuming.  The
+*ready_for_merge* label is usually attached when the LAMMPS developer
+assigned to the pull request considers this request complete and to
+trigger a final full test evaluation.
 
 **Reviews**
 
-As of Summer 2018, a pull request needs at least 1 approving review
-from a LAMMPS developer with write access to the repository.
-In case your changes touch code that certain developers are associated
-with, they are auto-requested by the GitHub software.  Those associations
-are set in the file
-`.github/CODEOWNERS <https://github.com/lammps/lammps/blob/master/.github/CODEOWNERS>`_
-Thus if you want to be automatically notified to review when anybody
-changes files or packages, that you have contributed to LAMMPS, you can
-add suitable patterns to that file, or a LAMMPS developer may add you.
+As of Fall 2021, a pull request needs to pass all automatic tests and at
+least 1 approving review from a LAMMPS developer with write access to
+the repository before it is eligible for merging.  In case your changes
+touch code that certain developers are associated with, they are
+auto-requested by the GitHub software.  Those associations are set in
+the file `.github/CODEOWNERS
+<https://github.com/lammps/lammps/blob/develop/.github/CODEOWNERS>`_ Thus
+if you want to be automatically notified to review when anybody changes
+files or packages, that **you** have contributed to LAMMPS, you can add
+suitable patterns to that file, or a LAMMPS developer may add you.
 
 Otherwise, you can also manually request reviews from specific developers,
 or LAMMPS developers - in their assessment of your pull request - may
@@ -329,7 +352,7 @@ LAMMPS developer (including him/herself) or c) Axel Kohlmeyer (akohlmey).
   After the review, the developer can choose to implement changes directly
   or suggest them to you.
 * Case c) means that the pull request has been assigned to the developer
-  overseeing the merging of pull requests into the master branch.
+  overseeing the merging of pull requests into the *develop* branch.
 
 In this case, Axel assigned the tutorial to Steve:
 
@@ -351,11 +374,11 @@ Sometimes, however, you might not feel comfortable having other people
 push changes into your own branch, or maybe the maintainers are not sure
 their idea was the right one.  In such a case, they can make changes,
 reassign you as the assignee, and file a "reverse pull request", i.e.
-file a pull request in your GitHub repository to include changes in the
-branch, that you have submitted as a pull request yourself.  In that
-case, you can choose to merge their changes back into your branch,
-possibly make additional changes or corrections and proceed from there.
-It looks something like this:
+file a pull request in **your** forked GitHub repository to include
+changes in the branch, that you have submitted as a pull request
+yourself.  In that case, you can choose to merge their changes back into
+your branch, possibly make additional changes or corrections and proceed
+from there.  It looks something like this:
 
 .. image:: JPG/tutorial_reverse_pull_request.png
    :align: center
@@ -419,7 +442,7 @@ This merge also shows up on the lammps GitHub page:
 
 **After a merge**
 
-When everything is fine, the feature branch is merged into the master branch:
+When everything is fine, the feature branch is merged into the *develop* branch:
 
 .. image:: JPG/tutorial_merged.png
    :align: center
@@ -433,8 +456,8 @@ branch!
 
 .. code-block:: bash
 
-   $ git checkout master
-   $ git pull master
+   $ git checkout develop
+   $ git pull https://github.com/lammps/lammps develop
    $ git branch -d github-tutorial-update
 
 If you do not pull first, it is not really a problem but git will warn
@@ -442,6 +465,7 @@ you at the next statement that you are deleting a local branch that
 was not yet fully merged into HEAD. This is because git does not yet
 know your branch just got merged into LAMMPS upstream. If you
 first delete and then pull, everything should still be fine.
+You can display all branches that are fully merged by:
 
 Finally, if you delete the branch locally, you might want to push this
 to your remote(s) as well:
@@ -453,14 +477,14 @@ to your remote(s) as well:
 **Recent changes in the workflow**
 
 Some changes to the workflow are not captured in this tutorial.  For
-example, in addition to the master branch, to which all new features
-should be submitted, there is now also an "unstable" and a "stable"
-branch; these have the same content as "master", but are only updated
-after a patch release or stable release was made.
-Furthermore, the naming of the patches now follow the pattern
-"patch_<Day><Month><Year>" to simplify comparisons between releases.
-Finally, all patches and submissions are subject to automatic testing
-and code checks to make sure they at the very least compile.
+example, in addition to the *develop* branch, to which all new features
+should be submitted, there is also a *release* and a *stable* branch;
+these have the same content as *develop*, but are only updated after a
+patch release or stable release was made.  Furthermore, the naming of
+the patches now follow the pattern "patch_<Day><Month><Year>" to
+simplify comparisons between releases.  Finally, all patches and
+submissions are subject to automatic testing and code checks to make
+sure they at the very least compile.
 
 A discussion of the LAMMPS developer GitHub workflow can be found in the file
-`doc/github-development-workflow.md <https://github.com/lammps/lammps/blob/master/doc/github-development-workflow.md>`_
+`doc/github-development-workflow.md <https://github.com/lammps/lammps/blob/develop/doc/github-development-workflow.md>`_

doc/src/Install_git.rst

@@ -9,7 +9,8 @@ has several advantages:
   command.
 * You can create your own development branches to add code to LAMMPS.
 * You can submit your new features back to GitHub for inclusion in
-  LAMMPS.
+  LAMMPS.  For that you should first create your own :doc:`fork on
+  GitHub <Howto_github>`.
 
 You must have `git <git_>`_ installed on your system to use the
 commands explained below to communicate with the git servers on
@@ -20,35 +21,56 @@ provides `limited support for subversion clients <svn_>`_.
 
    As of October 2016, the official home of public LAMMPS development is
    on GitHub.  The previously advertised LAMMPS git repositories on
-   git.lammps.org and bitbucket.org are now deprecated or offline.
+   git.lammps.org and bitbucket.org are now offline or deprecated.
 
 .. _git: https://git-scm.com
 .. _svn: https://help.github.com/en/github/importing-your-projects-to-github/working-with-subversion-on-github
 
-You can follow LAMMPS development on 3 different git branches:
+You can follow the LAMMPS development on 3 different git branches:
 
-* **stable**   :  this branch is updated with every stable release
-* **unstable** :  this branch is updated with every patch release
-* **master**   :  this branch continuously follows ongoing development
+* **stable**   :  this branch is updated from the *release* branch with
+  every stable release version and also has selected bug fixes and updates
+  back-ported from the *develop* branch
+* **release**  :  this branch is updated with every patch release;
+  updates are always "fast forward" merges from *develop*
+* **develop**  :  this branch follows the ongoing development and
+  is updated with every merge commit of a pull request
 
 To access the git repositories on your box, use the clone command to
 create a local copy of the LAMMPS repository with a command like:
 
 .. code-block:: bash
 
-   $ git clone -b unstable https://github.com/lammps/lammps.git mylammps
+   $ git clone -b release https://github.com/lammps/lammps.git mylammps
 
 where "mylammps" is the name of the directory you wish to create on
-your machine and "unstable" is one of the 3 branches listed above.
+your machine and "release" is one of the 3 branches listed above.
 (Note that you actually download all 3 branches; you can switch
 between them at any time using "git checkout <branch name>".)
 
+.. admonition:: Saving time and disk space when using ``git clone``
+
+   The complete git history of the LAMMPS project is quite large because
+   it contains the entire commit history of the project since fall 2006,
+   which includes the time when LAMMPS was managed with subversion.
+   This includes a few commits that have added and removed some large
+   files (mostly by accident).  If you do not need access to the entire
+   commit history (most people don't), you can speed up the "cloning"
+   process and reduce local disk space requirements by using the
+   *--depth* git command line flag.  That will create a "shallow clone"
+   of the repository containing only a subset of the git history.  Using
+   a depth of 1000 is usually sufficient to include the head commits of
+   the *develop* and the *release* branches.  To include the head commit
+   of the *stable* branch you may need a depth of up to 10000.  If you
+   later need more of the git history, you can always convert the
+   shallow clone into a "full clone".
+
 Once the command completes, your directory will contain the same files
 as if you unpacked a current LAMMPS tarball, with the exception, that
 the HTML documentation files are not included.  They can be fetched
 from the LAMMPS website by typing ``make fetch`` in the doc directory.
-Or they can be generated from the content provided in doc/src by
-typing ``make html`` from the doc directory.
+Or they can be generated from the content provided in ``doc/src`` by
+typing ``make html`` from the ``doc`` directory.
 
 After initial cloning, as bug fixes and new features are added to
 LAMMPS you can stay up-to-date by typing the following git commands
@@ -56,9 +78,9 @@ from within the "mylammps" directory:
 
 .. code-block:: bash
 
-   $ git checkout unstable      # not needed if you always stay in this branch
-   $ git checkout stable        # use one of these 3 checkout commands
-   $ git checkout master        # to choose the branch to follow
+   $ git checkout release      # not needed if you always stay in this branch
+   $ git checkout stable       # use one of these 3 checkout commands
+   $ git checkout develop      # to choose the branch to follow
    $ git pull
 
 Doing a "pull" will not change any files you have added to the LAMMPS
@@ -81,7 +103,7 @@ Stable versions and what tagID to use for a particular stable version
 are discussed on `this page <https://www.lammps.org/bug.html#version>`_.
 Note that this command will print some warnings, because in order to get
 back to the latest revision and to be able to update with ``git pull``
-again, you will need to do ``git checkout unstable`` (or
+again, you will need to do ``git checkout release`` (or
 check out any other desired branch) first.
 
 Once you have updated your local files with a ``git pull`` (or ``git
@@ -137,9 +159,9 @@ changed.  How to do this depends on the build system you are using.
 .. admonition:: Git protocols
    :class: note
 
-   The servers at github.com support the "git://" and "https://" access
-   protocols for anonymous, read-only access.  If you have a suitably
-   configured GitHub account, you may also use SSH protocol with the
+   The servers at github.com support the "https://" access protocol for
+   anonymous, read-only access.  If you have a suitably configured GitHub
+   account, you may also use SSH protocol with the
    URL "git@github.com:lammps/lammps.git".
 
 The LAMMPS GitHub project is currently managed by Axel Kohlmeyer

doc/src/Intro_citing.rst

@@ -16,7 +16,7 @@ source code design, the program structure, the spatial decomposition
 approach, the neighbor finding, basic communications algorithms, and how
 users and developers have contributed to LAMMPS is:
 
-  `LAMMPS - A flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales, Comp. Phys. Comm. (accepted 09/2021), DOI:10.1016/j.cpc.2021.108171 <https://doi.org/10.1016/j.cpc.2021.108171>`_
+  `LAMMPS - A flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales, Comp. Phys. Comm. 271, 108171 (2022) <https://doi.org/10.1016/j.cpc.2021.108171>`_
 
 So a project using LAMMPS or a derivative application that uses LAMMPS
 as a simulation engine should cite this paper.  The paper is expected to

doc/src/Intro_opensource.rst

@@ -19,7 +19,7 @@ software and open-source distribution, see `www.gnu.org <gnuorg_>`_
 or `www.opensource.org <opensource_>`_.  The legal text of the GPL as it
 applies to LAMMPS is in the LICENSE file included in the LAMMPS distribution.
 
-.. _gpl: https://github.com/lammps/lammps/blob/master/LICENSE
+.. _gpl: https://github.com/lammps/lammps/blob/develop/LICENSE
 
 .. _lgpl: https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html
 

doc/src/Manual_version.rst

@@ -7,26 +7,34 @@ correctly and reliably at all times.  You can follow its development
 in a public `git repository on GitHub <https://github.com/lammps/lammps>`_.
 
 Whenever we fix a bug or update or add a feature, it will be merged into
-the `master` branch of the git repository.  When a sufficient number of
+the *develop* branch of the git repository.  When a sufficient number of
 changes have accumulated *and* the software passes a set of automated
 tests, we release it in the next *patch* release, which are made every
-few weeks.  Info on patch releases are on `this website page
+few weeks.  The *release* branch of the git repository is updated with
+every such release.  Info on patch releases are on `this website page
 <https://www.lammps.org/bug.html>`_.
 
-Once or twice a year, only bug fixes and small, non-intrusive changes are
-included for a period of time, and the code is subjected to more detailed
+Once or twice a year, we apply only bug fixes and small, non-intrusive
+changes to the *develop* branch and the code is subjected to more detailed
 and thorough testing than the default automated testing.  The latest
-patch release after such a period is then labeled as a *stable* version.
+patch release after such a period is then also labeled as a *stable* version
+and the *stable* branch is updated with it.  Between stable releases
+we occasionally release some updates to the stable release containing
+only bug fixes and updates back-ported from *develop* but no new features
+and update the *stable* branch accordingly.
 
-Each version of LAMMPS contains all the features and bug-fixes up to
-and including its version date.
+Each version of LAMMPS contains all the documented features up to and
+including its version date.
 
 The version date is printed to the screen and logfile every time you
 run LAMMPS. It is also in the file src/version.h and in the LAMMPS
 directory name created when you unpack a tarball.  And it is on the
 first page of the :doc:`manual <Manual>`.
 
-* If you browse the HTML pages on the LAMMPS WWW site, they always
-  describe the most current patch release of LAMMPS.
+* If you browse the HTML pages on the LAMMPS WWW site, they will by
+  default describe the most current patch release version of LAMMPS.
+  In the navigation bar on the bottom left, there is the option to
+  view instead the documentation for the most recent *stable* version
+  or the latest version from the current development branch.
 * If you browse the HTML pages included in your tarball, they
   describe the version you have, which may be older.

doc/src/Modify_pair.rst

@@ -12,24 +12,24 @@ includes some optional methods to enable its use with rRESPA.
 
 Here is a brief description of the class methods in pair.h:
 
-+---------------------------------+-------------------------------------------------------------------+
-| compute                         | workhorse routine that computes pairwise interactions             |
-+---------------------------------+-------------------------------------------------------------------+
-| settings                        | reads the input script line with arguments you define             |
-+---------------------------------+-------------------------------------------------------------------+
-| coeff                           | set coefficients for one i,j type pair                            |
-+---------------------------------+-------------------------------------------------------------------+
-| init_one                        | perform initialization for one i,j type pair                      |
-+---------------------------------+-------------------------------------------------------------------+
-| init_style                      | initialization specific to this pair style                        |
-+---------------------------------+-------------------------------------------------------------------+
-| write & read_restart            | write/read i,j pair coeffs to restart files                       |
-+---------------------------------+-------------------------------------------------------------------+
-| write & read_restart_settings   | write/read global settings to restart files                       |
-+---------------------------------+-------------------------------------------------------------------+
-| single                          | force and energy of a single pairwise interaction between 2 atoms |
-+---------------------------------+-------------------------------------------------------------------+
-| compute_inner/middle/outer      | versions of compute used by rRESPA                                |
-+---------------------------------+-------------------------------------------------------------------+
++---------------------------------+---------------------------------------------------------------------+
+| compute                         | workhorse routine that computes pairwise interactions               |
++---------------------------------+---------------------------------------------------------------------+
+| settings                        | reads the input script line with arguments you define               |
++---------------------------------+---------------------------------------------------------------------+
+| coeff                           | set coefficients for one i,j type pair                              |
++---------------------------------+---------------------------------------------------------------------+
+| init_one                        | perform initialization for one i,j type pair                        |
++---------------------------------+---------------------------------------------------------------------+
+| init_style                      | initialization specific to this pair style                          |
++---------------------------------+---------------------------------------------------------------------+
+| write & read_restart            | write/read i,j pair coeffs to restart files                         |
++---------------------------------+---------------------------------------------------------------------+
+| write & read_restart_settings   | write/read global settings to restart files                         |
++---------------------------------+---------------------------------------------------------------------+
+| single                          | force/r and energy of a single pairwise interaction between 2 atoms |
++---------------------------------+---------------------------------------------------------------------+
+| compute_inner/middle/outer      | versions of compute used by rRESPA                                  |
++---------------------------------+---------------------------------------------------------------------+
 
 The inner/middle/outer routines are optional.

doc/src/dump_modify.rst

@@ -1011,7 +1011,9 @@ can be disabled with the :code:`checksum` parameter.
 
 Restrictions
 """"""""""""
- none
+
+*dump_modify sort* is not supported for dumps of groups containing
+more than 2 billion atoms.
 
 Related commands
 """"""""""""""""

doc/src/kspace_style.rst

@@ -310,7 +310,7 @@ Forschungszentrum Juelich.
 
 The library is available for download at "http://scafacos.de" or can
 be cloned from the git-repository
-"git://github.com/scafacos/scafacos.git".
+"https://github.com/scafacos/scafacos.git".
 
 In order to use this KSpace style, you must download and build the
 ScaFaCoS library, then build LAMMPS with the SCAFACOS package

doc/src/pair_granular.rst

@@ -205,7 +205,7 @@ For *damping mass_velocity*, the normal damping is given by:
    \eta_n = \eta_{n0} m_{eff}
 
 Here, :math:`\eta_{n0}` is the damping coefficient specified for the normal
-contact model, in units of *mass*\ /\ *time* and
+contact model, in units of 1/\ *time* and
 :math:`m_{eff} = m_i m_j/(m_i + m_j)` is the effective mass.
 Use *damping mass_velocity* to reproduce the damping behavior of
 *pair gran/hooke/\**.

doc/src/pair_lebedeva_z.rst

@@ -26,15 +26,29 @@ Examples
 Description
 """""""""""
 
-The *lebedeva/z* style computes the Lebedeva interaction
-potential as described in :ref:`(Lebedeva et al.) <Leb01>`. An important simplification is made,
-which is to take all normals along the z-axis.
+The *lebedeva/z* pair style computes the Lebedeva interaction potential
+as described in :ref:`(Lebedeva1) <Leb01>` and :ref:`(Lebedeva2)
+<Leb02>`.  An important simplification is made, which is to take all
+normals along the z-axis.
+
+The Lebedeva potential is intended for the description of the interlayer
+interaction between graphene layers.  To perform a realistic simulation,
+this potential must be used in combination with an intralayer potential
+such as :doc:`AIREBO <pair_airebo>` or :doc:`Tersoff <pair_tersoff>`
+facilitated by using pair style :doc:`hybrid/overlay <pair_hybrid>`.  To
+keep the intralayer properties unaffected, the interlayer interaction
+within the same layers should be avoided.  This can be achieved by
+assigning different atom types to atoms of different layers (e.g. 1 and
+2 in the examples above).
+
+Other interactions can be set to zero using pair_style *none*\ .
+
 
 .. math::
 
-   E       = & \frac{1}{2} \sum_i \sum_{i \neq j} V_{ij}\\
+   E       = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij}\\
    V_{ij}  = & B e^{-\alpha(r_{ij} - z_0)} \\
-             & + C(1 + D_1\rho^2_{ij} + D_2\rho^4_{ij} e^{-\lambda_1\rho^2_{ij}} e^{-\lambda_2 (z^2_{ij} - z^2_0)} \\
+             & + C(1 + D_1\rho^2_{ij} + D_2\rho^4_{ij}) e^{-\lambda_1\rho^2_{ij}} e^{-\lambda_2 (z^2_{ij} - z^2_0)} \\
              & - A \left(\frac{z_0}{r_ij}\right)^6 + A \left( \frac{z_0}{r_c} \right)^6 \\
    \rho^2_{ij} = & x^2_{ij} + y^2_{ij} \qquad (\mathbf{n_i} \equiv \mathbf{\hat{z}})
 
@@ -43,12 +57,15 @@ Energies are shifted so that they go continuously to zero at the cutoff assuming
 that the exponential part of :math:`V_{ij}` (first term) decays sufficiently fast.
 This shift is achieved by the last term in the equation for :math:`V_{ij}` above.
 
-The parameter file (e.g. CC.Lebedeva), is intended for use with metal
-:doc:`units <units>`, with energies in meV. An additional parameter, *S*,
-is available to facilitate scaling of energies.
+The provided parameter file (CC.Lebedeva) contains two sets of parameters.
 
-This potential must be used in combination with hybrid/overlay.
-Other interactions can be set to zero using pair_style *none*\ .
+- The first set (element name "C") is suitable for normal conditions and
+  is taken from :ref:`(Popov1) <Popov>`
+- The second set (element name "C1") is suitable for high-pressure
+  conditions and is taken from :ref:`(Koziol1) <Koziol>`
+
+Both sets contain an additional parameter, *S*, that can be used to
+facilitate scaling of energies and is set to 1.0 by default.
 
 Restrictions
 """"""""""""
@@ -77,4 +94,16 @@ none
 
 .. _Leb01:
 
-**(Lebedeva et al.)** I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Phys. Rev. B, 84, 245437 (2011)
+**(Lebedeva1)** I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Phys. Rev. B, 84, 245437 (2011)
+
+.. _Leb02:
+
+**(Lebedeva2)** I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Physica E: 44, 949-954 (2012)
+
+.. _Popov:
+
+**(Popov1)** A.M. Popov, I. V. Lebedeva, A. A. Knizhnik, Y. E. Lozovik and B. V. Potapkin, Chem. Phys. Lett. 536, 82-86 (2012).
+
+.. _Koziol:
+
+**(Koziol1)** Z. Koziol, G. Gawlik and J. Jagielski, Chinese Phys. B 28, 096101 (2019).

doc/src/pair_local_density.rst

@@ -26,23 +26,25 @@ Examples
 Description
 """""""""""
 
-The local density (LD) potential is a mean-field manybody potential, and, in some
-sense,a generalization of embedded atom models (EAM). The name "local density
-potential" arises from the fact that it assigns an energy to an atom depending
-on the number of neighboring atoms of given type around it within a predefined
-spherical volume (i.e., within a cutoff). The bottom-up coarse-graining (CG)
-literature suggests that such potentials can be widely useful  in capturing
-effective multibody forces in a computationally efficient manner so as to
-improve the quality of CG models of implicit solvation:ref:`(Sanyal1) <Sanyal1>` and
-phase-segregation in liquid mixtures:ref:`(Sanyal2) <Sanyal2>`, and provide guidelines
-to determine the extent of manybody correlations present in a CG
-model.:ref:`(Rosenberger) <Rosenberger>` The LD potential in LAMMPS is primarily
-intended to be used as a corrective potential over traditional pair potentials
-in bottom-up CG models, i.e., as a hybrid pair style with
-other explicit pair interaction terms (e.g., table spline, Lennard Jones, etc.).
-Because the LD potential is not a pair potential per se,  it is implemented
-simply as a single auxiliary file with all specifications that will be read
-upon initialization.
+The local density (LD) potential is a mean-field manybody potential,
+and, in some way, a generalization of embedded atom models (EAM).  The
+name "local density potential" arises from the fact that it assigns an
+energy to an atom depending on the number of neighboring atoms of a
+given type around it within a predefined spherical volume (i.e., within
+the cutoff).  The bottom-up coarse-graining (CG) literature suggests
+that such potentials can be widely useful in capturing effective
+multibody forces in a computationally efficient manner and thus improve
+the quality of CG models of implicit solvation :ref:`(Sanyal1)
+<Sanyal1>` and phase-segregation in liquid mixtures :ref:`(Sanyal2)
+<Sanyal2>`, and provide guidelines to determine the extent of manybody
+correlations present in a CG model :ref:`(Rosenberger) <Rosenberger>`.
+The LD potential in LAMMPS is primarily intended to be used as a
+corrective potential over traditional pair potentials in bottom-up CG
+models via :doc:`hybrid/overlay pair style <pair_hybrid>` with other
+explicit pair interaction terms (e.g., tabulated, Lennard-Jones, Morse
+etc.).  Because the LD potential is not a pair potential per se, it is
+implemented simply as a single auxiliary file with all specifications
+that will be read upon initialization.
 
 .. note::
 

doc/src/pair_python.rst

@@ -126,11 +126,11 @@ and *compute_energy*, which both take 3 numerical arguments:
 * itype = the (numerical) type of the first atom
 * jtype = the (numerical) type of the second atom
 
-This functions need to compute the force and the energy, respectively,
-and use the result as return value. The functions need to use the
-*pmap* dictionary to convert the LAMMPS atom type number to the symbolic
-value of the internal potential parameter data structure. Following
-the *LJCutMelt* example, here are the two functions:
+This functions need to compute the (scaled) force and the energy,
+respectively, and use the result as return value. The functions need
+to use the *pmap* dictionary to convert the LAMMPS atom type number
+to the symbolic value of the internal potential parameter data structure.
+Following the *LJCutMelt* example, here are the two functions:
 
 .. code-block:: python
 
@@ -154,10 +154,10 @@ the *LJCutMelt* example, here are the two functions:
 
    for consistency with the C++ pair styles in LAMMPS, the
    *compute_force* function follows the conventions of the Pair::single()
-   methods and does not return the full force, but the force scaled by
-   the distance between the two atoms, so this value only needs to be
-   multiplied by delta x, delta y, and delta z to conveniently obtain the
-   three components of the force vector between these two atoms.
+   methods and does not return the pairwise force directly, but the force
+   divided by the distance between the two atoms, so this value only needs
+   to be  multiplied by delta x, delta y, and delta z to conveniently obtain
+   the three components of the force vector between these two atoms.
 
 ----------
 

doc/utils/requirements.txt

@@ -1,6 +1,6 @@
-Sphinx==4.0.3
+Sphinx==4.2.0
 sphinxcontrib-spelling==7.2.1
-git+git://github.com/akohlmey/sphinx-fortran@parallel-read
+git+https://github.com/akohlmey/sphinx-fortran@parallel-read
 sphinx_tabs==3.2.0
 breathe==4.31.0
 Pygments==2.10.0

doc/utils/sphinx-config/false_positives.txt

@@ -1122,6 +1122,7 @@ gaussian
 gaussians
 Gaussians
 Gavhane
+Gawlik
 gayberne
 gcc
 gcmc
@@ -1476,6 +1477,7 @@ Izz
 Jacobsen
 Jadhao
 Jadhav
+Jagielski
 jagreat
 Jahn
 Jalalvand
@@ -1602,6 +1604,7 @@ Koslowski
 Kosovan
 Koster
 Kosztin
+Koziol
 Kp
 kradius
 Kraker

examples/PACKAGES/local_density/benzene_water/log.04Sep19.g++.1

@@ -1,267 +0,0 @@
-LAMMPS (7 Aug 2019)
-# LAMMPS input file for 26.5% benzene mole fraction solution
-# with 380 benzene and 1000 water molecules,
-# using all possible local density potentials
-# between benzene and water
-#
-# Author: Tanmoy Sanyal, Shell Group, UC Santa Barbara
-#
-# Refer: Sanyal and Shell, JPC-B, 2018, 122 (21), 5678-5693
-
-
-
-# Initialize simulation box
-dimension       3
-boundary        p p p
-units           real
-atom_style      molecular
-
-# Set potential styles
-pair_style      hybrid/overlay table spline 500 local/density
-
-# Read molecule data and set initial velocities
-read_data       benzene_water.data
-  orthogonal box = (-12.865 -12.865 -64.829) to (12.865 12.865 64.829)
-  1 by 1 by 8 MPI processor grid
-  reading atoms ...
-  1380 atoms
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-  special bonds CPU = 0.000566959 secs
-  read_data CPU = 0.00661397 secs
-velocity        all create  3.0000e+02 16611 rot yes dist gaussian
-
-# Assign potentials
-pair_coeff          1     1    table          benzene_water.pair.table      PairBB
-WARNING: 33 of 500 force values in table are inconsistent with -dE/dr.
-  Should only be flagged at inflection points (../pair_table.cpp:483)
-WARNING: 150 of 500 distance values in table with relative error
-  over 1e-06 to re-computed values (../pair_table.cpp:492)
-pair_coeff          1     2    table          benzene_water.pair.table      PairWW
-WARNING: 61 of 500 force values in table are inconsistent with -dE/dr.
-  Should only be flagged at inflection points (../pair_table.cpp:483)
-WARNING: 90 of 500 distance values in table with relative error
-  over 1e-06 to re-computed values (../pair_table.cpp:492)
-pair_coeff          2     2    table          benzene_water.pair.table      PairBW
-WARNING: 108 of 500 force values in table are inconsistent with -dE/dr.
-  Should only be flagged at inflection points (../pair_table.cpp:483)
-WARNING: 135 of 500 distance values in table with relative error
-  over 1e-06 to re-computed values (../pair_table.cpp:492)
-pair_coeff          *     *    local/density  benzene_water.localdensity.table
-
-# Recentering during minimization and equilibration
-fix recentering all recenter 0.0 0.0 0.0 units box
-
-# Thermostat & time integration
-timestep        2.0
-thermo          100
-thermo_style    custom temp ke pe etotal ebond eangle edihed evdwl
-
-# Minimization
-minimize        1.e-4 0.0 10000 10000
-WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 15.25
-  ghost atom cutoff = 15.25
-  binsize = 7.625, bins = 4 4 18
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair table, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-  (2) pair local/density, perpetual, copy from (1)
-      attributes: half, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 8.061 | 8.32 | 8.674 Mbytes
-Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
-         300    1233.1611    4162.3053    5395.4665            0            0            0    4162.3053 
-         300    1233.1611     2275.526    3508.6871            0            0            0     2275.526 
-Loop time of 0.352822 on 8 procs for 40 steps with 1380 atoms
-
-71.3% CPU use with 8 MPI tasks x no OpenMP threads
-
-Minimization stats:
-  Stopping criterion = linesearch alpha is zero
-  Energy initial, next-to-last, final = 
-         4162.30533361      2208.86525108      2275.52597861
-  Force two-norm initial, final = 259.364 69.3915
-  Force max component initial, final = 22.2077 8.31436
-  Final line search alpha, max atom move = 2.90022e-12 2.41135e-11
-  Iterations, force evaluations = 40 110
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.053192   | 0.23903    | 0.32779    |  17.2 | 67.75
-Bond    | 9.0599e-06 | 1.6302e-05 | 2.5272e-05 |   0.0 |  0.00
-Neigh   | 0.00044513 | 0.0023614  | 0.0063851  |   5.1 |  0.67
-Comm    | 0.015469   | 0.090432   | 0.20295    |  20.0 | 25.63
-Output  | 0          | 0          | 0          |   0.0 |  0.00
-Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 0.02098    |            |       |  5.95
-
-Nlocal:    172.5 ave 348 max 72 min
-Histogram: 5 0 0 0 0 0 0 0 1 2
-Nghost:    2193.62 ave 4352 max 932 min
-Histogram: 3 0 0 2 0 0 2 0 0 1
-Neighs:    9700.5 ave 20535 max 3685 min
-Histogram: 5 0 0 0 0 0 0 1 0 2
-
-Total # of neighbors = 77604
-Ave neighs/atom = 56.2348
-Ave special neighs/atom = 0
-Neighbor list builds = 2
-Dangerous builds = 0
-
-# Set up integration parameters
-fix             timeintegration all nve
-fix             thermostat all langevin  3.0000e+02  3.0000e+02  1.0000e+02 81890
-
-# Equilibration (for realistic results, run for 5000000 steps)
-reset_timestep  0
-run             5000
-WARNING: Fix recenter should come after all other integration fixes (../fix_recenter.cpp:131)
-Per MPI rank memory allocation (min/avg/max) = 6.936 | 7.195 | 7.552 Mbytes
-Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
-         300    1233.1611    2866.9109    4100.0721            0            0            0    2866.9109 
-   273.33541    1123.5553    3983.2007     5106.756            0            0            0    3983.2007 
-   293.68078    1207.1857    3319.6601    4526.8458            0            0            0    3319.6601 
-   314.21462    1291.5908    3389.2178    4680.8086            0            0            0    3389.2178 
-   323.77563    1330.8917    3332.9828    4663.8745            0            0            0    3332.9828 
-    302.5902    1243.8082    3461.7692    4705.5774            0            0            0    3461.7692 
-   295.39324    1214.2249    3411.5727    4625.7976            0            0            0    3411.5727 
-   320.52341    1317.5234    3453.1931    4770.7164            0            0            0    3453.1931 
-   312.00777    1282.5195    3403.3443    4685.8638            0            0            0    3403.3443 
-   307.96774    1265.9128    3429.7809    4695.6937            0            0            0    3429.7809 
-   294.75922    1211.6187    3388.8404    4600.4591            0            0            0    3388.8404 
-   311.24567    1279.3869    3514.9603    4794.3472            0            0            0    3514.9603 
-    306.6152    1260.3531    3447.2011    4707.5542            0            0            0    3447.2011 
-   305.23306    1254.6718    3375.5092     4630.181            0            0            0    3375.5092 
-   321.62889    1322.0675    3460.2581    4782.3256            0            0            0    3460.2581 
-   316.37725    1300.4804    3437.0312    4737.5116            0            0            0    3437.0312 
-   322.90522    1327.3139    3389.1262      4716.44            0            0            0    3389.1262 
-   307.57893    1264.3146    3359.8491    4624.1637            0            0            0    3359.8491 
-   302.22607    1242.3115    3406.1711    4648.4826            0            0            0    3406.1711 
-   302.73997    1244.4239    3220.2582    4464.6821            0            0            0    3220.2582 
-   303.66194    1248.2137    3318.4629    4566.6765            0            0            0    3318.4629 
-   308.73862    1269.0815    3369.5894     4638.671            0            0            0    3369.5894 
-   315.60294    1297.2976    3411.2405    4708.5381            0            0            0    3411.2405 
-    310.0113    1274.3129    3360.1054    4634.4183            0            0            0    3360.1054 
-   302.36229    1242.8714    3326.9845    4569.8559            0            0            0    3326.9845 
-   317.78659    1306.2735    3355.4976    4661.7711            0            0            0    3355.4976 
-   302.50479    1243.4571    3317.6846    4561.1417            0            0            0    3317.6846 
-   304.29249    1250.8056    3423.5068    4674.3124            0            0            0    3423.5068 
-   305.99948    1257.8222    3432.9395    4690.7617            0            0            0    3432.9395 
-   309.93363    1273.9937     3393.657    4667.6506            0            0            0     3393.657 
-   316.14884    1299.5415    3463.0636    4762.6051            0            0            0    3463.0636 
-   300.38817    1234.7567    3309.2495    4544.0062            0            0            0    3309.2495 
-   311.05735    1278.6128    3304.4418    4583.0546            0            0            0    3304.4418 
-   311.11872     1278.865    3291.1891    4570.0542            0            0            0    3291.1891 
-   315.74338    1297.8749    3341.3063    4639.1812            0            0            0    3341.3063 
-    297.5658    1223.1552    3316.3862    4539.5414            0            0            0    3316.3862 
-   311.79033    1281.6257    3357.4556    4639.0813            0            0            0    3357.4556 
-   310.93666    1278.1167    3414.7694    4692.8861            0            0            0    3414.7694 
-   307.37298     1263.468    3337.3889    4600.8569            0            0            0    3337.3889 
-   298.84185    1228.4005    3329.6173    4558.0178            0            0            0    3329.6173 
-   310.54684    1276.5143    3351.0852    4627.5995            0            0            0    3351.0852 
-    300.0871    1233.5191    3302.2315    4535.7506            0            0            0    3302.2315 
-   304.69078    1252.4427    3324.2508    4576.6935            0            0            0    3324.2508 
-   313.50714    1288.6827    3330.4088    4619.0915            0            0            0    3330.4088 
-   329.80018    1355.6559      3301.86    4657.5159            0            0            0      3301.86 
-   304.57609    1251.9713    3365.2938    4617.2652            0            0            0    3365.2938 
-   308.73584    1269.0701    3344.4155    4613.4856            0            0            0    3344.4155 
-   306.90951    1261.5629    3304.4698    4566.0327            0            0            0    3304.4698 
-   308.85761    1269.5707    3392.1511    4661.7218            0            0            0    3392.1511 
-   302.78788    1244.6208    3317.0849    4561.7057            0            0            0    3317.0849 
-   321.68092    1322.2813    3321.5755    4643.8568            0            0            0    3321.5755 
-Loop time of 16.3061 on 8 procs for 5000 steps with 1380 atoms
-
-Performance: 52.986 ns/day, 0.453 hours/ns, 306.634 timesteps/s
-69.6% CPU use with 8 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 2.1872     | 10.542     | 14.607     | 116.7 | 64.65
-Bond    | 0.00044084 | 0.00069669 | 0.00095081 |   0.0 |  0.00
-Neigh   | 0.026948   | 0.15225    | 0.44344    |  42.0 |  0.93
-Comm    | 0.63452    | 4.2953     | 9.49       | 133.9 | 26.34
-Output  | 0.0016391  | 0.012378   | 0.050919   |  13.9 |  0.08
-Modify  | 0.45894    | 1.2107     | 4.4629     | 116.4 |  7.42
-Other   |            | 0.09292    |            |       |  0.57
-
-Nlocal:    172.5 ave 380 max 70 min
-Histogram: 5 0 0 0 0 0 0 1 1 1
-Nghost:    2213 ave 4440 max 903 min
-Histogram: 3 0 0 2 0 0 2 0 0 1
-Neighs:    10042.5 ave 24051 max 3500 min
-Histogram: 5 0 0 0 0 0 0 1 1 1
-
-Total # of neighbors = 80340
-Ave neighs/atom = 58.2174
-Ave special neighs/atom = 0
-Neighbor list builds = 123
-Dangerous builds = 1
-
-# Turn off recentering during production phase
-unfix recentering
-
-# Setup trajectory output
-dump            myDump all custom 100 benzene_water.lammpstrj.gz id type x y z element
-dump_modify     myDump element B W
-dump_modify     myDump sort id
-
-# Production (for realistic results, run for 10000000 steps)
-reset_timestep  0
-run             1000
-Per MPI rank memory allocation (min/avg/max) = 8.232 | 8.492 | 8.851 Mbytes
-Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
-   321.68092    1322.2813    3784.0834    5106.3647            0            0            0    3784.0834 
-   310.59763    1276.7231    3318.3283    4595.0513            0            0            0    3318.3283 
-   303.39445    1247.1141    3324.1191    4571.2332            0            0            0    3324.1191 
-   311.37275    1279.9092    3305.0901    4584.9993            0            0            0    3305.0901 
-   311.29071     1279.572     3248.216     4527.788            0            0            0     3248.216 
-   314.53456     1292.906    3283.4563    4576.3623            0            0            0    3283.4563 
-   316.52595    1301.0916    3258.9171    4560.0087            0            0            0    3258.9171 
-   318.92447    1310.9509    3235.6256    4546.5765            0            0            0    3235.6256 
-   311.79212    1281.6331     3308.099    4589.7321            0            0            0     3308.099 
-   305.52477    1255.8709    3267.6907    4523.5616            0            0            0    3267.6907 
-   301.07457    1237.5782    3206.3997    4443.9779            0            0            0    3206.3997 
-Loop time of 4.44139 on 8 procs for 1000 steps with 1380 atoms
-
-Performance: 38.907 ns/day, 0.617 hours/ns, 225.155 timesteps/s
-60.8% CPU use with 8 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.656      | 2.5078     | 3.5775     |  57.7 | 56.46
-Bond    | 0.00013375 | 0.0001854  | 0.0002377  |   0.0 |  0.00
-Neigh   | 0.0048757  | 0.029188   | 0.090432   |  18.9 |  0.66
-Comm    | 0.51836    | 1.4427     | 2.6285     |  56.9 | 32.48
-Output  | 0.083084   | 0.089199   | 0.10333    |   2.3 |  2.01
-Modify  | 0.0087376  | 0.019705   | 0.038437   |   8.4 |  0.44
-Other   |            | 0.3526     |            |       |  7.94
-
-Nlocal:    172.5 ave 388 max 69 min
-Histogram: 5 0 0 0 0 0 0 2 0 1
-Nghost:    2207.88 ave 4429 max 896 min
-Histogram: 3 0 0 2 0 0 2 0 0 1
-Neighs:    10094.1 ave 24847 max 3403 min
-Histogram: 5 0 0 0 0 0 1 1 0 1
-
-Total # of neighbors = 80753
-Ave neighs/atom = 58.5167
-Ave special neighs/atom = 0
-Neighbor list builds = 23
-Dangerous builds = 0
-
-
-Total wall time: 0:00:21

examples/PACKAGES/local_density/benzene_water/log.27Oct21.benzene_water.g++.1

@@ -0,0 +1,300 @@
+LAMMPS (27 Oct 2021)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# LAMMPS input file for 26.5% benzene mole fraction solution
+# with 380 benzene and 1000 water molecules,
+# using all possible local density potentials
+# between benzene and water
+#
+# Author: Tanmoy Sanyal, Shell Group, UC Santa Barbara
+#
+# Refer: Sanyal and Shell, JPC-B, 2018, 122 (21), 5678-5693
+
+
+
+# Initialize simulation box
+dimension       3
+boundary        p p p
+units           real
+atom_style      molecular
+
+# Set potential styles
+pair_style      hybrid/overlay table spline 500 local/density
+
+# Read molecule data and set initial velocities
+read_data       benzene_water.data
+Reading data file ...
+  orthogonal box = (-12.865000 -12.865000 -64.829000) to (12.865000 12.865000 64.829000)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1380 atoms
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     0 = max # of 1-2 neighbors
+     0 = max # of 1-3 neighbors
+     0 = max # of 1-4 neighbors
+     1 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.006 seconds
+velocity        all create  3.0000e+02 16611 rot yes dist gaussian
+
+# Assign potentials
+pair_coeff          1     1    table          benzene_water.pair.table      PairBB
+WARNING: 33 of 500 force values in table PairBB are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
+WARNING: 150 of 500 distance values in table 1e-06 with relative error
+WARNING:  over PairBB to re-computed values (src/pair_table.cpp:473)
+pair_coeff          1     2    table          benzene_water.pair.table      PairWW
+WARNING: 61 of 500 force values in table PairWW are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
+WARNING: 90 of 500 distance values in table 1e-06 with relative error
+WARNING:  over PairWW to re-computed values (src/pair_table.cpp:473)
+pair_coeff          2     2    table          benzene_water.pair.table      PairBW
+WARNING: 108 of 500 force values in table PairBW are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
+WARNING: 135 of 500 distance values in table 1e-06 with relative error
+WARNING:  over PairBW to re-computed values (src/pair_table.cpp:473)
+pair_coeff          *     *    local/density  benzene_water.localdensity.table
+
+# Recentering during minimization and equilibration
+fix recentering all recenter 0.0 0.0 0.0 units box
+
+# Thermostat & time integration
+timestep        2.0
+thermo          100
+thermo_style    custom temp ke pe etotal ebond eangle edihed evdwl
+
+# Minimization
+minimize        1.e-4 0.0 10000 10000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- pair_style  local/density  command:
+
+@Article{Sanyal16,
+ author =  {T.Sanyal and M.Scott Shell},
+ title =   {Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation},
+ journal = {J.~Chem.~Phys.},
+ year =    2016,
+ DOI = doi.org/10.1063/1.4958629}
+
+@Article{Sanyal18,
+ author =  {T.Sanyal and M.Scott Shell},
+ title =   {Transferable coarse-grained models of liquid-liquid equilibrium using local density potentials optimized with the relative entropy},
+ journal = {J.~Phys.~Chem. B},
+ year =    2018,
+ DOI = doi.org/10.1021/acs.jpcb.7b12446}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
+  generated 0 of 1 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 = 15.25
+  ghost atom cutoff = 15.25
+  binsize = 7.625, bins = 4 4 18
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+  (2) pair local/density, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 8.754 | 8.754 | 8.754 Mbytes
+Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
+         300    1233.1611    2374.6749     3607.836            0            0            0    2374.6749 
+         300    1233.1611    985.54829    2218.7094            0            0            0    985.54829 
+         300    1233.1611    962.66036    2195.8215            0            0            0    962.66036 
+Loop time of 0.812343 on 1 procs for 134 steps with 1380 atoms
+
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+  Stopping criterion = energy tolerance
+  Energy initial, next-to-last, final = 
+      2374.67491482358   962.664796664787   962.660357218268
+  Force two-norm initial, final = 263.77519 15.741017
+  Force max component initial, final = 22.412654 7.9360139
+  Final line search alpha, max atom move = 0.014975513 0.11884588
+  Iterations, force evaluations = 134 240
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.78539    | 0.78539    | 0.78539    |   0.0 | 96.68
+Bond    | 2.0149e-05 | 2.0149e-05 | 2.0149e-05 |   0.0 |  0.00
+Neigh   | 0.016759   | 0.016759   | 0.016759   |   0.0 |  2.06
+Comm    | 0.0045     | 0.0045     | 0.0045     |   0.0 |  0.55
+Output  | 2.9402e-05 | 2.9402e-05 | 2.9402e-05 |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.005647   |            |       |  0.70
+
+Nlocal:        1380.00 ave        1380 max        1380 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        5832.00 ave        5832 max        5832 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:        78165.0 ave       78165 max       78165 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 78165
+Ave neighs/atom = 56.641304
+Ave special neighs/atom = 0.0000000
+Neighbor list builds = 5
+Dangerous builds = 0
+
+# Set up integration parameters
+fix             timeintegration all nve
+fix             thermostat all langevin  3.0000e+02  3.0000e+02  1.0000e+02 81890
+
+# Equilibration (for realistic results, run for 5000000 steps)
+reset_timestep  0
+run             5000
+  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+WARNING: Fix recenter should come after all other integration fixes (src/fix_recenter.cpp:133)
+Per MPI rank memory allocation (min/avg/max) = 7.629 | 7.629 | 7.629 Mbytes
+Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
+         300    1233.1611    962.66036    2195.8215            0            0            0    962.66036 
+    253.1913    1040.7522     1803.711    2844.4633            0            0            0     1803.711 
+   290.31049     1193.332    2059.0637    3252.3958            0            0            0    2059.0637 
+   299.30778    1230.3157     2140.226    3370.5417            0            0            0     2140.226 
+   309.81524     1273.507    2178.3782    3451.8853            0            0            0    2178.3782 
+   299.79526    1232.3195    2229.9248    3462.2444            0            0            0    2229.9248 
+   299.24909    1230.0745    2260.7129    3490.7874            0            0            0    2260.7129 
+    299.5898     1231.475    2244.2384    3475.7134            0            0            0    2244.2384 
+   297.81223    1224.1682      2320.27    3544.4382            0            0            0      2320.27 
+   301.53975    1239.4903    2277.0431    3516.5334            0            0            0    2277.0431 
+   292.00572    1200.3003    2292.3073    3492.6076            0            0            0    2292.3073 
+   309.19709    1270.9661    2303.6055    3574.5716            0            0            0    2303.6055 
+   297.54933    1223.0876     2304.127    3527.2146            0            0            0     2304.127 
+   303.48106    1247.4702    2303.5673    3551.0375            0            0            0    2303.5673 
+   296.46047    1218.6118    2256.1591    3474.7709            0            0            0    2256.1591 
+    299.4835     1231.038    2280.0452    3511.0832            0            0            0    2280.0452 
+   306.25958    1258.8914    2307.9795    3566.8709            0            0            0    2307.9795 
+   304.67335    1252.3711    2284.8252    3537.1963            0            0            0    2284.8252 
+   298.33637    1226.3227    2289.8499    3516.1726            0            0            0    2289.8499 
+    303.1338    1246.0427    2342.2148    3588.2575            0            0            0    2342.2148 
+   305.86051     1257.251    2341.0106    3598.2616            0            0            0    2341.0106 
+   297.75418    1223.9296    2303.5613    3527.4909            0            0            0    2303.5613 
+   296.79348    1219.9806    2327.5207    3547.5013            0            0            0    2327.5207 
+   307.25403    1262.9791    2288.4219     3551.401            0            0            0    2288.4219 
+   301.26976    1238.3805    2291.2465     3529.627            0            0            0    2291.2465 
+   297.17249    1221.5385    2283.3926    3504.9311            0            0            0    2283.3926 
+   313.99072    1290.6705    2293.9661    3584.6366            0            0            0    2293.9661 
+   301.70804    1240.1821    2331.1694    3571.3515            0            0            0    2331.1694 
+   300.62599    1235.7343    2325.4367     3561.171            0            0            0    2325.4367 
+   292.13495    1200.8316     2315.631    3516.4626            0            0            0     2315.631 
+    313.9981    1290.7008    2286.0536    3576.7545            0            0            0    2286.0536 
+   300.25311    1234.2015    2324.2379    3558.4394            0            0            0    2324.2379 
+    309.3746    1271.6958    2322.2298    3593.9256            0            0            0    2322.2298 
+   300.23041    1234.1082    2332.7521    3566.8603            0            0            0    2332.7521 
+   302.97054    1245.3716    2303.1689    3548.5405            0            0            0    2303.1689 
+   294.77155    1211.6694    2334.5087    3546.1781            0            0            0    2334.5087 
+   296.81476    1220.0681    2322.5932    3542.6613            0            0            0    2322.5932 
+   301.83238    1240.6932    2345.4841    3586.1773            0            0            0    2345.4841 
+    295.0399    1212.7724    2312.3889    3525.1614            0            0            0    2312.3889 
+   300.73565     1236.185    2338.8384    3575.0235            0            0            0    2338.8384 
+   303.02264    1245.5858    2310.0868    3555.6726            0            0            0    2310.0868 
+   302.86404    1244.9339    2332.2001     3577.134            0            0            0    2332.2001 
+   293.77916    1207.5901    2293.2799    3500.8701            0            0            0    2293.2799 
+   299.30072    1230.2867    2317.5065    3547.7933            0            0            0    2317.5065 
+   311.05029    1278.5837    2311.0476    3589.6313            0            0            0    2311.0476 
+   293.25646    1205.4416    2314.7398    3520.1814            0            0            0    2314.7398 
+   310.49018    1276.2814    2337.4909    3613.7723            0            0            0    2337.4909 
+   302.37336    1242.9169    2340.3197    3583.2366            0            0            0    2340.3197 
+   297.06862    1221.1116    2323.9136    3545.0252            0            0            0    2323.9136 
+   300.54817    1235.4144    2315.2405    3550.6549            0            0            0    2315.2405 
+   309.10643    1270.5934    2333.1848    3603.7783            0            0            0    2333.1848 
+Loop time of 15.2696 on 1 procs for 5000 steps with 1380 atoms
+
+Performance: 56.583 ns/day, 0.424 hours/ns, 327.447 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 14.432     | 14.432     | 14.432     |   0.0 | 94.51
+Bond    | 0.00032375 | 0.00032375 | 0.00032375 |   0.0 |  0.00
+Neigh   | 0.41541    | 0.41541    | 0.41541    |   0.0 |  2.72
+Comm    | 0.0975     | 0.0975     | 0.0975     |   0.0 |  0.64
+Output  | 0.0013044  | 0.0013044  | 0.0013044  |   0.0 |  0.01
+Modify  | 0.30336    | 0.30336    | 0.30336    |   0.0 |  1.99
+Other   |            | 0.01973    |            |       |  0.13
+
+Nlocal:        1380.00 ave        1380 max        1380 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        5843.00 ave        5843 max        5843 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:        76949.0 ave       76949 max       76949 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 76949
+Ave neighs/atom = 55.760145
+Ave special neighs/atom = 0.0000000
+Neighbor list builds = 121
+Dangerous builds = 1
+
+# Turn off recentering during production phase
+unfix recentering
+
+# Setup trajectory output
+dump            myDump all custom 100 benzene_water.lammpstrj.gz id type x y z element
+dump_modify     myDump element B W
+dump_modify     myDump sort id
+
+# Production (for realistic results, run for 10000000 steps)
+reset_timestep  0
+run             1000
+  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 9.022 | 9.022 | 9.022 Mbytes
+Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
+   309.10643    1270.5934    2333.1848    3603.7783            0            0            0    2333.1848 
+   300.84572    1236.6375    2331.3493    3567.9868            0            0            0    2331.3493 
+   300.90599    1236.8852    2337.6775    3574.5627            0            0            0    2337.6775 
+   302.77895    1244.5841    2341.7778     3586.362            0            0            0    2341.7778 
+   291.66639    1198.9055    2320.3512    3519.2567            0            0            0    2320.3512 
+    298.7003    1227.8187    2292.8195    3520.6382            0            0            0    2292.8195 
+   301.11163    1237.7305     2310.017    3547.7475            0            0            0     2310.017 
+   305.22515    1254.6393    2315.1355    3569.7748            0            0            0    2315.1355 
+   295.15921    1213.2629     2310.184    3523.4468            0            0            0     2310.184 
+    299.2024    1229.8826    2332.2118    3562.0943            0            0            0    2332.2118 
+   302.80078    1244.6738    2320.3763    3565.0502            0            0            0    2320.3763 
+Loop time of 3.07208 on 1 procs for 1000 steps with 1380 atoms
+
+Performance: 56.249 ns/day, 0.427 hours/ns, 325.512 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.8993     | 2.8993     | 2.8993     |   0.0 | 94.37
+Bond    | 6.5327e-05 | 6.5327e-05 | 6.5327e-05 |   0.0 |  0.00
+Neigh   | 0.083502   | 0.083502   | 0.083502   |   0.0 |  2.72
+Comm    | 0.019967   | 0.019967   | 0.019967   |   0.0 |  0.65
+Output  | 0.012268   | 0.012268   | 0.012268   |   0.0 |  0.40
+Modify  | 0.052801   | 0.052801   | 0.052801   |   0.0 |  1.72
+Other   |            | 0.004203   |            |       |  0.14
+
+Nlocal:        1380.00 ave        1380 max        1380 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        5860.00 ave        5860 max        5860 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:        77055.0 ave       77055 max       77055 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 77055
+Ave neighs/atom = 55.836957
+Ave special neighs/atom = 0.0000000
+Neighbor list builds = 24
+Dangerous builds = 0
+
+
+Total wall time: 0:00:19

examples/PACKAGES/local_density/benzene_water/log.27Oct21.benzene_water.g++.4

@@ -0,0 +1,299 @@
+LAMMPS (27 Oct 2021)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# LAMMPS input file for 26.5% benzene mole fraction solution
+# with 380 benzene and 1000 water molecules,
+# using all possible local density potentials
+# between benzene and water
+#
+# Author: Tanmoy Sanyal, Shell Group, UC Santa Barbara
+#
+# Refer: Sanyal and Shell, JPC-B, 2018, 122 (21), 5678-5693
+
+
+
+# Initialize simulation box
+dimension       3
+boundary        p p p
+units           real
+atom_style      molecular
+
+# Set potential styles
+pair_style      hybrid/overlay table spline 500 local/density
+
+# Read molecule data and set initial velocities
+read_data       benzene_water.data
+Reading data file ...
+  orthogonal box = (-12.865000 -12.865000 -64.829000) to (12.865000 12.865000 64.829000)
+  1 by 1 by 4 MPI processor grid
+  reading atoms ...
+  1380 atoms
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     0 = max # of 1-2 neighbors
+     0 = max # of 1-3 neighbors
+     0 = max # of 1-4 neighbors
+     1 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.007 seconds
+velocity        all create  3.0000e+02 16611 rot yes dist gaussian
+
+# Assign potentials
+pair_coeff          1     1    table          benzene_water.pair.table      PairBB
+WARNING: 33 of 500 force values in table PairBB are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
+WARNING: 150 of 500 distance values in table 1e-06 with relative error
+WARNING:  over PairBB to re-computed values (src/pair_table.cpp:473)
+pair_coeff          1     2    table          benzene_water.pair.table      PairWW
+WARNING: 61 of 500 force values in table PairWW are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
+WARNING: 90 of 500 distance values in table 1e-06 with relative error
+WARNING:  over PairWW to re-computed values (src/pair_table.cpp:473)
+pair_coeff          2     2    table          benzene_water.pair.table      PairBW
+WARNING: 108 of 500 force values in table PairBW are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
+WARNING: 135 of 500 distance values in table 1e-06 with relative error
+WARNING:  over PairBW to re-computed values (src/pair_table.cpp:473)
+pair_coeff          *     *    local/density  benzene_water.localdensity.table
+
+# Recentering during minimization and equilibration
+fix recentering all recenter 0.0 0.0 0.0 units box
+
+# Thermostat & time integration
+timestep        2.0
+thermo          100
+thermo_style    custom temp ke pe etotal ebond eangle edihed evdwl
+
+# Minimization
+minimize        1.e-4 0.0 10000 10000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- pair_style  local/density  command:
+
+@Article{Sanyal16,
+ author =  {T.Sanyal and M.Scott Shell},
+ title =   {Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation},
+ journal = {J.~Chem.~Phys.},
+ year =    2016,
+ DOI = doi.org/10.1063/1.4958629}
+
+@Article{Sanyal18,
+ author =  {T.Sanyal and M.Scott Shell},
+ title =   {Transferable coarse-grained models of liquid-liquid equilibrium using local density potentials optimized with the relative entropy},
+ journal = {J.~Phys.~Chem. B},
+ year =    2018,
+ DOI = doi.org/10.1021/acs.jpcb.7b12446}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
+  generated 0 of 1 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 = 15.25
+  ghost atom cutoff = 15.25
+  binsize = 7.625, bins = 4 4 18
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+  (2) pair local/density, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 8.441 | 8.589 | 8.688 Mbytes
+Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
+         300    1233.1611    2374.6749     3607.836            0            0            0    2374.6749 
+         300    1233.1611    1024.8113    2257.9724            0            0            0    1024.8113 
+Loop time of 0.240559 on 4 procs for 74 steps with 1380 atoms
+
+98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+  Stopping criterion = energy tolerance
+  Energy initial, next-to-last, final = 
+      2374.67491482358   1024.89407898645   1024.81130011575
+  Force two-norm initial, final = 263.77519 20.459697
+  Force max component initial, final = 22.412654 8.6082349
+  Final line search alpha, max atom move = 0.027790997 0.23923143
+  Iterations, force evaluations = 74 118
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.15928    | 0.1873     | 0.22814    |   6.5 | 77.86
+Bond    | 3.857e-06  | 4.4012e-06 | 5.496e-06  |   0.0 |  0.00
+Neigh   | 0.00064142 | 0.0028761  | 0.0058864  |   4.2 |  1.20
+Comm    | 0.0040776  | 0.039595   | 0.074187   |  12.6 | 16.46
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.01078    |            |       |  4.48
+
+Nlocal:        345.000 ave         664 max         147 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+Nghost:        2850.50 ave        4438 max        1208 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Neighs:        19377.5 ave       37718 max        7456 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 77510
+Ave neighs/atom = 56.166667
+Ave special neighs/atom = 0.0000000
+Neighbor list builds = 3
+Dangerous builds = 0
+
+# Set up integration parameters
+fix             timeintegration all nve
+fix             thermostat all langevin  3.0000e+02  3.0000e+02  1.0000e+02 81890
+
+# Equilibration (for realistic results, run for 5000000 steps)
+reset_timestep  0
+run             5000
+  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+WARNING: Fix recenter should come after all other integration fixes (src/fix_recenter.cpp:133)
+Per MPI rank memory allocation (min/avg/max) = 7.316 | 7.465 | 7.563 Mbytes
+Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
+         300    1233.1611    1024.8113    2257.9724            0            0            0    1024.8113 
+   263.61917    1083.6164     1866.745    2950.3614            0            0            0     1866.745 
+    296.0253     1216.823    2122.8463    3339.6692            0            0            0    2122.8463 
+   301.93846    1241.1292    2172.9802    3414.1095            0            0            0    2172.9802 
+    293.9491    1208.2887    2205.4892    3413.7779            0            0            0    2205.4892 
+   286.33795    1177.0027    2204.8908    3381.8935            0            0            0    2204.8908 
+   295.48217    1214.5904    2230.8849    3445.4753            0            0            0    2230.8849 
+   293.88908    1208.0419    2218.7563    3426.7982            0            0            0    2218.7563 
+   295.13798    1213.1756    2277.4515    3490.6271            0            0            0    2277.4515 
+   290.39538     1193.681    2273.4385    3467.1195            0            0            0    2273.4385 
+   297.56782    1223.1635    2268.7182    3491.8817            0            0            0    2268.7182 
+   306.45578    1259.6978    2289.1507    3548.8486            0            0            0    2289.1507 
+   308.54582     1268.289    2284.8514    3553.1404            0            0            0    2284.8514 
+   302.17353    1242.0955    2262.5577    3504.6532            0            0            0    2262.5577 
+   295.30087    1213.8452    2315.8853    3529.7305            0            0            0    2315.8853 
+   308.59197    1268.4787    2291.8314    3560.3101            0            0            0    2291.8314 
+   297.75618    1223.9378    2287.2003    3511.1381            0            0            0    2287.2003 
+   303.43395    1247.2765    2297.7158    3544.9923            0            0            0    2297.7158 
+   307.16233    1262.6021    2255.9769    3518.5791            0            0            0    2255.9769 
+   301.34428    1238.6868     2284.416    3523.1028            0            0            0     2284.416 
+   295.43209    1214.3846    2294.1043    3508.4889            0            0            0    2294.1043 
+   287.86904    1183.2963    2257.0204    3440.3168            0            0            0    2257.0204 
+    297.2661    1221.9233    2251.4194    3473.3428            0            0            0    2251.4194 
+   298.90221    1228.6486     2261.834    3490.4826            0            0            0     2261.834 
+   288.07202    1184.1307    2284.1918    3468.3225            0            0            0    2284.1918 
+   300.41201    1234.8547    2303.9573     3538.812            0            0            0    2303.9573 
+   283.91279     1167.034    2329.7936    3496.8277            0            0            0    2329.7936 
+   297.27507    1221.9602    2337.0516    3559.0118            0            0            0    2337.0516 
+   296.22263    1217.6341    2335.6424    3553.2765            0            0            0    2335.6424 
+   296.13784    1217.2856    2364.7034     3581.989            0            0            0    2364.7034 
+   308.17642    1266.7706    2320.2753    3587.0459            0            0            0    2320.2753 
+   310.26592    1275.3596    2301.9318    3577.2914            0            0            0    2301.9318 
+   292.97391    1204.2801    2289.8116    3494.0917            0            0            0    2289.8116 
+   294.81231    1211.8369    2315.0388    3526.8757            0            0            0    2315.0388 
+   298.66155    1227.6594    2317.2844    3544.9437            0            0            0    2317.2844 
+   302.77939    1244.5859    2301.2063    3545.7922            0            0            0    2301.2063 
+   291.47597    1198.1228    2285.1757    3483.2985            0            0            0    2285.1757 
+   286.19045    1176.3964    2265.2665    3441.6629            0            0            0    2265.2665 
+   295.58144    1214.9984    2272.3165     3487.315            0            0            0    2272.3165 
+   283.86988    1166.8577    2320.6142    3487.4719            0            0            0    2320.6142 
+    300.0576    1233.3979    2330.8962    3564.2941            0            0            0    2330.8962 
+   299.86413    1232.6026    2321.2281    3553.8308            0            0            0    2321.2281 
+   292.79017    1203.5248    2334.2308    3537.7557            0            0            0    2334.2308 
+    291.5027    1198.2327    2335.2119    3533.4446            0            0            0    2335.2119 
+   299.55471    1231.3307    2332.5216    3563.8524            0            0            0    2332.5216 
+   293.29613    1205.6046    2295.3263    3500.9309            0            0            0    2295.3263 
+   303.13151    1246.0333    2310.0548    3556.0881            0            0            0    2310.0548 
+   298.83954     1228.391    2297.3117    3525.7027            0            0            0    2297.3117 
+   297.44775      1222.67    2307.2483    3529.9183            0            0            0    2307.2483 
+   309.59874    1272.6171    2309.2439     3581.861            0            0            0    2309.2439 
+   307.47844    1263.9015     2274.998    3538.8995            0            0            0     2274.998 
+Loop time of 11.2235 on 4 procs for 5000 steps with 1380 atoms
+
+Performance: 76.982 ns/day, 0.312 hours/ns, 445.495 timesteps/s
+98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.1444     | 8.5074     | 10.534     |  44.9 | 75.80
+Bond    | 0.00017048 | 0.00020672 | 0.00030488 |   0.0 |  0.00
+Neigh   | 0.026174   | 0.12108    | 0.26052    |  28.2 |  1.08
+Comm    | 0.21788    | 1.8597     | 3.3375     |  81.2 | 16.57
+Output  | 0.0008989  | 0.0069895  | 0.021647   |  10.2 |  0.06
+Modify  | 0.19418    | 0.7044     | 2.1378     |  98.6 |  6.28
+Other   |            | 0.02368    |            |       |  0.21
+
+Nlocal:        345.000 ave         678 max         148 min
+Histogram: 2 0 0 0 1 0 0 0 0 1
+Nghost:        2854.25 ave        4464 max        1181 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Neighs:        19366.8 ave       38533 max        7481 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 77467
+Ave neighs/atom = 56.135507
+Ave special neighs/atom = 0.0000000
+Neighbor list builds = 121
+Dangerous builds = 1
+
+# Turn off recentering during production phase
+unfix recentering
+
+# Setup trajectory output
+dump            myDump all custom 100 benzene_water.lammpstrj.gz id type x y z element
+dump_modify     myDump element B W
+dump_modify     myDump sort id
+
+# Production (for realistic results, run for 10000000 steps)
+reset_timestep  0
+run             1000
+  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 8.640 | 8.791 | 8.894 Mbytes
+Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
+   307.47844    1263.9015     2274.998    3538.8995            0            0            0     2274.998 
+   309.46142    1272.0526    2274.8499    3546.9026            0            0            0    2274.8499 
+   300.70977    1236.0787    2301.0588    3537.1374            0            0            0    2301.0588 
+   300.53659    1235.3668    2316.1008    3551.4675            0            0            0    2316.1008 
+   300.48582    1235.1581    2296.3009     3531.459            0            0            0    2296.3009 
+    299.2618    1230.1267    2325.7501    3555.8768            0            0            0    2325.7501 
+   303.00905    1245.5299    2321.8238    3567.3537            0            0            0    2321.8238 
+   300.07018    1233.4496    2339.2833    3572.7329            0            0            0    2339.2833 
+   304.20292    1250.4374    2353.1018    3603.5392            0            0            0    2353.1018 
+   304.19487    1250.4043    2334.5087     3584.913            0            0            0    2334.5087 
+   294.24283    1209.4961    2335.0535    3544.5496            0            0            0    2335.0535 
+Loop time of 2.90512 on 4 procs for 1000 steps with 1380 atoms
+
+Performance: 59.481 ns/day, 0.403 hours/ns, 344.220 timesteps/s
+98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.8627     | 2.2082     | 2.7289     |  22.6 | 76.01
+Bond    | 4.042e-05  | 5.3677e-05 | 8.4044e-05 |   0.0 |  0.00
+Neigh   | 0.0066184  | 0.030172   | 0.064523   |  13.9 |  1.04
+Comm    | 0.05914    | 0.51145    | 0.86887    |  40.7 | 17.61
+Output  | 0.0057814  | 0.0073478  | 0.011158   |   2.6 |  0.25
+Modify  | 0.0085337  | 0.020869   | 0.042248   |   9.4 |  0.72
+Other   |            | 0.127      |            |       |  4.37
+
+Nlocal:        345.000 ave         682 max         147 min
+Histogram: 2 0 0 0 1 0 0 0 0 1
+Nghost:        2836.25 ave        4427 max        1175 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Neighs:        19249.8 ave       38683 max        7433 min
+Histogram: 2 0 0 0 1 0 0 0 0 1
+
+Total # of neighbors = 76999
+Ave neighs/atom = 55.796377
+Ave special neighs/atom = 0.0000000
+Neighbor list builds = 23
+Dangerous builds = 0
+
+
+Total wall time: 0:00:14

examples/PACKAGES/local_density/methanol_implicit_water/log.04Sep19.g++.1

@@ -1,226 +0,0 @@
-LAMMPS (7 Aug 2019)
-# LAMMPS input file for 50.0% methanol mole fraction solution
-# with 2500 methanol molecules in implicit water.
-#
-#
-# Author: David Rosenberger, van der Vegt Group, TU Darmstadt
-#
-# Refer: Rosenberger, Sanyal, Shell, van der Vegt, J. Chem. Theory Comput. 15, 2881-2895 (2019)
-
-
-# Initialize simulation box
-dimension       3
-boundary        p p p
-units           real
-atom_style      molecular
-
-# Set potential styles
-pair_style      hybrid/overlay table spline 500 local/density
-
-# Read molecule data and set initial velocities
-read_data       methanol_implicit_water.data
-  orthogonal box = (-31.123 -31.123 -31.123) to (31.123 31.123 31.123)
-  2 by 2 by 2 MPI processor grid
-  reading atoms ...
-  2500 atoms
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-  special bonds CPU = 0.00063014 secs
-  read_data CPU = 0.00599909 secs
-velocity        all create  3.0000e+02 12142 rot yes dist gaussian
-
-# Assign potentials
-pair_coeff          1     1 table         methanol_implicit_water.pair.table PairMM
-WARNING: 93 of 500 force values in table are inconsistent with -dE/dr.
-  Should only be flagged at inflection points (../pair_table.cpp:483)
-WARNING: 254 of 500 distance values in table with relative error
-  over 1e-06 to re-computed values (../pair_table.cpp:492)
-pair_coeff          *     * local/density methanol_implicit_water.localdensity.table
-
-
-
-
-#Recentering during minimization and equilibration
-fix recentering all recenter 0.0 0.0 0.0 units box
-
-#Thermostat & time integration
-timestep        1.0
-thermo          100
-thermo_style    custom etotal ke pe temp evdwl
-
-#minimization
-minimize        1.e-4 0.0 1000 1000
-WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 17
-  ghost atom cutoff = 17
-  binsize = 8.5, bins = 8 8 8
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair table, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-  (2) pair local/density, perpetual, copy from (1)
-      attributes: half, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 7.411 | 7.411 | 7.412 Mbytes
-TotEng KinEng PotEng Temp E_vdwl 
-   1470.3564    2234.7133   -764.35689          300   -764.35689 
-   46.496766    2234.7133   -2188.2165          300   -2188.2165 
-   7.9030246    2234.7133   -2226.8103          300   -2226.8103 
-Loop time of 0.463996 on 8 procs for 121 steps with 2500 atoms
-
-91.4% CPU use with 8 MPI tasks x no OpenMP threads
-
-Minimization stats:
-  Stopping criterion = linesearch alpha is zero
-  Energy initial, next-to-last, final = 
-        -764.356892369     -2227.85589084     -2226.81026984
-  Force two-norm initial, final = 134.911 3.83896
-  Force max component initial, final = 14.1117 1.07422
-  Final line search alpha, max atom move = 5.06747e-10 5.44356e-10
-  Iterations, force evaluations = 121 154
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.41442    | 0.41976    | 0.42434    |   0.5 | 90.47
-Bond    | 1.1683e-05 | 2.0713e-05 | 3.5048e-05 |   0.0 |  0.00
-Neigh   | 0.0084722  | 0.0090862  | 0.010038   |   0.5 |  1.96
-Comm    | 0.022712   | 0.028157   | 0.034072   |   1.9 |  6.07
-Output  | 3.1948e-05 | 3.6925e-05 | 6.6996e-05 |   0.0 |  0.01
-Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 0.006937   |            |       |  1.50
-
-Nlocal:    312.5 ave 333 max 299 min
-Histogram: 2 2 0 0 1 0 2 0 0 1
-Nghost:    2546 ave 2580 max 2517 min
-Histogram: 1 1 0 3 0 1 0 0 0 2
-Neighs:    33215.4 ave 37251 max 29183 min
-Histogram: 1 0 0 1 2 2 0 1 0 1
-
-Total # of neighbors = 265723
-Ave neighs/atom = 106.289
-Ave special neighs/atom = 0
-Neighbor list builds = 6
-Dangerous builds = 0
-
-#set up integration parameters
-fix             timeintegration all nve
-fix             thermostat all langevin  3.0000e+02  3.0000e+02  1.0000e+02 59915
-
-#Equilibration (for realistic results, run for 2000000  steps)
-reset_timestep  0
-thermo          200
-thermo_style    custom etotal ke pe temp evdwl
-
-#run equilibration
-run             2000
-WARNING: Fix recenter should come after all other integration fixes (../fix_recenter.cpp:131)
-Per MPI rank memory allocation (min/avg/max) = 6.286 | 6.286 | 6.287 Mbytes
-TotEng KinEng PotEng Temp E_vdwl 
-   177.26822    2234.7133   -2057.4451          300   -2057.4451 
-   736.24287    2151.2608   -1415.0179    288.79688   -1415.0179 
-   963.07617    2090.6433   -1127.5671    280.65926   -1127.5671 
-   1148.9049    2173.1327   -1024.2279    291.73309   -1024.2279 
-   1303.6409    2279.8586   -976.21767    306.06055   -976.21767 
-     1355.42    2281.0383   -925.61826    306.21892   -925.61826 
-   1394.5206    2276.2093   -881.68863    305.57064   -881.68863 
-   1346.9764    2215.2973   -868.32091     297.3935   -868.32091 
-   1381.3654    2248.8061   -867.44063    301.89189   -867.44063 
-   1315.8059    2189.3193   -873.51332    293.90606   -873.51332 
-   1314.4456    2209.7431   -895.29752    296.64787   -895.29752 
-Loop time of 6.38989 on 8 procs for 2000 steps with 2500 atoms
-
-Performance: 27.043 ns/day, 0.887 hours/ns, 312.994 timesteps/s
-80.5% CPU use with 8 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 5.2693     | 5.3572     | 5.457      |   2.1 | 83.84
-Bond    | 0.00028825 | 0.00033835 | 0.00039148 |   0.0 |  0.01
-Neigh   | 0.0296     | 0.032337   | 0.035071   |   0.9 |  0.51
-Comm    | 0.64679    | 0.73397    | 0.80847    |   5.2 | 11.49
-Output  | 0.00033498 | 0.00051582 | 0.0015228  |   0.0 |  0.01
-Modify  | 0.16395    | 0.18919    | 0.21056    |   3.9 |  2.96
-Other   |            | 0.07636    |            |       |  1.19
-
-Nlocal:    312.5 ave 337 max 295 min
-Histogram: 2 2 0 1 0 0 0 1 1 1
-Nghost:    2551.62 ave 2582 max 2525 min
-Histogram: 2 1 0 0 1 1 1 0 1 1
-Neighs:    33241.8 ave 37659 max 29705 min
-Histogram: 2 0 0 2 2 0 0 0 1 1
-
-Total # of neighbors = 265934
-Ave neighs/atom = 106.374
-Ave special neighs/atom = 0
-Neighbor list builds = 21
-Dangerous builds = 0
-
-#turn off recentering during production run
-unfix recentering
-
-
-#setup trajectory output
-dump            myDump all custom 100 methanol_implicit_water.lammpstrj.gz id type x y z element
-dump_modify     myDump element M
-dump_modify     myDump sort id
-
-#run production (for realistic results, run for 10000000 steps)
-reset_timestep  0
-thermo          1000
-thermo_style    custom etotal ke pe temp  evdwl
-run             10000
-Per MPI rank memory allocation (min/avg/max) = 7.588 | 7.589 | 7.589 Mbytes
-TotEng KinEng PotEng Temp E_vdwl 
-   1442.5428    2209.7431   -767.20027    296.64787   -767.20027 
-   1391.8624    2262.6889   -870.82656     303.7556   -870.82656 
-    1375.914    2244.6176    -868.7036     301.3296    -868.7036 
-   1345.9064    2227.2324   -881.32599    298.99573   -881.32599 
-   1379.2334    2278.1156   -898.88222    305.82657   -898.88222 
-   1389.7928    2255.8062   -866.01341    302.83163   -866.01341 
-   1380.4549    2258.2108   -877.75582    303.15443   -877.75582 
-   1380.8489    2256.9432   -876.09428    302.98426   -876.09428 
-   1326.5151    2225.7408   -899.22577    298.79549   -899.22577 
-   1376.6025    2253.0128   -876.41028    302.45662   -876.41028 
-   1331.0008    2218.1033   -887.10258    297.77019   -887.10258 
-Loop time of 25.4591 on 8 procs for 10000 steps with 2500 atoms
-
-Performance: 33.937 ns/day, 0.707 hours/ns, 392.787 timesteps/s
-89.3% CPU use with 8 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 21.635     | 21.916     | 22.237     |   3.9 | 86.08
-Bond    | 0.0011308  | 0.0013149  | 0.0016932  |   0.5 |  0.01
-Neigh   | 0.14593    | 0.15675    | 0.16667    |   1.9 |  0.62
-Comm    | 1.3789     | 1.7502     | 1.9558     |  13.7 |  6.87
-Output  | 0.34664    | 0.82927    | 1.2013     |  32.8 |  3.26
-Modify  | 0.24904    | 0.25842    | 0.26907    |   1.2 |  1.02
-Other   |            | 0.5475     |            |       |  2.15
-
-Nlocal:    312.5 ave 327 max 298 min
-Histogram: 2 0 0 1 1 0 1 1 1 1
-Nghost:    2575 ave 2601 max 2559 min
-Histogram: 2 0 3 1 0 0 0 0 1 1
-Neighs:    33223.2 ave 35920 max 30303 min
-Histogram: 1 1 1 1 0 1 0 0 0 3
-
-Total # of neighbors = 265786
-Ave neighs/atom = 106.314
-Ave special neighs/atom = 0
-Neighbor list builds = 103
-Dangerous builds = 0
-
-
-Total wall time: 0:00:32

examples/PACKAGES/local_density/methanol_implicit_water/log.27Oct21.methanol_implicit_water.g++.1

@@ -0,0 +1,259 @@
+LAMMPS (27 Oct 2021)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# LAMMPS input file for 50.0% methanol mole fraction solution
+# with 2500 methanol molecules in implicit water.
+#
+#
+# Author: David Rosenberger, van der Vegt Group, TU Darmstadt
+#
+# Refer: Rosenberger, Sanyal, Shell, van der Vegt, J. Chem. Theory Comput. 15, 2881-2895 (2019)
+
+
+# Initialize simulation box
+dimension       3
+boundary        p p p
+units           real
+atom_style      molecular
+
+# Set potential styles
+pair_style      hybrid/overlay table spline 500 local/density
+
+# Read molecule data and set initial velocities
+read_data       methanol_implicit_water.data
+Reading data file ...
+  orthogonal box = (-31.123000 -31.123000 -31.123000) to (31.123000 31.123000 31.123000)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  2500 atoms
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     0 = max # of 1-2 neighbors
+     0 = max # of 1-3 neighbors
+     0 = max # of 1-4 neighbors
+     1 = max # of special neighbors
+  special bonds CPU = 0.001 seconds
+  read_data CPU = 0.016 seconds
+velocity        all create  3.0000e+02 12142 rot yes dist gaussian
+
+# Assign potentials
+pair_coeff          1     1 table         methanol_implicit_water.pair.table PairMM
+WARNING: 93 of 500 force values in table PairMM are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
+WARNING: 254 of 500 distance values in table 1e-06 with relative error
+WARNING:  over PairMM to re-computed values (src/pair_table.cpp:473)
+pair_coeff          *     * local/density methanol_implicit_water.localdensity.table
+
+
+
+
+#Recentering during minimization and equilibration
+fix recentering all recenter 0.0 0.0 0.0 units box
+
+#Thermostat & time integration
+timestep        1.0
+thermo          100
+thermo_style    custom etotal ke pe temp evdwl
+
+#minimization
+minimize        1.e-4 0.0 1000 1000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- pair_style  local/density  command:
+
+@Article{Sanyal16,
+ author =  {T.Sanyal and M.Scott Shell},
+ title =   {Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation},
+ journal = {J.~Chem.~Phys.},
+ year =    2016,
+ DOI = doi.org/10.1063/1.4958629}
+
+@Article{Sanyal18,
+ author =  {T.Sanyal and M.Scott Shell},
+ title =   {Transferable coarse-grained models of liquid-liquid equilibrium using local density potentials optimized with the relative entropy},
+ journal = {J.~Phys.~Chem. B},
+ year =    2018,
+ DOI = doi.org/10.1021/acs.jpcb.7b12446}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
+  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 = 17
+  ghost atom cutoff = 17
+  binsize = 8.5, bins = 8 8 8
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+  (2) pair local/density, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 9.535 | 9.535 | 9.535 Mbytes
+TotEng KinEng PotEng Temp E_vdwl 
+   1283.8556    2234.7133   -950.85771          300   -950.85771 
+  -10.187232    2234.7133   -2244.9005          300   -2244.9005 
+  -124.79406    2234.7133   -2359.5074          300   -2359.5074 
+   -126.7619    2234.7133   -2361.4752          300   -2361.4752 
+Loop time of 3.74581 on 1 procs for 205 steps with 2500 atoms
+
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+  Stopping criterion = energy tolerance
+  Energy initial, next-to-last, final = 
+     -950.857712502514  -2361.24417962983  -2361.47519428972
+  Force two-norm initial, final = 135.25170 2.8038329
+  Force max component initial, final = 14.083102 1.1154133
+  Final line search alpha, max atom move = 0.16981022 0.18940857
+  Iterations, force evaluations = 205 223
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.5678     | 3.5678     | 3.5678     |   0.0 | 95.25
+Bond    | 7.5831e-05 | 7.5831e-05 | 7.5831e-05 |   0.0 |  0.00
+Neigh   | 0.12962    | 0.12962    | 0.12962    |   0.0 |  3.46
+Comm    | 0.019204   | 0.019204   | 0.019204   |   0.0 |  0.51
+Output  | 0.00023948 | 0.00023948 | 0.00023948 |   0.0 |  0.01
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.02886    |            |       |  0.77
+
+Nlocal:        2500.00 ave        2500 max        2500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        6729.00 ave        6729 max        6729 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:        265637.0 ave      265637 max      265637 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 265637
+Ave neighs/atom = 106.25480
+Ave special neighs/atom = 0.0000000
+Neighbor list builds = 11
+Dangerous builds = 0
+
+#set up integration parameters
+fix             timeintegration all nve
+fix             thermostat all langevin  3.0000e+02  3.0000e+02  1.0000e+02 59915
+
+#Equilibration (for realistic results, run for 2000000  steps)
+reset_timestep  0
+thermo          200
+thermo_style    custom etotal ke pe temp evdwl
+
+#run equilibration
+run             2000
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+WARNING: Fix recenter should come after all other integration fixes (src/fix_recenter.cpp:133)
+Per MPI rank memory allocation (min/avg/max) = 8.410 | 8.410 | 8.410 Mbytes
+TotEng KinEng PotEng Temp E_vdwl 
+   -126.7619    2234.7133   -2361.4752          300   -2361.4752 
+   517.05047    2015.8636   -1498.8131    270.62043   -1498.8131 
+   931.78263    2135.4332   -1203.6506     286.6721   -1203.6506 
+   1162.6209    2242.1662   -1079.5453    301.00051   -1079.5453 
+   1164.2129    2211.6204   -1047.4075    296.89989   -1047.4075 
+   1258.0085    2286.5942   -1028.5857    306.96477   -1028.5857 
+   1231.1937     2200.814   -969.62032    295.44917   -969.62032 
+   1251.2144    2245.0533   -993.83885     301.3881   -993.83885 
+   1237.2495    2239.8802   -1002.6307    300.69363   -1002.6307 
+   1232.3342    2224.3415   -992.00722    298.60763   -992.00722 
+   1235.3228     2197.191   -961.86817     294.9628   -961.86817 
+Loop time of 23.6478 on 1 procs for 2000 steps with 2500 atoms
+
+Performance: 7.307 ns/day, 3.284 hours/ns, 84.575 timesteps/s
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 22.797     | 22.797     | 22.797     |   0.0 | 96.40
+Bond    | 0.00070412 | 0.00070412 | 0.00070412 |   0.0 |  0.00
+Neigh   | 0.2249     | 0.2249     | 0.2249     |   0.0 |  0.95
+Comm    | 0.12259    | 0.12259    | 0.12259    |   0.0 |  0.52
+Output  | 0.00088925 | 0.00088925 | 0.00088925 |   0.0 |  0.00
+Modify  | 0.46447    | 0.46447    | 0.46447    |   0.0 |  1.96
+Other   |            | 0.03711    |            |       |  0.16
+
+Nlocal:        2500.00 ave        2500 max        2500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        6752.00 ave        6752 max        6752 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:        265940.0 ave      265940 max      265940 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 265940
+Ave neighs/atom = 106.37600
+Ave special neighs/atom = 0.0000000
+Neighbor list builds = 20
+Dangerous builds = 0
+
+#turn off recentering during production run
+unfix recentering
+
+
+#setup trajectory output
+dump            myDump all custom 100 methanol_implicit_water.lammpstrj.gz id type x y z element
+dump_modify     myDump element M
+dump_modify     myDump sort id
+
+#run production (for realistic results, run for 10000000 steps)
+reset_timestep  0
+thermo          1000
+thermo_style    custom etotal ke pe temp  evdwl
+run             10000
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 9.918 | 9.918 | 9.918 Mbytes
+TotEng KinEng PotEng Temp E_vdwl 
+   1235.3228     2197.191   -961.86817     294.9628   -961.86817 
+   1289.8463    2236.1425   -946.29622    300.19186   -946.29622 
+   1348.0825    2305.0295   -956.94703    309.43963   -956.94703 
+   1279.5478    2241.1582   -961.61041    300.86521   -961.61041 
+   1231.8597    2201.9591   -970.09949    295.60291   -970.09949 
+   1277.3424    2221.3696   -944.02725    298.20867   -944.02725 
+   1296.0116    2222.0998   -926.08818     298.3067   -926.08818 
+   1266.2849    2206.3727   -940.08782     296.1954   -940.08782 
+   1313.2808    2260.5077   -947.22683    303.46278   -947.22683 
+   1309.3076    2234.3895   -925.08198    299.95654   -925.08198 
+   1275.9792    2221.3037   -945.32449    298.19982   -945.32449 
+Loop time of 67.3224 on 1 procs for 10000 steps with 2500 atoms
+
+Performance: 12.834 ns/day, 1.870 hours/ns, 148.539 timesteps/s
+99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 64.476     | 64.476     | 64.476     |   0.0 | 95.77
+Bond    | 0.0014504  | 0.0014504  | 0.0014504  |   0.0 |  0.00
+Neigh   | 0.71333    | 0.71333    | 0.71333    |   0.0 |  1.06
+Comm    | 0.32846    | 0.32846    | 0.32846    |   0.0 |  0.49
+Output  | 0.46997    | 0.46997    | 0.46997    |   0.0 |  0.70
+Modify  | 1.2336     | 1.2336     | 1.2336     |   0.0 |  1.83
+Other   |            | 0.09996    |            |       |  0.15
+
+Nlocal:        2500.00 ave        2500 max        2500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        6662.00 ave        6662 max        6662 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:        265774.0 ave      265774 max      265774 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 265774
+Ave neighs/atom = 106.30960
+Ave special neighs/atom = 0.0000000
+Neighbor list builds = 104
+Dangerous builds = 0
+
+
+Total wall time: 0:01:34

examples/PACKAGES/local_density/methanol_implicit_water/log.27Oct21.methanol_implicit_water.g++.4

@@ -0,0 +1,259 @@
+LAMMPS (27 Oct 2021)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# LAMMPS input file for 50.0% methanol mole fraction solution
+# with 2500 methanol molecules in implicit water.
+#
+#
+# Author: David Rosenberger, van der Vegt Group, TU Darmstadt
+#
+# Refer: Rosenberger, Sanyal, Shell, van der Vegt, J. Chem. Theory Comput. 15, 2881-2895 (2019)
+
+
+# Initialize simulation box
+dimension       3
+boundary        p p p
+units           real
+atom_style      molecular
+
+# Set potential styles
+pair_style      hybrid/overlay table spline 500 local/density
+
+# Read molecule data and set initial velocities
+read_data       methanol_implicit_water.data
+Reading data file ...
+  orthogonal box = (-31.123000 -31.123000 -31.123000) to (31.123000 31.123000 31.123000)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  2500 atoms
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     0 = max # of 1-2 neighbors
+     0 = max # of 1-3 neighbors
+     0 = max # of 1-4 neighbors
+     1 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.005 seconds
+velocity        all create  3.0000e+02 12142 rot yes dist gaussian
+
+# Assign potentials
+pair_coeff          1     1 table         methanol_implicit_water.pair.table PairMM
+WARNING: 93 of 500 force values in table PairMM are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
+WARNING: 254 of 500 distance values in table 1e-06 with relative error
+WARNING:  over PairMM to re-computed values (src/pair_table.cpp:473)
+pair_coeff          *     * local/density methanol_implicit_water.localdensity.table
+
+
+
+
+#Recentering during minimization and equilibration
+fix recentering all recenter 0.0 0.0 0.0 units box
+
+#Thermostat & time integration
+timestep        1.0
+thermo          100
+thermo_style    custom etotal ke pe temp evdwl
+
+#minimization
+minimize        1.e-4 0.0 1000 1000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- pair_style  local/density  command:
+
+@Article{Sanyal16,
+ author =  {T.Sanyal and M.Scott Shell},
+ title =   {Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation},
+ journal = {J.~Chem.~Phys.},
+ year =    2016,
+ DOI = doi.org/10.1063/1.4958629}
+
+@Article{Sanyal18,
+ author =  {T.Sanyal and M.Scott Shell},
+ title =   {Transferable coarse-grained models of liquid-liquid equilibrium using local density potentials optimized with the relative entropy},
+ journal = {J.~Phys.~Chem. B},
+ year =    2018,
+ DOI = doi.org/10.1021/acs.jpcb.7b12446}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
+  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 = 17
+  ghost atom cutoff = 17
+  binsize = 8.5, bins = 8 8 8
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+  (2) pair local/density, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 7.855 | 7.855 | 7.855 Mbytes
+TotEng KinEng PotEng Temp E_vdwl 
+   1283.8556    2234.7133   -950.85771          300   -950.85771 
+  -10.187232    2234.7133   -2244.9005          300   -2244.9005 
+   -124.3661    2234.7133   -2359.0794          300   -2359.0794 
+   -146.7158    2234.7133   -2381.4291          300   -2381.4291 
+Loop time of 0.528503 on 4 procs for 244 steps with 2500 atoms
+
+99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+  Stopping criterion = energy tolerance
+  Energy initial, next-to-last, final = 
+     -950.857712502527   -2381.2294195605  -2381.42909821383
+  Force two-norm initial, final = 135.25170 2.3117934
+  Force max component initial, final = 14.083102 0.60833889
+  Final line search alpha, max atom move = 0.18347073 0.11161238
+  Iterations, force evaluations = 244 278
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.48518    | 0.48843    | 0.49223    |   0.4 | 92.42
+Bond    | 1.0084e-05 | 1.0861e-05 | 1.1483e-05 |   0.0 |  0.00
+Neigh   | 0.018199   | 0.019153   | 0.020036   |   0.5 |  3.62
+Comm    | 0.010229   | 0.014832   | 0.018994   |   2.6 |  2.81
+Output  | 3.7985e-05 | 4.2069e-05 | 5.3874e-05 |   0.0 |  0.01
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.006032   |            |       |  1.14
+
+Nlocal:        625.000 ave         638 max         618 min
+Histogram: 2 0 0 0 1 0 0 0 0 1
+Nghost:        3613.75 ave        3640 max        3580 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Neighs:        66411.2 ave       70713 max       62416 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+
+Total # of neighbors = 265645
+Ave neighs/atom = 106.25800
+Ave special neighs/atom = 0.0000000
+Neighbor list builds = 13
+Dangerous builds = 0
+
+#set up integration parameters
+fix             timeintegration all nve
+fix             thermostat all langevin  3.0000e+02  3.0000e+02  1.0000e+02 59915
+
+#Equilibration (for realistic results, run for 2000000  steps)
+reset_timestep  0
+thermo          200
+thermo_style    custom etotal ke pe temp evdwl
+
+#run equilibration
+run             2000
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+WARNING: Fix recenter should come after all other integration fixes (src/fix_recenter.cpp:133)
+Per MPI rank memory allocation (min/avg/max) = 6.730 | 6.730 | 6.731 Mbytes
+TotEng KinEng PotEng Temp E_vdwl 
+   -146.7158    2234.7133   -2381.4291          300   -2381.4291 
+   540.68168      2041.44   -1500.7584    274.05395   -1500.7584 
+    945.4949    2163.7509    -1218.256    290.47363    -1218.256 
+   1118.7729    2195.7579    -1076.985    294.77042    -1076.985 
+   1215.0058    2233.2445   -1018.2387    299.80282   -1018.2387 
+   1251.8045    2240.8439   -989.03944      300.823   -989.03944 
+    1206.649    2149.5807   -942.93169    288.57134   -942.93169 
+   1290.6111    2248.3623   -957.75117    301.83231   -957.75117 
+   1312.8944     2219.147   -906.25264     297.9103   -906.25264 
+    1260.002    2211.4176   -951.41561    296.87266   -951.41561 
+   1335.0956    2270.1367   -935.04108    304.75543   -935.04108 
+Loop time of 3.56721 on 4 procs for 2000 steps with 2500 atoms
+
+Performance: 48.441 ns/day, 0.495 hours/ns, 560.663 timesteps/s
+99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.3122     | 3.3399     | 3.3633     |   1.0 | 93.63
+Bond    | 7.5941e-05 | 8.062e-05  | 8.7627e-05 |   0.0 |  0.00
+Neigh   | 0.03524    | 0.036666   | 0.037864   |   0.6 |  1.03
+Comm    | 0.080116   | 0.10444    | 0.13373    |   6.1 |  2.93
+Output  | 0.00019977 | 0.00022502 | 0.00029007 |   0.0 |  0.01
+Modify  | 0.077781   | 0.078206   | 0.078752   |   0.1 |  2.19
+Other   |            | 0.007641   |            |       |  0.21
+
+Nlocal:        625.000 ave         637 max         616 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Nghost:        3597.25 ave        3610 max        3586 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Neighs:        66468.2 ave       69230 max       62721 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+
+Total # of neighbors = 265873
+Ave neighs/atom = 106.34920
+Ave special neighs/atom = 0.0000000
+Neighbor list builds = 20
+Dangerous builds = 0
+
+#turn off recentering during production run
+unfix recentering
+
+
+#setup trajectory output
+dump            myDump all custom 100 methanol_implicit_water.lammpstrj.gz id type x y z element
+dump_modify     myDump element M
+dump_modify     myDump sort id
+
+#run production (for realistic results, run for 10000000 steps)
+reset_timestep  0
+thermo          1000
+thermo_style    custom etotal ke pe temp  evdwl
+run             10000
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 8.071 | 8.071 | 8.071 Mbytes
+TotEng KinEng PotEng Temp E_vdwl 
+   1335.0956    2270.1367   -935.04108    304.75543   -935.04108 
+   1266.2305    2227.2123   -960.98186    298.99303   -960.98186 
+   1304.2289    2238.1343   -933.90544    300.45925   -933.90544 
+   1311.3201    2232.0862    -920.7661    299.64733    -920.7661 
+   1289.9028    2241.3533   -951.45049    300.89139   -951.45049 
+   1314.2234    2244.8514   -930.62797      301.361   -930.62797 
+   1282.2744    2240.6716   -958.39719    300.79987   -958.39719 
+    1239.302    2181.5711    -942.2691    292.86591    -942.2691 
+   1327.0954    2242.6441   -915.54875    301.06468   -915.54875 
+   1334.9799    2239.6841   -904.70423    300.66731   -904.70423 
+   1320.6105    2263.4912   -942.88066     303.8633   -942.88066 
+Loop time of 23.3399 on 4 procs for 10000 steps with 2500 atoms
+
+Performance: 37.018 ns/day, 0.648 hours/ns, 428.451 timesteps/s
+99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 21.343     | 21.606     | 21.766     |   3.7 | 92.57
+Bond    | 0.00045963 | 0.0004817  | 0.0005083  |   0.0 |  0.00
+Neigh   | 0.20708    | 0.22081    | 0.22733    |   1.7 |  0.95
+Comm    | 0.63014    | 0.80326    | 1.0801     |  19.8 |  3.44
+Output  | 0.11791    | 0.14443    | 0.22211    |  11.8 |  0.62
+Modify  | 0.37291    | 0.389      | 0.41719    |   2.7 |  1.67
+Other   |            | 0.1761     |            |       |  0.75
+
+Nlocal:        625.000 ave         636 max         613 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Nghost:        3597.00 ave        3613 max        3580 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Neighs:        66408.5 ave       69186 max       61728 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+
+Total # of neighbors = 265634
+Ave neighs/atom = 106.25360
+Ave special neighs/atom = 0.0000000
+Neighbor list builds = 102
+Dangerous builds = 0
+
+
+Total wall time: 0:00:27

lib/gpu/Makefile.cuda_mps

@@ -1,5 +1,5 @@
 # /* ----------------------------------------------------------------------
-#  Generic Linux Makefile for CUDA
+#  Generic Linux Makefile for CUDA with the Multi-Process Service (MPS)
 #     - change CUDA_ARCH for your GPU
 # ------------------------------------------------------------------------- */
 

lib/gpu/Makefile.hip

@@ -39,11 +39,9 @@ HIP_PLATFORM=$(shell $(HIP_PATH)/bin/hipconfig --platform)
 HIP_COMPILER=$(shell $(HIP_PATH)/bin/hipconfig --compiler)
 
 ifeq (hcc,$(HIP_PLATFORM))
-	HIP_OPTS  += -ffast-math
 	# possible values: gfx803,gfx900,gfx906
 	HIP_ARCH = gfx906
 else ifeq (amd,$(HIP_PLATFORM))
-	HIP_OPTS  += -ffast-math
 	# possible values: gfx803,gfx900,gfx906
 	HIP_ARCH = gfx906
 else ifeq (nvcc,$(HIP_PLATFORM))

lib/gpu/Makefile.linux

@@ -1,5 +1,5 @@
 # /* ----------------------------------------------------------------------   
-#  Generic Linux Makefile for CUDA 
+#  Generic Linux Makefile for CUDA
 #     - Change CUDA_ARCH for your GPU
 # ------------------------------------------------------------------------- */
 
@@ -13,7 +13,7 @@ endif
 
 NVCC = nvcc
 
-# obsolete hardware. not supported by current drivers anymore.
+# obsolete hardware. not supported by current drivers and toolkits anymore.
 #CUDA_ARCH = -arch=sm_13
 #CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
 
@@ -28,11 +28,11 @@ NVCC = nvcc
 #CUDA_ARCH = -arch=sm_37
 
 # Maxwell hardware
-CUDA_ARCH = -arch=sm_50
+#CUDA_ARCH = -arch=sm_50
 #CUDA_ARCH = -arch=sm_52
 
 # Pascal hardware
-#CUDA_ARCH = -arch=sm_60
+CUDA_ARCH = -arch=sm_60
 #CUDA_ARCH = -arch=sm_61
 
 # Volta hardware
@@ -70,7 +70,7 @@ LIB_DIR = ./
 AR = ar
 BSH = /bin/sh
 
-# GPU binning not recommended with modern GPUs
+# GPU binning not recommended for most modern GPUs
 CUDPP_OPT = #-DUSE_CUDPP -Icudpp_mini
 
 include Nvidia.makefile

lib/gpu/Makefile.linux_multi

@@ -1,6 +1,6 @@
 # /* ----------------------------------------------------------------------   
-#  Generic Linux Makefile for CUDA 
-#     - Change CUDA_ARCH for your GPU
+#  Generic Linux Makefile for CUDA complied for multiple compute capabilities
+#     - Add your GPU to CUDA_CODE
 # ------------------------------------------------------------------------- */
 
 # which file will be copied to Makefile.lammps

lib/gpu/Makefile.mpi

@@ -0,0 +1 @@
+Makefile.linux

lib/gpu/Makefile.serial

@@ -1,5 +1,5 @@
 # /* ----------------------------------------------------------------------   
-#  Generic Linux Makefile for CUDA 
+#  Generic Linux Makefile for CUDA without MPI libraries
 #     - Change CUDA_ARCH for your GPU
 # ------------------------------------------------------------------------- */
 
@@ -28,11 +28,11 @@ NVCC = nvcc
 #CUDA_ARCH = -arch=sm_37
 
 # Maxwell hardware
-CUDA_ARCH = -arch=sm_50
+#CUDA_ARCH = -arch=sm_50
 #CUDA_ARCH = -arch=sm_52
 
 # Pascal hardware
-#CUDA_ARCH = -arch=sm_60
+CUDA_ARCH = -arch=sm_60
 #CUDA_ARCH = -arch=sm_61
 
 # Volta hardware
@@ -41,6 +41,10 @@ CUDA_ARCH = -arch=sm_50
 # Turing hardware
 #CUDA_ARCH = -arch=sm_75
 
+# Ampere hardware
+#CUDA_ARCH = -arch=sm_80
+#CUDA_ARCH = -arch=sm_86
+
 # this setting should match LAMMPS Makefile
 # one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
 

lib/gpu/Makefile.turing

@@ -1,23 +0,0 @@
-NVCC  = $(CUDA_HOME)/bin/nvcc
-EXTRAMAKE = Makefile.lammps.standard
-
-CUDA_ARCH = -arch=sm_75
-CUDA_PRECISION = -D_SINGLE_DOUBLE
-CUDA_INCLUDE = -I$(CUDA_HOME)/include
-CUDA_LIB = -L$(CUDA_HOME)/lib64 -Xlinker -rpath -Xlinker $(CUDA_HOME)/lib64 -lcudart
-CUDA_OPTS = -DUNIX -O3 --use_fast_math --ftz=true
-
-CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -I$(CUDA_HOME)/include
-CUDR_OPTS = -O3 -ffast-math -funroll-loops -DMPI_GERYON -DLAMMPS_SMALLBIG
-
-BIN_DIR = .
-OBJ_DIR = obj
-LIB_DIR = .
-AR = ar
-BSH = /bin/sh
-
-# GPU binning not recommended with most modern GPUs
-CUDPP_OPT = #-DUSE_CUDPP -Icudpp_mini
-
-include Nvidia.makefile
-

lib/gpu/lal_atom.cu

@@ -18,7 +18,7 @@
 #endif
 
 __kernel void kernel_cast_x(__global numtyp4 *restrict x_type,
-                            const __global double *restrict x,
+                            const __global numtyp *restrict x,
                             const __global int *restrict type,
                             const int nall) {
   int ii=GLOBAL_ID_X;

lib/gpu/lal_atom.h

@@ -475,7 +475,7 @@ class Atom {
   UCL_Vector<numtyp,numtyp> v;
 
   #ifdef GPU_CAST
-  UCL_Vector<double,double> x_cast;
+  UCL_Vector<numtyp,numtyp> x_cast;
   UCL_Vector<int,int> type_cast;
   #endif
 

lib/gpu/lal_device.cpp

@@ -1039,10 +1039,18 @@ Device<PRECISION,ACC_PRECISION> global_device;
 
 using namespace LAMMPS_AL;
 
-bool lmp_has_gpu_device()
+// check if a suitable GPU is present.
+// for mixed and double precision GPU library compilation
+// also the GPU needs to support double precision.
+bool lmp_has_compatible_gpu_device()
 {
   UCL_Device gpu;
-  return (gpu.num_platforms() > 0);
+  bool compatible_gpu = gpu.num_platforms() > 0;
+  #if defined(_SINGLE_DOUBLE) || defined(_DOUBLE_DOUBLE)
+  if (compatible_gpu && !gpu.double_precision(0))
+    compatible_gpu = false;
+  #endif
+  return compatible_gpu;
 }
 
 std::string lmp_gpu_device_info()

lib/gpu/lal_zbl.cu

@@ -82,9 +82,9 @@ __kernel void k_zbl(const __global numtyp4 *restrict x_,
                     const __global numtyp4 *restrict coeff1,
                     const __global numtyp4 *restrict coeff2,
                     const __global numtyp4 *restrict coeff3,
-                    const double cut_globalsq,
-                    const double cut_innersq,
-                    const double cut_inner,
+                    const numtyp cut_globalsq,
+                    const numtyp cut_innersq,
+                    const numtyp cut_inner,
                     const int lj_types,
                     const __global int *dev_nbor,
                     const __global int *dev_packed,
@@ -174,9 +174,9 @@ __kernel void k_zbl_fast(const __global numtyp4 *restrict x_,
                          const __global numtyp4 *restrict coeff1_in,
                          const __global numtyp4 *restrict coeff2_in,
                          const __global numtyp4 *restrict coeff3_in,
-                         const double cut_globalsq,
-                         const double cut_innersq,
-                         const double cut_inner,
+                         const numtyp cut_globalsq,
+                         const numtyp cut_innersq,
+                         const numtyp cut_inner,
                          const __global int *dev_nbor,
                          const __global int *dev_packed,
                          __global acctyp4 *restrict ans,

lib/gpu/lal_zbl.h

@@ -67,9 +67,9 @@ class ZBL : public BaseAtomic<numtyp, acctyp> {
   /// If atom type constants fit in shared memory, use fast kernels
   bool shared_types;
 
-  double _cut_globalsq;
-  double _cut_innersq;
-  double _cut_inner;
+  numtyp _cut_globalsq;
+  numtyp _cut_innersq;
+  numtyp _cut_inner;
 
   /// Number of atom types
   int _lj_types;

lib/machdyn/Install.py

@@ -17,11 +17,12 @@ parser = ArgumentParser(prog='Install.py',
 
 # settings
 
-version = '3.3.9'
+version = '3.4.0'
 tarball = "eigen.tar.gz"
 
 # known checksums for different Eigen versions. used to validate the download.
 checksums = { \
+              '3.4.0' : '4c527a9171d71a72a9d4186e65bea559', \
               '3.3.9' : '609286804b0f79be622ccf7f9ff2b660', \
               '3.3.7' : '9e30f67e8531477de4117506fe44669b' \
 }
@@ -35,7 +36,7 @@ Syntax from src dir: make lib-smd args="-b"
 
 Syntax from lib dir: python Install.py -b
                  or: python Install.py -p /usr/include/eigen3"
-                 or: python Install.py -v 3.3.7 -b
+                 or: python Install.py -v 3.4.0 -b
 
 Example:
 
@@ -77,7 +78,7 @@ if pathflag:
 if buildflag:
   print("Downloading Eigen ...")
   eigentar = os.path.join(homepath, tarball)
-  url = "https://gitlab.com/libeigen/eigen/-/archive/%s/eigen-%s.tar.gz" %  (version,version)
+  url = "https://download.lammps.org/thirdparty/eigen-%s.tar.gz" %  version
   geturl(url, eigentar)
 
   # verify downloaded archive integrity via md5 checksum, if known.

lib/qmmm/pwqmmm.c

@@ -26,6 +26,8 @@
 #error "Unsupported QE coupling API. Want API version 1."
 #endif
 
+// we need to pass an MPI communicator to the LAMMPS library interface
+#define  LAMMPS_LIB_MPI
 #include "library.h"
 
 static const char delim[] = " \t\n\r";
@@ -67,8 +69,8 @@ int main(int argc, char **argv)
 #if 1    // AK: temporary hack
     if ( qmmmcfg.nmm != 2 ) {
         if (me == 0) {
-            fprintf( stderr, "\n Error in the number of processors for MM code"
-            "\n for the time being only two processor are allowed\n");
+            fprintf( stderr, "\n Error in the number of processors for the MM code.\n"
+            " Currently only requesting 2 MM processors is allowed.\n");
         }
         MPI_Finalize();
         return -1;

potentials/CC.Lebedeva

@@ -1,12 +1,13 @@
-# DATE: 2018-11-28  UNITS: metal  CONTRIBUTOR: Zbigniew Koziol softquake@gmail.com CITATION: Z. Koziol et al.: https://arxiv.org/abs/1803.05162
+# DATE: 2021-11-04  UNITS: metal  CONTRIBUTOR: Zbigniew Koziol softquake@gmail.com CITATION: Z. Koziol et al.: https://arxiv.org/abs/1803.05162
 #
-# Lebedeva Potential. https://doi.org/10.1016/j.physe.2011.07.018
+# Lebedeva potential: https://doi.org/10.1039/C0CP02614J and https://doi.org/10.1016/j.physe.2011.07.018
 
 # Parameters must be in this order as here, otherwise their values may be changed.
+# Energies here are given in meV.
 # The last one, S, is convenient for scaling the potential amplitude. S is a multiplication factor for A, B, C
 #        A       B           C       z0     alpha   D1      D2       lambda1   lambda2     S
-# These are values according to Levedeva et al
-#C  C   10.510  11.6523.34  35.883  3.34    4.16   -0.86232 0.10049  0.48703   0.46445     1.0
+# These are values according to Lebedeva et al.: https://doi.org/10.1016/j.cplett.2012.03.082
+C  C   10.510  11.652  29.5  3.34    4.16   -0.86232 0.10049  0.48703   0.46445     1.0
 #
 # These are values by Z. Koziol et al.: https://arxiv.org/abs/1803.05162
-C  C    14.558  21.204      1.8     3.198   4.16   -0.862   0.10049  0.6       0.4         1.0
+C1  C1    14.558  21.204      1.8     3.198   4.16   -0.862   0.10049  0.6       0.4         1.0

src/EXTRA-COMPUTE/compute_temp_rotate.h

@@ -43,7 +43,6 @@ class ComputeTempRotate : public Compute {
   double memory_usage();
 
  private:
-  int fix_dof;
   double tfactor, masstotal;
   double **vbiasall;    // stored velocity bias for all atoms
   int maxbias;          // size of vbiasall array

src/EXTRA-MOLECULE/angle_gaussian.cpp

@@ -176,20 +176,20 @@ void AngleGaussian::compute(int eflag, int vflag)
 void AngleGaussian::allocate()
 {
   allocated = 1;
-  int n = atom->nangletypes;
+  int n = atom->nangletypes+1;
 
-  memory->create(nterms,n+1,"angle:nterms");
-  memory->create(angle_temperature,n+1,"angle:angle_temperature");
+  memory->create(nterms,n,"angle:nterms");
+  memory->create(angle_temperature,n,"angle:angle_temperature");
 
-  alpha = new double *[n+1];
-  width = new double *[n+1];
-  theta0 = new double *[n+1];
-  memset(alpha,0,sizeof(double)*(n+1));
-  memset(width,0,sizeof(double)*(n+1));
-  memset(theta0,0,sizeof(double)*(n+1));
+  alpha = new double*[n];
+  width = new double*[n];
+  theta0 = new double*[n];
+  memset(alpha,0,sizeof(double *)*n);
+  memset(width,0,sizeof(double *)*n);
+  memset(theta0,0,sizeof(double *)*n);
 
-  memory->create(setflag,n+1,"angle:setflag");
-  for (int i = 1; i <= n; i++) setflag[i] = 0;
+  memory->create(setflag,n,"angle:setflag");
+  memset(setflag,0,sizeof(int)*n);
 }
 
 /* ----------------------------------------------------------------------

src/EXTRA-MOLECULE/bond_gaussian.cpp

@@ -14,8 +14,6 @@
 
 #include "bond_gaussian.h"
 
-#include <cmath>
-#include <cstring>
 #include "atom.h"
 #include "neighbor.h"
 #include "comm.h"
@@ -24,6 +22,8 @@
 #include "memory.h"
 #include "error.h"
 
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -131,20 +131,20 @@ void BondGaussian::compute(int eflag, int vflag)
 void BondGaussian::allocate()
 {
   allocated = 1;
-  int n = atom->nbondtypes;
+  int n = atom->nbondtypes+1;
 
-  memory->create(nterms,n+1,"bond:nterms");
-  memory->create(bond_temperature,n+1,"bond:bond_temperature");
+  memory->create(nterms,n,"bond:nterms");
+  memory->create(bond_temperature,n,"bond:bond_temperature");
 
-  alpha = new double *[n+1];
-  width = new double *[n+1];
-  r0 = new double *[n+1];
-  memset(alpha,0,sizeof(double)*(n+1));
-  memset(width,0,sizeof(double)*(n+1));
-  memset(r0,0,sizeof(double)*(n+1));
+  alpha = new double *[n];
+  width = new double *[n];
+  r0 = new double *[n];
+  memset(alpha,0,sizeof(double *)*n);
+  memset(width,0,sizeof(double *)*n);
+  memset(r0,0,sizeof(double *)*n);
 
-  memory->create(setflag,n+1,"bond:setflag");
-  for (int i = 1; i <= n; i++) setflag[i] = 0;
+  memory->create(setflag,n,"bond:setflag");
+  memset(setflag,0,sizeof(int)*n);
 }
 
 /* ----------------------------------------------------------------------

src/GPU/fix_nve_gpu.cpp

@@ -37,7 +37,7 @@ using namespace FixConst;
 FixNVEGPU::FixNVEGPU(LAMMPS *lmp, int narg, char **arg) :
   FixNVE(lmp, narg, arg)
 {
-  _dtfm = 0;
+  _dtfm = nullptr;
   _nlocal_max = 0;
 }
 
@@ -57,7 +57,11 @@ void FixNVEGPU::setup(int vflag)
     _respa_on = 1;
   else
     _respa_on = 0;
-  if (atom->ntypes > 1) reset_dt();
+
+  // ensure that _dtfm array is initialized if the group is not "all"
+  // or there is more than one atom type as that re-ordeted array is used for
+  // per-type/per-atom masses and group membership detection.
+  if ((igroup != 0) || (atom->ntypes > 1)) reset_dt();
 }
 
 /* ----------------------------------------------------------------------

src/INTERLAYER/pair_drip.cpp

@@ -31,7 +31,6 @@
 #include "neigh_request.h"
 #include "neighbor.h"
 #include "potential_file_reader.h"
-#include "tokenizer.h"
 
 #include <cmath>
 #include <cstring>
@@ -59,6 +58,7 @@ PairDRIP::PairDRIP(LAMMPS *lmp) : Pair(lmp)
 {
   single_enable = 0;
   restartinfo = 0;
+  one_coeff = 1;
   manybody_flag = 1;
   centroidstressflag = CENTROID_NOTAVAIL;
   unit_convert_flag = utils::get_supported_conversions(utils::ENERGY);
@@ -241,17 +241,17 @@ void PairDRIP::read_file(char *filename)
 
       nparams++;
     }
-
-    MPI_Bcast(&nparams, 1, MPI_INT, 0, world);
-    MPI_Bcast(&maxparam, 1, MPI_INT, 0, world);
-
-    if (comm->me != 0) {
-      params = (Param *) memory->srealloc(params, maxparam * sizeof(Param), "pair:params");
-    }
-
-    MPI_Bcast(params, maxparam * sizeof(Param), MPI_BYTE, 0, world);
   }
 
+  MPI_Bcast(&nparams, 1, MPI_INT, 0, world);
+  MPI_Bcast(&maxparam, 1, MPI_INT, 0, world);
+
+  if (comm->me != 0) {
+    params = (Param *) memory->srealloc(params, maxparam * sizeof(Param), "pair:params");
+  }
+
+  MPI_Bcast(params, maxparam * sizeof(Param), MPI_BYTE, 0, world);
+
   memory->destroy(elem2param);
   memory->create(elem2param, nelements, nelements, "pair:elem2param");
   for (int i = 0; i < nelements; i++) {
@@ -259,7 +259,7 @@ void PairDRIP::read_file(char *filename)
       int n = -1;
       for (int m = 0; m < nparams; m++) {
         if (i == params[m].ielement && j == params[m].jelement) {
-          if (n >= 0) error->all(FLERR, "Potential file has duplicate entry");
+          if (n >= 0) error->all(FLERR, "DRIP potential file has duplicate entry");
           n = m;
         }
       }

src/INTERLAYER/pair_ilp_graphene_hbn.cpp

@@ -142,8 +142,8 @@ void PairILPGrapheneHBN::allocate()
 void PairILPGrapheneHBN::settings(int narg, char **arg)
 {
   if (narg < 1 || narg > 2) error->all(FLERR, "Illegal pair_style command");
-  if (strcmp(force->pair_style, "hybrid/overlay") != 0)
-    error->all(FLERR, "ERROR: requires hybrid/overlay pair_style");
+  if (!utils::strmatch(force->pair_style, "^hybrid/overlay"))
+    error->all(FLERR, "Pair style ilp/graphene/hbn must be used as sub-style with hybrid/overlay");
 
   cut_global = utils::numeric(FLERR, arg[0], false, lmp);
   if (narg == 2) tap_flag = utils::numeric(FLERR, arg[1], false, lmp);
@@ -273,16 +273,17 @@ void PairILPGrapheneHBN::read_file(char *filename)
 
       nparams++;
     }
-
-    MPI_Bcast(&nparams, 1, MPI_INT, 0, world);
-    MPI_Bcast(&maxparam, 1, MPI_INT, 0, world);
-
-    if (comm->me != 0) {
-      params = (Param *) memory->srealloc(params, maxparam * sizeof(Param), "pair:params");
-    }
-
-    MPI_Bcast(params, maxparam * sizeof(Param), MPI_BYTE, 0, world);
   }
+
+  MPI_Bcast(&nparams, 1, MPI_INT, 0, world);
+  MPI_Bcast(&maxparam, 1, MPI_INT, 0, world);
+
+  if (comm->me != 0) {
+    params = (Param *) memory->srealloc(params, maxparam * sizeof(Param), "pair:params");
+  }
+
+  MPI_Bcast(params, maxparam * sizeof(Param), MPI_BYTE, 0, world);
+
   memory->destroy(elem2param);
   memory->destroy(cutILPsq);
   memory->create(elem2param, nelements, nelements, "pair:elem2param");
@@ -292,7 +293,7 @@ void PairILPGrapheneHBN::read_file(char *filename)
       int n = -1;
       for (int m = 0; m < nparams; m++) {
         if (i == params[m].ielement && j == params[m].jelement) {
-          if (n >= 0) error->all(FLERR, "ILP Potential file has duplicate entry");
+          if (n >= 0) error->all(FLERR, "ILP potential file has duplicate entry");
           n = m;
         }
       }

src/INTERLAYER/pair_kolmogorov_crespi_full.cpp

@@ -34,7 +34,6 @@
 #include "neigh_request.h"
 #include "neighbor.h"
 #include "potential_file_reader.h"
-#include "tokenizer.h"
 
 #include <cmath>
 #include <cstring>
@@ -142,8 +141,8 @@ void PairKolmogorovCrespiFull::allocate()
 void PairKolmogorovCrespiFull::settings(int narg, char **arg)
 {
   if (narg < 1 || narg > 2) error->all(FLERR, "Illegal pair_style command");
-  if (strcmp(force->pair_style, "hybrid/overlay") != 0)
-    error->all(FLERR, "ERROR: requires hybrid/overlay pair_style");
+  if (!utils::strmatch(force->pair_style, "^hybrid/overlay"))
+    error->all(FLERR, "Pair style kolmogorov/crespi/full must be used as sub-style with hybrid/overlay");
 
   cut_global = utils::numeric(FLERR, arg[0], false, lmp);
   if (narg == 2) tap_flag = utils::numeric(FLERR, arg[1], false, lmp);
@@ -270,17 +269,17 @@ void PairKolmogorovCrespiFull::read_file(char *filename)
 
       nparams++;
     }
-
-    MPI_Bcast(&nparams, 1, MPI_INT, 0, world);
-    MPI_Bcast(&maxparam, 1, MPI_INT, 0, world);
-
-    if (comm->me != 0) {
-      params = (Param *) memory->srealloc(params, maxparam * sizeof(Param), "pair:params");
-    }
-
-    MPI_Bcast(params, maxparam * sizeof(Param), MPI_BYTE, 0, world);
   }
 
+  MPI_Bcast(&nparams, 1, MPI_INT, 0, world);
+  MPI_Bcast(&maxparam, 1, MPI_INT, 0, world);
+
+  if (comm->me != 0) {
+    params = (Param *) memory->srealloc(params, maxparam * sizeof(Param), "pair:params");
+  }
+
+  MPI_Bcast(params, maxparam * sizeof(Param), MPI_BYTE, 0, world);
+
   memory->destroy(elem2param);
   memory->destroy(cutKCsq);
   memory->create(elem2param, nelements, nelements, "pair:elem2param");
@@ -290,7 +289,7 @@ void PairKolmogorovCrespiFull::read_file(char *filename)
       int n = -1;
       for (int m = 0; m < nparams; m++) {
         if (i == params[m].ielement && j == params[m].jelement) {
-          if (n >= 0) error->all(FLERR, "KC Potential file has duplicate entry");
+          if (n >= 0) error->all(FLERR, "KC potential file has duplicate entry");
           n = m;
         }
       }

src/KOKKOS/bond_class2_kokkos.cpp

@@ -68,14 +68,14 @@ void BondClass2Kokkos<DeviceType>::compute(int eflag_in, int vflag_in)
     //if(k_eatom.extent(0)<maxeatom) { // won't work without adding zero functor
       memoryKK->destroy_kokkos(k_eatom,eatom);
       memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"improper:eatom");
-      d_eatom = k_eatom.template view<DeviceType>();
+      d_eatom = k_eatom.template view<KKDeviceType>();
     //}
   }
   if (vflag_atom) {
     //if(k_vatom.extent(0)<maxvatom) { // won't work without adding zero functor
       memoryKK->destroy_kokkos(k_vatom,vatom);
       memoryKK->create_kokkos(k_vatom,vatom,maxvatom,"improper:vatom");
-      d_vatom = k_vatom.template view<DeviceType>();
+      d_vatom = k_vatom.template view<KKDeviceType>();
     //}
   }
 
@@ -210,10 +210,10 @@ void BondClass2Kokkos<DeviceType>::coeff(int narg, char **arg)
   BondClass2::coeff(narg, arg);
 
   int n = atom->nbondtypes;
-  Kokkos::DualView<F_FLOAT*,DeviceType> k_k2("BondClass2::k2",n+1);
-  Kokkos::DualView<F_FLOAT*,DeviceType> k_k3("BondClass2::k3",n+1);
-  Kokkos::DualView<F_FLOAT*,DeviceType> k_k4("BondClass2::k4",n+1);
-  Kokkos::DualView<F_FLOAT*,DeviceType> k_r0("BondClass2::r0",n+1);
+  typename AT::tdual_ffloat_1d k_k2("BondClass2::k2",n+1);
+  typename AT::tdual_ffloat_1d k_k3("BondClass2::k3",n+1);
+  typename AT::tdual_ffloat_1d k_k4("BondClass2::k4",n+1);
+  typename AT::tdual_ffloat_1d k_r0("BondClass2::r0",n+1);
 
   d_k2 = k_k2.template view<DeviceType>();
   d_k3 = k_k3.template view<DeviceType>();
@@ -247,10 +247,10 @@ void BondClass2Kokkos<DeviceType>::read_restart(FILE *fp)
   BondClass2::read_restart(fp);
 
   int n = atom->nbondtypes;
-  Kokkos::DualView<F_FLOAT*,DeviceType> k_k2("BondClass2::k2",n+1);
-  Kokkos::DualView<F_FLOAT*,DeviceType> k_k3("BondClass2::k3",n+1);
-  Kokkos::DualView<F_FLOAT*,DeviceType> k_k4("BondClass2::k4",n+1);
-  Kokkos::DualView<F_FLOAT*,DeviceType> k_r0("BondClass2::r0",n+1);
+  typename AT::tdual_ffloat_1d k_k2("BondClass2::k2",n+1);
+  typename AT::tdual_ffloat_1d k_k3("BondClass2::k3",n+1);
+  typename AT::tdual_ffloat_1d k_k4("BondClass2::k4",n+1);
+  typename AT::tdual_ffloat_1d k_r0("BondClass2::r0",n+1);
 
   d_k2 = k_k2.template view<DeviceType>();
   d_k3 = k_k3.template view<DeviceType>();

src/KOKKOS/bond_class2_kokkos.h

@@ -67,10 +67,11 @@ class BondClass2Kokkos : public BondClass2 {
   typename Kokkos::View<double*[3],typename AT::t_f_array::array_layout,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<Kokkos::Atomic> > f;
   typename AT::t_int_2d bondlist;
 
-  Kokkos::DualView<E_FLOAT*,Kokkos::LayoutRight,DeviceType> k_eatom;
-  Kokkos::DualView<F_FLOAT*[6],Kokkos::LayoutRight,DeviceType> k_vatom;
-  Kokkos::View<E_FLOAT*,Kokkos::LayoutRight,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<Kokkos::Atomic> > d_eatom;
-  Kokkos::View<F_FLOAT*[6],Kokkos::LayoutRight,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<Kokkos::Atomic> > d_vatom;
+  typedef typename KKDevice<DeviceType>::value KKDeviceType;
+  Kokkos::DualView<E_FLOAT*,Kokkos::LayoutRight,KKDeviceType> k_eatom;
+  Kokkos::DualView<F_FLOAT*[6],Kokkos::LayoutRight,KKDeviceType> k_vatom;
+  Kokkos::View<E_FLOAT*,Kokkos::LayoutRight,KKDeviceType,Kokkos::MemoryTraits<Kokkos::Atomic> > d_eatom;
+  Kokkos::View<F_FLOAT*[6],Kokkos::LayoutRight,KKDeviceType,Kokkos::MemoryTraits<Kokkos::Atomic> > d_vatom;
 
   int nlocal,newton_bond;
   int eflag,vflag;

src/KOKKOS/compute_orientorder_atom_kokkos.cpp

@@ -173,8 +173,6 @@ void ComputeOrientOrderAtomKokkos<DeviceType>::compute_peratom()
   x = atomKK->k_x.view<DeviceType>();
   mask = atomKK->k_mask.view<DeviceType>();
 
-  Kokkos::deep_copy(d_qnm,{0.0,0.0});
-
   int vector_length_default = 1;
   int team_size_default = 1;
   if (!host_flag)
@@ -185,6 +183,8 @@ void ComputeOrientOrderAtomKokkos<DeviceType>::compute_peratom()
     if (chunk_size > inum - chunk_offset)
       chunk_size = inum - chunk_offset;
 
+    Kokkos::deep_copy(d_qnm,{0.0,0.0});
+
     //Neigh
     {
       int vector_length = vector_length_default;
@@ -286,7 +286,7 @@ void ComputeOrientOrderAtomKokkos<DeviceType>::operator() (TagComputeOrientOrder
   const int i = d_ilist[ii + chunk_offset];
   const int ncount = d_ncount(ii);
 
-  // if not nnn neighbors, order parameter = 0;
+  // if not nnn neighbors, order parameter = 0
 
   if ((ncount == 0) || (ncount < nnn)) {
     for (int jj = 0; jj < ncol; jj++)
@@ -316,7 +316,7 @@ void ComputeOrientOrderAtomKokkos<DeviceType>::operator() (TagComputeOrientOrder
   const int ncount = d_ncount(ii);
   if (jj >= ncount) return;
 
-  // if not nnn neighbors, order parameter = 0;
+  // if not nnn neighbors, order parameter = 0
 
   if ((ncount == 0) || (ncount < nnn))
     return;
@@ -328,6 +328,12 @@ template<class DeviceType>
 KOKKOS_INLINE_FUNCTION
 void ComputeOrientOrderAtomKokkos<DeviceType>::operator() (TagComputeOrientOrderAtomBOOP2,const int& ii) const {
   const int ncount = d_ncount(ii);
+
+  // if not nnn neighbors, order parameter = 0
+
+  if ((ncount == 0) || (ncount < nnn))
+    return;
+
   calc_boop2(ncount, ii);
 }
 

src/KOKKOS/modify_kokkos.cpp

@@ -38,7 +38,20 @@ ModifyKokkos::ModifyKokkos(LAMMPS *lmp) : Modify(lmp)
 void ModifyKokkos::setup(int vflag)
 {
   // compute setup needs to come before fix setup
-  // b/c NH fixes need use DOF of temperature computes
+  //   b/c NH fixes need DOF of temperature computes
+  // fix group setup() is special case since populates a dynamic group
+  //   needs to be done before temperature compute setup
+
+  for (int i = 0; i < nfix; i++) {
+    if (strcmp(fix[i]->style,"GROUP") == 0) {
+      atomKK->sync(fix[i]->execution_space,fix[i]->datamask_read);
+      int prev_auto_sync = lmp->kokkos->auto_sync;
+      if (!fix[i]->kokkosable) lmp->kokkos->auto_sync = 1;
+      fix[i]->setup(vflag);
+      lmp->kokkos->auto_sync = prev_auto_sync;
+      atomKK->modified(fix[i]->execution_space,fix[i]->datamask_modify);
+    }
+  }
 
   for (int i = 0; i < ncompute; i++) compute[i]->setup();
 
@@ -124,6 +137,37 @@ void ModifyKokkos::setup_pre_neighbor()
     }
 }
 
+/* ----------------------------------------------------------------------
+   setup post_neighbor call, only for fixes that define post_neighbor
+   called from Verlet, RESPA
+------------------------------------------------------------------------- */
+
+void ModifyKokkos::setup_post_neighbor()
+{
+  if (update->whichflag == 1)
+    for (int i = 0; i < n_post_neighbor; i++) {
+      atomKK->sync(fix[list_post_neighbor[i]]->execution_space,
+                   fix[list_post_neighbor[i]]->datamask_read);
+      int prev_auto_sync = lmp->kokkos->auto_sync;
+      if (!fix[list_post_neighbor[i]]->kokkosable) lmp->kokkos->auto_sync = 1;
+      fix[list_post_neighbor[i]]->setup_post_neighbor();
+      lmp->kokkos->auto_sync = prev_auto_sync;
+      atomKK->modified(fix[list_post_neighbor[i]]->execution_space,
+                       fix[list_post_neighbor[i]]->datamask_modify);
+    }
+  else if (update->whichflag == 2)
+    for (int i = 0; i < n_min_post_neighbor; i++) {
+      atomKK->sync(fix[list_min_post_neighbor[i]]->execution_space,
+                   fix[list_min_post_neighbor[i]]->datamask_read);
+      int prev_auto_sync = lmp->kokkos->auto_sync;
+      if (!fix[list_min_post_neighbor[i]]->kokkosable) lmp->kokkos->auto_sync = 1;
+      fix[list_min_post_neighbor[i]]->setup_post_neighbor();
+      lmp->kokkos->auto_sync = prev_auto_sync;
+      atomKK->modified(fix[list_min_post_neighbor[i]]->execution_space,
+                       fix[list_min_post_neighbor[i]]->datamask_modify);
+    }
+}
+
 /* ----------------------------------------------------------------------
    setup pre_force call, only for fixes that define pre_force
    called from Verlet, RESPA, Min
@@ -258,6 +302,24 @@ void ModifyKokkos::pre_neighbor()
   }
 }
 
+/* ----------------------------------------------------------------------
+   post_neighbor call, only for relevant fixes
+------------------------------------------------------------------------- */
+
+void ModifyKokkos::post_neighbor()
+{
+  for (int i = 0; i < n_post_neighbor; i++) {
+    atomKK->sync(fix[list_post_neighbor[i]]->execution_space,
+                 fix[list_post_neighbor[i]]->datamask_read);
+    int prev_auto_sync = lmp->kokkos->auto_sync;
+    if (!fix[list_post_neighbor[i]]->kokkosable) lmp->kokkos->auto_sync = 1;
+    fix[list_post_neighbor[i]]->post_neighbor();
+    lmp->kokkos->auto_sync = prev_auto_sync;
+    atomKK->modified(fix[list_post_neighbor[i]]->execution_space,
+                     fix[list_post_neighbor[i]]->datamask_modify);
+  }
+}
+
 /* ----------------------------------------------------------------------
    pre_force call, only for relevant fixes
 ------------------------------------------------------------------------- */
@@ -420,6 +482,12 @@ void ModifyKokkos::post_run()
     atomKK->modified(fix[i]->execution_space,
                      fix[i]->datamask_modify);
   }
+
+  // must reset this to its default value, since computes may be added
+  // or removed between runs and with this change we will redirect any
+  // calls to addstep_compute() to addstep_compute_all() instead.
+  n_timeflag = -1;
+
 }
 
 /* ----------------------------------------------------------------------
@@ -567,6 +635,24 @@ void ModifyKokkos::min_pre_neighbor()
   }
 }
 
+/* ----------------------------------------------------------------------
+   minimizer post-neighbor call, only for relevant fixes
+------------------------------------------------------------------------- */
+
+void ModifyKokkos::min_post_neighbor()
+{
+  for (int i = 0; i < n_min_post_neighbor; i++) {
+    atomKK->sync(fix[list_min_post_neighbor[i]]->execution_space,
+                 fix[list_min_post_neighbor[i]]->datamask_read);
+    int prev_auto_sync = lmp->kokkos->auto_sync;
+    if (!fix[list_min_post_neighbor[i]]->kokkosable) lmp->kokkos->auto_sync = 1;
+    fix[list_min_post_neighbor[i]]->min_post_neighbor();
+    lmp->kokkos->auto_sync = prev_auto_sync;
+    atomKK->modified(fix[list_min_post_neighbor[i]]->execution_space,
+                     fix[list_min_post_neighbor[i]]->datamask_modify);
+  }
+}
+
 /* ----------------------------------------------------------------------
    minimizer pre-force call, only for relevant fixes
 ------------------------------------------------------------------------- */
@@ -646,7 +732,7 @@ double ModifyKokkos::min_energy(double *fextra)
 }
 
 /* ----------------------------------------------------------------------
-   store current state of extra dof, only for relevant fixes
+   store current state of extra minimizer dof, only for relevant fixes
 ------------------------------------------------------------------------- */
 
 void ModifyKokkos::min_store()
@@ -664,7 +750,7 @@ void ModifyKokkos::min_store()
 }
 
 /* ----------------------------------------------------------------------
-   mange state of extra dof on a stack, only for relevant fixes
+   manage state of extra minimizer dof on a stack, only for relevant fixes
 ------------------------------------------------------------------------- */
 
 void ModifyKokkos::min_clearstore()
@@ -710,7 +796,7 @@ void ModifyKokkos::min_popstore()
 }
 
 /* ----------------------------------------------------------------------
-   displace extra dof along vector hextra, only for relevant fixes
+   displace extra minimizer dof along vector hextra, only for relevant fixes
 ------------------------------------------------------------------------- */
 
 void ModifyKokkos::min_step(double alpha, double *hextra)
@@ -755,7 +841,7 @@ double ModifyKokkos::max_alpha(double *hextra)
 }
 
 /* ----------------------------------------------------------------------
-   extract extra dof for minimization, only for relevant fixes
+   extract extra minimizer dof, only for relevant fixes
 ------------------------------------------------------------------------- */
 
 int ModifyKokkos::min_dof()
@@ -775,7 +861,7 @@ int ModifyKokkos::min_dof()
 }
 
 /* ----------------------------------------------------------------------
-   reset reference state of fix, only for relevant fixes
+   reset minimizer reference state of fix, only for relevant fixes
 ------------------------------------------------------------------------- */
 
 int ModifyKokkos::min_reset_ref()
@@ -788,8 +874,8 @@ int ModifyKokkos::min_reset_ref()
     int prev_auto_sync = lmp->kokkos->auto_sync;
     if (!fix[list_min_energy[i]]->kokkosable) lmp->kokkos->auto_sync = 1;
     itmp = fix[list_min_energy[i]]->min_reset_ref();
-    lmp->kokkos->auto_sync = prev_auto_sync;
     if (itmp) itmpall = 1;
+    lmp->kokkos->auto_sync = prev_auto_sync;
     atomKK->modified(fix[list_min_energy[i]]->execution_space,
                      fix[list_min_energy[i]]->datamask_modify);
   }

src/KOKKOS/modify_kokkos.h

@@ -26,6 +26,7 @@ class ModifyKokkos : public Modify {
   void setup(int);
   void setup_pre_exchange();
   void setup_pre_neighbor();
+  void setup_post_neighbor();
   void setup_pre_force(int);
   void setup_pre_reverse(int, int);
   void initial_integrate(int);
@@ -33,6 +34,7 @@ class ModifyKokkos : public Modify {
   void pre_decide();
   void pre_exchange();
   void pre_neighbor();
+  void post_neighbor();
   void pre_force(int);
   void pre_reverse(int,int);
   void post_force(int);
@@ -52,6 +54,7 @@ class ModifyKokkos : public Modify {
 
   void min_pre_exchange();
   void min_pre_neighbor();
+  void min_post_neighbor();
   void min_pre_force(int);
   void min_pre_reverse(int,int);
   void min_post_force(int);

src/KOKKOS/npair_kokkos.cpp

@@ -29,6 +29,8 @@ namespace LAMMPS_NS {
 template<class DeviceType, int HALF_NEIGH, int GHOST, int TRI, int SIZE>
 NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI,SIZE>::NPairKokkos(LAMMPS *lmp) : NPair(lmp) {
 
+  last_stencil_old = -1;
+
   // use 1D view for scalars to reduce GPU memory operations
 
   d_scalars = typename AT::t_int_1d("neighbor:scalars",2);
@@ -112,9 +114,11 @@ void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI,SIZE>::copy_stencil_info()
   NPair::copy_stencil_info();
   nstencil = ns->nstencil;
 
-  if (ns->last_stencil == update->ntimestep) {
+  if (ns->last_stencil != last_stencil_old) {
     // copy stencil to device as it may have changed
 
+    last_stencil_old = ns->last_stencil;
+
     int maxstencil = ns->get_maxstencil();
 
     if (maxstencil > (int)k_stencil.extent(0))

src/KOKKOS/npair_kokkos.h

@@ -138,7 +138,7 @@ class NPairKokkos : public NPair {
 
   // data from NStencil class
 
-  int nstencil;
+  int nstencil,last_stencil_old;
   DAT::tdual_int_1d k_stencil;  // # of J neighs for each I
   DAT::tdual_int_1d_3 k_stencilxyz;
 };

src/MACHDYN/atom_vec_smd.cpp

@@ -115,6 +115,7 @@ void AtomVecSMD::grow_pointers()
   vfrac = atom->vfrac;
   rmass = atom->rmass;
   x0 = atom->x0;
+  x = atom->x;
   radius = atom->radius;
   contact_radius = atom->contact_radius;
   molecule = atom->molecule;
@@ -129,13 +130,11 @@ void AtomVecSMD::grow_pointers()
 /* ----------------------------------------------------------------------
    clear extra forces starting at atom N
    nbytes = # of bytes to clear for a per-atom vector
-   NOTE: does f need to be re-cleared?
 ------------------------------------------------------------------------- */
 
 void AtomVecSMD::force_clear(int n, size_t nbytes)
 {
   memset(&desph[n],0,nbytes);
-  memset(&f[n][0],0,3*nbytes);
 }
 
 /* ----------------------------------------------------------------------

src/MACHDYN/compute_smd_triangle_vertices.cpp

@@ -53,7 +53,7 @@ ComputeSMDTriangleVertices::ComputeSMDTriangleVertices(LAMMPS *lmp, int narg, ch
 /* ---------------------------------------------------------------------- */
 
 ComputeSMDTriangleVertices::~ComputeSMDTriangleVertices() {
-    memory->sfree(outputVector);
+    memory->destroy(outputVector);
 }
 
 /* ---------------------------------------------------------------------- */

src/MACHDYN/pair_smd_ulsph.cpp

@@ -85,7 +85,8 @@ PairULSPH::PairULSPH(LAMMPS *lmp) :
 
 PairULSPH::~PairULSPH() {
         if (allocated) {
-                //printf("... deallocating\n");
+                memory->destroy(setflag);
+                memory->destroy(cutsq);
                 memory->destroy(Q1);
                 memory->destroy(rho0);
                 memory->destroy(eos);

src/MANYBODY/pair_eam_cd.cpp

@@ -20,9 +20,6 @@
 
 #include "pair_eam_cd.h"
 
-#include <cmath>
-
-#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
@@ -31,11 +28,11 @@
 #include "error.h"
 #include "tokenizer.h"
 
-
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
-#define ASSERT(cond)
 #define MAXLINE 1024        // This sets the maximum line length in EAM input files.
 
 PairEAMCD::PairEAMCD(LAMMPS *lmp, int _cdeamVersion)
@@ -298,7 +295,7 @@ void PairEAMCD::compute(int eflag, int vflag)
     // It will be replaced by the concentration at site i if atom i is either A or B.
 
     double x_i = -1.0;
-    double D_i, h_prime_i;
+    double D_i = 0.0, h_prime_i;
 
     // This if-clause is only required for ternary alloys.
 
@@ -307,7 +304,6 @@ void PairEAMCD::compute(int eflag, int vflag)
       // Compute local concentration at site i.
 
       x_i = rhoB[i]/rho[i];
-      ASSERT(x_i >= 0 && x_i<=1.0);
 
       if (cdeamVersion == 1) {
 
@@ -317,8 +313,6 @@ void PairEAMCD::compute(int eflag, int vflag)
         D_i = D_values[i] * h_prime_i / (2.0 * rho[i] * rho[i]);
       } else if (cdeamVersion == 2) {
         D_i = D_values[i];
-      } else {
-        ASSERT(false);
       }
     }
 
@@ -354,14 +348,11 @@ void PairEAMCD::compute(int eflag, int vflag)
 
         // This code line is required for ternary alloy.
 
-        if (jtype == speciesA || jtype == speciesB) {
-          ASSERT(rho[i] != 0.0);
-          ASSERT(rho[j] != 0.0);
+        if ((jtype == speciesA || jtype == speciesB) && rho[j] != 0.0) {
 
           // Compute local concentration at site j.
 
           x_j = rhoB[j]/rho[j];
-          ASSERT(x_j >= 0 && x_j<=1.0);
 
           double D_j=0.0;
           if (cdeamVersion == 1) {
@@ -372,8 +363,6 @@ void PairEAMCD::compute(int eflag, int vflag)
             D_j = D_values[j] * h_prime_j / (2.0 * rho[j] * rho[j]);
           } else if (cdeamVersion == 2) {
             D_j = D_values[j];
-          } else {
-            ASSERT(false);
           }
           double t2 = -rhoB[j];
           if (itype == speciesB) t2 += rho[j];
@@ -422,8 +411,6 @@ void PairEAMCD::compute(int eflag, int vflag)
             // Calculate h(x_ij) polynomial function.
 
             h = evalH(x_ij);
-          } else {
-            ASSERT(false);
           }
           fpair += h * phip;
           phi *= h;
@@ -460,7 +447,8 @@ void PairEAMCD::coeff(int narg, char **arg)
   // Make sure the EAM file is a CD-EAM binary alloy.
 
   if (setfl->nelements < 2)
-    error->all(FLERR,"The EAM file must contain at least 2 elements to be used with the eam/cd pair style.");
+    error->all(FLERR,"The EAM file must contain at least 2 elements to be "
+                    "used with the eam/cd pair style.");
 
   // Read in the coefficients of the h polynomial from the end of the EAM file.
 
@@ -502,22 +490,19 @@ void PairEAMCD::read_h_coeff(char *filename)
     // Open potential file
 
     FILE *fptr;
-    char line[MAXLINE];
-    char nextline[MAXLINE];
-    int convert_flag = unit_convert_flag;
+    char line[2][MAXLINE];
+    int convert_flag = unit_convert_flag, toggle = 0;
     fptr = utils::open_potential(filename, lmp, &convert_flag);
     if (fptr == nullptr)
-      error->one(FLERR,"Cannot open EAMCD potential file {}",
-                                   filename);
+      error->one(FLERR,"Cannot open EAMCD potential file {}", filename);
 
     // h coefficients are stored at the end of the file.
     // Skip to last line of file.
 
-    while (fgets(nextline, MAXLINE, fptr) != nullptr) {
-      strcpy(line, nextline);
-    }
+    while (fgets(line[toggle], MAXLINE, fptr) != nullptr)
+      toggle = !toggle;
 
-    ValueTokenizer values(line);
+    ValueTokenizer values(line[!toggle]);
     int degree = values.next_int();
     nhcoeff = degree+1;
 
@@ -527,10 +512,8 @@ void PairEAMCD::read_h_coeff(char *filename)
     delete[] hcoeff;
     hcoeff = new double[nhcoeff];
 
-    int i = 0;
-    while (values.has_next()) {
-      hcoeff[i++] = values.next_double();
-    }
+    for (int i = 0; i < nhcoeff; ++i)
+      hcoeff[i] = values.next_double();
 
     // Close the potential file.
 
@@ -545,7 +528,6 @@ void PairEAMCD::read_h_coeff(char *filename)
   MPI_Bcast(hcoeff, nhcoeff, MPI_DOUBLE, 0, world);
 }
 
-
 /* ---------------------------------------------------------------------- */
 
 int PairEAMCD::pack_forward_comm(int n, int *list, double *buf,
@@ -572,7 +554,7 @@ int PairEAMCD::pack_forward_comm(int n, int *list, double *buf,
         buf[m++] = rhoB[j];
       }
       return m;
-    } else { ASSERT(false); return 0; }
+    } else return 0;
   } else if (communicationStage == 4) {
     for (i = 0; i < n; i++) {
       j = list[i];
@@ -604,8 +586,6 @@ void PairEAMCD::unpack_forward_comm(int n, int first, double *buf)
         rho[i] = buf[m++];
         rhoB[i] = buf[m++];
       }
-    } else {
-      ASSERT(false);
     }
   } else if (communicationStage == 4) {
     for (i = first; i < last; i++) {
@@ -636,7 +616,7 @@ int PairEAMCD::pack_reverse_comm(int n, int first, double *buf)
         buf[m++] = rhoB[i];
       }
       return m;
-    } else { ASSERT(false); return 0; }
+    } else return 0;
   } else if (communicationStage == 3) {
     for (i = first; i < last; i++) {
       buf[m++] = D_values[i];
@@ -666,8 +646,6 @@ void PairEAMCD::unpack_reverse_comm(int n, int *list, double *buf)
         rho[j] += buf[m++];
         rhoB[j] += buf[m++];
       }
-    } else {
-      ASSERT(false);
     }
   } else if (communicationStage == 3) {
     for (i = 0; i < n; i++) {

src/MANYBODY/pair_eam_cd.h

@@ -120,6 +120,7 @@ class PairEAMCD : public PairEAMAlloy {
     index.p = r * rdr + 1.0;
     index.m = static_cast<int>(index.p);
     index.m = index.m <= (nr - 1) ? index.m : (nr - 1);
+    index.m = index.m > 1 ? index.m : 1;
     index.p -= index.m;
     index.p = index.p <= 1.0 ? index.p : 1.0;
     return index;
@@ -132,6 +133,7 @@ class PairEAMCD : public PairEAMAlloy {
     index.p = rho * rdrho + 1.0;
     index.m = static_cast<int>(index.p);
     index.m = index.m <= (nrho - 1) ? index.m : (nrho - 1);
+    index.m = index.m > 1 ? index.m : 1;
     index.p -= index.m;
     index.p = index.p <= 1.0 ? index.p : 1.0;
     return index;

src/MANYBODY/pair_local_density.cpp

@@ -86,9 +86,8 @@ PairLocalDensity::PairLocalDensity(LAMMPS *lmp) : Pair(lmp)
   fp = nullptr;
   localrho = nullptr;
 
-  // set comm size needed by this pair
-  comm_forward = 1;
-  comm_reverse = 1;
+  // comm sizes needed by this pair style will be set when reading the potential file
+  comm_forward = comm_reverse = 0;
 
   // cite publication
   if (lmp->citeme) lmp->citeme->add(cite_pair_local_density);
@@ -686,6 +685,11 @@ void PairLocalDensity::parse_file(char *filename) {
 
   MPI_Bcast(&nLD,1,MPI_INT,0,world);
   MPI_Bcast(&nrho,1,MPI_INT,0,world);
+  comm_forward = comm_reverse = nLD;
+
+  if ((me == 0) && (nLD != atom->ntypes*atom->ntypes))
+    error->warning(FLERR, "Expected {} local density potentials but got {}",
+                   atom->ntypes*atom->ntypes, nLD);
 
   // setting up all arrays to be read from files and broadcasted
   memory->create(uppercut, nLD, "pairLD:uppercut");
@@ -807,8 +811,8 @@ void PairLocalDensity::parse_file(char *filename) {
    communication routines
 ------------------------------------------------------------------------- */
 
-int PairLocalDensity::pack_comm(int n, int *list, double *buf,
-                                int /* pbc_flag */, int * /* pbc */) {
+int PairLocalDensity::pack_forward_comm(int n, int *list, double *buf,
+                                        int /* pbc_flag */, int * /* pbc */) {
   int i,j,k;
   int m;
 
@@ -820,12 +824,12 @@ int PairLocalDensity::pack_comm(int n, int *list, double *buf,
     }
   }
 
-  return nLD;
+  return m;
 }
 
 /* ---------------------------------------------------------------------- */
 
-void PairLocalDensity::unpack_comm(int n, int first, double *buf) {
+void PairLocalDensity::unpack_forward_comm(int n, int first, double *buf) {
 
   int i,k,m,last;
 
@@ -851,7 +855,7 @@ int PairLocalDensity::pack_reverse_comm(int n, int first, double *buf) {
       buf[m++] = localrho[k][i];
     }
   }
-  return nLD;
+  return m;
 }
 
 /* ---------------------------------------------------------------------- */

src/MANYBODY/pair_local_density.h

@@ -39,8 +39,8 @@ class PairLocalDensity : public Pair {
   double init_one(int, int);
   double single(int, int, int, int, double, double, double, double &);
 
-  virtual int pack_comm(int, int *, double *, int, int *);
-  virtual void unpack_comm(int, int, double *);
+  virtual int pack_forward_comm(int, int *, double *, int, int *);
+  virtual void unpack_forward_comm(int, int, double *);
   int pack_reverse_comm(int, int, double *);
   void unpack_reverse_comm(int, int *, double *);
   double memory_usage();

src/MC/fix_charge_regulation.cpp

@@ -75,7 +75,7 @@ FixChargeRegulation::FixChargeRegulation(LAMMPS *lmp, int narg, char **arg) :
   size_vector = 8;
   global_freq = 1;
   extvector = 0;
-  restart_global = 1;
+  restart_global = 0;
   time_depend = 1;
   cr_nmax = 0;
   overlap_flag = 0;
@@ -985,9 +985,17 @@ int FixChargeRegulation::insert_particle(int ptype, double charge, double rd, do
     modify->create_attribute(m);
 
   }
-  atom->nghost = 0;
-  comm->borders();
   atom->natoms++;
+  atom->nghost = 0;
+  if (atom->tag_enable) {
+    if (atom->tag_enable) {
+      atom->tag_extend();
+      if (atom->map_style != Atom::MAP_NONE) atom->map_init();
+    }
+  }
+  if (triclinic) domain->x2lamda(atom->nlocal);
+  comm->borders();
+  if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
   return m;
 }
 

src/MOLECULE/angle_table.cpp

@@ -470,9 +470,9 @@ void AngleTable::compute_table(Table *tb)
 
   memory->create(tb->ang,tablength,"angle:ang");
   memory->create(tb->e,tablength,"angle:e");
-  memory->create(tb->de,tlm1,"angle:de");
+  memory->create(tb->de,tablength,"angle:de");
   memory->create(tb->f,tablength,"angle:f");
-  memory->create(tb->df,tlm1,"angle:df");
+  memory->create(tb->df,tablength,"angle:df");
   memory->create(tb->e2,tablength,"angle:e2");
   memory->create(tb->f2,tablength,"angle:f2");
 
@@ -488,6 +488,9 @@ void AngleTable::compute_table(Table *tb)
     tb->de[i] = tb->e[i+1] - tb->e[i];
     tb->df[i] = tb->f[i+1] - tb->f[i];
   }
+  // get final elements from linear extrapolation
+  tb->de[tlm1] = 2.0*tb->de[tlm1-1] - tb->de[tlm1-2];
+  tb->df[tlm1] = 2.0*tb->df[tlm1-1] - tb->df[tlm1-2];
 
   double ep0 = - tb->f[0];
   double epn = - tb->f[tlm1];

src/MOLECULE/bond_table.cpp

@@ -435,9 +435,9 @@ void BondTable::compute_table(Table *tb)
 
   memory->create(tb->r,tablength,"bond:r");
   memory->create(tb->e,tablength,"bond:e");
-  memory->create(tb->de,tlm1,"bond:de");
+  memory->create(tb->de,tablength,"bond:de");
   memory->create(tb->f,tablength,"bond:f");
-  memory->create(tb->df,tlm1,"bond:df");
+  memory->create(tb->df,tablength,"bond:df");
   memory->create(tb->e2,tablength,"bond:e2");
   memory->create(tb->f2,tablength,"bond:f2");
 
@@ -453,6 +453,9 @@ void BondTable::compute_table(Table *tb)
     tb->de[i] = tb->e[i+1] - tb->e[i];
     tb->df[i] = tb->f[i+1] - tb->f[i];
   }
+  // get final elements from linear extrapolation
+  tb->de[tlm1] = 2.0*tb->de[tlm1-1] - tb->de[tlm1-2];
+  tb->df[tlm1] = 2.0*tb->df[tlm1-1] - tb->df[tlm1-2];
 
   double ep0 = - tb->f[0];
   double epn = - tb->f[tlm1];

src/NETCDF/dump_netcdf.cpp

@@ -65,6 +65,10 @@ static constexpr int THIS_IS_A_COMPUTE  = -2;
 static constexpr int THIS_IS_A_VARIABLE = -3;
 static constexpr int THIS_IS_A_BIGINT   = -4;
 
+// to be used instead of NC_MAX_VAR_DIMS which was expected
+// to be no larger than 1024 but that is not guaranteed anymore.
+static constexpr int LMP_MAX_VAR_DIMS = 1024;
+
 /* ---------------------------------------------------------------------- */
 
 #define NCERR(x) ncerr(x, nullptr, __LINE__)
@@ -339,8 +343,8 @@ void DumpNetCDF::openfile()
       if (framei != 0 && !multifile)
         error->all(FLERR,"at keyword requires use of 'append yes'");
 
-      int dims[NC_MAX_VAR_DIMS];
-      size_t index[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
+      int dims[LMP_MAX_VAR_DIMS];
+      size_t index[LMP_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
       double d[1];
 
       if (singlefile_opened) return;
@@ -735,8 +739,8 @@ void DumpNetCDF::write_header(bigint n)
 
 void DumpNetCDF::write_data(int n, double *mybuf)
 {
-  size_t start[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
-  ptrdiff_t stride[NC_MAX_VAR_DIMS];
+  size_t start[LMP_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
+  ptrdiff_t stride[LMP_MAX_VAR_DIMS];
 
   if (!int_buffer) {
     n_buffer = n;

src/NETCDF/dump_netcdf_mpiio.cpp

@@ -65,6 +65,10 @@ static constexpr int THIS_IS_A_COMPUTE  = -2;
 static constexpr int THIS_IS_A_VARIABLE = -3;
 static constexpr int THIS_IS_A_BIGINT   = -4;
 
+// to be used instead of NC_MAX_VAR_DIMS which was expected
+// to be no larger than 1024 but that is not guaranteed anymore.
+static constexpr int LMP_MAX_VAR_DIMS = 1024;
+
 /* ---------------------------------------------------------------------- */
 
 #define NCERR(x) ncerr(x, nullptr, __LINE__)
@@ -275,7 +279,7 @@ void DumpNetCDFMPIIO::openfile()
     if (not utils::file_is_readable(filecurrent))
       error->all(FLERR, "cannot append to non-existent file {}", filecurrent);
 
-    MPI_Offset index[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
+    MPI_Offset index[LMP_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
     double d[1];
 
     if (singlefile_opened) return;
@@ -340,8 +344,8 @@ void DumpNetCDFMPIIO::openfile()
     if (framei != 0 && !multifile)
       error->all(FLERR,"at keyword requires use of 'append yes'");
 
-    int dims[NC_MAX_VAR_DIMS];
-    MPI_Offset index[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
+    int dims[LMP_MAX_VAR_DIMS];
+    MPI_Offset index[LMP_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
     double d[1];
 
     if (singlefile_opened) return;
@@ -753,8 +757,8 @@ void DumpNetCDFMPIIO::write_time_and_cell()
 
 void DumpNetCDFMPIIO::write_data(int n, double *mybuf)
 {
-  MPI_Offset start[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
-  MPI_Offset stride[NC_MAX_VAR_DIMS];
+  MPI_Offset start[LMP_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
+  MPI_Offset stride[LMP_MAX_VAR_DIMS];
 
   if (!int_buffer) {
     n_buffer = std::max(1, n);

src/REAXFF/fix_reaxff_species.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -62,9 +61,9 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
   MPI_Comm_size(world,&nprocs);
   ntypes = atom->ntypes;
 
-  nevery = atoi(arg[3]);
-  nrepeat = atoi(arg[4]);
-  global_freq = nfreq = atoi(arg[5]);
+  nevery = utils::inumeric(FLERR,arg[3],false,lmp);
+  nrepeat = utils::inumeric(FLERR,arg[4],false,lmp);
+  global_freq = nfreq = utils::inumeric(FLERR,arg[5],false,lmp);
 
   comm_forward = 4;
 
@@ -95,15 +94,9 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
     rene_flag = 1;
   }
 
-  if (me == 0 && rene_flag) {
-    error->warning(FLERR,"Resetting reneighboring criteria for fix reaxff/species");
-  }
-
-  tmparg = nullptr;
-  memory->create(tmparg,4,4,"reaxff/species:tmparg");
-  strcpy(tmparg[0],arg[3]);
-  strcpy(tmparg[1],arg[4]);
-  strcpy(tmparg[2],arg[5]);
+  if (me == 0 && rene_flag)
+    error->warning(FLERR,"Resetting reneighboring criteria to 'delay {} every {} check no' "
+                   "for fix reaxff/species",neighbor->delay, neighbor->every);
 
   if (me == 0) {
     char *suffix = strrchr(arg[6],'.');
@@ -121,8 +114,7 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
     } else fp = fopen(arg[6],"w");
 
     if (!fp)
-      error->one(FLERR,fmt::format("Cannot open fix reaxff/species file {}: "
-                                   "{}",arg[6],utils::getsyserror()));
+      error->one(FLERR,"Cannot open fix reaxff/species file {}: {}",arg[6],utils::getsyserror());
   }
 
   x0 = nullptr;
@@ -169,9 +161,9 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
     // set BO cutoff
     if (strcmp(arg[iarg],"cutoff") == 0) {
       if (iarg+4 > narg) error->all(FLERR,"Illegal fix reaxff/species command");
-      itype = atoi(arg[iarg+1]);
-      jtype = atoi(arg[iarg+2]);
-      bo_cut = atof(arg[iarg+3]);
+      itype = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
+      jtype = utils::inumeric(FLERR,arg[iarg+2],false,lmp);
+      bo_cut = utils::numeric(FLERR,arg[iarg+3],false,lmp);
       if (itype > ntypes || jtype > ntypes)
         error->all(FLERR,"Illegal fix reaxff/species command");
       if (itype <= 0 || jtype <= 0)
@@ -201,7 +193,7 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
     } else if (strcmp(arg[iarg],"position") == 0) {
       if (iarg+3 > narg) error->all(FLERR,"Illegal fix reaxff/species command");
       posflag = 1;
-      posfreq = atoi(arg[iarg+1]);
+      posfreq = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
       if (posfreq < nfreq || (posfreq%nfreq != 0))
         error->all(FLERR,"Illegal fix reaxff/species command");
 
@@ -259,8 +251,8 @@ FixReaxFFSpecies::~FixReaxFFSpecies()
   if (me == 0) fclose(fp);
   if (me == 0 && posflag && multipos_opened) fclose(pos);
 
-  modify->delete_compute("SPECATOM");
-  modify->delete_fix("SPECBOND");
+  modify->delete_compute(fmt::format("SPECATOM_{}",id));
+  modify->delete_fix(fmt::format("SPECBOND_{}",id));
 }
 
 /* ---------------------------------------------------------------------- */
@@ -300,22 +292,16 @@ void FixReaxFFSpecies::init()
   if (nvalid != update->ntimestep)
     nvalid = update->ntimestep+nfreq;
 
-  // check if this fix has been called twice
-  int count = 0;
-  for (int i = 0; i < modify->nfix; i++)
-    if (strcmp(modify->fix[i]->style,"reaxff/species") == 0) count++;
-  if (count > 1 && comm->me == 0)
-    error->warning(FLERR,"More than one fix reaxff/species");
-
   if (!setupflag) {
     // create a compute to store properties
-    modify->add_compute("SPECATOM all SPEC/ATOM q x y z vx vy vz abo01 abo02 abo03 abo04 "
-                        "abo05 abo06 abo07 abo08 abo09 abo10 abo11 abo12 abo13 abo14 "
-                        "abo15 abo16 abo17 abo18 abo19 abo20 abo21 abo22 abo23 abo24");
+    modify->add_compute(fmt::format("SPECATOM_{} all SPEC/ATOM q x y z vx vy vz abo01 abo02 "
+                                    "abo03 abo04 abo05 abo06 abo07 abo08 abo09 abo10 abo11 "
+                                    "abo12 abo13 abo14 abo15 abo16 abo17 abo18 abo19 abo20 "
+                                    "abo21 abo22 abo23 abo24",id));
 
     // create a fix to point to fix_ave_atom for averaging stored properties
-    auto fixcmd = fmt::format("SPECBOND all ave/atom {} {} {}",tmparg[0],tmparg[1],tmparg[2]);
-    for (int i = 1; i < 32; ++i) fixcmd += " c_SPECATOM[" + std::to_string(i) + "]";
+    auto fixcmd = fmt::format("SPECBOND_{} all ave/atom {} {} {}",id,nevery,nrepeat,nfreq);
+    for (int i = 1; i < 32; ++i) fixcmd += fmt::format(" c_SPECATOM_{}[{}]",id,i);
     f_SPECBOND = (FixAveAtom *) modify->add_fix(fixcmd);
     setupflag = 1;
   }
@@ -683,8 +669,7 @@ void FixReaxFFSpecies::OpenPos()
   char *ptr = strchr(filepos,'*');
   *ptr = '\0';
   if (padflag == 0)
-    sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
-            filepos,ntimestep,ptr+1);
+    sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",filepos,ntimestep,ptr+1);
   else {
     char bif[8],pad[16];
     strcpy(bif,BIGINT_FORMAT);

src/REAXFF/reaxff_ffield.cpp

@@ -583,6 +583,7 @@ namespace ReaxFF {
       } catch (std::exception &e) {
         error->one(FLERR,e.what());
       }
+      fclose(fp);
     }
 
     // broadcast global parameters and allocate list on ranks != 0

src/VTK/dump_vtk.cpp

@@ -31,6 +31,7 @@
 #include "domain.h"
 #include "error.h"
 #include "fix.h"
+#include "fix_store.h"
 #include "force.h"
 #include "group.h"
 #include "input.h"
@@ -87,9 +88,9 @@ enum{X,Y,Z, // required for vtk, must come first
      Q,MUX,MUY,MUZ,MU,RADIUS,DIAMETER,
      OMEGAX,OMEGAY,OMEGAZ,ANGMOMX,ANGMOMY,ANGMOMZ,
      TQX,TQY,TQZ,
-     VARIABLE,COMPUTE,FIX,INAME,DNAME,
+     COMPUTE,FIX,VARIABLE,IVEC,DVEC,IARRAY,DARRAY,
      ATTRIBUTES}; // must come last
-enum{LT,LE,GT,GE,EQ,NEQ};
+enum{LT,LE,GT,GE,EQ,NEQ,XOR};
 enum{VTK,VTP,VTU,PVTP,PVTU}; // file formats
 
 #define ONEFIELD 32
@@ -119,11 +120,10 @@ DumpVTK::DumpVTK(LAMMPS *lmp, int narg, char **arg) :
   // ioptional = start of additional optional args
   // only dump image and dump movie styles process optional args
 
-  ioptional = parse_fields(narg,arg);
+  ioptional = parse_fields(nargnew,earg);
 
-  if (ioptional < narg &&
-      strcmp(style,"image") != 0 && strcmp(style,"movie") != 0)
-    error->all(FLERR,"Invalid attribute in dump vtk command");
+  if (ioptional < nargnew)
+    error->all(FLERR,"Invalid attribute {} in dump vtk command", earg[ioptional]);
   size_one = pack_choice.size();
   current_pack_choice_key = -1;
 
@@ -210,38 +210,40 @@ void DumpVTK::init_style()
   else
     write_choice = &DumpVTK::write_vtk;
 
-  // find current ptr for each compute,fix,variable
+  // find current ptr for each compute,fix,variable and custom atom property
   // check that fix frequency is acceptable
 
-  int icompute;
   for (int i = 0; i < ncompute; i++) {
-    icompute = modify->find_compute(id_compute[i]);
+    int icompute = modify->find_compute(id_compute[i]);
     if (icompute < 0) error->all(FLERR,"Could not find dump vtk compute ID");
     compute[i] = modify->compute[icompute];
   }
 
-  int ifix;
   for (int i = 0; i < nfix; i++) {
-    ifix = modify->find_fix(id_fix[i]);
+    int ifix = modify->find_fix(id_fix[i]);
     if (ifix < 0) error->all(FLERR,"Could not find dump vtk fix ID");
     fix[i] = modify->fix[ifix];
     if (nevery % modify->fix[ifix]->peratom_freq)
       error->all(FLERR,"Dump vtk and fix not computed at compatible times");
   }
 
-  int ivariable;
   for (int i = 0; i < nvariable; i++) {
-    ivariable = input->variable->find(id_variable[i]);
+    int ivariable = input->variable->find(id_variable[i]);
     if (ivariable < 0)
       error->all(FLERR,"Could not find dump vtk variable name");
     variable[i] = ivariable;
   }
 
-  int icustom;
+  int icustom,flag,cols;
   for (int i = 0; i < ncustom; i++) {
-    icustom = atom->find_custom(id_custom[i],flag_custom[i]);
+    icustom = atom->find_custom(id_custom[i],flag,cols);
     if (icustom < 0)
       error->all(FLERR,"Could not find custom per-atom property ID");
+    custom[i] = icustom;
+    if (!flag && !cols) custom_flag[i] = IVEC;
+    else if (flag && !cols) custom_flag[i] = DVEC;
+    else if (!flag && cols) custom_flag[i] = IARRAY;
+    else if (flag && cols) custom_flag[i] = DARRAY;
   }
 
   // set index and check validity of region
@@ -275,7 +277,7 @@ int DumpVTK::count()
 
   // grow choose and variable vbuf arrays if needed
 
-  int nlocal = atom->nlocal;
+  const int nlocal = atom->nlocal;
   if (atom->nmax > maxlocal) {
     maxlocal = atom->nmax;
 
@@ -345,10 +347,10 @@ int DumpVTK::count()
   // un-choose if any threshold criterion isn't met
 
   if (nthresh) {
-    double *ptr;
+    double *ptr,*ptrhold;
+    double *values;
     double value;
-    int nstride;
-    int nlocal = atom->nlocal;
+    int nstride,lastflag;
 
     for (int ithresh = 0; ithresh < nthresh; ithresh++) {
 
@@ -635,26 +637,22 @@ int DumpVTK::count()
         nstride = 1;
       } else if (thresh_array[ithresh] == MUX) {
         if (!atom->mu_flag)
-          error->all(FLERR,
-                     "Threshold for an atom property that isn't allocated");
+          error->all(FLERR,"Threshold for an atom property that isn't allocated");
         ptr = &atom->mu[0][0];
         nstride = 4;
       } else if (thresh_array[ithresh] == MUY) {
         if (!atom->mu_flag)
-          error->all(FLERR,
-                     "Threshold for an atom property that isn't allocated");
+          error->all(FLERR,"Threshold for an atom property that isn't allocated");
         ptr = &atom->mu[0][1];
         nstride = 4;
       } else if (thresh_array[ithresh] == MUZ) {
         if (!atom->mu_flag)
-          error->all(FLERR,
-                     "Threshold for an atom property that isn't allocated");
+          error->all(FLERR,"Threshold for an atom property that isn't allocated");
         ptr = &atom->mu[0][2];
         nstride = 4;
       } else if (thresh_array[ithresh] == MU) {
         if (!atom->mu_flag)
-          error->all(FLERR,
-                     "Threshold for an atom property that isn't allocated");
+          error->all(FLERR,"Threshold for an atom property that isn't allocated");
         ptr = &atom->mu[0][3];
         nstride = 4;
 
@@ -753,9 +751,8 @@ int DumpVTK::count()
         nstride = 1;
 
       } else if (thresh_array[ithresh] == IVEC) {
-        int iwhich,flag,cols
         i = ATTRIBUTES + nfield + ithresh;
-        iwhich = atom->find_custom(id_custom[field2index[i]],flag,cols);
+        int iwhich = custom[field2index[i]];
         int *ivector = atom->ivector[iwhich];
         for (i = 0; i < nlocal; i++)
           dchoose[i] = ivector[i];
@@ -763,16 +760,14 @@ int DumpVTK::count()
         nstride = 1;
 
       } else if (thresh_array[ithresh] == DVEC) {
-        int iwhich,flag,cols;
         i = ATTRIBUTES + nfield + ithresh;
-        iwhich = atom->find_custom(id_custom[field2index[i]],flag,cols);
+        int iwhich = custom[field2index[i]];
         ptr = atom->dvector[iwhich];
         nstride = 1;
 
       } else if (thresh_array[ithresh] == IARRAY) {
-        int iwhich,flag,cols;
         i = ATTRIBUTES + nfield + ithresh;
-        iwhich = atom->find_custom(id_custom[field2index[i]],flag,cols);
+        int iwhich = custom[field2index[i]];
         int **iarray = atom->iarray[iwhich];
         int icol = argindex[i] - 1;
         for (i = 0; i < nlocal; i++)
@@ -781,43 +776,99 @@ int DumpVTK::count()
         nstride = 1;
 
       } else if (thresh_array[ithresh] == DARRAY) {
-        int iwhich,flag,cols;
         i = ATTRIBUTES + nfield + ithresh;
-        iwhich = atom->find_custom(id_custom[field2index[i]],flag,cols)
+        int iwhich = custom[field2index[i]];
         double **darray = atom->darray[iwhich];
         ptr = &darray[0][argindex[i]-1];
         nstride = atom->dcols[iwhich];
       }
 
       // unselect atoms that don't meet threshold criterion
+      // compare to single value or values stored in threshfix
+      // copy ptr attribute into thresh_fix if this is first comparison
 
-      value = thresh_value[ithresh];
+      if (thresh_last[ithresh] < 0) {
+        lastflag = 0;
+        value = thresh_value[ithresh];
+      } else {
+        lastflag = 1;
+        int ilast = thresh_last[ithresh];
+        values = thresh_fix[ilast]->vstore;
+        ptrhold = ptr;
+        if (thresh_first[ilast]) {
+          thresh_first[ilast] = 0;
+          for (i = 0; i < nlocal; i++, ptr += nstride) values[i] = *ptr;
+          ptr = ptrhold;
+        }
+      }
 
-      switch (thresh_op[ithresh]) {
-      case LT:
-        for (i = 0; i < nlocal; i++, ptr += nstride)
-          if (choose[i] && *ptr >= value) choose[i] = 0;
-        break;
-      case LE:
-        for (i = 0; i < nlocal; i++, ptr += nstride)
-          if (choose[i] && *ptr > value) choose[i] = 0;
-        break;
-      case GT:
-        for (i = 0; i < nlocal; i++, ptr += nstride)
-          if (choose[i] && *ptr <= value) choose[i] = 0;
-        break;
-      case GE:
-        for (i = 0; i < nlocal; i++, ptr += nstride)
-          if (choose[i] && *ptr < value) choose[i] = 0;
-        break;
-      case EQ:
-        for (i = 0; i < nlocal; i++, ptr += nstride)
-          if (choose[i] && *ptr != value) choose[i] = 0;
-        break;
-      case NEQ:
-        for (i = 0; i < nlocal; i++, ptr += nstride)
-          if (choose[i] && *ptr == value) choose[i] = 0;
-        break;
+      if (thresh_op[ithresh] == LT) {
+        if (lastflag) {
+          for (i = 0; i < nlocal; i++, ptr += nstride)
+            if (choose[i] && *ptr >= values[i]) choose[i] = 0;
+        } else {
+          for (i = 0; i < nlocal; i++, ptr += nstride)
+            if (choose[i] && *ptr >= value) choose[i] = 0;
+        }
+      } else if (thresh_op[ithresh] == LE) {
+        if (lastflag) {
+          for (i = 0; i < nlocal; i++, ptr += nstride)
+            if (choose[i] && *ptr > values[i]) choose[i] = 0;
+        } else {
+          for (i = 0; i < nlocal; i++, ptr += nstride)
+            if (choose[i] && *ptr > value) choose[i] = 0;
+        }
+      } else if (thresh_op[ithresh] == GT) {
+        if (lastflag) {
+          for (i = 0; i < nlocal; i++, ptr += nstride)
+            if (choose[i] && *ptr <= values[i]) choose[i] = 0;
+        } else {
+          for (i = 0; i < nlocal; i++, ptr += nstride)
+            if (choose[i] && *ptr <= value) choose[i] = 0;
+        }
+      } else if (thresh_op[ithresh] == GE) {
+        if (lastflag) {
+          for (i = 0; i < nlocal; i++, ptr += nstride)
+            if (choose[i] && *ptr < values[i]) choose[i] = 0;
+        } else {
+          for (i = 0; i < nlocal; i++, ptr += nstride)
+            if (choose[i] && *ptr < value) choose[i] = 0;
+        }
+      } else if (thresh_op[ithresh] == EQ) {
+        if (lastflag) {
+          for (i = 0; i < nlocal; i++, ptr += nstride)
+            if (choose[i] && *ptr != values[i]) choose[i] = 0;
+        } else {
+          for (i = 0; i < nlocal; i++, ptr += nstride)
+            if (choose[i] && *ptr != value) choose[i] = 0;
+        }
+      } else if (thresh_op[ithresh] == NEQ) {
+        if (lastflag) {
+          for (i = 0; i < nlocal; i++, ptr += nstride)
+            if (choose[i] && *ptr == values[i]) choose[i] = 0;
+        } else {
+          for (i = 0; i < nlocal; i++, ptr += nstride)
+            if (choose[i] && *ptr == value) choose[i] = 0;
+        }
+      } else if (thresh_op[ithresh] == XOR) {
+        if (lastflag) {
+          for (i = 0; i < nlocal; i++, ptr += nstride)
+            if ((choose[i] && *ptr == 0.0 && values[i] == 0.0) ||
+                (*ptr != 0.0 && values[i] != 0.0))
+              choose[i] = 0;
+        } else {
+          for (i = 0; i < nlocal; i++, ptr += nstride)
+            if ((choose[i] && *ptr == 0.0 && value == 0.0) ||
+                (*ptr != 0.0 && value != 0.0))
+              choose[i] = 0;
+        }
+      }
+
+      // update values stored in threshfix
+
+      if (lastflag) {
+        ptr = ptrhold;
+        for (i = 0; i < nlocal; i++, ptr += nstride) values[i] = *ptr;
       }
     }
   }
@@ -1754,15 +1805,16 @@ int DumpVTK::parse_fields(int narg, char **arg)
 
     } else {
 
-      int n,tmp;
+      int n,flag,cols;
       ArgInfo argi(arg[iarg],ArgInfo::COMPUTE|ArgInfo::FIX|ArgInfo::VARIABLE
-                   |ArgInfo::DVEC|ArgInfo::IVEC);
+                   |ArgInfo::DNAME|ArgInfo::INAME);
       argindex[ATTRIBUTES+i] = argi.get_index1();
+      auto aname = argi.get_name();
 
       switch (argi.get_type()) {
 
       case ArgInfo::UNKNOWN:
-        error->all(FLERR,"Invalid attribute in dump vtk command");
+        error->all(FLERR,"Invalid attribute in dump vtk command: {}",arg[iarg]);
         break;
 
       // compute value = c_ID
@@ -1772,21 +1824,19 @@ int DumpVTK::parse_fields(int narg, char **arg)
         pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_compute;
         vtype[ATTRIBUTES+i] = Dump::DOUBLE;
 
-        n = modify->find_compute(argi.get_name());
-        if (n < 0) error->all(FLERR,"Could not find dump vtk compute ID");
+        n = modify->find_compute(aname);
+        if (n < 0) error->all(FLERR,"Could not find dump vtk compute ID: {}",aname);
         if (modify->compute[n]->peratom_flag == 0)
-          error->all(FLERR,"Dump vtk compute does not compute per-atom info");
+          error->all(FLERR,"Dump vtk compute {} does not compute per-atom info",aname);
         if (argi.get_dim() == 0 && modify->compute[n]->size_peratom_cols > 0)
-          error->all(FLERR,
-                     "Dump vtk compute does not calculate per-atom vector");
+          error->all(FLERR,"Dump vtk compute {} does not calculate per-atom vector",aname);
         if (argi.get_dim() > 0 && modify->compute[n]->size_peratom_cols == 0)
-          error->all(FLERR,
-                     "Dump vtk compute does not calculate per-atom array");
+          error->all(FLERR,"Dump vtk compute {} does not calculate per-atom array",aname);
         if (argi.get_dim() > 0 &&
             argi.get_index1() > modify->compute[n]->size_peratom_cols)
-          error->all(FLERR,"Dump vtk compute vector is accessed out-of-range");
+          error->all(FLERR,"Dump vtk compute {} vector is accessed out-of-range",aname);
 
-        field2index[ATTRIBUTES+i] = add_compute(argi.get_name());
+        field2index[ATTRIBUTES+i] = add_compute(aname);
         name[ATTRIBUTES+i] = arg[iarg];
         break;
 
@@ -1797,19 +1847,19 @@ int DumpVTK::parse_fields(int narg, char **arg)
         pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_fix;
         vtype[ATTRIBUTES+i] = Dump::DOUBLE;
 
-        n = modify->find_fix(argi.get_name());
-        if (n < 0) error->all(FLERR,"Could not find dump vtk fix ID");
+        n = modify->find_fix(aname);
+        if (n < 0) error->all(FLERR,"Could not find dump vtk fix ID: {}",aname);
         if (modify->fix[n]->peratom_flag == 0)
-          error->all(FLERR,"Dump vtk fix does not compute per-atom info");
+          error->all(FLERR,"Dump vtk fix {} does not compute per-atom info",aname);
         if (argi.get_dim() == 0 && modify->fix[n]->size_peratom_cols > 0)
-          error->all(FLERR,"Dump vtk fix does not compute per-atom vector");
+          error->all(FLERR,"Dump vtk fix {} does not compute per-atom vector",aname);
         if (argi.get_dim() > 0 && modify->fix[n]->size_peratom_cols == 0)
-          error->all(FLERR,"Dump vtk fix does not compute per-atom array");
+          error->all(FLERR,"Dump vtk fix {} does not compute per-atom array",aname);
         if (argi.get_dim() > 0 &&
             argi.get_index1() > modify->fix[n]->size_peratom_cols)
-          error->all(FLERR,"Dump vtk fix vector is accessed out-of-range");
+          error->all(FLERR,"Dump vtk fix {} vector is accessed out-of-range",aname);
 
-        field2index[ATTRIBUTES+i] = add_fix(argi.get_name());
+        field2index[ATTRIBUTES+i] = add_fix(aname);
         name[ATTRIBUTES+i] = arg[iarg];
         break;
 
@@ -1819,61 +1869,62 @@ int DumpVTK::parse_fields(int narg, char **arg)
         pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_variable;
         vtype[ATTRIBUTES+i] = Dump::DOUBLE;
 
-        n = input->variable->find(argi.get_name());
-        if (n < 0) error->all(FLERR,"Could not find dump vtk variable name");
+        n = input->variable->find(aname);
+        if (n < 0) error->all(FLERR,"Could not find dump vtk variable name {}",aname);
         if (input->variable->atomstyle(n) == 0)
-          error->all(FLERR,"Dump vtk variable is not atom-style variable");
+          error->all(FLERR,"Dump vtk variable {} is not atom-style variable",aname);
 
-        field2index[ATTRIBUTES+i] = add_variable(argi.get_name());
+        field2index[ATTRIBUTES+i] = add_variable(aname);
         name[ATTRIBUTES+i] = arg[iarg];
         break;
 
-      // custom per-atom integer vector = i_ID
-
-      case ArgInfo::INAME:
-        pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_custom;
-        vtype[ATTRIBUTES+i] = Dump::INT;
-
-        tmp = -1;
-        n = atom->find_custom(argi.get_name(),tmp);
-        if (n < 0)
-          error->all(FLERR,"Could not find custom per-atom property ID");
-
-        if (tmp != 0)
-          error->all(FLERR,"Custom per-atom property ID is not integer");
-
-        field2index[ATTRIBUTES+i] = add_custom(argi.get_name(),0);
-        name[ATTRIBUTES+i] = arg[iarg];
-        break;
-
-      // custom per-atom floating point vector = d_ID
+      // custom per-atom floating point vector or array = d_ID d2_ID
 
       case ArgInfo::DNAME:
         pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_custom;
         vtype[ATTRIBUTES+i] = Dump::DOUBLE;
 
-        tmp = -1;
-        n = atom->find_custom(argi.get_name(),tmp);
+        n = atom->find_custom(aname,flag,cols);
+
         if (n < 0)
-          error->all(FLERR,"Could not find custom per-atom property ID");
-
-        if (tmp != 1)
-          error->all(FLERR,"Custom per-atom property ID is not floating point");
-
-        field2index[ATTRIBUTES+i] = add_custom(argi.get_name(),1);
+          error->all(FLERR,"Could not find custom per-atom property ID: {}", aname);
+        if (argindex[ATTRIBUTES+i] == 0) {
+          if (!flag || cols)
+            error->all(FLERR,"Property double vector {} for dump vtk does not exist",aname);
+        } else {
+          if (!flag || !cols)
+            error->all(FLERR,"Property double array {} for dump vtk does not exist",aname);
+          if (argindex[ATTRIBUTES+i] > atom->dcols[n])
+            error->all(FLERR,"Dump vtk property array {} is accessed out-of-range",aname);
+        }
+        field2index[ATTRIBUTES+i] = add_custom(aname,1);
         name[ATTRIBUTES+i] = arg[iarg];
         break;
 
-      // NEWSTYLE
-      // custom per-atom integer array = i2_ID
+      // custom per-atom integer vector or array = i_ID or i2_ID
 
-      case ArgInfo::IARRAY:
-        return iarg;
+      case ArgInfo::INAME:
+        pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_custom;
+        vtype[ATTRIBUTES+i] = Dump::INT;
 
-      // custom per-atom floating point array = d2_ID
+        n = atom->find_custom(aname,flag,cols);
 
-      case ArgInfo::DARRAY:
-        return iarg;
+        if (n < 0)
+          error->all(FLERR,"Could not find custom per-atom property ID: {}", aname);
+        if (argindex[ATTRIBUTES+i] == 0) {
+          if (flag || cols)
+            error->all(FLERR,"Property integer vector {} for dump vtk does not exist",aname);
+        } else {
+          if (flag || !cols)
+            error->all(FLERR,"Property integer array {} for dump vtk does not exist",aname);
+          if (argindex[ATTRIBUTES+i] > atom->icols[n])
+            error->all(FLERR,"Dump vtk property array {} is accessed out-of-range",aname);
+        }
+        field2index[ATTRIBUTES+i] = add_custom(aname,0);
+        name[ATTRIBUTES+i] = arg[iarg];
+        break;
+
+      // no match
 
       default:
         return iarg;
@@ -1948,12 +1999,10 @@ int DumpVTK::add_compute(const char *id)
 
   id_compute = (char **)
     memory->srealloc(id_compute,(ncompute+1)*sizeof(char *),"dump:id_compute");
-  delete [] compute;
+  delete[] compute;
   compute = new Compute*[ncompute+1];
 
-  int n = strlen(id) + 1;
-  id_compute[ncompute] = new char[n];
-  strcpy(id_compute[ncompute],id);
+  id_compute[ncompute] = utils::strdup(id);
   ncompute++;
   return ncompute-1;
 }
@@ -1973,12 +2022,10 @@ int DumpVTK::add_fix(const char *id)
 
   id_fix = (char **)
     memory->srealloc(id_fix,(nfix+1)*sizeof(char *),"dump:id_fix");
-  delete [] fix;
+  delete[] fix;
   fix = new Fix*[nfix+1];
 
-  int n = strlen(id) + 1;
-  id_fix[nfix] = new char[n];
-  strcpy(id_fix[nfix],id);
+  id_fix[nfix] = utils::strdup(id);
   nfix++;
   return nfix-1;
 }
@@ -1999,22 +2046,20 @@ int DumpVTK::add_variable(const char *id)
   id_variable = (char **)
     memory->srealloc(id_variable,(nvariable+1)*sizeof(char *),
                      "dump:id_variable");
-  delete [] variable;
+  delete[] variable;
   variable = new int[nvariable+1];
-  delete [] vbuf;
+  delete[] vbuf;
   vbuf = new double*[nvariable+1];
   for (int i = 0; i <= nvariable; i++) vbuf[i] = nullptr;
 
-  int n = strlen(id) + 1;
-  id_variable[nvariable] = new char[n];
-  strcpy(id_variable[nvariable],id);
+  id_variable[nvariable] = utils::strdup(id);
   nvariable++;
   return nvariable-1;
 }
 
 /* ----------------------------------------------------------------------
    add custom atom property to list used by dump
-   return index of where this property is in list
+   return index of where this property is in Atom class custom lists
    if already in list, do not add, just return index, else add to list
 ------------------------------------------------------------------------- */
 
@@ -2022,21 +2067,17 @@ int DumpVTK::add_custom(const char *id, int flag)
 {
   int icustom;
   for (icustom = 0; icustom < ncustom; icustom++)
-    if ((strcmp(id,id_custom[icustom]) == 0)
-        && (flag == flag_custom[icustom])) break;
+    if (strcmp(id,id_custom[icustom]) == 0) break;
   if (icustom < ncustom) return icustom;
 
-  id_custom = (char **)
-    memory->srealloc(id_custom,(ncustom+1)*sizeof(char *),"dump:id_custom");
-  flag_custom = (int *)
-    memory->srealloc(flag_custom,(ncustom+1)*sizeof(int),"dump:flag_custom");
-
-  int n = strlen(id) + 1;
-  id_custom[ncustom] = new char[n];
-  strcpy(id_custom[ncustom],id);
-  flag_custom[ncustom] = flag;
+  id_custom = (char **) memory->srealloc(id_custom,(ncustom+1)*sizeof(char *),"dump:id_custom");
+  custom = (int *) memory->srealloc(custom,(ncustom+1)*sizeof(int),"dump:custom");
+  custom_flag = (int *) memory->srealloc(custom_flag,(ncustom+1)*sizeof(int),"dump:custom_flag");
 
+  id_custom[ncustom] = utils::strdup(id);
+  custom_flag[ncustom] = flag;
   ncustom++;
+
   return ncustom-1;
 }
 
@@ -2050,21 +2091,17 @@ int DumpVTK::modify_param(int narg, char **arg)
     else {
       iregion = domain->find_region(arg[1]);
       if (iregion == -1)
-        error->all(FLERR,"Dump_modify region ID does not exist");
-      delete [] idregion;
-      int n = strlen(arg[1]) + 1;
-      idregion = new char[n];
-      strcpy(idregion,arg[1]);
+        error->all(FLERR,"Dump_modify region ID {} does not exist",arg[1]);
+      delete[] idregion;
+      idregion = utils::strdup(arg[1]);
     }
     return 2;
   }
 
   if (strcmp(arg[0],"label") == 0) {
      if (narg < 2) error->all(FLERR,"Illegal dump_modify command [label]");
-     delete [] label;
-     int n = strlen(arg[1]) + 1;
-     label = new char[n];
-     strcpy(label,arg[1]);
+     delete[] label;
+     label = utils::strdup(arg[1]);
      return 2;
    }
 
@@ -2078,23 +2115,29 @@ int DumpVTK::modify_param(int narg, char **arg)
 
   if (strcmp(arg[0],"element") == 0) {
     if (narg < ntypes+1)
-      error->all(FLERR,"Dump modify: number of element names do not match atom types");
-
-    if (typenames) {
-      for (int i = 1; i <= ntypes; i++) delete [] typenames[i];
-      delete [] typenames;
-      typenames = nullptr;
-    }
+      error->all(FLERR,"Number of dump_modify element names does not match number of atom types");
 
+    for (int i = 1; i <= ntypes; i++) delete[] typenames[i];
+    delete[] typenames;
     typenames = new char*[ntypes+1];
     for (int itype = 1; itype <= ntypes; itype++) {
-      int n = strlen(arg[itype]) + 1;
-      typenames[itype] = new char[n];
-      strcpy(typenames[itype],arg[itype]);
+      typenames[itype] = utils::strdup(arg[itype]);
     }
     return ntypes+1;
   }
 
+  if (strcmp(arg[0],"refresh") == 0) {
+    if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
+    ArgInfo argi(arg[1],ArgInfo::COMPUTE);
+    if ((argi.get_type() != ArgInfo::COMPUTE) || (argi.get_dim() != 0))
+      error->all(FLERR,"Illegal dump_modify command");
+    if (refreshflag) error->all(FLERR,"Dump_modify can only have one refresh");
+
+    refreshflag = 1;
+    refresh = argi.copy_name();
+    return 2;
+  }
+
   if (strcmp(arg[0],"thresh") == 0) {
     if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
     if (strcmp(arg[1],"none") == 0) {
@@ -2105,8 +2148,16 @@ int DumpVTK::modify_param(int narg, char **arg)
         thresh_array = nullptr;
         thresh_op = nullptr;
         thresh_value = nullptr;
+        thresh_last = nullptr;
+        for (int i = 0; i < nthreshlast; i++) {
+          modify->delete_fix(thresh_fixID[i]);
+          delete[] thresh_fixID[i];
+        }
+        thresh_fix = nullptr;
+        thresh_fixID = nullptr;
+        thresh_first = nullptr;
       }
-      nthresh = 0;
+      nthresh = nthreshlast = 0;
       return 2;
     }
 
@@ -2117,6 +2168,7 @@ int DumpVTK::modify_param(int narg, char **arg)
     memory->grow(thresh_array,nthresh+1,"dump:thresh_array");
     memory->grow(thresh_op,(nthresh+1),"dump:thresh_op");
     memory->grow(thresh_value,(nthresh+1),"dump:thresh_value");
+    memory->grow(thresh_last,(nthresh+1),"dump:thresh_last");
 
     // set attribute type of threshold
     // customize by adding to if statement
@@ -2199,98 +2251,125 @@ int DumpVTK::modify_param(int narg, char **arg)
     else if (strcmp(arg[1],"tqy") == 0) thresh_array[nthresh] = TQY;
     else if (strcmp(arg[1],"tqz") == 0) thresh_array[nthresh] = TQZ;
 
-    // compute value = c_ID
-    // if no trailing [], then arg is set to 0, else arg is between []
+    // compute or fix or variable or custom vector/array
 
-    else if (strncmp(arg[1],"c_",2) == 0) {
-      thresh_array[nthresh] = COMPUTE;
-      int n = strlen(arg[1]);
-      char *suffix = new char[n];
-      strcpy(suffix,&arg[1][2]);
+    else {
+      int n,flag,cols;
+      ArgInfo argi(arg[1],ArgInfo::COMPUTE|ArgInfo::FIX|ArgInfo::VARIABLE
+                   |ArgInfo::DNAME|ArgInfo::INAME);
+      argindex[ATTRIBUTES+nfield+nthresh] = argi.get_index1();
+      auto aname = argi.get_name();
 
-      char *ptr = strchr(suffix,'[');
-      if (ptr) {
-        if (suffix[strlen(suffix)-1] != ']')
-          error->all(FLERR,"Invalid attribute in dump modify command");
-        argindex[ATTRIBUTES+nfield+nthresh] = atoi(ptr+1);
-        *ptr = '\0';
-      } else argindex[ATTRIBUTES+nfield+nthresh] = 0;
+      switch (argi.get_type()) {
 
-      n = modify->find_compute(suffix);
-      if (n < 0) error->all(FLERR,"Could not find dump modify compute ID");
+      case ArgInfo::UNKNOWN:
+        error->all(FLERR,"Invalid attribute in dump modify command");
+        break;
 
-      if (modify->compute[n]->peratom_flag == 0)
-        error->all(FLERR,
-                   "Dump modify compute ID does not compute per-atom info");
-      if (argindex[ATTRIBUTES+nfield+nthresh] == 0 &&
-          modify->compute[n]->size_peratom_cols > 0)
-        error->all(FLERR,
-                   "Dump modify compute ID does not compute per-atom vector");
-      if (argindex[ATTRIBUTES+nfield+nthresh] > 0 &&
-          modify->compute[n]->size_peratom_cols == 0)
-        error->all(FLERR,
-                   "Dump modify compute ID does not compute per-atom array");
-      if (argindex[ATTRIBUTES+nfield+nthresh] > 0 &&
-          argindex[ATTRIBUTES+nfield+nthresh] > modify->compute[n]->size_peratom_cols)
-        error->all(FLERR,"Dump modify compute ID vector is not large enough");
+      // compute value = c_ID
+      // if no trailing [], then arg is set to 0, else arg is between []
 
-      field2index[ATTRIBUTES+nfield+nthresh] = add_compute(suffix);
-      delete [] suffix;
+      case ArgInfo::COMPUTE:
+        thresh_array[nthresh] = COMPUTE;
+        n = modify->find_compute(aname);
+        if (n < 0) error->all(FLERR,"Could not find dump modify compute ID: {}",aname);
 
-    // fix value = f_ID
-    // if no trailing [], then arg is set to 0, else arg is between []
+        if (modify->compute[n]->peratom_flag == 0)
+          error->all(FLERR,"Dump modify compute ID {} does not compute per-atom info",aname);
+        if (argi.get_dim() == 0 && modify->compute[n]->size_peratom_cols > 0)
+          error->all(FLERR,"Dump modify compute ID {} does not compute per-atom vector",aname);
+        if (argi.get_index1() > 0 && modify->compute[n]->size_peratom_cols == 0)
+          error->all(FLERR,"Dump modify compute ID {} does not compute per-atom array",aname);
+        if (argi.get_index1() > 0 &&
+            argi.get_index1() > modify->compute[n]->size_peratom_cols)
+          error->all(FLERR,"Dump modify compute ID {} vector is not large enough",aname);
 
-    } else if (strncmp(arg[1],"f_",2) == 0) {
-      thresh_array[nthresh] = FIX;
-      int n = strlen(arg[1]);
-      char *suffix = new char[n];
-      strcpy(suffix,&arg[1][2]);
+        field2index[ATTRIBUTES+nfield+nthresh] = add_compute(aname);
+        break;
 
-      char *ptr = strchr(suffix,'[');
-      if (ptr) {
-        if (suffix[strlen(suffix)-1] != ']')
-          error->all(FLERR,"Invalid attribute in dump modify command");
-        argindex[ATTRIBUTES+nfield+nthresh] = atoi(ptr+1);
-        *ptr = '\0';
-      } else argindex[ATTRIBUTES+nfield+nthresh] = 0;
+      // fix value = f_ID
+      // if no trailing [], then arg is set to 0, else arg is between []
 
-      n = modify->find_fix(suffix);
-      if (n < 0) error->all(FLERR,"Could not find dump modify fix ID");
+      case ArgInfo::FIX:
+        thresh_array[nthresh] = FIX;
+        n = modify->find_fix(aname);
+        if (n < 0) error->all(FLERR,"Could not find dump modify fix ID: {}",aname);
 
-      if (modify->fix[n]->peratom_flag == 0)
-        error->all(FLERR,"Dump modify fix ID does not compute per-atom info");
-      if (argindex[ATTRIBUTES+nfield+nthresh] == 0 &&
-          modify->fix[n]->size_peratom_cols > 0)
-        error->all(FLERR,"Dump modify fix ID does not compute per-atom vector");
-      if (argindex[ATTRIBUTES+nfield+nthresh] > 0 &&
-          modify->fix[n]->size_peratom_cols == 0)
-        error->all(FLERR,"Dump modify fix ID does not compute per-atom array");
-      if (argindex[ATTRIBUTES+nfield+nthresh] > 0 &&
-          argindex[ATTRIBUTES+nfield+nthresh] > modify->fix[n]->size_peratom_cols)
-        error->all(FLERR,"Dump modify fix ID vector is not large enough");
+        if (modify->fix[n]->peratom_flag == 0)
+          error->all(FLERR,"Dump modify fix ID {} does not compute per-atom info",aname);
+        if (argi.get_dim() == 0 && modify->fix[n]->size_peratom_cols > 0)
+          error->all(FLERR,"Dump modify fix ID {} does not compute per-atom vector",aname);
+        if (argi.get_index1() > 0 && modify->fix[n]->size_peratom_cols == 0)
+          error->all(FLERR,"Dump modify fix ID {} does not compute per-atom array",aname);
+        if (argi.get_index1() > 0 && argi.get_index1() > modify->fix[n]->size_peratom_cols)
+          error->all(FLERR,"Dump modify fix ID {} vector is not large enough",aname);
 
-      field2index[ATTRIBUTES+nfield+nthresh] = add_fix(suffix);
-      delete [] suffix;
+        field2index[ATTRIBUTES+nfield+nthresh] = add_fix(aname);
+        break;
 
-    // variable value = v_ID
+      // variable value = v_ID
 
-    } else if (strncmp(arg[1],"v_",2) == 0) {
-      thresh_array[nthresh] = VARIABLE;
-      int n = strlen(arg[1]);
-      char *suffix = new char[n];
-      strcpy(suffix,&arg[1][2]);
+      case ArgInfo::VARIABLE:
+        thresh_array[nthresh] = VARIABLE;
+        n = input->variable->find(aname);
+        if (n < 0) error->all(FLERR,"Could not find dump modify variable name: {}",aname);
+        if (input->variable->atomstyle(n) == 0)
+          error->all(FLERR,"Dump modify variable {} is not atom-style variable",aname);
 
-      argindex[ATTRIBUTES+nfield+nthresh] = 0;
+        field2index[ATTRIBUTES+nfield+nthresh] = add_variable(aname);
+        break;
 
-      n = input->variable->find(suffix);
-      if (n < 0) error->all(FLERR,"Could not find dump modify variable name");
-      if (input->variable->atomstyle(n) == 0)
-        error->all(FLERR,"Dump modify variable is not atom-style variable");
+      // custom per atom floating point vector or array
 
-      field2index[ATTRIBUTES+nfield+nthresh] = add_variable(suffix);
-      delete [] suffix;
+      case ArgInfo::DNAME:
+        n = atom->find_custom(aname,flag,cols);
 
-    } else error->all(FLERR,"Invalid dump_modify threshold operator");
+        if (n < 0)
+          error->all(FLERR,"Could not find custom per-atom property ID: {}", aname);
+        if (argindex[ATTRIBUTES+nfield+nthresh] == 0) {
+          if (!flag || cols)
+            error->all(FLERR,"Property double vector for dump custom does not exist");
+          thresh_array[nthresh] = DVEC;
+        } else {
+          if (!flag || !cols)
+            error->all(FLERR,"Property double array for dump custom does not exist");
+          if (argindex[ATTRIBUTES+nfield+nthresh] > atom->dcols[n])
+            error->all(FLERR,"Dump custom property array is accessed out-of-range");
+          thresh_array[nthresh] = DARRAY;
+        }
+
+        field2index[ATTRIBUTES+nfield+nthresh] = add_custom(aname,thresh_array[nthresh]);
+        break;
+
+      // custom per atom integer vector or array
+
+      case ArgInfo::INAME:
+        n = atom->find_custom(aname,flag,cols);
+
+        if (n < 0)
+          error->all(FLERR,"Could not find custom per-atom property ID: {}", aname);
+        if (argindex[ATTRIBUTES+nfield+nthresh] == 0) {
+          if (flag || cols)
+            error->all(FLERR,"Property integer vector for dump custom does not exist");
+          thresh_array[nthresh] = IVEC;
+        } else {
+          if (flag || !cols)
+            error->all(FLERR,"Property integer array for dump custom does not exist");
+          if (argindex[ATTRIBUTES+nfield+nthresh] > atom->icols[n])
+            error->all(FLERR,"Dump custom property array is accessed out-of-range");
+          thresh_array[nthresh] = IARRAY;
+        }
+
+        field2index[ATTRIBUTES+nfield+nthresh] = add_custom(aname,thresh_array[nthresh]);
+        break;
+
+      // no match
+
+      default:
+        error->all(FLERR,"Invalid dump_modify thresh attribute: {}",aname);
+        break;
+      }
+    }
 
     // set operation type of threshold
 
@@ -2300,11 +2379,32 @@ int DumpVTK::modify_param(int narg, char **arg)
     else if (strcmp(arg[2],">=") == 0) thresh_op[nthresh] = GE;
     else if (strcmp(arg[2],"==") == 0) thresh_op[nthresh] = EQ;
     else if (strcmp(arg[2],"!=") == 0) thresh_op[nthresh] = NEQ;
-    else error->all(FLERR,"Invalid dump_modify threshold operator");
+    else if (strcmp(arg[2],"|^") == 0) thresh_op[nthresh] = XOR;
+    else error->all(FLERR,"Invalid dump_modify thresh operator");
 
-    // set threshold value
+    // set threshold value as number or special LAST keyword
+    // create FixStore to hold LAST values, should work with restart
+    // id = dump-ID + nthreshlast + DUMP_STORE, fix group = dump group
 
-    thresh_value[nthresh] = utils::numeric(FLERR,arg[3],false,lmp);
+    if (strcmp(arg[3],"LAST") != 0) {
+      thresh_value[nthresh] = utils::numeric(FLERR,arg[3],false,lmp);
+      thresh_last[nthresh] = -1;
+    } else {
+      thresh_fix = (FixStore **)
+        memory->srealloc(thresh_fix,(nthreshlast+1)*sizeof(FixStore *),"dump:thresh_fix");
+      thresh_fixID = (char **)
+        memory->srealloc(thresh_fixID,(nthreshlast+1)*sizeof(char *),"dump:thresh_fixID");
+      memory->grow(thresh_first,(nthreshlast+1),"dump:thresh_first");
+
+      std::string threshid = fmt::format("{}{}_DUMP_STORE",id,nthreshlast);
+      thresh_fixID[nthreshlast] = utils::strdup(threshid);
+      threshid += fmt::format(" {} STORE peratom 1 1", group->names[igroup]);
+      thresh_fix[nthreshlast] = (FixStore *) modify->add_fix(threshid);
+
+      thresh_last[nthreshlast] = nthreshlast;
+      thresh_first[nthreshlast] = 1;
+      nthreshlast++;
+    }
 
     nthresh++;
     return 4;
@@ -2389,25 +2489,35 @@ void DumpVTK::pack_variable(int n)
 
 void DumpVTK::pack_custom(int n)
 {
-  int index = field2index[n];
-
-  if (flag_custom[index] == 0) { // integer
-    int iwhich,tmp;
-    iwhich = atom->find_custom(id_custom[index],tmp);
+  int flag = custom_flag[field2index[current_pack_choice_key]];
+  int iwhich = custom[field2index[current_pack_choice_key]];
+  int index = argindex[current_pack_choice_key];
 
+  if (flag == IVEC) {
     int *ivector = atom->ivector[iwhich];
     for (int i = 0; i < nchoose; i++) {
       buf[n] = ivector[clist[i]];
       n += size_one;
     }
-  } else if (flag_custom[index] == 1) { // double
-    int iwhich,tmp;
-    iwhich = atom->find_custom(id_custom[index],tmp);
-
+  } else if (flag == DVEC) {
     double *dvector = atom->dvector[iwhich];
     for (int i = 0; i < nchoose; i++) {
       buf[n] = dvector[clist[i]];
       n += size_one;
     }
+  } else if (flag == IARRAY) {
+    index--;
+    int **iarray = atom->iarray[iwhich];
+    for (int i = 0; i < nchoose; i++) {
+      buf[n] = iarray[clist[i]][index];
+      n += size_one;
+    }
+  } else if (flag == DARRAY) {
+    index--;
+    double **darray = atom->darray[iwhich];
+    for (int i = 0; i < nchoose; i++) {
+      buf[n] = darray[clist[i]][index];
+      n += size_one;
+    }
   }
 }

src/compute_orientorder_atom.cpp

@@ -198,6 +198,8 @@ void ComputeOrientOrderAtom::init()
     error->all(FLERR,"Compute orientorder/atom cutoff is "
                "longer than pairwise cutoff");
 
+  memory->destroy(qnm_r);
+  memory->destroy(qnm_i);
   memory->create(qnm_r,nqlist,2*qmax+1,"orientorder/atom:qnm_r");
   memory->create(qnm_i,nqlist,2*qmax+1,"orientorder/atom:qnm_i");
 
@@ -669,6 +671,7 @@ void ComputeOrientOrderAtom::init_clebsch_gordan()
         idxcg_count++;
   }
   idxcg_max = idxcg_count;
+  memory->destroy(cglist);
   memory->create(cglist, idxcg_max, "computeorientorderatom:cglist");
 
   idxcg_count = 0;

src/dump.cpp

@@ -371,16 +371,6 @@ void Dump::write()
   if (multiproc != nprocs) MPI_Allreduce(&nme,&nmax,1,MPI_INT,MPI_MAX,world);
   else nmax = nme;
 
-  // write timestep header
-  // for multiproc,
-  //   nheader = # of lines in this file via Allreduce on clustercomm
-
-  bigint nheader = ntotal;
-  if (multiproc)
-    MPI_Allreduce(&bnme,&nheader,1,MPI_LMP_BIGINT,MPI_SUM,clustercomm);
-
-  if (filewriter && write_header_flag) write_header(nheader);
-
   // insure buf is sized for packing and communicating
   // use nmax to insure filewriter proc can receive info from others
   // limit nmax*size_one to int since used as arg in MPI calls
@@ -433,6 +423,19 @@ void Dump::write()
   else pack(nullptr);
   if (sort_flag) sort();
 
+  // write timestep header
+  // for multiproc,
+  //   nheader = # of lines in this file via Allreduce on clustercomm
+  //   must come after sort, which can change nme
+
+  bigint nheader = ntotal;
+  if (multiproc) {
+    bnme = nme;
+    MPI_Allreduce(&bnme,&nheader,1,MPI_LMP_BIGINT,MPI_SUM,clustercomm);
+  }
+
+  if (filewriter && write_header_flag) write_header(nheader);
+
   // if buffering, convert doubles into strings
   // insure sbuf is sized for communicating
   // cannot buffer if output is to binary file

src/dump_custom.cpp

@@ -131,7 +131,7 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
 
   if (ioptional < nfield &&
       strcmp(style,"image") != 0 && strcmp(style,"movie") != 0)
-    error->all(FLERR,"Invalid attribute in dump custom command");
+    error->all(FLERR,"Invalid attribute {} in dump {} command",earg[ioptional],style);
 
   // noptional = # of optional args
   // reset nfield to subtract off optional args
@@ -238,9 +238,8 @@ DumpCustom::~DumpCustom()
 
   for (int i = 0; i < ncustom; i++) delete[] id_custom[i];
   memory->sfree(id_custom);
-  delete [] custom;
-  delete [] custom_flag;
-
+  memory->sfree(custom);
+  memory->sfree(custom_flag);
   memory->destroy(choose);
   memory->destroy(dchoose);
   memory->destroy(clist);
@@ -909,32 +908,27 @@ int DumpCustom::count()
 
       } else if (thresh_array[ithresh] == Q) {
         if (!atom->q_flag)
-          error->all(FLERR,
-                     "Threshold for an atom property that isn't allocated");
+          error->all(FLERR,"Threshold for an atom property that isn't allocated");
         ptr = atom->q;
         nstride = 1;
       } else if (thresh_array[ithresh] == MUX) {
         if (!atom->mu_flag)
-          error->all(FLERR,
-                     "Threshold for an atom property that isn't allocated");
+          error->all(FLERR,"Threshold for an atom property that isn't allocated");
         ptr = &atom->mu[0][0];
         nstride = 4;
       } else if (thresh_array[ithresh] == MUY) {
         if (!atom->mu_flag)
-          error->all(FLERR,
-                     "Threshold for an atom property that isn't allocated");
+          error->all(FLERR,"Threshold for an atom property that isn't allocated");
         ptr = &atom->mu[0][1];
         nstride = 4;
       } else if (thresh_array[ithresh] == MUZ) {
         if (!atom->mu_flag)
-          error->all(FLERR,
-                     "Threshold for an atom property that isn't allocated");
+          error->all(FLERR,"Threshold for an atom property that isn't allocated");
         ptr = &atom->mu[0][2];
         nstride = 4;
       } else if (thresh_array[ithresh] == MU) {
         if (!atom->mu_flag)
-          error->all(FLERR,
-                     "Threshold for an atom property that isn't allocated");
+          error->all(FLERR,"Threshold for an atom property that isn't allocated");
         ptr = &atom->mu[0][3];
         nstride = 4;
 
@@ -1521,7 +1515,7 @@ int DumpCustom::parse_fields(int narg, char **arg)
         field2index[iarg] = add_variable(name);
         break;
 
-      // custom per-atom floating point vector or array
+      // custom per-atom floating point vector or array = d_ID d2_ID
 
       case ArgInfo::DNAME:
         pack_choice[iarg] = &DumpCustom::pack_custom;
@@ -1533,18 +1527,18 @@ int DumpCustom::parse_fields(int narg, char **arg)
           error->all(FLERR,"Could not find custom per-atom property ID: {}", name);
         if (argindex[iarg] == 0) {
           if (!flag || cols)
-            error->all(FLERR,"Property double vector for dump custom does not exist");
+            error->all(FLERR,"Property double vector {} for dump custom does not exist",name);
         } else {
           if (!flag || !cols)
-            error->all(FLERR,"Property double array for dump custom does not exist");
+            error->all(FLERR,"Property double array {} for dump custom does not exist",name);
           if (argindex[iarg] > atom->dcols[n])
-            error->all(FLERR,"Dump custom property array is accessed out-of-range");
+            error->all(FLERR,"Dump custom property array {} is accessed out-of-range",name);
         }
 
         field2index[iarg] = add_custom(name,1);
         break;
 
-      // custom per-atom integer vector or array
+      // custom per-atom integer vector or array = i_ID or i2_ID
 
       case ArgInfo::INAME:
         pack_choice[iarg] = &DumpCustom::pack_custom;
@@ -1556,15 +1550,12 @@ int DumpCustom::parse_fields(int narg, char **arg)
           error->all(FLERR,"Could not find custom per-atom property ID: {}", name);
         if (argindex[iarg] == 0) {
           if (flag || cols)
-            error->all(FLERR,
-                       "Property integer vector for dump custom does not exist");
+            error->all(FLERR,"Property integer vector {} for dump custom does not exist",name);
         } else {
           if (flag || !cols)
-            error->all(FLERR,
-                       "Property integer array for dump custom does not exist");
+            error->all(FLERR,"Property integer array {} for dump custom does not exist",name);
           if (argindex[iarg] > atom->icols[n])
-            error->all(FLERR,
-                       "Dump custom property array is accessed out-of-range");
+            error->all(FLERR,"Dump custom property array {} is accessed out-of-range",name);
         }
 
         field2index[iarg] = add_custom(name,0);
@@ -1574,6 +1565,7 @@ int DumpCustom::parse_fields(int narg, char **arg)
 
       default:
         return iarg;
+        break;
       }
     }
   }
@@ -1667,13 +1659,9 @@ int DumpCustom::add_custom(const char *id, int flag)
     if (strcmp(id,id_custom[icustom]) == 0) break;
   if (icustom < ncustom) return icustom;
 
-  id_custom = (char **)
-    memory->srealloc(id_custom,(ncustom+1)*sizeof(char *),"dump:id_custom");
-
-  delete [] custom;
-  custom = new int[ncustom+1];
-  delete [] custom_flag;
-  custom_flag = new int[ncustom+1];
+  id_custom = (char **) memory->srealloc(id_custom,(ncustom+1)*sizeof(char *),"dump:id_custom");
+  custom = (int *) memory->srealloc(custom,(ncustom+1)*sizeof(int),"dump:custom");
+  custom_flag = (int *) memory->srealloc(custom_flag,(ncustom+1)*sizeof(int),"dump:custom_flag");
 
   id_custom[ncustom] = utils::strdup(id);
   custom_flag[ncustom] = flag;
@@ -1962,21 +1950,18 @@ int DumpCustom::modify_param(int narg, char **arg)
         if (n < 0)
           error->all(FLERR,"Could not find custom per-atom property ID: {}", name);
         if (argindex[nfield+nthresh] == 0) {
-          if (flag || cols)
-            error->all(FLERR,
-                       "Property double vector for dump custom does not exist");
+          if (!flag || cols)
+            error->all(FLERR,"Property double vector for dump custom does not exist");
           thresh_array[nthresh] = DVEC;
         } else {
-          if (flag || !cols)
-            error->all(FLERR,
-                       "Property double array for dump custom does not exist");
+          if (!flag || !cols)
+            error->all(FLERR,"Property double array for dump custom does not exist");
           if (argindex[nfield+nthresh] > atom->dcols[n])
-            error->all(FLERR,
-                       "Dump custom property array is accessed out-of-range");
+            error->all(FLERR,"Dump custom property array is accessed out-of-range");
           thresh_array[nthresh] = DARRAY;
         }
 
-        field2index[nfield+nthresh] = add_custom(name,0);
+        field2index[nfield+nthresh] = add_custom(name,thresh_array[nthresh]);
         break;
 
       // custom per atom integer vector or array
@@ -1988,20 +1973,17 @@ int DumpCustom::modify_param(int narg, char **arg)
           error->all(FLERR,"Could not find custom per-atom property ID: {}", name);
         if (argindex[nfield+nthresh] == 0) {
           if (flag || cols)
-            error->all(FLERR,
-                       "Property integer vector for dump custom does not exist");
+            error->all(FLERR,"Property integer vector for dump custom does not exist");
           thresh_array[nthresh] = IVEC;
         } else {
           if (flag || !cols)
-            error->all(FLERR,
-                       "Property integer array for dump custom does not exist");
+            error->all(FLERR,"Property integer array for dump custom does not exist");
           if (argindex[nfield+nthresh] > atom->icols[n])
-            error->all(FLERR,
-                       "Dump custom property array is accessed out-of-range");
+            error->all(FLERR,"Dump custom property array is accessed out-of-range");
           thresh_array[nthresh] = IARRAY;
         }
 
-        field2index[nfield+nthresh] = add_custom(name,0);
+        field2index[nfield+nthresh] = add_custom(name,thresh_array[nthresh]);
         break;
 
       // no match

src/error.cpp

@@ -195,7 +195,7 @@ void Error::one(const std::string &file, int line, const std::string &str)
   MPI_Comm_rank(world,&me);
 
   if (input && input->line) lastcmd = input->line;
-  std::string mesg = fmt::format("ERROR on proc {}: {} ({}:{})\n",
+  std::string mesg = fmt::format("ERROR on proc {}: {} ({}:{})\nLast command: {}\n",
                                  me,str,truncpath(file),line,lastcmd);
   utils::logmesg(lmp,mesg);
 

src/fix_vector.cpp

@@ -111,9 +111,9 @@ FixVector::FixVector(LAMMPS *lmp, int narg, char **arg) :
   for (int i = 0; i < nvalues; i++) {
     if (which[i] == ArgInfo::COMPUTE) {
       Compute *compute = modify->compute[modify->find_compute(ids[i])];
-      if (argindex[0] == 0) value = compute->extscalar;
+      if (argindex[i] == 0) value = compute->extscalar;
       else if (compute->extvector >= 0) value = compute->extvector;
-      else value = compute->extlist[argindex[0]-1];
+      else value = compute->extlist[argindex[i]-1];
     } else if (which[i] == ArgInfo::FIX) {
       Fix *fix = modify->fix[modify->find_fix(ids[i])];
       if (argindex[i] == 0) value = fix->extvector;

src/info.cpp

@@ -299,6 +299,7 @@ void Info::command(int narg, char **arg)
     if (has_png_support()) fputs("-DLAMMPS_PNG\n",out);
     if (has_jpeg_support()) fputs("-DLAMMPS_JPEG\n",out);
     if (has_ffmpeg_support()) fputs("-DLAMMPS_FFMPEG\n",out);
+    if (has_fft_single_support()) fputs("-DFFT_SINGLE\n",out);
     if (has_exceptions()) fputs("-DLAMMPS_EXCEPTIONS\n",out);
 
 #if defined(LAMMPS_BIGBIG)
@@ -895,6 +896,8 @@ bool Info::is_available(const char *category, const char *name)
       return has_jpeg_support();
     } else if (strcmp(name,"ffmpeg") == 0) {
       return has_ffmpeg_support();
+    } else if (strcmp(name,"fft_single") == 0) {
+      return has_fft_single_support();
     } else if (strcmp(name,"exceptions") == 0) {
       return has_exceptions();
     }
@@ -1143,6 +1146,14 @@ bool Info::has_ffmpeg_support() {
 #endif
 }
 
+bool Info::has_fft_single_support() {
+#ifdef FFT_SINGLE
+  return true;
+#else
+  return false;
+#endif
+}
+
 bool Info::has_exceptions() {
 #ifdef LAMMPS_EXCEPTIONS
   return true;
@@ -1162,12 +1173,14 @@ bool Info::has_package(const std::string &package_name) {
 
 #if defined(LMP_GPU)
 extern bool lmp_gpu_config(const std::string &, const std::string &);
-extern bool lmp_has_gpu_device();
+extern bool lmp_has_compatible_gpu_device();
 extern std::string lmp_gpu_device_info();
 
+// we will only report compatible GPUs, i.e. when a GPU device is
+// available *and* supports the required floating point precision
 bool Info::has_gpu_device()
 {
-  return lmp_has_gpu_device();
+  return lmp_has_compatible_gpu_device();
 }
 
 std::string Info::get_gpu_device_info()

src/info.h

@@ -42,6 +42,7 @@ class Info : public Command {
   static bool has_png_support();
   static bool has_jpeg_support();
   static bool has_ffmpeg_support();
+  static bool has_fft_single_support();
   static bool has_exceptions();
   static bool has_package(const std::string &);
   static bool has_accelerator_feature(const std::string &, const std::string &,

src/lammps.cpp

@@ -51,6 +51,10 @@
 #include "update.h"
 #include "version.h"
 
+#if defined(LMP_PLUGIN)
+#include "plugin.h"
+#endif
+
 #include <cctype>
 #include <cmath>
 #include <cstring>
@@ -65,6 +69,12 @@
 #include "lmpinstalledpkgs.h"
 #include "lmpgitversion.h"
 
+#if defined(LAMMPS_UPDATE)
+#define UPDATE_STRING " - " LAMMPS_UPDATE
+#else
+#define UPDATE_STRING ""
+#endif
+
 static void print_style(FILE *fp, const char *str, int &pos);
 
 struct LAMMPS_NS::package_styles_lists {
@@ -511,7 +521,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
     }
 
     if ((universe->me == 0) && !helpflag)
-      utils::logmesg(this,fmt::format("LAMMPS ({})\n",version));
+      utils::logmesg(this,fmt::format("LAMMPS ({}{})\n",version,UPDATE_STRING));
 
   // universe is one or more worlds, as setup by partition switch
   // split universe communicator into separate world communicators
@@ -905,6 +915,10 @@ void LAMMPS::init()
 
 void LAMMPS::destroy()
 {
+  // must wipe out all plugins first, if configured
+#if defined(LMP_PLUGIN)
+  plugin_clear(this);
+#endif
   delete update;
   update = nullptr;
 
@@ -1147,10 +1161,10 @@ void _noopt LAMMPS::help()
 
   if (has_git_info) {
     fprintf(fp,"\nLarge-scale Atomic/Molecular Massively Parallel Simulator - "
-            LAMMPS_VERSION "\nGit info (%s / %s)\n\n",git_branch, git_descriptor);
+            LAMMPS_VERSION UPDATE_STRING "\nGit info (%s / %s)\n\n",git_branch, git_descriptor);
   } else {
     fprintf(fp,"\nLarge-scale Atomic/Molecular Massively Parallel Simulator - "
-            LAMMPS_VERSION "\n\n");
+            LAMMPS_VERSION UPDATE_STRING "\n\n");
   }
   fprintf(fp,
           "Usage example: %s -var t 300 -echo screen -in in.alloy\n\n"
@@ -1350,7 +1364,7 @@ void LAMMPS::print_config(FILE *fp)
   fmt::print(fp,"Accelerator configuration:\n\n{}\n",
              Info::get_accelerator_info());
 #if defined(LMP_GPU)
-  fmt::print(fp,"GPU present: {}\n\n",Info::has_gpu_device() ? "yes" : "no");
+  fmt::print(fp,"Compatible GPU present: {}\n\n",Info::has_gpu_device() ? "yes" : "no");
 #endif
 
   fputs("Active compile time flags:\n\n",fp);
@@ -1358,6 +1372,7 @@ void LAMMPS::print_config(FILE *fp)
   if (Info::has_png_support()) fputs("-DLAMMPS_PNG\n",fp);
   if (Info::has_jpeg_support()) fputs("-DLAMMPS_JPEG\n",fp);
   if (Info::has_ffmpeg_support()) fputs("-DLAMMPS_FFMPEG\n",fp);
+  if (Info::has_fft_single_support()) fputs("-DFFT_SINGLE\n",fp);
   if (Info::has_exceptions()) fputs("-DLAMMPS_EXCEPTIONS\n",fp);
 #if defined(LAMMPS_BIGBIG)
   fputs("-DLAMMPS_BIGBIG\n",fp);

src/utils.cpp

@@ -676,7 +676,10 @@ int utils::expand_args(const char *file, int line, int narg, char **arg, int mod
       }
 
       for (int index = nlo; index <= nhi; index++) {
-        earg[newarg] = utils::strdup(fmt::format("{}2_{}[{}]{}", word[0], id, index, tail));
+        if (word[1] == '2')
+          earg[newarg] = utils::strdup(fmt::format("{}2_{}[{}]{}", word[0], id, index, tail));
+        else
+          earg[newarg] = utils::strdup(fmt::format("{}_{}[{}]{}", word[0], id, index, tail));
         newarg++;
       }
     } else {

src/version.h

@@ -1 +1,2 @@
 #define LAMMPS_VERSION "29 Sep 2021"
+#define LAMMPS_UPDATE "Update 2"

src/write_restart.cpp

@@ -269,7 +269,7 @@ void WriteRestart::write(const std::string &file)
 
   double *buf;
   memory->create(buf,max_size,"write_restart:buf");
-  memset(buf,0,max_size*sizeof(buf));
+  memset(buf,0,max_size*sizeof(double));
 
   // all procs write file layout info which may include per-proc sizes
 

tools/offline/scripts/use_git_cache.sh

@@ -8,12 +8,12 @@ fi
 
 export GIT_CONFIG_COUNT=1
 export GIT_CONFIG_KEY_0="url.$GITHUB_PROXY_DIR/.insteadOf"
-export GIT_CONFIG_VALUE_0=git://github.com/
+export GIT_CONFIG_VALUE_0=https://github.com/
 
-echo "Redirecting git://github.com urls to local cache..."
+echo "Redirecting https://github.com urls to local cache..."
 
 function deactivate_git_cache {
-    echo "Removing git://github.com redirect..."
+    echo "Removing https://github.com redirect..."
     unset GIT_CONFIG_COUNT
     unset GIT_CONFIG_KEY_0
     unset GIT_CONFIG_VALUE_0

tools/offline/use_caches.sh

@@ -63,7 +63,7 @@ echo "or"
 echo
 echo "-D LAMMPS_DOWNLOADS_URL=${HTTP_CACHE_URL} -C \"${LAMMPS_HTTP_CACHE_CONFIG}\""
 echo
-echo "pip installations and git clones (from git://) are automatically redirected"
+echo "pip installations and git clones (from https://) are automatically redirected"
 echo
 echo Use 'deactivate_caches' to revert changes
 echo

tools/singularity/README.md

@@ -21,7 +21,7 @@ built CentOS 7.x singularity container.
 
 ```
 cd some/work/directory
-git clone --depth 500  git://github.com/lammps/lammps.git lammps
+git clone --depth 500  https://github.com/lammps/lammps.git lammps
 mkdir build-centos7
 cd build-centos7
 sudo singularity build centos7.sif ../tools/singularity/centos7.def

unittest/CMakeLists.txt

@@ -8,7 +8,7 @@ add_test(NAME RunLammps
          WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
 set_tests_properties(RunLammps PROPERTIES
 	ENVIRONMENT "TSAN_OPTIONS=ignore_noninstrumented_modules=1;HWLOC_HIDE_ERRORS=1"
-        PASS_REGULAR_EXPRESSION "^LAMMPS \\([0-9]+ [A-Za-z]+ 2[0-9][0-9][0-9]\\)")
+        PASS_REGULAR_EXPRESSION "LAMMPS \\([0-9]+ [A-Za-z]+ 2[0-9][0-9][0-9]( - Update [0-9]+)?\\)")
 
 # check if the compiled executable will print the help message
 add_test(NAME HelpMessage
@@ -31,6 +31,10 @@ if(BUILD_MPI)
     set(MPI_TEST_NUM_PROCS 1)
     set(MPI_TEST_WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
     cmake_parse_arguments(MPI_TEST "" "NAME;NUM_PROCS;WORKING_DIRECTORY" "COMMAND" ${ARGN})
+    # Do not add test when oversubscribing
+    if(MPI_TEST_NUMPROCS GREATER MPIEXEC_MAX_NUMPROCS)
+      return()
+    endif()
     list(GET MPI_TEST_COMMAND 0 EXECUTABLE)
     list(REMOVE_AT MPI_TEST_COMMAND 0)
     set(ARGS ${MPI_TEST_COMMAND})

unittest/commands/test_groups.cpp

@@ -246,7 +246,7 @@ TEST_F(GroupTest, Molecular)
     ASSERT_DOUBLE_EQ(group->mass(group->find("half")), 40);
     ASSERT_DOUBLE_EQ(group->mass(group->find("half"), domain->find_region("top")), 10);
     ASSERT_NEAR(group->charge(group->find("top")), 0, 1.0e-14);
-    ASSERT_DOUBLE_EQ(group->charge(group->find("right"), domain->find_region("top")), 0);
+    ASSERT_NEAR(group->charge(group->find("right"), domain->find_region("top")), 0, 1.0e-14);
 
     TEST_FAILURE(".*ERROR: Illegal group command.*", command("group three include xxx"););
 }

unittest/force-styles/test_pair_style.cpp

@@ -858,6 +858,13 @@ TEST(PairStyle, gpu)
     if (!Info::has_gpu_device()) GTEST_SKIP();
     if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
 
+    // when testing PPPM styles with GPUs and GPU support is compiled with single precision
+    // we also must have single precision FFTs; otherwise skip since the test would abort
+    if (utils::strmatch(test_config.basename, ".*pppm.*") &&
+        (Info::has_accelerator_feature("GPU", "precision", "single")) &&
+        (!Info::has_fft_single_support()))
+        GTEST_SKIP();
+
     const char *args_neigh[]   = {"PairStyle", "-log",    "none", "-echo",
                                 "screen",    "-nocite", "-sf",  "gpu"};
     const char *args_noneigh[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite", "-sf",

unittest/force-styles/tests/manybody-pair-lebedeva_z.yaml

@@ -14,7 +14,7 @@ post_commands: ! ""
 input_file: in.bilayer
 pair_style: hybrid/overlay lebedeva/z 16.0
 pair_coeff: ! |
-  * * lebedeva/z CC.Lebedeva C C C
+  * * lebedeva/z CC.Lebedeva C1 C1 C1
 extract: ! ""
 natoms: 48
 init_vdwl: 2360.887727742073

unittest/formats/test_dump_atom.cpp

@@ -39,6 +39,21 @@ public:
         END_HIDE_OUTPUT();
     }
 
+    std::string dump_filename(std::string ident)
+    {
+        return fmt::format("dump_{}_{}.melt", dump_style, ident);
+    }
+
+    std::string text_dump_filename(std::string ident)
+    {
+        return fmt::format("dump_{}_text_{}.melt", dump_style, ident);
+    }
+
+    std::string binary_dump_filename(std::string ident)
+    {
+        return fmt::format("dump_{}_binary_{}.melt.bin", dump_style, ident);
+    }
+
     void generate_dump(std::string dump_file, std::string dump_modify_options, int ntimesteps)
     {
         BEGIN_HIDE_OUTPUT();
@@ -87,7 +102,7 @@ public:
 
 TEST_F(DumpAtomTest, run0)
 {
-    auto dump_file = "dump_run0.melt";
+    auto dump_file = dump_filename("run0");
     generate_dump(dump_file, "scale yes image no", 0);
 
     ASSERT_FILE_EXISTS(dump_file);
@@ -103,7 +118,7 @@ TEST_F(DumpAtomTest, run0)
 
 TEST_F(DumpAtomTest, format_line_run0)
 {
-    auto dump_file = "dump_format_line_run0.melt";
+    auto dump_file = dump_filename("format_line_run0");
     generate_dump(dump_file, "format line \"%d %d %20.15g %g %g\" scale yes image no", 0);
 
     ASSERT_FILE_EXISTS(dump_file);
@@ -119,7 +134,7 @@ TEST_F(DumpAtomTest, format_line_run0)
 
 TEST_F(DumpAtomTest, no_scale_run0)
 {
-    auto dump_file = "dump_no_scale_run0.melt";
+    auto dump_file = dump_filename("no_scale_run0");
     generate_dump(dump_file, "scale no", 0);
 
     ASSERT_FILE_EXISTS(dump_file);
@@ -134,7 +149,7 @@ TEST_F(DumpAtomTest, no_scale_run0)
 
 TEST_F(DumpAtomTest, no_buffer_no_scale_run0)
 {
-    auto dump_file = "dump_no_buffer_no_scale_run0.melt";
+    auto dump_file = dump_filename("no_buffer_no_scale_run0");
     generate_dump(dump_file, "buffer no scale no", 0);
 
     ASSERT_FILE_EXISTS(dump_file);
@@ -149,7 +164,7 @@ TEST_F(DumpAtomTest, no_buffer_no_scale_run0)
 
 TEST_F(DumpAtomTest, no_buffer_with_scale_run0)
 {
-    auto dump_file = "dump_no_buffer_with_scale_run0.melt";
+    auto dump_file = dump_filename("no_buffer_with_scale_run0");
     generate_dump(dump_file, "buffer no scale yes", 0);
 
     ASSERT_FILE_EXISTS(dump_file);
@@ -164,7 +179,7 @@ TEST_F(DumpAtomTest, no_buffer_with_scale_run0)
 
 TEST_F(DumpAtomTest, with_image_run0)
 {
-    auto dump_file = "dump_with_image_run0.melt";
+    auto dump_file = dump_filename("with_image_run0");
     generate_dump(dump_file, "scale no image yes", 0);
 
     ASSERT_FILE_EXISTS(dump_file);
@@ -177,7 +192,7 @@ TEST_F(DumpAtomTest, with_image_run0)
 
 TEST_F(DumpAtomTest, with_units_run0)
 {
-    auto dump_file = "dump_with_units_run0.melt";
+    auto dump_file = dump_filename("with_units_run0");
     generate_dump(dump_file, "scale no units yes", 0);
 
     ASSERT_FILE_EXISTS(dump_file);
@@ -192,7 +207,7 @@ TEST_F(DumpAtomTest, with_units_run0)
 
 TEST_F(DumpAtomTest, with_time_run0)
 {
-    auto dump_file = "dump_with_time_run0.melt";
+    auto dump_file = dump_filename("with_time_run0");
     generate_dump(dump_file, "scale no time yes", 0);
 
     ASSERT_FILE_EXISTS(dump_file);
@@ -206,7 +221,7 @@ TEST_F(DumpAtomTest, with_time_run0)
 
 TEST_F(DumpAtomTest, with_units_run1)
 {
-    auto dump_file = "dump_with_units_run1.melt";
+    auto dump_file = dump_filename("with_units_run1");
     generate_dump(dump_file, "scale no units yes", 1);
 
     ASSERT_FILE_EXISTS(dump_file);
@@ -221,7 +236,7 @@ TEST_F(DumpAtomTest, with_units_run1)
 
 TEST_F(DumpAtomTest, no_buffer_with_scale_and_image_run0)
 {
-    auto dump_file = "dump_no_buffer_with_scale_and_image_run0.melt";
+    auto dump_file = dump_filename("no_buffer_with_scale_and_image_run0");
     generate_dump(dump_file, "buffer no scale yes image yes", 0);
 
     ASSERT_FILE_EXISTS(dump_file);
@@ -235,7 +250,7 @@ TEST_F(DumpAtomTest, no_buffer_with_scale_and_image_run0)
 }
 TEST_F(DumpAtomTest, triclinic_run0)
 {
-    auto dump_file = "dump_triclinic_run0.melt";
+    auto dump_file = dump_filename("triclinic_run0");
     enable_triclinic();
     generate_dump(dump_file, "", 0);
 
@@ -251,7 +266,7 @@ TEST_F(DumpAtomTest, triclinic_run0)
 
 TEST_F(DumpAtomTest, triclinic_with_units_run0)
 {
-    auto dump_file = "dump_triclinic_with_units_run0.melt";
+    auto dump_file = dump_filename("triclinic_with_units_run0");
     enable_triclinic();
     generate_dump(dump_file, "units yes", 0);
 
@@ -269,7 +284,7 @@ TEST_F(DumpAtomTest, triclinic_with_units_run0)
 
 TEST_F(DumpAtomTest, triclinic_with_time_run0)
 {
-    auto dump_file = "dump_triclinic_with_time_run0.melt";
+    auto dump_file = dump_filename("triclinic_with_time_run0");
     enable_triclinic();
     generate_dump(dump_file, "time yes", 0);
 
@@ -286,7 +301,7 @@ TEST_F(DumpAtomTest, triclinic_with_time_run0)
 
 TEST_F(DumpAtomTest, triclinic_with_image_run0)
 {
-    auto dump_file = "dump_triclinic_with_image_run0.melt";
+    auto dump_file = dump_filename("triclinic_with_image_run0");
     enable_triclinic();
     generate_dump(dump_file, "image yes", 0);
 
@@ -308,8 +323,8 @@ TEST_F(DumpAtomTest, binary_run0)
 {
     if (!BINARY2TXT_BINARY) GTEST_SKIP();
 
-    auto text_file   = "dump_text_run0.melt";
-    auto binary_file = "dump_binary_run0.melt.bin";
+    auto text_file   = text_dump_filename("run0");
+    auto binary_file = binary_dump_filename("run0");
 
     generate_text_and_binary_dump(text_file, binary_file, "", 0);
 
@@ -329,8 +344,8 @@ TEST_F(DumpAtomTest, binary_with_units_run0)
 {
     if (!BINARY2TXT_BINARY) GTEST_SKIP();
 
-    auto text_file   = "dump_text_with_units_run0.melt";
-    auto binary_file = "dump_binary_with_units_run0.melt.bin";
+    auto text_file   = text_dump_filename("with_units_run0");
+    auto binary_file = binary_dump_filename("with_units_run0");
 
     generate_text_and_binary_dump(text_file, binary_file, "scale no units yes", 0);
 
@@ -350,8 +365,8 @@ TEST_F(DumpAtomTest, binary_with_time_run0)
 {
     if (!BINARY2TXT_BINARY) GTEST_SKIP();
 
-    auto text_file   = "dump_text_with_time_run0.melt";
-    auto binary_file = "dump_binary_with_time_run0.melt.bin";
+    auto text_file   = text_dump_filename("with_time_run0");
+    auto binary_file = binary_dump_filename("with_time_run0");
 
     generate_text_and_binary_dump(text_file, binary_file, "scale no time yes", 0);
 
@@ -371,8 +386,8 @@ TEST_F(DumpAtomTest, binary_triclinic_run0)
 {
     if (!BINARY2TXT_BINARY) GTEST_SKIP();
 
-    auto text_file   = "dump_text_tri_run0.melt";
-    auto binary_file = "dump_binary_tri_run0.melt.bin";
+    auto text_file   = text_dump_filename("tri_run0");
+    auto binary_file = binary_dump_filename("tri_run0");
 
     enable_triclinic();
     generate_text_and_binary_dump(text_file, binary_file, "", 0);
@@ -393,8 +408,8 @@ TEST_F(DumpAtomTest, binary_triclinic_with_units_run0)
 {
     if (!BINARY2TXT_BINARY) GTEST_SKIP();
 
-    auto text_file   = "dump_text_tri_with_units_run0.melt";
-    auto binary_file = "dump_binary_tri_with_units_run0.melt.bin";
+    auto text_file   = text_dump_filename("tri_with_units_run0");
+    auto binary_file = binary_dump_filename("tri_with_units_run0");
 
     enable_triclinic();
     generate_text_and_binary_dump(text_file, binary_file, "scale no units yes", 0);
@@ -415,8 +430,8 @@ TEST_F(DumpAtomTest, binary_triclinic_with_time_run0)
 {
     if (!BINARY2TXT_BINARY) GTEST_SKIP();
 
-    auto text_file   = "dump_text_tri_with_time_run0.melt";
-    auto binary_file = "dump_binary_tri_with_time_run0.melt.bin";
+    auto text_file   = text_dump_filename("tri_with_time_run0");
+    auto binary_file = binary_dump_filename("tri_with_time_run0");
 
     enable_triclinic();
     generate_text_and_binary_dump(text_file, binary_file, "scale no time yes", 0);
@@ -437,8 +452,8 @@ TEST_F(DumpAtomTest, binary_triclinic_with_image_run0)
 {
     if (!BINARY2TXT_BINARY) GTEST_SKIP();
 
-    auto text_file   = "dump_text_tri_with_image_run0.melt";
-    auto binary_file = "dump_binary_tri_with_image_run0.melt.bin";
+    auto text_file   = text_dump_filename("tri_with_image_run0");
+    auto binary_file = binary_dump_filename("tri_with_image_run0");
 
     enable_triclinic();
     generate_text_and_binary_dump(text_file, binary_file, "image yes", 0);
@@ -457,7 +472,7 @@ TEST_F(DumpAtomTest, binary_triclinic_with_image_run0)
 
 TEST_F(DumpAtomTest, run1plus1)
 {
-    auto dump_file = "dump_run1plus1.melt";
+    auto dump_file = dump_filename("run1plus1");
     generate_dump(dump_file, "", 1);
 
     ASSERT_FILE_EXISTS(dump_file);
@@ -470,7 +485,7 @@ TEST_F(DumpAtomTest, run1plus1)
 
 TEST_F(DumpAtomTest, run2)
 {
-    auto dump_file = "dump_run2.melt";
+    auto dump_file = dump_filename("run2");
     generate_dump(dump_file, "", 2);
 
     ASSERT_FILE_EXISTS(dump_file);
@@ -480,7 +495,7 @@ TEST_F(DumpAtomTest, run2)
 
 TEST_F(DumpAtomTest, rerun)
 {
-    auto dump_file = "dump_rerun.melt";
+    auto dump_file = dump_filename("rerun");
     HIDE_OUTPUT([&] {
         command("fix 1 all nve");
     });
@@ -508,38 +523,43 @@ TEST_F(DumpAtomTest, rerun)
 
 TEST_F(DumpAtomTest, multi_file_run1)
 {
-    auto dump_file = "dump_run1_*.melt";
+    auto dump_file = dump_filename("run1_*");
     generate_dump(dump_file, "", 1);
 
-    ASSERT_FILE_EXISTS("dump_run1_0.melt");
-    ASSERT_FILE_EXISTS("dump_run1_1.melt");
-    ASSERT_EQ(count_lines("dump_run1_0.melt"), 41);
-    ASSERT_EQ(count_lines("dump_run1_1.melt"), 41);
-    delete_file("dump_run1_0.melt");
-    delete_file("dump_run1_1.melt");
+    auto run1_0 = dump_filename("run1_0");
+    auto run1_1 = dump_filename("run1_1");
+    ASSERT_FILE_EXISTS(run1_0);
+    ASSERT_FILE_EXISTS(run1_1);
+    ASSERT_EQ(count_lines(run1_0), 41);
+    ASSERT_EQ(count_lines(run1_1), 41);
+    delete_file(run1_0);
+    delete_file(run1_1);
 }
 
 TEST_F(DumpAtomTest, per_processor_file_run1)
 {
-    auto dump_file = "dump_run1_p%.melt";
+    auto dump_file = dump_filename("run1_p%");
     generate_dump(dump_file, "", 1);
 
-    ASSERT_FILE_EXISTS("dump_run1_p0.melt");
-    ASSERT_EQ(count_lines("dump_run1_p0.melt"), 82);
-    delete_file("dump_run1_p0.melt");
+    auto run1_p0 = dump_filename("run1_p0");
+    ASSERT_FILE_EXISTS(run1_p0);
+    ASSERT_EQ(count_lines(run1_p0), 82);
+    delete_file(run1_p0);
 }
 
 TEST_F(DumpAtomTest, per_processor_multi_file_run1)
 {
-    auto dump_file = "dump_run1_p%_*.melt";
+    auto dump_file = dump_filename("run1_p%_*");
     generate_dump(dump_file, "", 1);
 
-    ASSERT_FILE_EXISTS("dump_run1_p0_0.melt");
-    ASSERT_FILE_EXISTS("dump_run1_p0_1.melt");
-    ASSERT_EQ(count_lines("dump_run1_p0_0.melt"), 41);
-    ASSERT_EQ(count_lines("dump_run1_p0_1.melt"), 41);
-    delete_file("dump_run1_p0_0.melt");
-    delete_file("dump_run1_p0_1.melt");
+    auto run1_p0_0 = dump_filename("run1_p0_0");
+    auto run1_p0_1 = dump_filename("run1_p0_1");
+    ASSERT_FILE_EXISTS(run1_p0_0);
+    ASSERT_FILE_EXISTS(run1_p0_1);
+    ASSERT_EQ(count_lines(run1_p0_0), 41);
+    ASSERT_EQ(count_lines(run1_p0_1), 41);
+    delete_file(run1_p0_0);
+    delete_file(run1_p0_1);
 }
 
 TEST_F(DumpAtomTest, dump_modify_scale_invalid)
@@ -571,16 +591,17 @@ TEST_F(DumpAtomTest, dump_modify_invalid)
 
 TEST_F(DumpAtomTest, write_dump)
 {
-    auto reference = "dump_ref_run0.melt";
-    auto dump_file = "write_dump_atom_run0.melt";
+    auto reference = dump_filename("run0_ref");
+    auto dump_file = fmt::format("write_{}", dump_filename("run*"));
 
     BEGIN_HIDE_OUTPUT();
     command(fmt::format("dump id all atom 1 {}", reference));
     command("dump_modify id scale no units yes");
     command("run 0");
-    command("write_dump all atom write_dump_atom_run*.melt modify scale no units yes");
+    command(fmt::format("write_dump all atom {} modify scale no units yes", dump_file));
     END_HIDE_OUTPUT();
 
+    dump_file = fmt::format("write_{}", dump_filename("run0"));
     ASSERT_FILE_EXISTS(reference);
     ASSERT_FILE_EXISTS(dump_file);
 
@@ -593,16 +614,17 @@ TEST_F(DumpAtomTest, binary_write_dump)
 {
     if (!BINARY2TXT_BINARY) GTEST_SKIP();
 
-    auto reference = "dump_run0.melt.bin";
-    auto dump_file = "write_dump_atom_run0_p0.melt.bin";
+    auto reference = binary_dump_filename("write_run0_ref");
+    auto dump_file = fmt::format("write_{}", binary_dump_filename("write_dump_atom_run*_p%"));
 
     BEGIN_HIDE_OUTPUT();
     command(fmt::format("dump id all atom 1 {}", reference));
     command("dump_modify id scale no units yes");
     command("run 0");
-    command("write_dump all atom write_dump_atom_run*_p%.melt.bin modify scale no units yes");
+    command(fmt::format("write_dump all atom {} modify scale no units yes", dump_file));
     END_HIDE_OUTPUT();
 
+    dump_file = fmt::format("write_{}", binary_dump_filename("write_dump_atom_run0_p0"));
     ASSERT_FILE_EXISTS(reference);
     ASSERT_FILE_EXISTS(dump_file);
 

unittest/formats/test_dump_custom.cpp

@@ -37,6 +37,21 @@ public:
         END_HIDE_OUTPUT();
     }
 
+    std::string dump_filename(std::string ident)
+    {
+        return fmt::format("dump_{}_{}.melt", dump_style, ident);
+    }
+
+    std::string text_dump_filename(std::string ident)
+    {
+        return fmt::format("dump_{}_text_{}.melt", dump_style, ident);
+    }
+
+    std::string binary_dump_filename(std::string ident)
+    {
+        return fmt::format("dump_{}_binary_{}.melt.bin", dump_style, ident);
+    }
+
     void generate_dump(std::string dump_file, std::string fields, std::string dump_modify_options,
                        int ntimesteps)
     {
@@ -87,7 +102,7 @@ public:
 
 TEST_F(DumpCustomTest, run1)
 {
-    auto dump_file = "dump_custom_run1.melt";
+    auto dump_file = dump_filename("run1");
     auto fields =
         "id type proc procp1 mass x y z ix iy iz xs ys zs xu yu zu xsu ysu zsu vx vy vz fx fy fz";
 
@@ -105,7 +120,7 @@ TEST_F(DumpCustomTest, run1)
 
 TEST_F(DumpCustomTest, thresh_run0)
 {
-    auto dump_file = "dump_custom_thresh_run0.melt";
+    auto dump_file = dump_filename("thresh_run0");
     auto fields    = "id type x y z";
 
     generate_dump(dump_file, fields, "units yes thresh x < 1 thresh y < 1 thresh z < 1", 0);
@@ -126,7 +141,7 @@ TEST_F(DumpCustomTest, compute_run0)
     command("compute comp all property/atom x y z");
     END_HIDE_OUTPUT();
 
-    auto dump_file = "dump_custom_compute_run0.melt";
+    auto dump_file = dump_filename("compute_run0");
     auto fields    = "id type x y z c_comp[1] c_comp[2] c_comp[3]";
 
     generate_dump(dump_file, fields, "units yes", 0);
@@ -149,7 +164,7 @@ TEST_F(DumpCustomTest, fix_run0)
     command("fix numdiff all numdiff 1 0.0001");
     END_HIDE_OUTPUT();
 
-    auto dump_file = "dump_custom_compute_run0.melt";
+    auto dump_file = dump_filename("fix_run0");
     auto fields    = "id x y z f_numdiff[1] f_numdiff[2] f_numdiff[3]";
 
     generate_dump(dump_file, fields, "units yes", 0);
@@ -171,7 +186,7 @@ TEST_F(DumpCustomTest, custom_run0)
     command("compute 1 all property/atom i_flag1 d_flag2");
     END_HIDE_OUTPUT();
 
-    auto dump_file = "dump_custom_custom_run0.melt";
+    auto dump_file = dump_filename("custom_run0");
     auto fields    = "id x y z i_flag1 d_flag2";
 
     generate_dump(dump_file, fields, "units yes", 0);
@@ -190,8 +205,8 @@ TEST_F(DumpCustomTest, binary_run1)
 {
     if (!BINARY2TXT_BINARY) GTEST_SKIP();
 
-    auto text_file   = "dump_custom_text_run1.melt";
-    auto binary_file = "dump_custom_binary_run1.melt.bin";
+    auto text_file   = text_dump_filename("run1");
+    auto binary_file = binary_dump_filename("run1");
     auto fields = "id type proc x y z ix iy iz xs ys zs xu yu zu xsu ysu zsu vx vy vz fx fy fz";
 
     generate_text_and_binary_dump(text_file, binary_file, fields, "units yes", 1);
@@ -210,7 +225,7 @@ TEST_F(DumpCustomTest, binary_run1)
 
 TEST_F(DumpCustomTest, triclinic_run1)
 {
-    auto dump_file = "dump_custom_tri_run1.melt";
+    auto dump_file = dump_filename("tri_run1");
     auto fields    = "id type proc x y z ix iy iz xs ys zs xu yu zu xsu ysu zsu vx vy vz fx fy fz";
 
     enable_triclinic();
@@ -231,8 +246,8 @@ TEST_F(DumpCustomTest, binary_triclinic_run1)
 {
     if (!BINARY2TXT_BINARY) GTEST_SKIP();
 
-    auto text_file   = "dump_custom_tri_text_run1.melt";
-    auto binary_file = "dump_custom_tri_binary_run1.melt.bin";
+    auto text_file   = text_dump_filename("tri_run1");
+    auto binary_file = binary_dump_filename("tri_run1");
     auto fields      = "id type proc x y z xs ys zs xsu ysu zsu vx vy vz fx fy fz";
 
     enable_triclinic();
@@ -258,7 +273,7 @@ TEST_F(DumpCustomTest, with_variable_run1)
     command("variable        p atom (c_1%10)+1");
     END_HIDE_OUTPUT();
 
-    auto dump_file = "dump_custom_with_variable_run1.melt";
+    auto dump_file = dump_filename("with_variable_run1");
     auto fields    = "id type x y z v_p";
 
     generate_dump(dump_file, fields, "units yes", 1);
@@ -275,7 +290,7 @@ TEST_F(DumpCustomTest, with_variable_run1)
 
 TEST_F(DumpCustomTest, run1plus1)
 {
-    auto dump_file = "dump_custom_run1plus1.melt";
+    auto dump_file = dump_filename("run1plus1");
     auto fields    = "id type x y z";
 
     generate_dump(dump_file, fields, "units yes", 1);
@@ -292,7 +307,7 @@ TEST_F(DumpCustomTest, run1plus1)
 
 TEST_F(DumpCustomTest, run2)
 {
-    auto dump_file = "dump_custom_run2.melt";
+    auto dump_file = dump_filename("run2");
     auto fields    = "id type x y z";
     generate_dump(dump_file, fields, "", 2);
 
@@ -303,7 +318,7 @@ TEST_F(DumpCustomTest, run2)
 
 TEST_F(DumpCustomTest, rerun)
 {
-    auto dump_file = "dump_rerun.melt";
+    auto dump_file = dump_filename("rerun");
     auto fields    = "id type xs ys zs";
 
     HIDE_OUTPUT([&] {

unittest/python/python-capabilities.py

@@ -166,9 +166,9 @@ class PythonCapabilities(unittest.TestCase):
                  self.assertIn('single',settings['GPU']['precision'])
 
         if self.cmake_cache['PKG_KOKKOS']:
-            if self.cmake_cache['Kokkos_ENABLE_OPENMP']:
+            if 'Kokkos_ENABLE_OPENMP' in self.cmake_cache and self.cmake_cache['Kokkos_ENABLE_OPENMP']:
                 self.assertIn('openmp',settings['KOKKOS']['api'])
-            if self.cmake_cache['Kokkos_ENABLE_SERIAL']:
+            if 'Kokkos_ENABLE_SERIAL' in self.cmake_cache and self.cmake_cache['Kokkos_ENABLE_SERIAL']:
                 self.assertIn('serial',settings['KOKKOS']['api'])
             self.assertIn('double',settings['KOKKOS']['precision'])