Merge pull request #2305 from akohlmey/next_patch_version

Update version strings for updated patch release

.gitattributes

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+.gitattributes export-ignore
+.gitignore export-ignore
+.github export-ignore

.github/CODEOWNERS

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+# This file contains file patterns that triggers automatic
+# code review requests from users that are owners of these files
+# Order matters, the last match has the highest precedence
+
+# library folders
+lib/colvars/*         @giacomofiorin
+lib/compress/*        @akohlmey
+lib/kokkos/*          @stanmoore1
+lib/molfile/*         @akohlmey
+lib/qmmm/*            @akohlmey
+lib/vtk/*             @rbberger
+lib/kim/*             @ellio167
+lib/mesont/*          @iafoss
+
+# whole packages
+src/COMPRESS/*        @akohlmey
+src/GPU/*             @ndtrung81
+src/KOKKOS/*          @stanmoore1
+src/KIM/*             @ellio167
+src/LATTE/*           @cnegre
+src/MESSAGE/*         @sjplimp
+src/SPIN/*            @julient31
+src/USER-CGDNA/*      @ohenrich
+src/USER-CGSDK/*      @akohlmey
+src/USER-COLVARS/*    @giacomofiorin
+src/USER-INTEL/*      @wmbrownintel
+src/USER-MANIFOLD/*   @Pakketeretet2
+src/USER-MEAMC/*      @martok
+src/USER-MESONT/*     @iafoss
+src/USER-MOFFF/*      @hheenen
+src/USER-MOLFILE/*    @akohlmey
+src/USER-NETCDF/*     @pastewka
+src/USER-PLUMED/*     @gtribello
+src/USER-PHONON/*     @lingtikong
+src/USER-PTM/*        @pmla
+src/USER-OMP/*        @akohlmey
+src/USER-QMMM/*       @akohlmey
+src/USER-REAXC/*      @hasanmetin
+src/USER-SCAFACOS/*   @rhalver
+src/USER-TALLY/*      @akohlmey
+src/USER-UEF/*        @danicholson
+src/USER-VTK/*        @rbberger
+
+
+# individual files in packages
+src/GPU/pair_vashishta_gpu.*        @andeplane
+src/KOKKOS/pair_vashishta_kokkos.*  @andeplane
+src/MANYBODY/pair_vashishta_table.* @andeplane
+src/MANYBODY/pair_atm.*             @sergeylishchuk
+src/USER-REACTION/fix_bond_react.*  @jrgissing
+src/USER-MISC/*_grem.*              @dstelter92
+src/USER-MISC/compute_stress_mop*.* @RomainVermorel
+
+# core LAMMPS classes
+src/lammps.*              @sjplimp
+src/pointers.h            @sjplimp
+src/atom.*                @sjplimp
+src/atom_vec.*            @sjplimp
+src/angle.*               @sjplimp
+src/bond.*                @sjplimp
+src/comm*.*               @sjplimp
+src/compute.*             @sjplimp
+src/dihedral.*            @sjplimp
+src/domain.*              @sjplimp
+src/dump*.*               @sjplimp
+src/error.*               @sjplimp
+src/finish.*              @sjplimp
+src/fix.*                 @sjplimp
+src/force.*               @sjplimp
+src/group.*               @sjplimp
+src/improper.*            @sjplimp
+src/kspace.*              @sjplimp
+src/lmptyp.h              @sjplimp
+src/library.*             @sjplimp
+src/main.cpp              @sjplimp
+src/memory.*              @sjplimp
+src/modify.*              @sjplimp
+src/molecule.*            @sjplimp
+src/my_page.h             @sjplimp
+src/my_pool_chunk.h       @sjplimp
+src/npair*.*              @sjplimp
+src/ntopo*.*              @sjplimp
+src/nstencil*.*           @sjplimp
+src/neighbor.*            @sjplimp
+src/nbin*.*               @sjplimp
+src/neigh_*.*             @sjplimp
+src/output.*              @sjplimp
+src/pair.*                @sjplimp
+src/rcb.*                 @sjplimp
+src/random_*.*            @sjplimp
+src/region*.*             @sjplimp
+src/rcb.*                 @sjplimp
+src/read*.*               @sjplimp
+src/rerun.*               @sjplimp
+src/run.*                 @sjplimp
+src/respa.*               @sjplimp
+src/set.*                 @sjplimp
+src/special.*             @sjplimp
+src/suffix.h              @sjplimp
+src/thermo.*              @sjplimp
+src/universe.*            @sjplimp
+src/update.*              @sjplimp
+src/variable.*            @sjplimp
+src/verlet.*              @sjplimp
+src/velocity.*            @sjplimp
+src/write_data.*          @sjplimp
+src/write_restart.*       @sjplimp
+
+# overrides for specific files
+src/dump_movie.*          @akohlmey
+src/exceptions.h          @rbberger
+src/fix_nh.*              @athomps
+src/info.*                @akohlmey @rbberger
+src/timer.*               @akohlmey
+src/min*                  @sjplimp @stanmoore1
+src/utils.*               @akohlmey @rbberger
+
+# tools
+tools/msi2lmp/*       @akohlmey
+tools/emacs/*         @HaoZeke
+tools/singularity/*   @akohlmey @rbberger
+tools/code_standard/* @rbberger
+tools/valgrind/*      @akohlmey
+
+# tests
+unittest/*            @akohlmey @rbberger
+
+# cmake
+cmake/*               @junghans @rbberger
+cmake/Modules/Packages/USER-COLVARS.cmake @junghans @rbberger @giacomofiorin
+cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
+cmake/presets/*.cmake @junghans @rbberger @akohlmey
+
+# python
+python/*              @rbberger
+
+# docs
+doc/utils/*/*         @rbberger
+doc/Makefile          @rbberger
+doc/README            @rbberger
+
+# for releases
+src/version.h         @sjplimp

.github/CODE_OF_CONDUCT.md

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+# Code of Conduct for the LAMMPS Project on GitHub
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as LAMMPS
+developers, contributors, and maintainers pledge to making participation in
+our project a harassment-free experience for everyone.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of explicit language or imagery
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, issues, and other contributions that are not
+aligned to this Code of Conduct, or to ban temporarily or permanently any
+developer, maintainer, or contributor for this or other behaviors that they
+deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies to all public exchanges in the LAMMPS project
+on GitHub and in submitted code.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at developer@lammps.org. All
+complaints will be reviewed and investigated and will result in a response
+that is deemed necessary and appropriate to the circumstances. The project
+team is obligated to maintain confidentiality with regard to the reporter
+of an incident.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq
+

.github/CONTRIBUTING.md

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+# Contributing to LAMMPS via GitHub
+
+Thank your for considering to contribute to the LAMMPS software project.
+
+The following is a set of guidelines as well as explanations of policies and work flows for contributing to the LAMMPS molecular dynamics software project. These guidelines focus on submitting issues or pull requests on the LAMMPS GitHub project.
+
+Thus please also have a look at:
+* [The Section on submitting new features for inclusion in LAMMPS of the Manual](https://lammps.sandia.gov/doc/Modify_contribute.html)
+* [The LAMMPS GitHub Tutorial in the Manual](http://lammps.sandia.gov/doc/Howto_github.html)
+
+## Table of Contents
+
+[I don't want to read this whole thing, I just have a question!](#i-dont-want-to-read-this-whole-thing-i-just-have-a-question)
+
+[How Can I Contribute?](#how-can-i-contribute)
+* [Discussing How To Use LAMMPS](#discussing-how-to-use-lammps)
+* [Reporting Bugs](#reporting-bugs)
+* [Suggesting Enhancements](#suggesting-enhancements)
+* [Contributing Code](#contributing-code)
+
+[GitHub Work flows](#github-workflows)
+* [Issues](#issues)
+* [Pull Requests](#pull-requests)
+
+__
+
+## I don't want to read this whole thing I just have a question!
+
+> **Note:** Please do not file an issue to ask a general question about LAMMPS, its features, how to use specific commands, or how perform simulations or analysis in LAMMPS. Instead post your question to the ['lammps-users' mailing list](https://lammps.sandia.gov/mail.html). You do not need to be subscribed to post to the list (but a mailing list subscription avoids having your post delayed until it is approved by a mailing list moderator). Most posts to the mailing list receive a response within less than 24 hours. Before posting to the mailing list, please read the [mailing list guidelines](https://lammps.sandia.gov/guidelines.html). Following those guidelines will help greatly to get a helpful response. Always mention which LAMMPS version you are using.
+
+## How Can I Contribute?
+
+There are several ways how you can actively contribute to the LAMMPS project: you can discuss compiling and using LAMMPS, and solving LAMMPS related problems with other LAMMPS users on the lammps-users mailing list, you can report bugs or suggest enhancements by creating issues on GitHub (or posting them to the lammps-users mailing list), and you can contribute by submitting pull requests on GitHub or e-mail your code
+to one of the [LAMMPS core developers](https://lammps.sandia.gov/authors.html). As you may see from the aforementioned developer page, the LAMMPS software package includes the efforts of a very large number of contributors beyond the principal authors and maintainers.
+
+### Discussing How To Use LAMMPS
+
+The LAMMPS mailing list is hosted at SourceForge. The mailing list began in 2005, and now includes tens of thousands of messages in thousands of threads. LAMMPS developers try to respond to posted questions in a timely manner, but there are no guarantees. Please consider that people live in different timezone and may not have time to answer e-mails outside of their work hours.
+You can post to list by sending your email to lammps-users at lists.sourceforge.net (no subscription required), but before posting, please read the [mailing list guidelines](https://lammps.sandia.gov/guidelines.html) to maximize your chances to receive a helpful response.
+
+Anyone can browse/search previous questions/answers in the archives. You do not have to subscribe to the list to post questions, receive answers (to your questions), or browse/search the archives. You **do** need to subscribe to the list if you want emails for **all** the posts (as individual messages or in digest form), or to answer questions yourself. Feel free to sign up and help us out! Answering questions from fellow LAMMPS users is a great way to pay back the community for providing you a useful tool for free, and to pass on the advice you have received yourself to others. It improves your karma and helps you understand your own research better.
+
+If you post a message and you are a subscriber, your message will appear immediately. If you are not a subscriber, your message will be moderated, which typically takes one business day. Either way, when someone replies the reply will usually be sent to both, your personal email address and the mailing list. When replying to people, that responded to your post to the list, please always included the mailing list in your replies (i.e. use "Reply All" and **not** "Reply"). Responses will appear on the list in a few minutes, but it can take a few hours for postings and replies to show up in the SourceForge archive. Sending replies also to the mailing list is important, so that responses are archived and people with a similar issue can search for possible solutions in the mailing list archive.
+
+### Reporting Bugs
+
+While developers writing code for LAMMPS are careful to test their code, LAMMPS is such a large and complex software, that it is impossible to test for all combinations of features under all normal and not so normal circumstances. Thus bugs do happen, and if you suspect, that you have encountered one, please try to document it and report it as an [Issue](https://github.com/lammps/lammps/issues) on the LAMMPS GitHub project web page. However, before reporting a bug, you need to check whether this is something that may have already been corrected. The [Latest Features and Bug Fixes in LAMMPS](https://lammps.sandia.gov/bug.html) web page lists all significant changes to LAMMPS over the years. It also tells you what the current latest development version of LAMMPS is, and you should test whether your issue still applies to that version.
+
+When you click on the green "New Issue" button, you will be provided with a text field, where you can enter your message. That text field with contain a template with several headlines and some descriptions. Keep the headlines that are relevant to your reported potential bug and replace the descriptions with the information as suggested by the descriptions.
+You can also attach small text files (please add the file name extension `.txt` or it will be rejected), images, or small compressed text files (using gzip, do not use RAR or 7-ZIP or similar tools that are uncommon outside of Windows machines). In many cases, bugs are best illustrated by providing a small input deck (do **not** attach your entire production input, but remove everything that is not required to reproduce the issue, and scale down your system size, that the resulting calculation runs fast and can be run on small desktop quickly).
+
+To be able to submit an issue on GitHub, you have to register for an account (for GitHub in general). If you do not want to do that, or have other reservations against submitting an issue there, you can - as an alternative and in decreasing preference - either send an e-mail to the lammps-users mailing list, the original authors of the feature that you suspect to be affected, or one or more of the core LAMMPS developers.
+
+### Suggesting Enhancements
+
+The LAMMPS developers welcome suggestions for enhancements or new features. These should be submitted using the [GitHub Issue Tracker](https://github.com/lammps/lammps/issues) of the LAMMPS project. This is particularly recommended, when you plan to implement the feature or enhancement yourself, as this allows to coordinate in case there are other similar or conflicting ongoing developments.
+The LAMMPS developers will review your submission and consider implementing it. Whether this will actually happen depends on many factors: how difficult it would be, how much effort it would take, how many users would benefit from it, how well the individual developer would understand the underlying physics of the feature, and whether this is a feature that would fit into a software like LAMMPS, or would be better implemented as a separate tool. Because of these factors, it matters how well the suggested enhancement is formulated and the overall benefit is argued convincingly.
+
+To be able to submit an issue on GitHub, you have to register for an account (for GitHub in general). If you do not want to do that, or have other reservations against submitting an issue there, you can - as an alternative - send an e-mail to the lammps-users mailing list.
+
+### Contributing Code
+
+We encourage users to submit new features or modifications for LAMMPS to the core developers so they can be added to the LAMMPS distribution. The preferred way to manage and coordinate this is by submitting a pull request at the LAMMPS project on GitHub. For any larger modifications or programming project, you are encouraged to contact the LAMMPS developers ahead of time, in order to discuss implementation strategies and coding guidelines, that will make it easier to integrate your contribution and result in less work for everybody involved. You are also encouraged to search through the list of open issues on GitHub and submit a new issue for a planned feature, so you would not duplicate the work of others (and possibly get scooped by them) or have your work duplicated by others.
+
+How quickly your contribution will be integrated depends largely on how much effort it will cause to integrate and test it, how much it requires changes to the core code base, and of how much interest it is to the larger LAMMPS community. Please see below for a checklist of typical requirements. Once you have prepared everything, see [this tutorial](https://lammps.sandia.gov/doc/Howto_github.html)
+ for instructions on how to submit your changes or new files through a GitHub pull request
+
+Here is a checklist of steps you need to follow to submit a single file or user package for our consideration. Following these steps will save both you and us time. See existing files in packages in the source directory for examples. If you are uncertain, please ask on the lammps-users mailing list.
+
+* All source files you provide must compile with the most current version of LAMMPS with multiple configurations. In particular you need to test compiling LAMMPS from scratch with `-DLAMMPS_BIGBIG` set in addition to the default `-DLAMMPS_SMALLBIG` setting. Your code will need to work correctly in serial and in parallel using MPI.
+* For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no trailing whitespace, no lines over 80 characters. I/O is done via the C-style stdio library, style class header files should not import any system headers, STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. There MUST NOT be any "using namespace XXX;" statements in headers. In the implementation file (<name>.cpp) system includes should be placed in angular brackets (<>) and for c-library functions the C++ style header files should be included (<cstdio> instead of <stdio.h>, or <cstring> instead of <string.h>). This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages.
+* Source, style name, and documentation file should follow the following naming convention: style names should be lowercase and words separated by a forward slash; for a new fix style 'foo/bar', the class should be named FixFooBar, the name of the source files should be 'fix_foo_bar.h' and 'fix_foo_bar.cpp' and the corresponding documentation should be in a file 'fix_foo_bar.rst'.
+* If you want your contribution to be added as a user-contributed feature, and it is a single file (actually a `<name>.cpp` and `<name>.h` file) it can be rapidly added to the USER-MISC directory. Include the one-line entry to add to the USER-MISC/README file in that directory, along with the 2 source files. You can do this multiple times if you wish to contribute several individual features.
+* If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like USER-FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this USER-FOO directory.
+* Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code.
+* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). The text files can include mathematical expressions and symbol in ".. math::" sections or ":math:" expressions or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html`, `make pdf` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file.  For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`.
+* For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/USER for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind
+* For new utility functions or class (i.e. anything that does not depend on a LAMMPS object), new unit tests should be added to the unittest tree.
+* When adding a new LAMMPS style, a .yaml file with a test configuration and reference data should be added for the styles where a suitable tester program already exists (e.g. pair styles, bond styles, etc.).
+* If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the <name>.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide.
+
+Finally, as a general rule-of-thumb, the more clear and self-explanatory you make your documentation and README files, and the easier you make it for people to get started, e.g. by providing example scripts, the more likely it is that users will try out your new feature.
+
+If the new features/files are broadly useful we may add them as core files to LAMMPS or as part of a standard package. Else we will add them as a user-contributed file or package. Examples of user packages are in src sub-directories that start with USER. The USER-MISC package is simply a collection of (mostly) unrelated single files, which is the simplest way to have your contribution quickly added to the LAMMPS distribution. You can see a list of the both standard and user packages by typing "make package" in the LAMMPS src directory.
+
+Note that by providing us files to release, you are agreeing to make them open-source, i.e. we can release them under the terms of the GPL, used as a license for the rest of LAMMPS. See Section 1.4 for details.
+
+With user packages and files, all we are really providing (aside from the fame and fortune that accompanies having your name in the source code and on the Authors page of the LAMMPS WWW site), is a means for you to distribute your work to the LAMMPS user community, and a mechanism for others to easily try out your new feature. This may help you find bugs or make contact with new collaborators. Note that you are also implicitly agreeing to support your code which means answer questions, fix bugs, and maintain it if LAMMPS changes in some way that breaks it (an unusual event).
+
+To be able to submit an issue on GitHub, you have to register for an account (for GitHub in general). If you do not want to do that, or have other reservations or difficulties to submit a pull request, you can - as an alternative - contact one or more of the core LAMMPS developers and ask if one of them would be interested in manually merging your code into LAMMPS and send them your source code. Since the effort to merge a pull request is a small fraction of the effort of integrating source code manually (which would usually be done by converting the contribution into a pull request), your chances to have your new code included quickly are the best with a pull request.
+
+If you prefer to submit patches or full files, you should first make certain, that your code works correctly with the latest patch-level version of LAMMPS and contains all bug fixes from it. Then create a gzipped tar file of all changed or added files or a corresponding patch file using 'diff -u' or 'diff -c' and compress it with gzip. Please only use gzip compression, as this works well on all platforms.
+
+## GitHub Workflows
+
+This section briefly summarizes the steps that will happen **after** you have submitted either an issue or a pull request on the LAMMPS GitHub project page. 
+
+### Issues
+
+After submitting an issue, one or more of the LAMMPS developers will review it and categorize it by assigning labels. Confirmed bug reports will be labeled `bug`; if the bug report also contains a suggestion for how to fix it, it will be labeled `bugfix`; if the issue is a feature request, it will be labeled `enhancement`. Other labels may be attached as well, depending on which parts of the LAMMPS code are affected. If the assessment is, that the issue does not warrant any changes, the `wontfix` label will be applied and if the submission is incorrect or something that should not be submitted as an issue, the `invalid` label will be applied. In both of the last two cases, the issue will then be closed without further action.
+
+For feature requests, what happens next is that developers may comment on the viability or relevance of the request, discuss and make suggestions for how to implement it. If a LAMMPS developer or user is planning to implement the feature, the issue will be assigned to that developer. For developers, that are not yet listed as LAMMPS project collaborators, they will receive an invitation to be added to the LAMMPS project as a collaborator so they can get assigned. If the requested feature or enhancement is implemented, it will usually be submitted as a pull request, which will contain a reference to the issue number. And once the pull request is reviewed and accepted for inclusion into LAMMPS, the issue will be closed. For details on how pull requests are processed, please see below.
+
+For bug reports, the next step is that one of the core LAMMPS developers will self-assign to the issue and try to confirm the bug. If confirmed, the `bug` label and potentially other labels are added to classify the issue and its impact to LAMMPS. Before confirming, further questions may be asked or requests for providing additional input files or details about the steps required to reproduce the issue. Any bugfix is likely to be submitted as a pull request (more about that below) and since most bugs require only local changes, the bugfix may be included in a pull request specifically set up to collect such local bugfixes or small enhancements. Once the bugfix is included in the master branch, the issue will be closed.
+
+### Pull Requests
+
+For submitting pull requests, there is a [detailed tutorial](https://lammps.sandia.gov/doc/Howto_github.html) in the LAMMPS manual. Thus only a brief breakdown of the steps is presented here. Please note, that the LAMMPS developers are still reviewing and trying to improve the process. If you are unsure about something, do not hesitate to post a question on the lammps-users mailing list or contact one fo the core LAMMPS developers.
+Immediately after the submission, the LAMMPS continuing integration server at ci.lammps.org will download your submitted branch and perform a simple compilation test, i.e. will test whether your submitted code can be compiled under various conditions. It will also do a check on whether your included documentation translates cleanly. Whether these tests are successful or fail will be recorded. If a test fails, please inspect the corresponding output on the CI server and take the necessary steps, if needed, so that the code can compile cleanly again. The test will be re-run each the pull request is updated with a push to the remote branch on GitHub.
+Next a LAMMPS core developer will self-assign and do an overall technical assessment of the submission. If you are not yet registered as a LAMMPS collaborator, you will receive an invitation for that. As part of the assesment, the pull request will be categorized with labels. There are two special labels: `needs_work` (indicates that work from the submitter of the pull request is needed) and `work_in_progress` (indicates, that the assigned LAMMPS developer will make changes, if not done by the contributor who made the submit). 
+You may also receive comments and suggestions on the overall submission or specific details and on occasion specific requests for changes as part of the review. If permitted, also additional changes may be pushed into your pull request branch or a pull request may be filed in your LAMMPS fork on GitHub to include those changes.
+The LAMMPS developer may then decide to assign the pull request to another developer (e.g. when that developer is more knowledgeable about the submitted feature or enhancement or has written the modified code). It may also happen, that additional developers are requested to provide a review and approve the changes. For submissions, that may change the general behavior of LAMMPS, or where a possibility of unwanted side effects exists, additional tests may be requested by the assigned developer.
+If the assigned developer is satisfied and considers the submission ready for inclusion into LAMMPS, the pull request will receive approvals and be merged into the master branch by one of the core LAMMPS developers. After the pull request is merged, you may delete the feature branch used for the pull request in your personal LAMMPS fork.
+Since the learning curve for git is quite steep for efficiently managing remote repositories, local and remote branches, pull requests and more, do not hesitate to ask questions, if you are not sure about how to do certain steps that are asked of you. Even if the changes asked of you do not make sense to you, they may be important for the LAMMPS developers. Please also note, that these all are guidelines and nothing set in stone. So depending on the nature of the contribution, the workflow may be adjusted.
+

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,32 @@
+---
+name: Bug report
+about: Create a bug report to help us eliminate issues and improve LAMMPS
+title: "[BUG] _Replace With Suitable Title_"
+labels: bug
+assignees: ''
+
+---
+
+**Summary**
+
+<!--Please provide a clear and concise description of what the bug is.-->
+
+**LAMMPS Version and Platform**
+
+<!--Please specify precisely which LAMMPS version this issue was detected with (the first line of the output) and what platform (operating system and its version, hardware) you are running on. If possible, test with the most recent LAMMPS patch version-->
+
+**Expected Behavior**
+
+<!--Describe the expected behavior.  Quote from the LAMMPS manual where needed, or explain why the expected behavior is meaningful, especially when it differs from the manual-->
+
+**Actual Behavior**
+
+<!--Describe the actual behavior, how it differs from the expected behavior, and how this can be observed.  Try to be specific and do **not** use vague terms like "doesn't work" or "wrong result".  Do not assume that the person reading this has any experience with or knowledge of your specific area of research.-->
+
+**Steps to Reproduce**
+
+<!--Describe the steps required to (quickly) reproduce the issue. You can attach (small) files to the section below or add URLs where to download an archive with all necessary files. Please try to create an input set that is as minimal and small as possible and reproduces the bug as quickly as possible. **NOTE:** the less effort and time it takes to reproduce your reported bug, the more likely it becomes, that somebody will look into it and fix the problem.-->
+
+**Further Information, Files, and Links**
+
+<!--Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications-->

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Make a suggestion for a new feature or a change to LAMMPS
+title: "[Feature Request] _Replace with Title_"
+labels: enhancement
+assignees: ''
+
+---
+
+**Summary**
+
+<!--Please provide a brief and concise description of the suggested feature or change-->
+
+**Detailed Description**
+
+<!--Please explain how you would like to see LAMMPS enhanced, what feature(s) you are looking for, what specific problems this will solve. If possible, provide references to relevant background information like publications or web pages, and whether you are planning to implement the enhancement yourself or would like to participate in the implementation. If applicable add a reference to an existing bug report or issue that this will address.-->
+
+**Further Information, Files, and Links**
+
+<!--Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications-->

.github/ISSUE_TEMPLATE/generic.md

@@ -0,0 +1,21 @@
+---
+name: Generic Issue
+about: For issues that do not fit any of the other categories
+title: "_Replace With a Descriptive Title_"
+labels: 
+assignees: ''
+
+---
+
+**Summary**
+
+<!--Please provide a clear and concise description of what this issue report is about.-->
+
+**LAMMPS Version and Platform**
+
+<!--Please specify precisely which LAMMPS version this issue was detected with (the first line of the output) and what platform (operating system and its version, hardware) you are running on. If possible, test with the most recent LAMMPS patch version-->
+
+**Details**
+
+<!--Please explain the issue in detail here-->
+

.github/ISSUE_TEMPLATE/help_request.md

@@ -0,0 +1,15 @@
+---
+name: Request for Help
+about: "Don't post help requests here, email the lammps-users mailing list"
+title: ""
+labels: invalid
+assignees: ''
+
+---
+
+Please **do not** post requests for help (e.g. with installing or using LAMMPS) here.
+Instead send an e-mail to the lammps-users mailing list.
+
+This issue tracker is for tracking LAMMPS development related issues only.
+
+Thanks for your cooperation.

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,45 @@
+**Summary**
+
+<!--Briefly describe the new feature(s), enhancement(s), or bugfix(es) included in this pull request.-->
+
+**Related Issues**
+
+<!--If this addresses an open GitHub issue for this project, please mention the issue number here, and describe the relation. Use the phrases `fixes #221` or `closes #135`, when you want an issue to be automatically closed when the pull request is merged-->
+
+**Author(s)**
+
+<!--Please state name and affiliation of the author or authors that should be credited with the changes in this pull request. If this pull request adds new files to the distribution, please also provide a suitable "long-lived" e-mail address (ideally something that can outlive your institution's e-mail, in case you change jobs) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this contributed code.-->
+
+**Licensing**
+
+By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).
+
+**Backward Compatibility**
+
+<!--Please state whether any changes in the pull request will break backward compatibility for inputs, and - if yes - explain what has been changed and why-->
+
+**Implementation Notes**
+
+<!--Provide any relevant details about how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected-->
+
+**Post Submission Checklist**
+
+<!--Please check the fields below as they are completed **after** the pull request has been submitted. Delete lines that don't apply-->
+
+- [ ] The feature or features in this pull request is complete
+- [ ] Licensing information is complete
+- [ ] Corresponding author information is complete
+- [ ] The source code follows the LAMMPS formatting guidelines
+- [ ] Suitable new documentation files and/or updates to the existing docs are included
+- [ ] The added/updated documentation is integrated and tested with the documentation build system
+- [ ] The feature has been verified to work with the conventional build system
+- [ ] The feature has been verified to work with the CMake based build system
+- [ ] Suitable tests have been added to the unittest tree.
+- [ ] A package specific README file has been included or updated
+- [ ] One or more example input decks are included
+
+**Further Information, Files, and Links**
+
+<!--Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)-->
+
+

.github/PULL_REQUEST_TEMPLATE/bug_fix.md

@@ -0,0 +1,42 @@
+---
+name: Bug fix
+about: Submit a pull request that fixes one or more bugs
+title: "[BUGFIX] _Replace With Suitable Title_"
+labels: bugfix
+assignees: ''
+
+---
+
+**Summary**
+
+<!--Briefly describe the bug or bugs, that are eliminated by this pull request.-->
+
+**Related Issue(s)**
+
+<!--If this request addresses or is related to an existing (open) GitHub issue, e.g. a bug report, mention the issue number number here following a pound sign (aka hashmark), e.g.`#222`.-->
+
+**Author(s)**
+
+<!--Please state name and affiliation of the author or authors that should be credited with the changes in this pull request-->
+
+**Licensing**
+
+By submitting this pull request I implicitly accept, that my submission is subject to the same licensing terms as the files that are modified.
+
+**Backward Compatibility**
+
+<!--Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why-->
+
+**Detailed Description**
+
+<!--Provide any relevant details about how the fixed bug can be reproduced, how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected-->
+
+## Post Submission Checklist
+
+<!--Please check the fields below as they are completed *after* the pull request is submitted-->
+- [ ] The code in this pull request is complete
+- [ ] The source code follows the LAMMPS formatting guidelines
+
+## Further Information, Files, and Links
+
+<!--Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. to download input decks for testing)-->

.github/PULL_REQUEST_TEMPLATE/maintenance_refactoring.md

@@ -0,0 +1,35 @@
+---
+name: Maintenance or Refactoring
+about: Submit a pull request that does code refactoring or other maintenance changes
+title: "[MAINTENANCE] _Replace With Suitable Title_"
+labels: maintenance
+assignees: ''
+
+---
+
+**Summary**
+
+<!--Briefly describe the included changes.-->
+
+**Related Issue(s)**
+
+<!--If this request addresses or is related to an existing (open) GitHub issue, e.g. a bug report, mention the issue number number here following a pound sign (aka hashmark), e.g.`#222`.
+
+**Author(s)**
+
+<!--Please state name and affiliation of the author or authors that should be credited with the changes in this pull request-->
+
+**Licensing**
+
+By submitting this pull request I implicitly accept, that my submission is subject to the same licensing terms as the files that are modified.
+
+**Detailed Description**
+
+<!--Provide any relevant details about the included changes.-->
+
+## Post Submission Checklist
+
+<!--Please check the fields below as they are completed *after* the pull request is submitted-->
+- [ ] The pull request is complete
+- [ ] The source code follows the LAMMPS formatting guidelines
+

.github/PULL_REQUEST_TEMPLATE/new_feature.md

@@ -0,0 +1,56 @@
+---
+name: New Feature
+about: Submit a pull request that adds new Features (complete files) to LAMMPS
+title: "[New Feature] _Replace With Suitable Title_"
+labels: enhancement
+assignees: ''
+
+---
+
+**Summary**
+
+<!--Briefly describe the new feature(s) included in this pull request.-->
+
+**Related Issues**
+
+<!--If this addresses an existing (open) GitHub issue, e.g. a feature request, mention the issue number here following a pound sign (aka hashmark), e.g. `#331`.-->
+
+**Author(s)**
+
+<!--Please state name and affiliation of the author or authors that should be credited with the features added in this pull request. Please provide a suitable "long-lived" e-mail address (e.g. from gmail, yahoo, outlook, etc.) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this code. now and in the future-->
+
+**Licensing**
+
+<!--Please add *yes* or *no* to the following two statements (please contact @lammps/core if you have questions about this)-->
+
+My contribution may be licensed as GPL v2 (default LAMMPS license):
+My contribution may be licensed as LGPL (for use as a library with proprietary software):
+
+**Backward Compatibility**
+
+<!--Please state if any of the changes in this pull request will affect backward compatibility for inputs, and - if yes - explain what has been changed and why-->
+
+**Implementation Notes**
+
+<!--Provide any relevant details about how the new features are implemented, how correctness was verified, what platforms (OS, compiler, MPI, hardware, number of processors, accelerator(s)) it was tested on-->
+
+## Post Submission Checklist
+
+<!--Please check the fields below as they are completed *after* the pull request has been submitted-->
+
+- [ ] The feature or features in this pull request is complete
+- [ ] Licensing information is complete
+- [ ] Corresponding author information is complete
+- [ ] The source code follows the LAMMPS formatting guidelines
+- [ ] Suitable new documentation files and/or updates to the existing docs are included
+- [ ] The added/updated documentation is integrated and tested with the documentation build system
+- [ ] The feature has been verified to work with the conventional build system
+- [ ] The feature has been verified to work with the CMake based build system
+- [ ] A package specific README file has been included or updated
+- [ ] One or more example input decks are included
+
+## Further Information, Files, and Links
+
+<!--Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)-->
+
+

.github/PULL_REQUEST_TEMPLATE/update_enhancement.md

@@ -0,0 +1,42 @@
+---
+name: Update or Enhancement
+about: Submit a pull request that provides update or enhancements for a package or feature in LAMMPS
+title: "[UPDATE] _Replace With Suitable Title_"
+labels: enhancement
+assignees: ''
+
+---
+
+**Summary**
+
+<!--Briefly describe what kind of updates or enhancements for a package or feature are included. If you are not the original author of the package or feature, please mention, whether your contribution was created independently or in collaboration/cooperation with the original author.-->
+
+**Author(s)**
+
+<!--Please state name and affiliation of the author or authors that should be credited with the changes in this pull request-->
+
+**Licensing**
+
+By submitting this pull request I implicitly accept, that my submission is subject to the same licensing terms as the original package or feature(s) that are updated or amended by this pull request.
+
+**Backward Compatibility**
+
+<!--Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why-->
+
+**Implementation Notes**
+
+<!--Provide any relevant details about how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected-->
+
+**Post Submission Checklist**
+
+<!--Please check the fields below as they are completed-->
+- [ ] The feature or features in this pull request is complete
+- [ ] Suitable updates to the existing docs are included
+- [ ] One or more example input decks are included
+- [ ] The source code follows the LAMMPS formatting guidelines
+
+**Further Information, Files, and Links**
+
+<!--Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)-->
+
+

.github/codecov.yml

@@ -0,0 +1,29 @@
+comment: false
+coverage:
+  notify:
+    slack:
+      default:
+        url: "secret:HWZbvgtc6OD7F3v3PfrK3/rzCJvScbh69Fi1CkLwuHK0+wIBIHVR+Q5i7q6F9Ln4OChbiRGtYAEUUsT8/jmBu4qDpIi8mx746codc0z/Z3aafLd24pBrCEPLvdCfIZxqPnw3TuUgGhwmMDZf0+thg8YNUr/MbOZ7Li2L6+ZbYuA="
+        threshold: 10%
+        only_pulls: false
+        branches:
+          - "master"
+        flags:
+          - "unit"
+        paths:
+          - "src"
+  status:
+    project:
+        default:
+            branches:
+              - "master"
+            paths:
+              - "src"
+            informational: true
+    patch:
+        default:
+            branches:
+              - "master"
+            paths:
+              - "src"
+            informational: true

.gitignore

@@ -1,6 +1,7 @@
 *~
 *.o
 *.so
+*.lo
 *.cu_o
 *.ptx
 *_ptx.h
@@ -8,6 +9,7 @@
 *.d
 *.x
 *.exe
+*.sif
 *.dll
 *.pyc
 __pycache__
@@ -21,9 +23,11 @@ log.cite
 .*.swp
 *.orig
 *.rej
+vgcore.*
 .vagrant
 \#*#
 .#*
+.vscode
 
 .DS_Store
 .DS_Store?
@@ -32,3 +36,12 @@ log.cite
 .Trashes
 ehthumbs.db
 Thumbs.db
+.clang-format
+
+#cmake
+/build*
+/CMakeCache.txt
+/CMakeFiles/
+/Makefile
+/cmake_install.cmake
+/lmp

LICENSE

@@ -3,7 +3,7 @@ GNU GENERAL PUBLIC LICENSE
 Version 2, June 1991 
 
 Copyright (C) 1989, 1991 Free Software Foundation, Inc.  
-59 Temple Place - Suite 330, Boston, MA  02111-1307, USA
+51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 
 Everyone is permitted to copy and distribute verbatim copies of this
 license document, but changing it is not allowed.

README

@@ -25,7 +25,7 @@ The LAMMPS distribution includes the following files and directories:
 README			   this file
 LICENSE			   the GNU General Public License (GPL)
 bench			   benchmark problems
-couple			   code coupling examples using LAMMPS as a library
+cmake			   CMake build system
 doc			   documentation
 examples		   simple test problems
 lib			   libraries LAMMPS can be linked with
@@ -36,7 +36,14 @@ tools			   pre- and post-processing tools
 
 Point your browser at any of these files to get started:
 
-doc/Manual.html	           the LAMMPS manual
-doc/Section_intro.html	   hi-level introduction to LAMMPS
-doc/Section_start.html	   how to build and use LAMMPS
-doc/Developer.pdf          LAMMPS developer guide
+http://lammps.sandia.gov/doc/Manual.html         the LAMMPS manual
+http://lammps.sandia.gov/doc/Intro.html          hi-level introduction
+http://lammps.sandia.gov/doc/Build.html          how to build LAMMPS
+http://lammps.sandia.gov/doc/Run_head.html       how to run LAMMPS
+http://lammps.sandia.gov/doc/Developer.pdf       LAMMPS developer guide
+
+You can also create these doc pages locally:
+
+% cd doc
+% make html                # creates HTML pages in doc/html
+% make pdf                 # creates Manual.pdf and Developer.pdf

bench/FERMI/README

@@ -1,103 +0,0 @@
-These are input scripts used to run versions of several of the
-benchmarks in the top-level bench directory using the GPU and
-USER-CUDA accelerator packages.  The results of running these scripts
-on two different machines (a desktop with 2 Tesla GPUs and the ORNL
-Titan supercomputer) are shown on the "GPU (Fermi)" section of the
-Benchmark page of the LAMMPS WWW site: lammps.sandia.gov/bench.
-
-Examples are shown below of how to run these scripts.  This assumes
-you have built 3 executables with both the GPU and USER-CUDA packages
-installed, e.g.
-
-lmp_linux_single
-lmp_linux_mixed
-lmp_linux_double
-
-The precision (single, mixed, double) refers to the GPU and USER-CUDA
-pacakge precision.  See the README files in the lib/gpu and lib/cuda
-directories for instructions on how to build the packages with
-different precisions.  The GPU and USER-CUDA sub-sections of the
-doc/Section_accelerate.html file also describes this process.
-
-Make.py -d ~/lammps -j 16 -p #all orig -m linux -o cpu -a exe
-Make.py -d ~/lammps -j 16 -p #all opt orig -m linux -o opt -a exe
-Make.py -d ~/lammps -j 16 -p #all omp orig -m linux -o omp -a exe
-Make.py -d ~/lammps -j 16 -p #all gpu orig -m linux \
-        -gpu mode=double arch=20 -o gpu_double -a libs exe
-Make.py -d ~/lammps -j 16 -p #all gpu orig -m linux \
-        -gpu mode=mixed arch=20 -o gpu_mixed -a libs exe
-Make.py -d ~/lammps -j 16 -p #all gpu orig -m linux \
-        -gpu mode=single arch=20 -o gpu_single -a libs exe
-Make.py -d ~/lammps -j 16 -p #all cuda orig -m linux \
-        -cuda mode=double arch=20 -o cuda_double -a libs exe
-Make.py -d ~/lammps -j 16 -p #all cuda orig -m linux \
-        -cuda mode=mixed arch=20 -o cuda_mixed -a libs exe
-Make.py -d ~/lammps -j 16 -p #all cuda orig -m linux \
-        -cuda mode=single arch=20 -o cuda_single -a libs exe
-Make.py -d ~/lammps -j 16 -p #all intel orig -m linux -o intel_cpu -a exe
-Make.py -d ~/lammps -j 16 -p #all kokkos orig -m linux -o kokkos_omp -a exe
-Make.py -d ~/lammps -j 16 -p #all kokkos orig -kokkos cuda arch=20 \
-        -m cuda -o kokkos_cuda -a exe
-
-Make.py -d ~/lammps -j 16 -p #all opt omp gpu cuda intel kokkos orig \
-        -gpu mode=double arch=20 -cuda mode=double arch=20 -m linux \
-        -o all -a libs exe
-
-Make.py -d ~/lammps -j 16 -p #all opt omp gpu cuda intel kokkos orig \
-        -kokkos cuda arch=20 -gpu mode=double arch=20 \
-        -cuda mode=double arch=20 -m cuda -o all_cuda -a libs exe
-
-------------------------------------------------------------------------
-
-To run on just CPUs (without using the GPU or USER-CUDA styles),
-do something like the following:
-
-mpirun -np 1 lmp_linux_double -v x 8 -v y 8 -v z 8 -v t 100 < in.lj
-mpirun -np 12 lmp_linux_double -v x 16 -v y 16 -v z 16 -v t 100 < in.eam
-
-The "xyz" settings determine the problem size.  The "t" setting
-determines the number of timesteps.
-
-These mpirun commands run on a single node.  To run on multiple
-nodes, scale up the "-np" setting.
-
-------------------------------------------------------------------------
-
-To run with the GPU package, do something like the following:
-
-mpirun -np 12 lmp_linux_single -sf gpu -v x 32 -v y 32 -v z 64 -v t 100 < in.lj
-mpirun -np 8 lmp_linux_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 64 -v t 100 < in.eam
-
-The "xyz" settings determine the problem size.  The "t" setting
-determines the number of timesteps.  The "np" setting determines how
-many MPI tasks (per node) the problem will run on.  The numeric
-argument to the "-pk" setting is the number of GPUs (per node); 1 GPU
-is the default.  Note that you can use more MPI tasks than GPUs (per
-node) with the GPU package.
-
-These mpirun commands run on a single node.  To run on multiple nodes,
-scale up the "-np" setting, and control the number of MPI tasks per
-node via a "-ppn" setting.
-
-------------------------------------------------------------------------
-
-To run with the USER-CUDA package, do something like the following:
-
-mpirun -np 1 lmp_linux_single -c on -sf cuda -v x 16 -v y 16 -v z 16 -v t 100 < in.lj
-mpirun -np 2 lmp_linux_double -c on -sf cuda -pk cuda 2 -v x 32 -v y 64 -v z 64 -v t 100 < in.eam
-
-The "xyz" settings determine the problem size.  The "t" setting
-determines the number of timesteps.  The "np" setting determines how
-many MPI tasks (per node) the problem will run on.  The numeric
-argument to the "-pk" setting is the number of GPUs (per node); 1 GPU
-is the default.  Note that the number of MPI tasks must equal the
-number of GPUs (both per node) with the USER-CUDA package.
-
-These mpirun commands run on a single node.  To run on multiple nodes,
-scale up the "-np" setting, and control the number of MPI tasks per
-node via a "-ppn" setting.
-
-------------------------------------------------------------------------
-
-If the script has "titan" in its name, it was run on the Titan
-supercomputer at ORNL.

bench/FERMI/in.eam

@@ -1,24 +0,0 @@
-# bulk Cu lattice
-
-units		metal
-atom_style	atomic
-
-lattice		fcc 3.615
-region		box block 0 $x 0 $y 0 $z
-create_box	1 box
-create_atoms	1 box
-
-pair_style	eam
-pair_coeff	1 1 Cu_u3.eam
-
-velocity	all create 1600.0 376847 loop geom
-
-neighbor	1.0 bin
-neigh_modify    every 1 delay 5 check yes
-
-fix		1 all nve
-
-timestep	0.005
-thermo		50
-
-run		$t

bench/FERMI/in.eam.titan

@@ -1,37 +0,0 @@
-# bulk Cu lattice
-
-newton          off
-package         gpu force/neigh 0 0 1
-processors      * * * grid numa
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	yy equal 20*$y
-variable	zz equal 20*$z
-
-units		metal
-atom_style	atomic
-
-lattice		fcc 3.615
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-create_box	1 box
-create_atoms	1 box
-
-pair_style	eam/gpu
-pair_coeff	1 1 Cu_u3.eam
-
-velocity	all create 1600.0 376847 loop geom
-
-neighbor	1.0 bin
-neigh_modify    every 1 delay 5 check yes
-
-fix		1 all nve
-
-timestep	0.005
-thermo		50
-
-run             15
-run		100

bench/FERMI/in.lj.titan

@@ -1,35 +0,0 @@
-# 3d Lennard-Jones melt
-
-newton          off
-package         gpu force/neigh 0 0 1
-processors      * * * grid numa
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	yy equal 20*$y
-variable	zz equal 20*$z
-
-units		lj
-atom_style	atomic
-
-lattice		fcc 0.8442
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-create_box	1 box
-create_atoms	1 box
-mass		1 1.0
-
-velocity	all create 1.44 87287 loop geom
-
-pair_style	lj/cut/gpu 2.5
-pair_coeff	1 1 1.0 1.0 2.5
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 20 check no
-
-fix		1 all nve
-
-run             15
-run		100

bench/FERMI/in.rhodo

@@ -1,30 +0,0 @@
-# Rhodopsin model
-
-units           real  
-neigh_modify    delay 5 every 1   
-
-atom_style      full  
-atom_modify	map hash
-bond_style      harmonic 
-angle_style     charmm 
-dihedral_style  charmm 
-improper_style  harmonic 
-pair_style      lj/charmm/coul/long 8.0 10.0 
-pair_modify     mix arithmetic 
-kspace_style    pppm 1e-4 
-
-read_data       data.rhodo
-
-replicate	$x $y $z
-
-fix             1 all shake 0.0001 5 0 m 1.0 a 232
-fix             2 all npt temp 300.0 300.0 100.0 &
-		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
-
-special_bonds   charmm
- 
-thermo          50
-thermo_style    multi 
-timestep        2.0
-
-run		$t

bench/FERMI/in.rhodo.scaled.titan

@@ -1,39 +0,0 @@
-# Rhodopsin model
-
-newton          off
-package         gpu force/neigh 0 0 1
-processors      * * * grid numa
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-units           real  
-neigh_modify    delay 5 every 1   
-
-atom_style      full  
-atom_modify	map hash
-bond_style      harmonic 
-angle_style     charmm 
-dihedral_style  charmm 
-improper_style  harmonic 
-pair_style      lj/charmm/coul/long/gpu 8.0 ${cutoff}
-pair_modify     mix arithmetic 
-kspace_style    pppm/gpu 1e-4 
-
-read_data       data.rhodo
-
-replicate	$x $y $z
-
-fix             1 all shake 0.0001 5 0 m 1.0 a 232
-fix             2 all npt temp 300.0 300.0 100.0 &
-		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
-
-special_bonds   charmm
- 
-thermo          50
-# thermo_style    multi 
-timestep        2.0
-
-run             15
-run		100

bench/FERMI/in.rhodo.split.titan

@@ -1,42 +0,0 @@
-# Rhodopsin model
-
-newton          off
-package         gpu force/neigh 0 0 1
-partition	yes 1 processors * * * grid twolevel ${grid} * * * &
-		part 1 2 multiple
-partition	yes 2 processors * * * part 1 2 multiple
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-units           real  
-neigh_modify    delay 5 every 1   
-
-atom_style      full  
-atom_modify	map hash
-bond_style      harmonic 
-angle_style     charmm 
-dihedral_style  charmm 
-improper_style  harmonic 
-pair_style      lj/charmm/coul/long/gpu 8.0 ${cutoff}
-pair_modify     mix arithmetic 
-kspace_style    pppm/gpu 1e-4 
-
-read_data       data.rhodo
-
-replicate	$x $y $z
-
-fix             1 all shake 0.0001 5 0 m 1.0 a 232
-fix             2 all npt temp 300.0 300.0 100.0 &
-		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
-
-special_bonds   charmm
- 
-thermo          50
-# thermo_style    multi 
-timestep        2.0
-
-run_style       verlet/split
-run             15
-run		100

bench/POTENTIALS/CH.airebo

@@ -0,0 +1 @@
+../../potentials/CH.airebo

bench/POTENTIALS/CdTe.bop

@@ -1,44 +0,0 @@
-elements:
-   2
-  48   1.124118e+02 Cd
-  52   1.276030e+02 Te
-
-global:
-  1.00e-05   1.00e-05   1.00e-05   1.00e-05   1.00e-05   1.00e-03   1.00e-05
-  2   9.900000e-01   1.000000e-02
-  2.0 0.625  1
-  1.573798e+01   1.137622e+00   2.087779e+00
-  2.218068e+01   2.689731e+00
-  2.000000e+00   0.000000e+00
-
-ptrs:
-  0.000000e+00   1.000000e+00   4.200000e-01
-  0.000000e+00   1.000000e+00   4.606863e-01
-
-pairs:
-  3.127600e+00   3.127600e+00   3.730300e+00   4.333000e+00
-  3.263155e+00   1.553883e+00   2.800000e+00
-  1.863695e-01   2.383177e-01   9.759853e-02
-  0.000000e+00   5.611298e-01   0.000000e+00
-  1.000000e+00   1.000000e+00   0.000000e+00
-  4.318628e-01   1.500000e+01   1.000000e+06
-  3.127600e+00   3.127600e+00   4.013800e+00   4.900000e+00
-  2.587831e+00   1.287478e+00   2.811251e+00
-  6.314400e-01   8.252896e-01   3.174259e-02
-  0.000000e+00   1.286955e+00   0.000000e+00
-  1.000000e+00   1.000000e+00   0.000000e+00
-  5.000000e-01   0.000000e+00   1.000000e+06
-  3.162600e+00   3.162600e+00   3.804600e+00   4.446500e+00
-  2.458846e+00   1.223306e+00   2.799998e+00
-  8.769118e-01   7.826353e-01   5.312050e-01
-  0.000000e+00   1.014809e+00   0.000000e+00
-  1.000000e+00   1.000000e+00   0.000000e+00
-  3.312269e-01  -2.860190e+00   1.000000e+06
-
-tris:
-  3.968701e-01   8.810195e-01  -2.778897e-01
- -1.007128e-01  10.000000e-01   1.007128e-01
-  2.007322e-01   6.000000e-01   1.992678e-01
-  2.095238e-01   6.000000e-01   1.904762e-01
-  3.928496e-03   9.999272e-01  -3.855665e-03
-  1.171817e-01   8.348116e-01   4.800670e-02

bench/POTENTIALS/CdTe.bop.table

@@ -0,0 +1 @@
+../../potentials/CdTe.bop.table

bench/POTENTIALS/Cu_u3.eam

@@ -1,305 +0,0 @@
-Cu functions (universal 3), SM Foiles et al, PRB, 33, 7983 (1986)
-   29     63.550         3.6150    FCC
-  500  5.0100200400801306e-04  500  1.0000000000000009e-02  4.9499999999999886e+00
-  0.                     -3.1561636903424350e-01 -5.2324876182494506e-01 -6.9740831416804383e-01 -8.5202525457518519e-01
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- -2.0604838665854572e+00 -2.1476762477372944e+00 -2.2327843595560068e+00 -2.3159713409697673e+00 -2.3973797031286352e+00
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-  1.4298804471386687e-05  1.3623982748522034e-05  1.2966096406226424e-05  1.2324739993882115e-05  1.1699517181902770e-05
-  1.1090040573734860e-05  1.0495931521266495e-05  9.9168199435395021e-06  9.3523441487842465e-06  8.8021506596591475e-06
-  8.2658940417265321e-06  7.7432367350197678e-06  7.2338488887770244e-06  6.7374081991923703e-06  6.2535997501888662e-06
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-  3.5992828942305738e-06  3.1956709623667747e-06  2.8024197531120341e-06  2.4192741502208947e-06  2.0459849890155880e-06
-  1.6823089274468580e-06  1.3280083196495871e-06  9.8285109196557868e-07  6.4661062138351467e-07  3.1906561636122974e-07
-  0.                      0.                      0.                      0.                      0.
-
-

bench/POTENTIALS/Cu_u3.eam

@@ -0,0 +1 @@
+../../potentials/Cu_u3.eam

bench/POTENTIALS/Ni.adp

@@ -0,0 +1 @@
+../../potentials/Ni.adp

bench/POTENTIALS/Ni.meam

@@ -1,2 +0,0 @@
-rc = 4.0
-delr = 0.1

bench/POTENTIALS/Ni.meam

@@ -0,0 +1 @@
+../../potentials/Ni.meam

bench/POTENTIALS/README

@@ -5,7 +5,7 @@ the Benchmark page of the LAMMPS WWW site (lammps.sandia.gov/bench).
 
 Examples are shown below of how to run these scripts.  Log files for
 running them on 1 and 4 processors of a Linux box are included in the
-directory.  This assumes that the executable lmp_linux has been built
+directory.  This assumes that the executable lmp_mpi has been built
 with the appropriate packages installed in order to run with a
 particular potential.  For the ReaxFF potential invoked by the in.reax
 script, you should build the Fortran ReaxFF library in lib/reax, using
@@ -15,18 +15,10 @@ the in.reax file.
 Any potential parameter file(s) used by the input scripts are also
 included in this directory.
 
-Note that some of the input scripts read data files of atomic
-coordinates via the "read_data" command.  Those data files are NOT
-included in this directory, to make the LAMMPS download tarball
-smaller.  They are available on the Benchmark page of the LAMMPS WWW
-site (lammps.sandia.gov/bench), via the tarball link in the table
-under the Potentials section.  If you download and unpack the tarball
-for a particular potential, the data file is included.
-
 ------------------------------------------------------------------------
 
-lmp_linux < in.fene
-lmp_linux < in.tersoff
+lmp_mpi -in in.fene
+lmp_mpi -in in.tersoff
 
-mpirun -np 4 lmp_linux < in.fene
-mpirun -np 4 lmp_linux < in.protein
+mpirun -np 4 lmp_mpi -in in.fene
+mpirun -np 4 lmp_mpi -in in.protein

bench/POTENTIALS/Si.sw

@@ -1,17 +0,0 @@
-# Stillinger-Weber parameters for various elements and mixtures
-# multiple entries can be added to this file, LAMMPS reads the ones it needs
-# these entries are in LAMMPS "metal" units:
-#   epsilon = eV; sigma = Angstroms
-#   other quantities are unitless
-
-# format of a single entry (one or more lines):
-#   element 1, element 2, element 3, 
-#   epsilon, sigma, a, lambda, gamma, costheta0, A, B, p, q, tol
-
-# Here are the original parameters in metal units, for Silicon from:
-#
-# Stillinger and Weber,  Phys. Rev. B, v. 31, p. 5262, (1985)
-#
-
-Si Si Si 2.1683  2.0951  1.80  21.0  1.20  -0.333333333333
-         7.049556277  0.6022245584  4.0  0.0 0.0

bench/POTENTIALS/Si.sw

@@ -0,0 +1 @@
+../../potentials/Si.sw

bench/POTENTIALS/Si.tersoff

@@ -1,16 +0,0 @@
-# Tersoff parameters for various elements and mixtures
-# multiple entries can be added to this file, LAMMPS reads the ones it needs
-# these entries are in LAMMPS "metal" units:
-#   A,B = eV; lambda1,lambda2,lambda3 = 1/Angstroms; R,D = Angstroms
-#   other quantities are unitless
-
-# This is the Si parameterization from a particular Tersoff paper:
-# J. Tersoff, PRB, 37, 6991 (1988) 
-# See the SiCGe.tersoff file for different Si variants.
-
-# format of a single entry (one or more lines):
-#   element 1, element 2, element 3, 
-#   m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A
-
-Si  Si   Si  3.0 1.0 1.3258 4.8381 2.0417 0.0000 22.956
-             0.33675  1.3258  95.373  3.0  0.2  3.2394  3264.7

bench/POTENTIALS/Si.tersoff

@@ -0,0 +1 @@
+../../potentials/Si.tersoff

bench/POTENTIALS/data.airebo

@@ -0,0 +1,78 @@
+LAMMPS data file from restart file: timestep = 1, procs = 1
+
+60 atoms
+
+2 atom types
+
+-2.1 2.1 xlo xhi
+-2.1 2.1 ylo yhi
+0 25.5790000000 zlo zhi
+
+Masses
+
+1 12.01
+2 1.00794
+
+Atoms
+
+1 1 0.0000000000 0.0000000000 0.0000000000
+2 2 0.9010066786 -0.6310205743 0.0000000000
+3 2 -0.9010066786 -0.6310205743 0.0000000000
+4 1 0.0000000000 0.8470061967 1.2789591482
+5 2 0.9010066786 1.4780267710 1.2789591482
+6 2 -0.9010066786 1.4780267710 1.2789591482
+7 1 0.0000000000 0.0000000000 2.5579182965
+8 2 0.9010066786 -0.6310205743 2.5579182965
+9 2 -0.9010066786 -0.6310205743 2.5579182965
+10 1 0.0000000000 0.8470061967 3.8368774447
+11 2 0.9010066786 1.4780267710 3.8368774447
+12 2 -0.9010066786 1.4780267710 3.8368774447
+13 1 0.0000000000 0.0000000000 5.1158365929
+14 2 0.9010066786 -0.6310205743 5.1158365929
+15 2 -0.9010066786 -0.6310205743 5.1158365929
+16 1 0.0000000000 0.8470061967 6.3947957411
+17 2 0.9010066786 1.4780267710 6.3947957411
+18 2 -0.9010066786 1.4780267710 6.3947957411
+19 1 0.0000000000 0.0000000000 7.6737548894
+20 2 0.9010066786 -0.6310205743 7.6737548894
+21 2 -0.9010066786 -0.6310205743 7.6737548894
+22 1 0.0000000000 0.8470061967 8.9527140376
+23 2 0.9010066786 1.4780267710 8.9527140376
+24 2 -0.9010066786 1.4780267710 8.9527140376
+25 1 0.0000000000 0.0000000000 10.2316731858
+26 2 0.9010066786 -0.6310205743 10.2316731858
+27 2 -0.9010066786 -0.6310205743 10.2316731858
+28 1 0.0000000000 0.8470061967 11.5106323340
+29 2 0.9010066786 1.4780267710 11.5106323340
+30 2 -0.9010066786 1.4780267710 11.5106323340
+31 1 0.0000000000 0.0000000000 12.7895914823
+32 2 0.9010066786 -0.6310205743 12.7895914823
+33 2 -0.9010066786 -0.6310205743 12.7895914823
+34 1 0.0000000000 0.8470061967 14.0685506305
+35 2 0.9010066786 1.4780267710 14.0685506305
+36 2 -0.9010066786 1.4780267710 14.0685506305
+37 1 0.0000000000 0.0000000000 15.3475097787
+38 2 0.9010066786 -0.6310205743 15.3475097787
+39 2 -0.9010066786 -0.6310205743 15.3475097787
+40 1 0.0000000000 0.8470061967 16.6264689269
+41 2 0.9010066786 1.4780267710 16.6264689269
+42 2 -0.9010066786 1.4780267710 16.6264689269
+43 1 0.0000000000 0.0000000000 17.9054280752
+44 2 0.9010066786 -0.6310205743 17.9054280752
+45 2 -0.9010066786 -0.6310205743 17.9054280752
+46 1 0.0000000000 0.8470061967 19.1843872234
+47 2 0.9010066786 1.4780267710 19.1843872234
+48 2 -0.9010066786 1.4780267710 19.1843872234
+49 1 0.0000000000 0.0000000000 20.4633463716
+50 2 0.9010066786 -0.6310205743 20.4633463716
+51 2 -0.9010066786 -0.6310205743 20.4633463716
+52 1 0.0000000000 0.8470061967 21.7423055198
+53 2 0.9010066786 1.4780267710 21.7423055198
+54 2 -0.9010066786 1.4780267710 21.7423055198
+55 1 0.0000000000 0.0000000000 23.0212646681
+56 2 0.9010066786 -0.6310205743 23.0212646681
+57 2 -0.9010066786 -0.6310205743 23.0212646681
+58 1 0.0000000000 0.8470061967 24.3002238163
+59 2 0.9010066786 1.4780267710 24.3002238163
+60 2 -0.9010066786 1.4780267710 24.3002238163
+

bench/POTENTIALS/data.protein

@@ -0,0 +1 @@
+../data.rhodo

bench/POTENTIALS/data.reax

@@ -0,0 +1,77 @@
+# PETN-I unit cell (space group P4¯21c)
+
+58 atoms
+4 atom types	
+
+0.0 9.491065 xlo xhi
+0.0 9.491065 ylo yhi
+0.0 6.99123 zlo zhi
+
+Masses
+
+1 12.0000
+2 1.0080
+3 15.9990
+4 14.0000
+
+Atoms				
+
+       1        4     0.863455358E-13         1.732320000         4.630010000         0.892350000
+       2        3     0.863455358E-13         2.969950000         4.192650000         1.864890000
+       3        3     0.863455358E-13         1.373230000         3.777920000         0.096380000
+       4        3     0.863455358E-13         1.320990000         5.707670000         1.097690000
+       5        2     0.863455358E-13         2.884650000         5.896680000         3.317770000
+       6        2     0.863455358E-13         3.827980000         6.263410000         2.178970000
+       7        1     0.863455358E-13         5.909570000         4.291490000         2.540550000
+       8        4     0.863455358E-13         7.726490000         4.862430000         0.940970000
+       9        3     0.863455358E-13         6.554310000         5.406520000         1.911000000
+      10        3     0.863455358E-13         8.126280000         5.645810000         0.107790000
+      11        3     0.863455358E-13         8.070620000         3.697510000         1.039000000
+      12        2     0.863455358E-13         6.526620000         3.514030000         3.084250000
+      13        2     0.863455358E-13         5.500710000         3.475690000         1.894580000
+      14        1     0.863455358E-13         4.305160000         3.663690000         4.373270000
+      15        4     0.863455358E-13         4.891690000         1.789930000         5.975440000
+      16        3     0.863455358E-13         5.388500000         3.060710000         5.142620000
+      17        3     0.863455358E-13         5.709330000         1.320000000         6.723350000
+      18        3     0.863455358E-13         3.766570000         1.413750000         5.785210000
+      19        2     0.863455358E-13         3.859620000         2.802480000         3.723820000
+      20        2     0.863455358E-13         3.303550000         3.975170000         4.811250000
+      21        1     0.863455358E-13         5.224790000         5.919230000         4.377750000
+      22        4     0.863455358E-13         4.644030000         7.696520000         6.100900000
+      23        3     0.863455358E-13         4.146850000         6.645990000         4.999010000
+      24        3     0.863455358E-13         3.883440000         7.981690000         7.010630000
+      25        3     0.863455358E-13         5.786660000         8.025100000         5.996670000
+      26        2     0.863455358E-13         5.906020000         6.611630000         3.756700000
+      27        2     0.863455358E-13         6.077870000         5.531160000         4.915880000
+      28        1     0.863455358E-13         3.552720000         5.288480000         2.602930000
+      29        1     0.863455358E-13         4.757460000         4.786420000         3.446050000
+      30           1     0.863455358E-13        10.623310000        10.011360000         7.901960000
+      31           4     0.863455358E-13        12.340670000         9.278570000         9.658210000
+      32           3     0.863455358E-13        11.173160000         8.908900000         8.591070000
+      33           3     0.863455358E-13        12.634410000         8.404450000        10.434380000
+      34           3     0.863455358E-13        12.808850000        10.398130000         9.459970000
+      35           2     0.863455358E-13        11.336750000        10.607430000         7.235710000
+      36           2     0.863455358E-13        10.314820000        10.962610000         8.407430000
+      37           1     0.863455358E-13         8.366600000         8.930150000         7.823850000
+      38           4     0.863455358E-13         6.680390000         9.584210000         9.655230000
+      39           3     0.863455358E-13         7.796220000        10.005630000         8.544820000
+      40           3     0.863455358E-13         6.439700000        10.424020000        10.460020000
+      41           3     0.863455358E-13         6.239040000         8.465520000         9.442190000
+      42           2     0.863455358E-13         7.687150000         8.335850000         7.127770000
+      43           2     0.863455358E-13         8.728770000         7.913540000         8.234250000
+      44           1     0.863455358E-13        10.045160000         8.333570000         6.100600000
+      45           4     0.863455358E-13         9.373710000         6.690820000         4.302840000
+      46           3     0.863455358E-13         8.940460000         7.828420000         5.375480000
+      47           3     0.863455358E-13         8.526330000         6.420240000         3.522270000
+      48           3     0.863455358E-13        10.474540000         6.234360000         4.499290000
+      49           2     0.863455358E-13        10.719930000         7.694230000         6.776840000
+      50           2     0.863455358E-13        10.913160000         8.873910000         5.574960000
+      51           1     0.863455358E-13         8.940970000        10.671300000         6.139780000
+      52           4     0.863455358E-13         9.619090000        12.332990000         4.329510000
+      53           3     0.863455358E-13        10.055950000        11.263880000         5.506630000
+      54           3     0.863455358E-13        10.434090000        12.566040000         3.507610000
+      55           3     0.863455358E-13         8.506740000        12.768990000         4.512780000
+      56           2     0.863455358E-13         8.359930000        11.424490000         6.758000000
+      57           2     0.863455358E-13         8.018410000        10.320200000         5.568000000
+      58           1     0.863455358E-13         9.486900000         9.503450000         6.990810000
+

bench/POTENTIALS/data.rebo

@@ -0,0 +1 @@
+data.airebo

bench/POTENTIALS/in.bop

@@ -13,11 +13,11 @@ create_box	2 box
 create_atoms	1 box basis 2 2 basis 4 2 basis 6 2 basis 8 2
 
 pair_style	bop
-pair_coeff	* * CdTe.bop Cd Te
+pair_coeff	* * CdTe.bop.table Cd Te
 mass		1 112.4
 mass		2 127.6
 
-communicate	single cutoff 14.7
+comm_modify	cutoff 14.7
 
 velocity	all create 1000.0 376847 loop geom
 

bench/POTENTIALS/in.eff

@@ -10,7 +10,7 @@ pair_coeff	* *
 
 neigh_modify    one 6000 page 60000
 
-communicate	single vel yes
+comm_modify	vel yes
 
 compute         effTemp all temp/eff
 

bench/POTENTIALS/in.granular

@@ -4,7 +4,7 @@ units		lj
 atom_style	sphere
 boundary	p p fs
 newton		off
-communicate	single vel yes
+comm_modify	vel yes
 
 read_data	data.granular
 

bench/POTENTIALS/in.meam

@@ -1,24 +0,0 @@
-# bulk Ni in MEAM
-
-units		metal
-atom_style	atomic
-
-lattice		fcc 3.52
-region		box block 0 20 0 20 0 20
-create_box	1 box
-create_atoms	1 box
-
-pair_style	meam
-pair_coeff	* * library.meam Ni4 Ni.meam Ni4
-
-velocity	all create 1600.0 376847 loop geom
-
-neighbor	1.0 bin
-neigh_modify    delay 5 every 1
-
-fix		1 all nve
-
-timestep	0.005
-thermo		50
-
-run		100

bench/POTENTIALS/in.meamc

@@ -0,0 +1,24 @@
+# bulk Ni in MEAM
+
+units		metal
+atom_style	atomic
+
+lattice		fcc 3.52
+region		box block 0 20 0 20 0 20
+create_box	1 box
+create_atoms	1 box
+
+pair_style	meam/c
+pair_coeff	* * library.meam Ni4 Ni.meam Ni4
+
+velocity	all create 1600.0 376847 loop geom
+
+neighbor	1.0 bin
+neigh_modify    delay 5 every 1
+
+fix		1 all nve
+
+timestep	0.005
+thermo		50
+
+run		100

bench/POTENTIALS/in.reax

@@ -1,22 +0,0 @@
-# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
-
-units		real
-atom_style	charge
-
-read_data	data.reax
-
-#replicate	7 8 10
-replicate	7 8 5
-
-velocity	all create 300.0 9999
-
-pair_style	reax
-pair_coeff      * * ffield.reax 1 2 3 4
-
-timestep	0.1
-fix		2 all nve 
-
-thermo		10
-thermo_style	custom step temp ke pe pxx pyy pzz etotal
-
-run		100

bench/POTENTIALS/in.reaxc

@@ -10,7 +10,7 @@ replicate	7 8 10
 velocity	all create 300.0 9999
 
 pair_style	reax/c NULL
-pair_coeff      * * ffield.reax 1 2 3 4
+pair_coeff      * * ffield.reax C H O N
 
 timestep	0.1
 fix		1 all nve 

bench/POTENTIALS/library.meam

@@ -1,162 +0,0 @@
-# meam data from vax files fcc,bcc,dia    11/4/92
-# elt        lat     z       ielement     atwt
-# alpha      b0      b1      b2           b3    alat    esub    asub
-# t0         t1              t2           t3            rozero  ibar
-
-'Sn5'       'dia'   4.      50           118.
-5.09        5.00   16.0    04.0          5.0  6.483   3.14     1.00
-1.0         2.00            5.756        -0.30         1.      0
-'Sn'        'dia'   4.      50           118.
-5.09        5.42    8.0     5.0          6.0  6.483   3.14     1.12
-1.0         3.0             5.707        +0.30         1.      0
-'Cu'        'fcc'   12.     29           63.54
-5.10570729  3.634   2.20    6            2.20  3.62    3.54    1.07
-1.0         3.13803254      2.49438711   2.95269237    1.      0
-'Ag'        'fcc'   12.     47           107.870
-5.89222008  4.456   2.20    6            2.20  4.08    2.85    1.06
-1.0         5.54097609      2.45015783   1.28843988    1.      0
-'Au'        'fcc'   12.     79           196.967
-6.34090112  5.449   2.20    6            2.20  4.07    3.93    1.04
-1.0         1.58956328      1.50776392   2.60609758    1.      0
-'Ni1'        'fcc'   12.     28           58.71
-4.99        2.45    2.20    6            2.20  3.52    4.45    1.10
-1.0         3.57            1.60         3.70           1.0    0
-'Ni2'        'fcc'   12.     28           58.71
-4.99        2.45    2.20    6            2.20  3.52    4.45    1.10
-1.0         3.57            1.60         3.70           1.0    3
-'Ni3'        'fcc'   12.     28           58.71
-4.99        2.45    1.50    6            1.50  3.52    4.45    1.10
-1.0         3.57            1.60         3.70           1.0    3
-'Ni4'        'fcc'   12.     28           58.71
-4.99        2.45    1.50    6            1.50  3.52    4.45    1.10
-1.0         3.57            1.60         3.70           1.0    0
-'Ni'        'fcc'   12.     28           58.71
-4.99        2.64    1.50    4.50         1.50  3.52    4.45    1.10
-1.0         1.692           4.987        3.683          1.0    1 
-'Nix'        'fcc'   12.     28           58.71
-4.99        2.64    1.50    4.50         1.50  3.52    4.45    1.10
-1.0         0.00            0.000        3.683          1.0    1 
-'Ni'        'fcc'   12.     28           58.71
-4.99        3.25    0.80    4            1.50  3.52    4.45    1.07
-1.0         -4.052          13.14        3.786		1.0    1
-'Pd'        'fcc'   12.     46           106.4
-6.43230473  4.975   2.20    6            2.20  3.89    3.91    1.01
-1.0         2.33573516      1.38343023   4.47989049    1.      0
-'Pt'        'fcc'   12.     78           195.09
-6.44221724  4.673   2.20    6            2.20  3.92    5.77    1.04
-1.0         2.73335406      -1.3759593   3.29322278    1.      0
-'Al'        'fcc'   12.     13           26.9815
-4.61        2.21    2.20    6.0          2.20  4.05    3.58    1.07
-1.0         -1.78           -2.21        8.01          0.6     0
-'Al'        'fcc'   12.     13           26.9815
-4.69        1.56    4.00    5.5          0.60  4.05    3.36    1.09
-1.0         -0.251          -3.450       8.298         0.6     1
-'Al'        'fcc'   12.     13           26.9815
-4.69	    1.58    1.00    6.0          0.60  4.05    3.36    1.09
-1.0         -0.808          -2.614       8.298         0.6     1
-'Pb'        'fcc'   12.     82           207.19
-6.0564428   5.306   2.20    6            2.20  4.95    2.04    1.01
-1.0         2.74022352      3.06323991   1.2           1.      0
-'Rh'        'fcc'   12.     45           102.905
-6.0045385   1.131   1.00    2            1.00  3.8     5.75    1.05
-1.0         2.9900          4.60231784   4.8           1.      0
-'Ir'        'fcc'   12.     77           192.2
-6.52315787  1.13    1.00    2            1.00  3.84    6.93    1.05
-1.0         1.50000         8.09942666   4.8           1.      0
-'Li'        'bcc'   8.      3            6.939
-2.97244804  1.425   1.00    1.00169907   1.00  3.509   1.65    0.87
-1.0         0.26395017      0.44431129   -0.2          1.      0 
-'Na'        'bcc'   8.      11           22.9898
-3.64280541  2.313   1.00    1.00173951   1.00  4.291   1.13    0.9
-1.0         3.55398839      0.68807569   -0.2          1.      0
-'K'         'bcc'   8.      19           39.102
-3.90128376  2.687   1.00    1.00186667   1.00  5.344   0.94    0.92
-1.0         5.09756981      0.69413264   -0.2          1.      0
-'V'         'bcc'   8.      23           50.942
-4.83265262  4.113   1.00    1.00095022   1.00  3.04    5.3     1
-1.0         4.20161301      4.09946561   -1            1.      0
-'Nb'        'bcc'   8.      41           92.906
-4.79306197  4.374   1.00    1.00101441   1.00  3.301   7.47    1
-1.0         3.75762849      3.82514598   -1            1.      0
-'Ta'        'bcc'   8.      73           180.948
-4.89528669  3.709   1.00    1.00099783   1.00  3.303   8.09    0.99
-1.0         6.08617812      3.35255804   -2.9          1.      0
-'Cr'        'bcc'   8.      24           51.996
-5.12169218  3.224   1.00    1.00048646   1.00  2.885   4.1     0.94
-1.0         -0.207535       12.2600006   -1.9          1.      0
-'Mo'        'bcc'   8.      42           95.94
-5.84872871  4.481   1.00    1.00065204   1.00  3.15    6.81    0.99
-1.0         3.47727181      9.48582009   -2.9          1.      0
-'W'         'bcc'   8.      74           183.85
-5.62777409  3.978   1.00    1.00065894   1.00  3.165   8.66    0.98
-1.0         3.16353338      8.24586928   -2.7          1.      0
-'WL'	    'bcc'   8	    74	         183.85
-5.6831	    6.54    1	    1	         1     3.1639  8.66    0.4
-1	    -0.6	    0.3	         -8.7	       1       3
-'Fe'        'bcc'   8.      26           55.847
-5.07292627  2.935   1.00    1.00080073   1.00  2.866   4.29    0.89
-1.0         5.13579244      4.12042448   -2.7          1.      0
-'Si'        'dia'   4.      14           28.086
-4.87        4.8     4.8     4.8          4.8   5.431   4.63    1.
-1.0         3.30            5.105        -0.80         1.      1
-'Si97'        'dia'   4.      14           28.086
-4.87        4.4     5.5     5.5          5.5   5.431   4.63    1.
-1.0         3.13            4.47         -1.80         2.05    0
-'Si92'        'dia'   4.      14           28.086
-4.87        4.4     5.5     5.5          5.5   5.431   4.63    1.
-1.0         3.13            4.47        -1.80          2.35    0
-'Six'	    'dia'   4	    14	         28.086
-4.87	    4.4	    5.5	    5.5	         5.5   5.431   4.63    1.0
-1.0	    2.05            4.47         -1.8	       2.05     0
-'Sixb'	    'dia'   4	    14	         28.086
-4.87	    4.4	    5.5	    5.5	         5.5   5.431   4.63    1.0
-1.0	    2.05            4.47         -1.8	       2.5     0
-'Mg'       'hcp'   12.      12           24.305
-5.45        2.70    0.0     0.35         3.0   3.20    1.55    1.11
-1.0         8.00            04.1         -02.0         1.0     0
-'C'         'dia'   4.      6            12.0111
-4.38        4.10    4.200   5.00         3.00  3.567   7.37    1.000
-1.0         5.0             9.34         -1.00         2.25    1
-'C'         'dia'   4.      6            12.0111
-4.38        5.20    3.87    4.00         4.50  3.567   7.37    1.278
-1.0         15.             2.09         -6.00         2.5     1
-'C'         'dia'   4.      6            12.0111
-4.38        4.50    4.00    3.50         4.80  3.567   7.37    1.00
-1.0         10.5            1.54         -8.75         3.2     1 
-'C'         'dia'   4.      6            12.0111
-4.38        3.30    2.80    1.50         3.20  3.567   7.37    1.00 
-1.0         10.3            1.54         -8.80         2.5     1 
-'C'         'dia'   4.      6            12.0111
-4.38        4.60    3.45    4.00         4.20  3.567   7.37    1.061
-1.0         15.0            1.74         -8.00         2.5     1
-'C'         'dia'   4.      6            12.0111
-4.38        4.50    4.00    3.50         4.80  3.567   7.37    1.00
-1.0         10.5            1.54         -8.75         3.2     1
-'h'         'dim'   1.      1            1.0079
-2.96        2.70    3.5     3.4          3.4   0.74    2.235   2.27
-1.0         0.19            0.00         0.00          20.00    0
-'h'         'dim'   1.      1            1.0079
-2.96        2.00    4.0     4.0          0.0   0.74    2.235   1.00
-1.0         -0.60           -0.80        -0.0          01.0    1
-'H'         'dim'   1.      1            1.0079
-2.96        2.96    3.0     3.0          3.0   0.74    2.235   2.50
-1.0         0.20            -0.10        0.0           0.5     0
-'H'         'dim'   1.      1            1.0079
-2.96        2.0     3.0     4.0          0.0   0.74    2.225   1.00
-1.0         -0.5            -1.00        0.0           0.15    1
-'H'         'dim'   1.      1            1.0079
-2.96        2.00    2.0     2.0          2.0   0.74    2.235   1.00
-1.0         -0.60           -0.80        -0.0          01.0    2
-'Hni'       'dim'   1.      1            1.0079
-2.96        2.96    3.0     3.0          3.0   0.74    2.235   2.50
-1.0         0.2             -0.1         0.0           0.5     0
-'Hni'         'dim'   1.      1            1.0079
-2.96        2.96    3.0     2.0          3.0   0.74    2.235   36.4
-1.0         0.2             6.0         0.0           22.8     0
-'Vac'       'fcc'   12.     1            1.
-0           0       0.0     0            0.0   1E+08   0       1  
-0           0               0             0             1.     0
-'zz'        'zzz'   99.     1            1.
-0           0       0.0     0            0.0    0.     0.     0.
-0           0               0             0             1.     0
-                                 

bench/POTENTIALS/library.meam

@@ -0,0 +1 @@
+../../potentials/library.meam

bench/POTENTIALS/log.16Mar18.adp.1

@@ -0,0 +1,75 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# bulk Ni in ADP
+
+units		metal
+atom_style	atomic
+
+lattice		fcc 3.52
+Lattice spacing in x,y,z = 3.52 3.52 3.52
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  Time spent = 0.00184107 secs
+
+pair_style	adp
+pair_coeff	* * Ni.adp Ni
+
+velocity	all create 1600.0 376847 loop geom
+
+neighbor	1.0 bin
+neigh_modify    delay 5 every 1
+
+fix		1 all nve
+
+timestep	0.005
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.168
+  ghost atom cutoff = 6.168
+  binsize = 3.084, bins = 23 23 23
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair adp, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 27.56 | 27.56 | 27.56 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1600      -142400            0   -135782.09    20259.105 
+     100    793.05485   -139023.13            0    -135742.9    32175.694 
+Loop time of 11.9854 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 3.604 ns/day, 6.659 hours/ns, 8.344 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 11.447     | 11.447     | 11.447     |   0.0 | 95.51
+Neigh   | 0.48465    | 0.48465    | 0.48465    |   0.0 |  4.04
+Comm    | 0.019317   | 0.019317   | 0.019317   |   0.0 |  0.16
+Output  | 0.00011063 | 0.00011063 | 0.00011063 |   0.0 |  0.00
+Modify  | 0.025319   | 0.025319   | 0.025319   |   0.0 |  0.21
+Other   |            | 0.009125   |            |       |  0.08
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    19911 ave 19911 max 19911 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.33704e+06 ave 1.33704e+06 max 1.33704e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1337035
+Ave neighs/atom = 41.7823
+Neighbor list builds = 13
+Dangerous builds = 0
+
+Total wall time: 0:00:12

bench/POTENTIALS/log.16Mar18.adp.4

@@ -0,0 +1,75 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# bulk Ni in ADP
+
+units		metal
+atom_style	atomic
+
+lattice		fcc 3.52
+Lattice spacing in x,y,z = 3.52 3.52 3.52
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  Time spent = 0.000586033 secs
+
+pair_style	adp
+pair_coeff	* * Ni.adp Ni
+
+velocity	all create 1600.0 376847 loop geom
+
+neighbor	1.0 bin
+neigh_modify    delay 5 every 1
+
+fix		1 all nve
+
+timestep	0.005
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.168
+  ghost atom cutoff = 6.168
+  binsize = 3.084, bins = 23 23 23
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair adp, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 12.45 | 12.45 | 12.45 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1600      -142400            0   -135782.09    20259.105 
+     100    793.05485   -139023.13            0    -135742.9    32175.694 
+Loop time of 3.49752 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 12.352 ns/day, 1.943 hours/ns, 28.592 timesteps/s
+99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.3203     | 3.3261     | 3.3317     |   0.3 | 95.10
+Neigh   | 0.12544    | 0.12594    | 0.12634    |   0.1 |  3.60
+Comm    | 0.024059   | 0.03001    | 0.035574   |   2.9 |  0.86
+Output  | 4.8161e-05 | 6.8128e-05 | 0.00011802 |   0.0 |  0.00
+Modify  | 0.010666   | 0.010841   | 0.011109   |   0.2 |  0.31
+Other   |            | 0.00457    |            |       |  0.13
+
+Nlocal:    8000 ave 8044 max 7960 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Nghost:    9131 ave 9171 max 9087 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+Neighs:    334259 ave 336108 max 332347 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+
+Total # of neighbors = 1337035
+Ave neighs/atom = 41.7823
+Neighbor list builds = 13
+Dangerous builds = 0
+
+Total wall time: 0:00:03

bench/POTENTIALS/log.16Mar18.airebo.1

@@ -0,0 +1,87 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# AIREBO polyethelene benchmark
+
+units		    metal
+atom_style	    atomic
+
+read_data	    data.airebo
+  orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  60 atoms
+
+replicate	    17 16 2
+  orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
+  1 by 1 by 1 MPI processor grid
+  32640 atoms
+  Time spent = 0.00154901 secs
+
+neighbor	    0.5 bin
+neigh_modify	    delay 5 every 1
+
+pair_style	    airebo 3.0 1 1
+pair_coeff	    * * CH.airebo C H
+
+velocity	    all create 300.0 761341
+
+fix		    1 all nve
+timestep	    0.0005
+
+thermo		    10
+run		    100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.7
+  ghost atom cutoff = 10.7
+  binsize = 5.35, bins = 14 13 10
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair airebo, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 106.4 | 106.4 | 106.4 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          300    -139299.7            0   -138034.03    7998.7287 
+      10    161.33916   -138711.85            0   -138031.17    33242.273 
+      20    208.59505   -138911.77            0   -138031.73   -3199.2371 
+      30    139.73485   -138617.76            0   -138028.23    10890.529 
+      40    142.15332   -138628.03            0    -138028.3    14614.022 
+      50    114.21945   -138509.87            0   -138027.98    24700.885 
+      60     164.9432   -138725.08            0   -138029.19    35135.722 
+      70    162.14928   -138714.86            0   -138030.77    5666.4609 
+      80    157.17575   -138694.81            0    -138031.7    19838.161 
+      90    196.16354   -138859.65            0   -138032.05   -7942.9718 
+     100    178.30378    -138783.8            0   -138031.55     31012.15 
+Loop time of 60.9424 on 1 procs for 100 steps with 32640 atoms
+
+Performance: 0.071 ns/day, 338.569 hours/ns, 1.641 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 55.299     | 55.299     | 55.299     |   0.0 | 90.74
+Neigh   | 5.5777     | 5.5777     | 5.5777     |   0.0 |  9.15
+Comm    | 0.027658   | 0.027658   | 0.027658   |   0.0 |  0.05
+Output  | 0.0011463  | 0.0011463  | 0.0011463  |   0.0 |  0.00
+Modify  | 0.024684   | 0.024684   | 0.024684   |   0.0 |  0.04
+Other   |            | 0.012      |            |       |  0.02
+
+Nlocal:    32640 ave 32640 max 32640 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    48190 ave 48190 max 48190 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  2.22179e+07 ave 2.22179e+07 max 2.22179e+07 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 22217870
+Ave neighs/atom = 680.695
+Neighbor list builds = 8
+Dangerous builds = 0
+Total wall time: 0:01:02

bench/POTENTIALS/log.16Mar18.airebo.4

@@ -0,0 +1,87 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# AIREBO polyethelene benchmark
+
+units		    metal
+atom_style	    atomic
+
+read_data	    data.airebo
+  orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
+  1 by 1 by 4 MPI processor grid
+  reading atoms ...
+  60 atoms
+
+replicate	    17 16 2
+  orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
+  2 by 2 by 1 MPI processor grid
+  32640 atoms
+  Time spent = 0.00070262 secs
+
+neighbor	    0.5 bin
+neigh_modify	    delay 5 every 1
+
+pair_style	    airebo 3.0 1 1
+pair_coeff	    * * CH.airebo C H
+
+velocity	    all create 300.0 761341
+
+fix		    1 all nve
+timestep	    0.0005
+
+thermo		    10
+run		    100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.7
+  ghost atom cutoff = 10.7
+  binsize = 5.35, bins = 14 13 10
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair airebo, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 29.37 | 29.75 | 30.13 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          300    -139299.7            0   -138034.03    7998.7287 
+      10    161.33916   -138711.85            0   -138031.17    33242.273 
+      20    208.59505   -138911.77            0   -138031.73   -3199.2371 
+      30    139.73485   -138617.76            0   -138028.23    10890.529 
+      40    142.15332   -138628.03            0    -138028.3    14614.022 
+      50    114.21945   -138509.87            0   -138027.98    24700.885 
+      60     164.9432   -138725.08            0   -138029.19    35135.722 
+      70    162.14928   -138714.86            0   -138030.77    5666.4609 
+      80    157.17575   -138694.81            0    -138031.7    19838.161 
+      90    196.16354   -138859.65            0   -138032.05   -7942.9718 
+     100    178.30378    -138783.8            0   -138031.55     31012.15 
+Loop time of 16.768 on 4 procs for 100 steps with 32640 atoms
+
+Performance: 0.258 ns/day, 93.156 hours/ns, 5.964 timesteps/s
+99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 14.538     | 14.589     | 14.654     |   1.3 | 87.00
+Neigh   | 1.8853     | 1.8992     | 1.9159     |   0.8 | 11.33
+Comm    | 0.18073    | 0.25896    | 0.31361    |  10.6 |  1.54
+Output  | 0.00050807 | 0.0040419  | 0.0077746  |   5.6 |  0.02
+Modify  | 0.0094635  | 0.0096973  | 0.0099616  |   0.2 |  0.06
+Other   |            | 0.007481   |            |       |  0.04
+
+Nlocal:    8160 ave 8174 max 8146 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Nghost:    22614.5 ave 22629 max 22601 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  5.55447e+06 ave 5.56557e+06 max 5.54193e+06 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+
+Total # of neighbors = 22217870
+Ave neighs/atom = 680.695
+Neighbor list builds = 8
+Dangerous builds = 0
+Total wall time: 0:00:17

bench/POTENTIALS/log.16Mar18.bop.1

@@ -0,0 +1,82 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# bulk CdTe via BOP
+
+units		metal
+atom_style	atomic
+
+lattice		custom 6.82884 		basis 0.0 0.0 0.0 basis 0.25 0.25 0.25 		basis 0.0 0.5 0.5 basis 0.25 0.75 0.75 		basis 0.5 0.0 0.5 basis 0.75 0.25 0.75 		basis 0.5 0.5 0.0 basis 0.75 0.75 0.25
+Lattice spacing in x,y,z = 6.82884 6.82884 6.82884
+region		box block 0 20 0 20 0 10
+create_box	2 box
+Created orthogonal box = (0 0 0) to (136.577 136.577 68.2884)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box basis 2 2 basis 4 2 basis 6 2 basis 8 2
+Created 32000 atoms
+  Time spent = 0.00191426 secs
+
+pair_style	bop
+pair_coeff	* * CdTe.bop.table Cd Te
+Reading potential file CdTe.bop.table with DATE: 2012-06-25
+Reading potential file CdTe.bop.table with DATE: 2012-06-25
+mass		1 112.4
+mass		2 127.6
+
+comm_modify	cutoff 14.7
+
+velocity	all create 1000.0 376847 loop geom
+
+neighbor	0.1 bin
+neigh_modify    delay 5 every 1
+
+fix		1 all nve
+
+timestep	0.001
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5
+  ghost atom cutoff = 14.7
+  binsize = 2.5, bins = 55 55 28
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair bop, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 19.39 | 19.39 | 19.39 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1000   -69539.487            0   -65403.292    3473.2595 
+     100    572.16481   -67769.936            0    -65403.35    1838.6993 
+Loop time of 24.1696 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 0.357 ns/day, 67.138 hours/ns, 4.137 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 23.355     | 23.355     | 23.355     |   0.0 | 96.63
+Neigh   | 0.7545     | 0.7545     | 0.7545     |   0.0 |  3.12
+Comm    | 0.026978   | 0.026978   | 0.026978   |   0.0 |  0.11
+Output  | 0.0001111  | 0.0001111  | 0.0001111  |   0.0 |  0.00
+Modify  | 0.024145   | 0.024145   | 0.024145   |   0.0 |  0.10
+Other   |            | 0.009326   |            |       |  0.04
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    35071 ave 35071 max 35071 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  141288 ave 141288 max 141288 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 141288
+Ave neighs/atom = 4.41525
+Neighbor list builds = 14
+Dangerous builds = 0
+Total wall time: 0:00:24

bench/POTENTIALS/log.16Mar18.bop.4

@@ -0,0 +1,82 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# bulk CdTe via BOP
+
+units		metal
+atom_style	atomic
+
+lattice		custom 6.82884 		basis 0.0 0.0 0.0 basis 0.25 0.25 0.25 		basis 0.0 0.5 0.5 basis 0.25 0.75 0.75 		basis 0.5 0.0 0.5 basis 0.75 0.25 0.75 		basis 0.5 0.5 0.0 basis 0.75 0.75 0.25
+Lattice spacing in x,y,z = 6.82884 6.82884 6.82884
+region		box block 0 20 0 20 0 10
+create_box	2 box
+Created orthogonal box = (0 0 0) to (136.577 136.577 68.2884)
+  2 by 2 by 1 MPI processor grid
+create_atoms	1 box basis 2 2 basis 4 2 basis 6 2 basis 8 2
+Created 32000 atoms
+  Time spent = 0.000597477 secs
+
+pair_style	bop
+pair_coeff	* * CdTe.bop.table Cd Te
+Reading potential file CdTe.bop.table with DATE: 2012-06-25
+Reading potential file CdTe.bop.table with DATE: 2012-06-25
+mass		1 112.4
+mass		2 127.6
+
+comm_modify	cutoff 14.7
+
+velocity	all create 1000.0 376847 loop geom
+
+neighbor	0.1 bin
+neigh_modify    delay 5 every 1
+
+fix		1 all nve
+
+timestep	0.001
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5
+  ghost atom cutoff = 14.7
+  binsize = 2.5, bins = 55 55 28
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair bop, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 8.497 | 8.497 | 8.497 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1000   -69539.487            0   -65403.292    3473.2595 
+     100    572.16481   -67769.936            0    -65403.35    1838.6993 
+Loop time of 6.50033 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 1.329 ns/day, 18.056 hours/ns, 15.384 timesteps/s
+99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.7879     | 5.975      | 6.1607     |   5.4 | 91.92
+Neigh   | 0.27603    | 0.27621    | 0.27647    |   0.0 |  4.25
+Comm    | 0.049869   | 0.23531    | 0.42241    |  27.2 |  3.62
+Output  | 4.9829e-05 | 5.9724e-05 | 8.5592e-05 |   0.0 |  0.00
+Modify  | 0.0089927  | 0.0090921  | 0.0092406  |   0.1 |  0.14
+Other   |            | 0.004665   |            |       |  0.07
+
+Nlocal:    8000 ave 8006 max 7994 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    15171 ave 15177 max 15165 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  35322 ave 35412 max 35267 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+
+Total # of neighbors = 141288
+Ave neighs/atom = 4.41525
+Neighbor list builds = 14
+Dangerous builds = 0
+Total wall time: 0:00:06

bench/POTENTIALS/log.16Mar18.comb.1

@@ -0,0 +1,94 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# SiO2 for COMB potential
+
+units		metal
+atom_style	charge
+
+read_data  	data.comb
+  triclinic box = (0 0 0) to (74.58 74.58 83.064) with tilt (0 0 0)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  32400 atoms
+
+mass		1 28.0855
+group    	type1 type 1
+10800 atoms in group type1
+compute   	charge1 type1 property/atom q
+compute   	q1 type1 reduce ave c_charge1
+mass		2 16.00
+group    	type2 type 2
+21600 atoms in group type2
+compute   	charge2 type2 property/atom q
+compute   	q2 type2 reduce ave c_charge2
+
+pair_style	comb
+pair_coeff	* * ffield.comb Si O
+neighbor	0.5 bin
+neigh_modify	every 10 delay 0 check yes
+
+timestep        0.0002
+
+thermo_style	custom step temp etotal pe evdwl ecoul c_q1 c_q2 press vol
+thermo_modify	norm yes
+velocity  	all create 300.0 3482028
+fix		1 all nvt temp 300.0 300.0 0.1
+fix  		2 all qeq/comb 10 0.001 file fq.out
+
+thermo   	10
+run    		100
+Neighbor list info ...
+  update every 10 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12.5
+  ghost atom cutoff = 12.5
+  binsize = 6.25, bins = 12 12 14
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair comb, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 106.2 | 106.2 | 106.2 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Press Volume 
+       0          300   -6.8032038   -6.8419806    4.6274455   -11.469426    2.8875895   -1.4437947    13386.415    462016.62 
+      10    273.21913   -6.8032489   -6.8385642    4.6221303   -11.460695    2.8872353   -1.4436176    13076.442    462016.62 
+      20     242.0051    -6.803367   -6.8346477    4.6208311   -11.455479    2.8870176   -1.4435087    12080.423    462016.62 
+      30     214.5618   -6.8034588   -6.8311922     4.620067   -11.451259    2.8870575   -1.4435287    10307.876    462016.62 
+      40    198.14521   -6.8035174   -6.8291289    4.6202931   -11.449422    2.8874526   -1.4437263     7765.732    462016.62 
+      50    197.15561   -6.8035468   -6.8290303    4.6219602   -11.450991    2.8883366   -1.4441683    4432.7134    462016.62 
+      60    212.04532   -6.8035584   -6.8309666    4.6260476   -11.457014    2.8896425   -1.4448212    324.71226    462016.62 
+      70    239.37999   -6.8035665   -6.8345078    4.6322984   -11.466806    2.8912723   -1.4456361   -4497.0492    462016.62 
+      80    272.98301    -6.803583   -6.8388677    4.6404093   -11.479277    2.8932784   -1.4466392   -9896.1704    462016.62 
+      90    305.77651   -6.8036184   -6.8431419    4.6512736   -11.494415    2.8953109   -1.4476554   -15675.983    462016.62 
+     100    331.58255   -6.8036753   -6.8465344     4.662727   -11.509261     2.897273   -1.4486365   -21675.515    462016.62 
+Loop time of 517.206 on 1 procs for 100 steps with 32400 atoms
+
+Performance: 0.003 ns/day, 7183.417 hours/ns, 0.193 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 114.18     | 114.18     | 114.18     |   0.0 | 22.08
+Neigh   | 0.47558    | 0.47558    | 0.47558    |   0.0 |  0.09
+Comm    | 0.030611   | 0.030611   | 0.030611   |   0.0 |  0.01
+Output  | 0.0024922  | 0.0024922  | 0.0024922  |   0.0 |  0.00
+Modify  | 402.51     | 402.51     | 402.51     |   0.0 | 77.82
+Other   |            | 0.006137   |            |       |  0.00
+
+Nlocal:    32400 ave 32400 max 32400 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    42518 ave 42518 max 42518 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  1.85317e+07 ave 1.85317e+07 max 1.85317e+07 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18531740
+Ave neighs/atom = 571.967
+Neighbor list builds = 1
+Dangerous builds = 0
+Total wall time: 0:09:18

bench/POTENTIALS/log.16Mar18.comb.4

@@ -0,0 +1,94 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# SiO2 for COMB potential
+
+units		metal
+atom_style	charge
+
+read_data  	data.comb
+  triclinic box = (0 0 0) to (74.58 74.58 83.064) with tilt (0 0 0)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  32400 atoms
+
+mass		1 28.0855
+group    	type1 type 1
+10800 atoms in group type1
+compute   	charge1 type1 property/atom q
+compute   	q1 type1 reduce ave c_charge1
+mass		2 16.00
+group    	type2 type 2
+21600 atoms in group type2
+compute   	charge2 type2 property/atom q
+compute   	q2 type2 reduce ave c_charge2
+
+pair_style	comb
+pair_coeff	* * ffield.comb Si O
+neighbor	0.5 bin
+neigh_modify	every 10 delay 0 check yes
+
+timestep        0.0002
+
+thermo_style	custom step temp etotal pe evdwl ecoul c_q1 c_q2 press vol
+thermo_modify	norm yes
+velocity  	all create 300.0 3482028
+fix		1 all nvt temp 300.0 300.0 0.1
+fix  		2 all qeq/comb 10 0.001 file fq.out
+
+thermo   	10
+run    		100
+Neighbor list info ...
+  update every 10 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12.5
+  ghost atom cutoff = 12.5
+  binsize = 6.25, bins = 12 12 14
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair comb, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 32.11 | 32.11 | 32.11 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Press Volume 
+       0          300   -6.8032038   -6.8419806    4.6274455   -11.469426    2.8875895   -1.4437947    13386.415    462016.62 
+      10    273.21913   -6.8032489   -6.8385642    4.6221303   -11.460695    2.8872353   -1.4436176    13076.442    462016.62 
+      20     242.0051    -6.803367   -6.8346477    4.6208311   -11.455479    2.8870176   -1.4435087    12080.423    462016.62 
+      30     214.5618   -6.8034588   -6.8311922     4.620067   -11.451259    2.8870575   -1.4435287    10307.876    462016.62 
+      40    198.14521   -6.8035174   -6.8291289    4.6202931   -11.449422    2.8874526   -1.4437263     7765.732    462016.62 
+      50    197.15561   -6.8035468   -6.8290303    4.6219602   -11.450991    2.8883366   -1.4441683    4432.7134    462016.62 
+      60    212.04532   -6.8035584   -6.8309666    4.6260476   -11.457014    2.8896425   -1.4448212    324.71226    462016.62 
+      70    239.37999   -6.8035665   -6.8345078    4.6322984   -11.466806    2.8912723   -1.4456361   -4497.0492    462016.62 
+      80    272.98301    -6.803583   -6.8388677    4.6404093   -11.479277    2.8932784   -1.4466392   -9896.1704    462016.62 
+      90    305.77651   -6.8036184   -6.8431419    4.6512736   -11.494415    2.8953109   -1.4476554   -15675.983    462016.62 
+     100    331.58255   -6.8036753   -6.8465344     4.662727   -11.509261     2.897273   -1.4486365   -21675.515    462016.62 
+Loop time of 131.437 on 4 procs for 100 steps with 32400 atoms
+
+Performance: 0.013 ns/day, 1825.518 hours/ns, 0.761 timesteps/s
+99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 28.847     | 28.874     | 28.913     |   0.5 | 21.97
+Neigh   | 0.10981    | 0.11084    | 0.11145    |   0.2 |  0.08
+Comm    | 0.28924    | 0.32866    | 0.3556     |   4.5 |  0.25
+Output  | 0.0010426  | 0.0011656  | 0.0015302  |   0.6 |  0.00
+Modify  | 102.12     | 102.12     | 102.12     |   0.0 | 77.69
+Other   |            | 0.003455   |            |       |  0.00
+
+Nlocal:    8100 ave 8110 max 8090 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Nghost:    20725.2 ave 20772 max 20694 min
+Histogram: 1 1 0 0 1 0 0 0 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  4.63294e+06 ave 4.63866e+06 max 4.62736e+06 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+
+Total # of neighbors = 18531740
+Ave neighs/atom = 571.967
+Neighbor list builds = 1
+Dangerous builds = 0
+Total wall time: 0:02:21

bench/POTENTIALS/log.16Mar18.dpd.1

@@ -0,0 +1,75 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# DPD benchmark
+
+units		lj
+atom_style	atomic
+comm_modify     mode single vel yes
+
+lattice		fcc 3.0
+Lattice spacing in x,y,z = 1.10064 1.10064 1.10064
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (22.0128 22.0128 22.0128)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  Time spent = 0.0018332 secs
+mass		1 1.0
+
+velocity	all create 1.0 87287 loop geom
+
+pair_style	dpd 1.0 1.0 928948
+pair_coeff	1 1 25.0 4.5
+
+neighbor	0.5 bin
+neigh_modify    delay 0 every 1
+
+fix		1 all nve
+timestep	0.04
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.5
+  ghost atom cutoff = 1.5
+  binsize = 0.75, bins = 30 30 30
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair dpd, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 11.32 | 11.32 | 11.32 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            1    3.6872574            0    5.1872105    28.880274 
+     100    1.0246036    4.5727353            0    6.1095927    23.859969 
+Loop time of 3.09286 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 111741.340 tau/day, 32.333 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.5326     | 1.5326     | 1.5326     |   0.0 | 49.55
+Neigh   | 1.4771     | 1.4771     | 1.4771     |   0.0 | 47.76
+Comm    | 0.044292   | 0.044292   | 0.044292   |   0.0 |  1.43
+Output  | 0.00011039 | 0.00011039 | 0.00011039 |   0.0 |  0.00
+Modify  | 0.022322   | 0.022322   | 0.022322   |   0.0 |  0.72
+Other   |            | 0.01648    |            |       |  0.53
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    14981 ave 14981 max 14981 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    660587 ave 660587 max 660587 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 660587
+Ave neighs/atom = 20.6433
+Neighbor list builds = 50
+Dangerous builds = 0
+Total wall time: 0:00:03

bench/POTENTIALS/log.16Mar18.dpd.4

@@ -0,0 +1,75 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# DPD benchmark
+
+units		lj
+atom_style	atomic
+comm_modify     mode single vel yes
+
+lattice		fcc 3.0
+Lattice spacing in x,y,z = 1.10064 1.10064 1.10064
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (22.0128 22.0128 22.0128)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  Time spent = 0.000589132 secs
+mass		1 1.0
+
+velocity	all create 1.0 87287 loop geom
+
+pair_style	dpd 1.0 1.0 928948
+pair_coeff	1 1 25.0 4.5
+
+neighbor	0.5 bin
+neigh_modify    delay 0 every 1
+
+fix		1 all nve
+timestep	0.04
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.5
+  ghost atom cutoff = 1.5
+  binsize = 0.75, bins = 30 30 30
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair dpd, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.874 | 3.874 | 3.874 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            1    3.6872574            0    5.1872105    28.911346 
+     100    1.0219182    4.5817845            0    6.1146139    23.803115 
+Loop time of 0.83904 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 411899.440 tau/day, 119.184 timesteps/s
+99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.39605    | 0.40101    | 0.40702    |   0.6 | 47.79
+Neigh   | 0.38186    | 0.38494    | 0.38738    |   0.4 | 45.88
+Comm    | 0.032073   | 0.039688   | 0.045953   |   2.9 |  4.73
+Output  | 4.4823e-05 | 5.4002e-05 | 7.844e-05  |   0.0 |  0.01
+Modify  | 0.0056572  | 0.0056887  | 0.0057547  |   0.1 |  0.68
+Other   |            | 0.007655   |            |       |  0.91
+
+Nlocal:    8000 ave 8014 max 7986 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Nghost:    6744 ave 6764 max 6726 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Neighs:    165107 ave 166433 max 163419 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+
+Total # of neighbors = 660428
+Ave neighs/atom = 20.6384
+Neighbor list builds = 50
+Dangerous builds = 0
+Total wall time: 0:00:00

bench/POTENTIALS/log.16Mar18.eam.1

@@ -0,0 +1,74 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# bulk Cu in EAM
+
+units		metal
+atom_style	atomic
+
+lattice		fcc 3.615
+Lattice spacing in x,y,z = 3.615 3.615 3.615
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  Time spent = 0.00185037 secs
+
+pair_style	eam
+pair_coeff	1 1 Cu_u3.eam
+
+velocity	all create 1600.0 376847 loop geom
+
+neighbor	1.0 bin
+neigh_modify    delay 5 every 1
+
+fix		1 all nve
+
+timestep	0.005
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.95
+  ghost atom cutoff = 5.95
+  binsize = 2.975, bins = 25 25 25
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair eam, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 16.83 | 16.83 | 16.83 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1600      -113280            0   -106662.09    18703.573 
+     100      801.832    -109957.3            0   -106640.77    51322.821 
+Loop time of 3.92295 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 11.012 ns/day, 2.179 hours/ns, 25.491 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.3913     | 3.3913     | 3.3913     |   0.0 | 86.45
+Neigh   | 0.48107    | 0.48107    | 0.48107    |   0.0 | 12.26
+Comm    | 0.01729    | 0.01729    | 0.01729    |   0.0 |  0.44
+Output  | 0.00011253 | 0.00011253 | 0.00011253 |   0.0 |  0.00
+Modify  | 0.024349   | 0.024349   | 0.024349   |   0.0 |  0.62
+Other   |            | 0.008847   |            |       |  0.23
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    19909 ave 19909 max 19909 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.20778e+06 ave 1.20778e+06 max 1.20778e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1207784
+Ave neighs/atom = 37.7433
+Neighbor list builds = 13
+Dangerous builds = 0
+Total wall time: 0:00:03

bench/POTENTIALS/log.16Mar18.eam.4

@@ -0,0 +1,74 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# bulk Cu in EAM
+
+units		metal
+atom_style	atomic
+
+lattice		fcc 3.615
+Lattice spacing in x,y,z = 3.615 3.615 3.615
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  Time spent = 0.000595331 secs
+
+pair_style	eam
+pair_coeff	1 1 Cu_u3.eam
+
+velocity	all create 1600.0 376847 loop geom
+
+neighbor	1.0 bin
+neigh_modify    delay 5 every 1
+
+fix		1 all nve
+
+timestep	0.005
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.95
+  ghost atom cutoff = 5.95
+  binsize = 2.975, bins = 25 25 25
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair eam, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.381 | 7.381 | 7.381 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1600      -113280            0   -106662.09    18703.573 
+     100      801.832    -109957.3            0   -106640.77    51322.821 
+Loop time of 1.04497 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 41.341 ns/day, 0.581 hours/ns, 95.697 timesteps/s
+99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.88513    | 0.88724    | 0.89191    |   0.3 | 84.91
+Neigh   | 0.12418    | 0.12458    | 0.12511    |   0.1 | 11.92
+Comm    | 0.015654   | 0.020543   | 0.022984   |   2.0 |  1.97
+Output  | 4.8637e-05 | 5.8711e-05 | 8.6546e-05 |   0.0 |  0.01
+Modify  | 0.0085199  | 0.0085896  | 0.0086446  |   0.1 |  0.82
+Other   |            | 0.003959   |            |       |  0.38
+
+Nlocal:    8000 ave 8008 max 7993 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost:    9130.25 ave 9138 max 9122 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    301946 ave 302392 max 301360 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+
+Total # of neighbors = 1207784
+Ave neighs/atom = 37.7433
+Neighbor list builds = 13
+Dangerous builds = 0
+Total wall time: 0:00:01

bench/POTENTIALS/log.16Mar18.eff.1

@@ -0,0 +1,97 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# eFF benchmark of H plasma
+
+units 		electron
+atom_style	electron
+
+read_data  	data.eff
+  orthogonal box = (0 0 0) to (41.9118 41.9118 41.9118)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+
+pair_style      eff/cut 12
+pair_coeff	* *
+
+neigh_modify    one 6000 page 60000
+
+comm_modify	vel yes
+
+compute         effTemp all temp/eff
+
+thermo          5
+thermo_style    custom step etotal pe ke temp press
+thermo_modify   temp effTemp
+
+fix		1 all nve/eff
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 6000, page size: 60000
+  master list distance cutoff = 14
+  ghost atom cutoff = 14
+  binsize = 7, bins = 6 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair eff/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 370.9 | 370.9 | 370.9 Mbytes
+Step TotEng PotEng KinEng Temp Press 
+       0    4046.5854    796.63785    3249.9475    42763.133 4.4764483e+12 
+       5    4046.5854    796.95799    3249.6274     42758.92 4.4728546e+12 
+      10    4046.5854    797.71165    3248.8737    42749.004 4.4690821e+12 
+      15    4046.5854     798.8949    3247.6905    42733.435 4.4651331e+12 
+      20    4046.5854    800.50332    3246.0821    42712.271 4.4610102e+12 
+      25    4046.5854    802.53206    3244.0534    42685.577 4.456716e+12 
+      30    4046.5855    804.97579    3241.6097    42653.422 4.4522535e+12 
+      35    4046.5855    807.82873    3238.7567    42615.883 4.4476257e+12 
+      40    4046.5855    811.08467    3235.5008    42573.041 4.4428357e+12 
+      45    4046.5855    814.73696    3231.8485    42524.984 4.437887e+12 
+      50    4046.5855    818.77851     3227.807    42471.806 4.432783e+12 
+      55    4046.5855    823.20183    3223.3837    42413.603 4.4275273e+12 
+      60    4046.5856    827.99901    3218.5866    42350.482 4.4221238e+12 
+      65    4046.5856    833.16176    3213.4238     42282.55 4.4165764e+12 
+      70    4046.5856    838.68137    3207.9042    42209.923 4.4108891e+12 
+      75    4046.5856    844.54877    3202.0369    42132.719 4.4050662e+12 
+      80    4046.5857    850.75454    3195.8311    42051.064 4.399112e+12 
+      85    4046.5857    857.28886    3189.2968    41965.085 4.393031e+12 
+      90    4046.5857    864.14162    3182.4441    41874.916 4.3868277e+12 
+      95    4046.5857    871.30234    3175.2834    41780.695 4.3805068e+12 
+     100    4046.5858    878.76023    3167.8255    41682.563 4.3740731e+12 
+Loop time of 323.031 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 26.747 fs/day, 0.897 hours/fs, 0.310 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 322.78     | 322.78     | 322.78     |   0.0 | 99.92
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.1876     | 0.1876     | 0.1876     |   0.0 |  0.06
+Output  | 0.0027025  | 0.0027025  | 0.0027025  |   0.0 |  0.00
+Modify  | 0.032475   | 0.032475   | 0.032475   |   0.0 |  0.01
+Other   |            | 0.02538    |            |       |  0.01
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    114349 ave 114349 max 114349 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    8.10572e+07 ave 8.10572e+07 max 8.10572e+07 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 81057159
+Ave neighs/atom = 2533.04
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:05:27

bench/POTENTIALS/log.16Mar18.eff.4

@@ -0,0 +1,97 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# eFF benchmark of H plasma
+
+units 		electron
+atom_style	electron
+
+read_data  	data.eff
+  orthogonal box = (0 0 0) to (41.9118 41.9118 41.9118)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+
+pair_style      eff/cut 12
+pair_coeff	* *
+
+neigh_modify    one 6000 page 60000
+
+comm_modify	vel yes
+
+compute         effTemp all temp/eff
+
+thermo          5
+thermo_style    custom step etotal pe ke temp press
+thermo_modify   temp effTemp
+
+fix		1 all nve/eff
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 6000, page size: 60000
+  master list distance cutoff = 14
+  ghost atom cutoff = 14
+  binsize = 7, bins = 6 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair eff/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 101.4 | 104.8 | 108.3 Mbytes
+Step TotEng PotEng KinEng Temp Press 
+       0    4046.5854    796.63785    3249.9475    42763.133 4.4764483e+12 
+       5    4046.5854    796.95799    3249.6274     42758.92 4.4728546e+12 
+      10    4046.5854    797.71165    3248.8737    42749.004 4.4690821e+12 
+      15    4046.5854     798.8949    3247.6905    42733.435 4.4651331e+12 
+      20    4046.5854    800.50332    3246.0821    42712.271 4.4610102e+12 
+      25    4046.5854    802.53206    3244.0534    42685.577 4.456716e+12 
+      30    4046.5855    804.97579    3241.6097    42653.422 4.4522535e+12 
+      35    4046.5855    807.82873    3238.7567    42615.883 4.4476257e+12 
+      40    4046.5855    811.08467    3235.5008    42573.041 4.4428357e+12 
+      45    4046.5855    814.73696    3231.8485    42524.984 4.437887e+12 
+      50    4046.5855    818.77851     3227.807    42471.806 4.432783e+12 
+      55    4046.5855    823.20183    3223.3837    42413.603 4.4275273e+12 
+      60    4046.5856    827.99901    3218.5866    42350.482 4.4221238e+12 
+      65    4046.5856    833.16176    3213.4238     42282.55 4.4165764e+12 
+      70    4046.5856    838.68137    3207.9042    42209.923 4.4108891e+12 
+      75    4046.5856    844.54877    3202.0369    42132.719 4.4050662e+12 
+      80    4046.5857    850.75454    3195.8311    42051.064 4.399112e+12 
+      85    4046.5857    857.28886    3189.2968    41965.085 4.393031e+12 
+      90    4046.5857    864.14162    3182.4441    41874.916 4.3868277e+12 
+      95    4046.5857    871.30234    3175.2834    41780.695 4.3805068e+12 
+     100    4046.5858    878.76023    3167.8255    41682.563 4.3740731e+12 
+Loop time of 90.1636 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 95.826 fs/day, 0.250 hours/fs, 1.109 timesteps/s
+99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 83.772     | 86.516     | 89.593     |  29.5 | 95.95
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.51677    | 3.5934     | 6.3368     | 144.6 |  3.99
+Output  | 0.0012872  | 0.0018208  | 0.0024981  |   1.0 |  0.00
+Modify  | 0.017231   | 0.018405   | 0.01983    |   0.8 |  0.02
+Other   |            | 0.03431    |            |       |  0.04
+
+Nlocal:    8000 ave 8112 max 7875 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Nghost:    65589 ave 66004 max 65177 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    2.02643e+07 ave 2.11126e+07 max 1.94058e+07 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 81057159
+Ave neighs/atom = 2533.04
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:01:31

bench/POTENTIALS/log.16Mar18.eim.1

@@ -0,0 +1,77 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# EIM benchmark
+# if run long enough (e.g. 1M steps), the unstable CsCl form of a NaCl single
+# crystal can be annealed to the correct NaCl type of NaCl polycrystals
+
+units		metal
+atom_style      atomic
+
+read_data       data.eim
+  orthogonal box = (-0.5 -0.5 -0.5) to (71.58 143.66 71.58)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+
+pair_style      eim
+pair_coeff      * * Na Cl ffield.eim Na Cl
+
+neighbor	0.3 bin
+neigh_modify    delay 0 every 1
+
+timestep        0.0005
+thermo_style    custom step pe pxx pyy pzz temp
+
+velocity        all create 1400.0 43454 dist gaussian mom yes
+
+fix             int all npt temp 1400.0 1400.0 0.1 aniso 0.0 0.0 0.1
+# anneal in much longer run
+#fix             int all npt temp 1400.0 300.0 0.1 aniso 0.0 0.0 0.1
+
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.906
+  ghost atom cutoff = 7.906
+  binsize = 3.953, bins = 19 37 19
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair eim, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 17.72 | 17.72 | 17.72 Mbytes
+Step PotEng Pxx Pyy Pzz Temp 
+       0    -90567.58    -117883.6   -118039.81   -117894.07         1400 
+     100   -91997.012   -4104.7052    -4138.276   -4145.8936    944.10136 
+Loop time of 11.4536 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 0.377 ns/day, 63.631 hours/ns, 8.731 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 9.8277     | 9.8277     | 9.8277     |   0.0 | 85.80
+Neigh   | 1.484      | 1.484      | 1.484      |   0.0 | 12.96
+Comm    | 0.028584   | 0.028584   | 0.028584   |   0.0 |  0.25
+Output  | 0.00023127 | 0.00023127 | 0.00023127 |   0.0 |  0.00
+Modify  | 0.09791    | 0.09791    | 0.09791    |   0.0 |  0.85
+Other   |            | 0.0152     |            |       |  0.13
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    21505 ave 21505 max 21505 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.5839e+06 ave 1.5839e+06 max 1.5839e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1583901
+Ave neighs/atom = 49.4969
+Neighbor list builds = 37
+Dangerous builds = 12
+Total wall time: 0:00:11

bench/POTENTIALS/log.16Mar18.eim.4

@@ -0,0 +1,77 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# EIM benchmark
+# if run long enough (e.g. 1M steps), the unstable CsCl form of a NaCl single
+# crystal can be annealed to the correct NaCl type of NaCl polycrystals
+
+units		metal
+atom_style      atomic
+
+read_data       data.eim
+  orthogonal box = (-0.5 -0.5 -0.5) to (71.58 143.66 71.58)
+  1 by 4 by 1 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+
+pair_style      eim
+pair_coeff      * * Na Cl ffield.eim Na Cl
+
+neighbor	0.3 bin
+neigh_modify    delay 0 every 1
+
+timestep        0.0005
+thermo_style    custom step pe pxx pyy pzz temp
+
+velocity        all create 1400.0 43454 dist gaussian mom yes
+
+fix             int all npt temp 1400.0 1400.0 0.1 aniso 0.0 0.0 0.1
+# anneal in much longer run
+#fix             int all npt temp 1400.0 300.0 0.1 aniso 0.0 0.0 0.1
+
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.906
+  ghost atom cutoff = 7.906
+  binsize = 3.953, bins = 19 37 19
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair eim, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.285 | 7.285 | 7.285 Mbytes
+Step PotEng Pxx Pyy Pzz Temp 
+       0    -90567.58    -117883.6   -118039.81   -117894.07         1400 
+     100   -91997.012   -4104.7052    -4138.276   -4145.8936    944.10136 
+Loop time of 3.12061 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 1.384 ns/day, 17.337 hours/ns, 32.045 timesteps/s
+98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.6504     | 2.6583     | 2.6685     |   0.5 | 85.18
+Neigh   | 0.36996    | 0.37847    | 0.39396    |   1.5 | 12.13
+Comm    | 0.037041   | 0.040586   | 0.04504    |   1.4 |  1.30
+Output  | 7.081e-05  | 8.75e-05   | 0.00012994 |   0.0 |  0.00
+Modify  | 0.029286   | 0.035978   | 0.047942   |   3.9 |  1.15
+Other   |            | 0.007206   |            |       |  0.23
+
+Nlocal:    8000 ave 8000 max 8000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    9460.25 ave 9469 max 9449 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+Neighs:    395975 ave 397239 max 394616 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+
+Total # of neighbors = 1583901
+Ave neighs/atom = 49.4969
+Neighbor list builds = 37
+Dangerous builds = 12
+Total wall time: 0:00:03

bench/POTENTIALS/log.16Mar18.fene.1

@@ -0,0 +1,84 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# FENE beadspring benchmark
+
+units		lj
+atom_style	bond
+special_bonds   fene
+
+read_data	data.fene
+  orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  31680 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of special neighbors
+
+neighbor	0.4 bin
+neigh_modify    delay 5 every 1
+
+bond_style      fene
+bond_coeff	1 30.0 1.5 1.0 1.0
+
+pair_style	lj/cut 1.12
+pair_modify	shift yes
+pair_coeff	1 1 1.0 1.0 1.12
+
+fix		1 all nve
+fix		2 all langevin 1.0 1.0 10.0 904297
+
+timestep	0.012
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.52
+  ghost atom cutoff = 1.52
+  binsize = 0.76, bins = 45 45 45
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 13.18 | 13.18 | 13.18 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0   0.97029772   0.44484087    20.494523    22.394765    4.6721833 
+     100    0.9729966    0.4361122    20.507698     22.40326    4.6548819 
+Loop time of 0.66285 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 156415.445 tau/day, 150.864 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.13075    | 0.13075    | 0.13075    |   0.0 | 19.73
+Bond    | 0.046363   | 0.046363   | 0.046363   |   0.0 |  6.99
+Neigh   | 0.3172     | 0.3172     | 0.3172     |   0.0 | 47.85
+Comm    | 0.016553   | 0.016553   | 0.016553   |   0.0 |  2.50
+Output  | 0.00010395 | 0.00010395 | 0.00010395 |   0.0 |  0.02
+Modify  | 0.14515    | 0.14515    | 0.14515    |   0.0 | 21.90
+Other   |            | 0.006728   |            |       |  1.02
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    9493 ave 9493 max 9493 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    155873 ave 155873 max 155873 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 155873
+Ave neighs/atom = 4.87103
+Ave special neighs/atom = 1.98
+Neighbor list builds = 20
+Dangerous builds = 20
+Total wall time: 0:00:00

bench/POTENTIALS/log.16Mar18.fene.4

@@ -0,0 +1,84 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# FENE beadspring benchmark
+
+units		lj
+atom_style	bond
+special_bonds   fene
+
+read_data	data.fene
+  orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  31680 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of special neighbors
+
+neighbor	0.4 bin
+neigh_modify    delay 5 every 1
+
+bond_style      fene
+bond_coeff	1 30.0 1.5 1.0 1.0
+
+pair_style	lj/cut 1.12
+pair_modify	shift yes
+pair_coeff	1 1 1.0 1.0 1.12
+
+fix		1 all nve
+fix		2 all langevin 1.0 1.0 10.0 904297
+
+timestep	0.012
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.52
+  ghost atom cutoff = 1.52
+  binsize = 0.76, bins = 45 45 45
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.605 | 4.605 | 4.606 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0   0.97029772   0.44484087    20.494523    22.394765    4.6721833 
+     100    0.9736748   0.44378481    20.502389     22.40664    4.7809557 
+Loop time of 0.184782 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 561093.346 tau/day, 541.178 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    | 0.033747   | 0.034391   | 0.035036   |   0.3 | 18.61
+Bond    | 0.012475   | 0.012579   | 0.012812   |   0.1 |  6.81
+Neigh   | 0.083916   | 0.083953   | 0.084022   |   0.0 | 45.43
+Comm    | 0.012409   | 0.01363    | 0.014534   |   0.7 |  7.38
+Output  | 4.1246e-05 | 5.9545e-05 | 0.00010443 |   0.0 |  0.03
+Modify  | 0.036675   | 0.037876   | 0.038357   |   0.4 | 20.50
+Other   |            | 0.002294   |            |       |  1.24
+
+Nlocal:    8000 ave 8023 max 7978 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Nghost:    4158.75 ave 4175 max 4145 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Neighs:    38940 ave 39184 max 38640 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+
+Total # of neighbors = 155760
+Ave neighs/atom = 4.8675
+Ave special neighs/atom = 1.98
+Neighbor list builds = 20
+Dangerous builds = 20
+Total wall time: 0:00:00

bench/POTENTIALS/log.16Mar18.gb.1

@@ -0,0 +1,103 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# Gay-Berne benchmark
+# biaxial ellipsoid mesogens in isotropic phase
+# shape: 2 1.5 1
+# cutoff 4.0 with skin 0.8
+# NPT, T=2.4, P=8.0
+
+units	      lj
+atom_style    ellipsoid
+
+# creation
+#lattice	      sc 0.22
+#region	      box block 0 32 0 32 0 32
+#create_box    1 box
+#create_atoms  1 box
+#set	      group all quat/random 982381
+
+read_data     data.gb
+  orthogonal box = (2.19575 2.19575 2.19575) to (50.8124 50.8124 50.8124)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  32768 atoms
+  reading velocities ...
+  32768 velocities
+  32768 ellipsoids
+
+compute	      rot all temp/asphere
+group	      spheroid type 1
+32768 atoms in group spheroid
+variable      dof equal count(spheroid)+3
+compute_modify rot extra ${dof}
+compute_modify rot extra 32771
+
+velocity      all create 2.4 41787 loop geom
+
+pair_style    gayberne 1.0 3.0 1.0 4.0
+pair_coeff    1 1 1.0 1.0 1.0 0.5 0.2 1.0 0.5 0.2
+
+neighbor      0.8 bin
+
+timestep      0.002
+thermo	      20
+
+# equilibration
+#fix	      1 all npt/asphere temp 2.4 2.4 0.1 iso 5.0 8.0 0.1
+#compute_modify 1_temp extra ${dof}
+#run	      100
+#write_restart tmp.restart
+
+fix	      1 all npt/asphere temp 2.4 2.4 0.2 iso 8.0 8.0 0.2
+run	      100
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.8
+  ghost atom cutoff = 4.8
+  binsize = 2.4, bins = 21 21 21
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gayberne, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 28.91 | 28.91 | 28.91 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume 
+       0          2.4   0.50438568            0    4.1042758    6.7818168    114909.09 
+      20    2.7357818   0.26045557            0     4.364003    6.8299368    111715.16 
+      40    2.9201296   0.22570735            0     4.605768    7.0767907    109473.23 
+      60    2.9820039   0.19733812            0    4.6702075    7.1507065    108393.77 
+      80    3.0148529   0.15114819            0    4.6732895    7.1699502    107672.24 
+     100    3.0206703   0.10567623            0    4.6365433     7.154345    107184.83 
+Loop time of 43.7894 on 1 procs for 100 steps with 32768 atoms
+
+Performance: 394.616 tau/day, 2.284 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 42.881     | 42.881     | 42.881     |   0.0 | 97.93
+Neigh   | 0.35071    | 0.35071    | 0.35071    |   0.0 |  0.80
+Comm    | 0.065153   | 0.065153   | 0.065153   |   0.0 |  0.15
+Output  | 0.00054383 | 0.00054383 | 0.00054383 |   0.0 |  0.00
+Modify  | 0.47852    | 0.47852    | 0.47852    |   0.0 |  1.09
+Other   |            | 0.01337    |            |       |  0.03
+
+Nlocal:    32768 ave 32768 max 32768 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    25669 ave 25669 max 25669 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    2.30433e+06 ave 2.30433e+06 max 2.30433e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2304332
+Ave neighs/atom = 70.3226
+Neighbor list builds = 6
+Dangerous builds = 3
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:44

bench/POTENTIALS/log.16Mar18.gb.4

@@ -0,0 +1,103 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# Gay-Berne benchmark
+# biaxial ellipsoid mesogens in isotropic phase
+# shape: 2 1.5 1
+# cutoff 4.0 with skin 0.8
+# NPT, T=2.4, P=8.0
+
+units	      lj
+atom_style    ellipsoid
+
+# creation
+#lattice	      sc 0.22
+#region	      box block 0 32 0 32 0 32
+#create_box    1 box
+#create_atoms  1 box
+#set	      group all quat/random 982381
+
+read_data     data.gb
+  orthogonal box = (2.19575 2.19575 2.19575) to (50.8124 50.8124 50.8124)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  32768 atoms
+  reading velocities ...
+  32768 velocities
+  32768 ellipsoids
+
+compute	      rot all temp/asphere
+group	      spheroid type 1
+32768 atoms in group spheroid
+variable      dof equal count(spheroid)+3
+compute_modify rot extra ${dof}
+compute_modify rot extra 32771
+
+velocity      all create 2.4 41787 loop geom
+
+pair_style    gayberne 1.0 3.0 1.0 4.0
+pair_coeff    1 1 1.0 1.0 1.0 0.5 0.2 1.0 0.5 0.2
+
+neighbor      0.8 bin
+
+timestep      0.002
+thermo	      20
+
+# equilibration
+#fix	      1 all npt/asphere temp 2.4 2.4 0.1 iso 5.0 8.0 0.1
+#compute_modify 1_temp extra ${dof}
+#run	      100
+#write_restart tmp.restart
+
+fix	      1 all npt/asphere temp 2.4 2.4 0.2 iso 8.0 8.0 0.2
+run	      100
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.8
+  ghost atom cutoff = 4.8
+  binsize = 2.4, bins = 21 21 21
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gayberne, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 11.78 | 11.78 | 11.78 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume 
+       0          2.4   0.50438568            0    4.1042758    6.7818168    114909.09 
+      20    2.7357818   0.26045557            0     4.364003    6.8299368    111715.16 
+      40    2.9201296   0.22570735            0     4.605768    7.0767907    109473.23 
+      60    2.9820039   0.19733812            0    4.6702075    7.1507065    108393.77 
+      80    3.0148529   0.15114819            0    4.6732895    7.1699502    107672.24 
+     100    3.0206703   0.10567623            0    4.6365433     7.154345    107184.83 
+Loop time of 11.3124 on 4 procs for 100 steps with 32768 atoms
+
+Performance: 1527.522 tau/day, 8.840 timesteps/s
+99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 10.778     | 10.849     | 10.934     |   2.0 | 95.90
+Neigh   | 0.088265   | 0.08871    | 0.089238   |   0.1 |  0.78
+Comm    | 0.1384     | 0.22518    | 0.29662    |  14.1 |  1.99
+Output  | 0.00020599 | 0.00024837 | 0.00036836 |   0.0 |  0.00
+Modify  | 0.13828    | 0.13899    | 0.13984    |   0.2 |  1.23
+Other   |            | 0.01053    |            |       |  0.09
+
+Nlocal:    8192 ave 8215 max 8166 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Nghost:    11972.5 ave 11984 max 11959 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+Neighs:    576083 ave 579616 max 572161 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 2304332
+Ave neighs/atom = 70.3226
+Neighbor list builds = 6
+Dangerous builds = 3
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:11

bench/POTENTIALS/log.16Mar18.granular.1

@@ -0,0 +1,85 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# granular chute flow
+
+units		lj
+atom_style	sphere
+boundary	p p fs
+newton		off
+comm_modify	vel yes
+
+read_data	data.granular
+  orthogonal box = (0 0 0) to (40 20 37.2886)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+
+pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
+pair_coeff	* *
+
+neighbor	0.1 bin
+neigh_modify    delay 5 every 1
+
+timestep	0.0001
+
+group		bottom type 2
+912 atoms in group bottom
+group		active subtract all bottom
+31088 atoms in group active
+neigh_modify	exclude group bottom bottom
+
+fix		1 all gravity 1.0 chute 26.0
+fix		2 bottom freeze
+fix		3 active nve/sphere
+
+compute		1 all erotate/sphere
+thermo_style	custom step atoms ke c_1 vol
+thermo_modify	norm no
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.1
+  ghost atom cutoff = 1.1
+  binsize = 0.55, bins = 73 37 68
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gran/hooke/history, perpetual
+      attributes: half, newton off, size, history
+      pair build: half/size/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 23.36 | 23.36 | 23.36 Mbytes
+Step Atoms KinEng c_1 Volume 
+       0    32000    784139.13    1601.1263    29833.783 
+     100    32000    784292.08    1571.0968    29834.707 
+Loop time of 0.292816 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 2950.657 tau/day, 341.511 timesteps/s
+99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.17449    | 0.17449    | 0.17449    |   0.0 | 59.59
+Neigh   | 0.031927   | 0.031927   | 0.031927   |   0.0 | 10.90
+Comm    | 0.010195   | 0.010195   | 0.010195   |   0.0 |  3.48
+Output  | 0.00019121 | 0.00019121 | 0.00019121 |   0.0 |  0.07
+Modify  | 0.064463   | 0.064463   | 0.064463   |   0.0 | 22.01
+Other   |            | 0.01155    |            |       |  3.94
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    5463 ave 5463 max 5463 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    115133 ave 115133 max 115133 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 115133
+Ave neighs/atom = 3.59791
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:00

bench/POTENTIALS/log.16Mar18.granular.4

@@ -0,0 +1,85 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# granular chute flow
+
+units		lj
+atom_style	sphere
+boundary	p p fs
+newton		off
+comm_modify	vel yes
+
+read_data	data.granular
+  orthogonal box = (0 0 0) to (40 20 37.2886)
+  2 by 1 by 2 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+
+pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
+pair_coeff	* *
+
+neighbor	0.1 bin
+neigh_modify    delay 5 every 1
+
+timestep	0.0001
+
+group		bottom type 2
+912 atoms in group bottom
+group		active subtract all bottom
+31088 atoms in group active
+neigh_modify	exclude group bottom bottom
+
+fix		1 all gravity 1.0 chute 26.0
+fix		2 bottom freeze
+fix		3 active nve/sphere
+
+compute		1 all erotate/sphere
+thermo_style	custom step atoms ke c_1 vol
+thermo_modify	norm no
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.1
+  ghost atom cutoff = 1.1
+  binsize = 0.55, bins = 73 37 68
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gran/hooke/history, perpetual
+      attributes: half, newton off, size, history
+      pair build: half/size/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 10.41 | 10.42 | 10.42 Mbytes
+Step Atoms KinEng c_1 Volume 
+       0    32000    784139.13    1601.1263    29833.783 
+     100    32000    784292.08    1571.0968    29834.707 
+Loop time of 0.0903978 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 9557.751 tau/day, 1106.221 timesteps/s
+98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.046331   | 0.049088   | 0.052195   |   1.2 | 54.30
+Neigh   | 0.0090401  | 0.0091327  | 0.0091863  |   0.1 | 10.10
+Comm    | 0.0073855  | 0.0080023  | 0.0086699  |   0.6 |  8.85
+Output  | 7.1049e-05 | 0.00010067 | 0.00012088 |   0.0 |  0.11
+Modify  | 0.017226   | 0.017449   | 0.01803    |   0.3 | 19.30
+Other   |            | 0.006625   |            |       |  7.33
+
+Nlocal:    8000 ave 8008 max 7992 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    2439 ave 2450 max 2428 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    29500.5 ave 30488 max 28513 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 118002
+Ave neighs/atom = 3.68756
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:00

bench/POTENTIALS/log.16Mar18.lj.1

@@ -0,0 +1,73 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# 3d Lennard-Jones melt
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  Time spent = 0.00183916 secs
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify    delay 5 every 1
+
+fix		1 all nve
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 24 24 24
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 15.82 | 15.82 | 15.82 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
+     100   0.75745998   -5.7584998            0   -4.6223453   0.20729996 
+Loop time of 1.721 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 25101.720 tau/day, 58.106 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.2551     | 1.2551     | 1.2551     |   0.0 | 72.93
+Neigh   | 0.41825    | 0.41825    | 0.41825    |   0.0 | 24.30
+Comm    | 0.015347   | 0.015347   | 0.015347   |   0.0 |  0.89
+Output  | 0.00010729 | 0.00010729 | 0.00010729 |   0.0 |  0.01
+Modify  | 0.023436   | 0.023436   | 0.023436   |   0.0 |  1.36
+Other   |            | 0.008766   |            |       |  0.51
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    19669 ave 19669 max 19669 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.20318e+06 ave 1.20318e+06 max 1.20318e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1203176
+Ave neighs/atom = 37.5992
+Neighbor list builds = 11
+Dangerous builds = 0
+Total wall time: 0:00:01

bench/POTENTIALS/log.16Mar18.lj.4

@@ -0,0 +1,73 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# 3d Lennard-Jones melt
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  Time spent = 0.000587225 secs
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify    delay 5 every 1
+
+fix		1 all nve
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 24 24 24
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.88 | 6.88 | 6.88 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
+     100   0.75745998   -5.7584998            0   -4.6223453   0.20729996 
+Loop time of 0.469936 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 91927.316 tau/day, 212.795 timesteps/s
+99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.32713    | 0.32917    | 0.33317    |   0.4 | 70.05
+Neigh   | 0.10836    | 0.10931    | 0.11007    |   0.2 | 23.26
+Comm    | 0.015526   | 0.020355   | 0.022399   |   2.0 |  4.33
+Output  | 4.2439e-05 | 5.8353e-05 | 0.00010061 |   0.0 |  0.01
+Modify  | 0.0071156  | 0.0072448  | 0.007309   |   0.1 |  1.54
+Other   |            | 0.003793   |            |       |  0.81
+
+Nlocal:    8000 ave 8041 max 7958 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    9011 ave 9065 max 8961 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+Neighs:    300794 ave 304843 max 297317 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+
+Total # of neighbors = 1203176
+Ave neighs/atom = 37.5992
+Neighbor list builds = 11
+Dangerous builds = 0
+Total wall time: 0:00:00

bench/POTENTIALS/log.16Mar18.meamc.1

@@ -0,0 +1,83 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# bulk Ni in MEAM
+
+units		metal
+atom_style	atomic
+
+lattice		fcc 3.52
+Lattice spacing in x,y,z = 3.52 3.52 3.52
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  Time spent = 0.00184226 secs
+
+pair_style	meam/c
+pair_coeff	* * library.meam Ni4 Ni.meam Ni4
+
+velocity	all create 1600.0 376847 loop geom
+
+neighbor	1.0 bin
+neigh_modify    delay 5 every 1
+
+fix		1 all nve
+
+timestep	0.005
+thermo		50
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5
+  ghost atom cutoff = 5
+  binsize = 2.5, bins = 29 29 29
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair meam/c, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair meam/c, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 55.91 | 55.91 | 55.91 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1600      -142400            0   -135782.09     20259.18 
+      50    885.10702   -139411.51            0   -135750.54    32425.431 
+     100    895.50973    -139454.3            0    -135750.3    31804.185 
+Loop time of 22.9343 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 1.884 ns/day, 12.741 hours/ns, 4.360 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 22.397     | 22.397     | 22.397     |   0.0 | 97.66
+Neigh   | 0.48781    | 0.48781    | 0.48781    |   0.0 |  2.13
+Comm    | 0.013967   | 0.013967   | 0.013967   |   0.0 |  0.06
+Output  | 0.00022793 | 0.00022793 | 0.00022793 |   0.0 |  0.00
+Modify  | 0.025412   | 0.025412   | 0.025412   |   0.0 |  0.11
+Other   |            | 0.009448   |            |       |  0.04
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    13576 ave 13576 max 13576 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    780360 ave 780360 max 780360 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  1.56072e+06 ave 1.56072e+06 max 1.56072e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1560720
+Ave neighs/atom = 48.7725
+Neighbor list builds = 8
+Dangerous builds = 0
+Total wall time: 0:00:23

bench/POTENTIALS/log.16Mar18.meamc.4

@@ -0,0 +1,83 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# bulk Ni in MEAM
+
+units		metal
+atom_style	atomic
+
+lattice		fcc 3.52
+Lattice spacing in x,y,z = 3.52 3.52 3.52
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  Time spent = 0.00058651 secs
+
+pair_style	meam/c
+pair_coeff	* * library.meam Ni4 Ni.meam Ni4
+
+velocity	all create 1600.0 376847 loop geom
+
+neighbor	1.0 bin
+neigh_modify    delay 5 every 1
+
+fix		1 all nve
+
+timestep	0.005
+thermo		50
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5
+  ghost atom cutoff = 5
+  binsize = 2.5, bins = 29 29 29
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair meam/c, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair meam/c, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 17.41 | 17.41 | 17.41 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1600      -142400            0   -135782.09     20259.18 
+      50    885.10702   -139411.51            0   -135750.54    32425.431 
+     100    895.50973    -139454.3            0    -135750.3    31804.185 
+Loop time of 6.45947 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 6.688 ns/day, 3.589 hours/ns, 15.481 timesteps/s
+98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 6.22       | 6.2385     | 6.265      |   0.7 | 96.58
+Neigh   | 0.12657    | 0.12691    | 0.12721    |   0.1 |  1.96
+Comm    | 0.052339   | 0.07915    | 0.097897   |   5.9 |  1.23
+Output  | 9.7752e-05 | 0.0001151  | 0.00016594 |   0.0 |  0.00
+Modify  | 0.010194   | 0.010291   | 0.010442   |   0.1 |  0.16
+Other   |            | 0.004529   |            |       |  0.07
+
+Nlocal:    8000 ave 8045 max 7947 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Nghost:    6066.75 ave 6120 max 6021 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Neighs:    195090 ave 196403 max 193697 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+FullNghs:  390180 ave 392616 max 387490 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+
+Total # of neighbors = 1560720
+Ave neighs/atom = 48.7725
+Neighbor list builds = 8
+Dangerous builds = 0
+Total wall time: 0:00:06

bench/POTENTIALS/log.16Mar18.peri.1

@@ -0,0 +1,217 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# Crack growth in notched 3D Peridynamic block
+
+# Mesh spacing
+variable    	h equal 5.00e-4
+# Peridynamic horizon
+variable    	delta equal 3.0*${h}
+variable    	delta equal 3.0*0.0005
+# Height of plate (meters)
+variable    	height equal 31.5*${h}
+variable    	height equal 31.5*0.0005
+# Width of plate (meters)
+variable    	width equal 39.5*${h}
+variable    	width equal 39.5*0.0005
+# Thickness of plate (meters)
+variable    	depth equal 24.5*${h}
+variable    	depth equal 24.5*0.0005
+# Height of notch
+variable	crackheight equal 10*${h}
+variable	crackheight equal 10*0.0005
+# Density of plate
+variable	mydensity equal 2440.0
+# Elastic modulus of material
+variable	myE equal 72.0e9
+# Strain energy release rate at branching
+variable	myG equal 135.0
+# constant, but define it as a variable here
+variable    	pi equal 3.14159265358979323846
+
+units 		si
+boundary        s s s
+atom_style      peri
+atom_modify	map array
+variable 	myskin equal 2.0*${h}
+variable 	myskin equal 2.0*0.0005
+neighbor	${myskin} bin
+neighbor	0.001 bin
+
+lattice         sc $h
+lattice         sc 0.0005
+Lattice spacing in x,y,z = 0.0005 0.0005 0.0005
+variable	myxmin equal 0.0
+variable	myxmax equal ${width}
+variable	myxmax equal 0.01975
+variable	myymin equal 0.0
+variable	myymax equal ${height}
+variable	myymax equal 0.01575
+variable	myzmin equal 0.0
+variable	myzmax equal ${depth}
+variable	myzmax equal 0.01225
+region          plate block 		${myxmin} ${myxmax} ${myymin} ${myymax} ${myzmin} ${myzmax} 		units box
+region          plate block 		0 ${myxmax} ${myymin} ${myymax} ${myzmin} ${myzmax} 		units box
+region          plate block 		0 0.01975 ${myymin} ${myymax} ${myzmin} ${myzmax} 		units box
+region          plate block 		0 0.01975 0 ${myymax} ${myzmin} ${myzmax} 		units box
+region          plate block 		0 0.01975 0 0.01575 ${myzmin} ${myzmax} 		units box
+region          plate block 		0 0.01975 0 0.01575 0 ${myzmax} 		units box
+region          plate block 		0 0.01975 0 0.01575 0 0.01225 		units box
+create_box      3 plate
+Created orthogonal box = (0 0 0) to (0.01975 0.01575 0.01225)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 region plate
+Created 32000 atoms
+  Time spent = 0.00362897 secs
+
+
+pair_style      peri/pmb
+variable	myk equal (2.0/3.0)*${myE}
+variable	myk equal (2.0/3.0)*72000000000
+
+variable	myc equal ((18.0*${myk})/(${pi}*(${delta}^4)))
+variable	myc equal ((18.0*48000000000)/(${pi}*(${delta}^4)))
+variable	myc equal ((18.0*48000000000)/(3.14159265358979*(${delta}^4)))
+variable	myc equal ((18.0*48000000000)/(3.14159265358979*(0.0015^4)))
+variable	mydelta equal (${delta}+(${delta}/100.0))
+variable	mydelta equal (0.0015+(${delta}/100.0))
+variable	mydelta equal (0.0015+(0.0015/100.0))
+variable	mys0 equal sqrt((5.0*${myG})/(9.0*${myk}*${delta}))
+variable	mys0 equal sqrt((5.0*135)/(9.0*${myk}*${delta}))
+variable	mys0 equal sqrt((5.0*135)/(9.0*48000000000*${delta}))
+variable	mys0 equal sqrt((5.0*135)/(9.0*48000000000*0.0015))
+
+variable	tmpvar1 equal ${myymax}-${crackheight}
+variable	tmpvar1 equal 0.01575-${crackheight}
+variable	tmpvar1 equal 0.01575-0.005
+variable	tmpvar2 equal 0.5*${width}
+variable	tmpvar2 equal 0.5*0.01975
+
+region		topleft  block 		0.0 ${tmpvar2} ${tmpvar1} ${myymax} ${myzmin} ${myzmax} 		units box
+region		topleft  block 		0.0 0.009875 ${tmpvar1} ${myymax} ${myzmin} ${myzmax} 		units box
+region		topleft  block 		0.0 0.009875 0.01075 ${myymax} ${myzmin} ${myzmax} 		units box
+region		topleft  block 		0.0 0.009875 0.01075 0.01575 ${myzmin} ${myzmax} 		units box
+region		topleft  block 		0.0 0.009875 0.01075 0.01575 0 ${myzmax} 		units box
+region		topleft  block 		0.0 0.009875 0.01075 0.01575 0 0.01225 		units box
+region		topright block 		${tmpvar2} ${myxmax} ${tmpvar1} ${myymax} ${myzmin} ${myzmax} 		units box
+region		topright block 		0.009875 ${myxmax} ${tmpvar1} ${myymax} ${myzmin} ${myzmax} 		units box
+region		topright block 		0.009875 0.01975 ${tmpvar1} ${myymax} ${myzmin} ${myzmax} 		units box
+region		topright block 		0.009875 0.01975 0.01075 ${myymax} ${myzmin} ${myzmax} 		units box
+region		topright block 		0.009875 0.01975 0.01075 0.01575 ${myzmin} ${myzmax} 		units box
+region		topright block 		0.009875 0.01975 0.01075 0.01575 0 ${myzmax} 		units box
+region		topright block 		0.009875 0.01975 0.01075 0.01575 0 0.01225 		units box
+set 		region topleft  type 2
+  5000 settings made for type
+set 		region topright type 3
+  5000 settings made for type
+pair_coeff      1 1 ${myc} ${mydelta} ${mys0} 0.0
+pair_coeff      1 1 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
+pair_coeff      1 1 5.43248872420337e+22 0.001515 ${mys0} 0.0
+pair_coeff      1 1 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
+pair_coeff      2 2 ${myc} ${mydelta} ${mys0} 0.0
+pair_coeff      2 2 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
+pair_coeff      2 2 5.43248872420337e+22 0.001515 ${mys0} 0.0
+pair_coeff      2 2 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
+pair_coeff      3 3 ${myc} ${mydelta} ${mys0} 0.0
+pair_coeff      3 3 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
+pair_coeff      3 3 5.43248872420337e+22 0.001515 ${mys0} 0.0
+pair_coeff      3 3 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
+pair_coeff      2 3 ${myc}        0.0 ${mys0} 0.0
+pair_coeff      2 3 5.43248872420337e+22        0.0 ${mys0} 0.0
+pair_coeff      2 3 5.43248872420337e+22        0.0 0.00102062072615966 0.0
+pair_coeff      1 2 ${myc} ${mydelta} ${mys0} 0.0
+pair_coeff      1 2 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
+pair_coeff      1 2 5.43248872420337e+22 0.001515 ${mys0} 0.0
+pair_coeff      1 2 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
+pair_coeff      1 3 ${myc} ${mydelta} ${mys0} 0.0
+pair_coeff      1 3 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
+pair_coeff      1 3 5.43248872420337e+22 0.001515 ${mys0} 0.0
+pair_coeff      1 3 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
+set             group all density ${mydensity}
+set             group all density 2440
+  32000 settings made for density
+variable	myvolume equal ($h)^3
+variable	myvolume equal (0.0005)^3
+set             group all volume ${myvolume}
+set             group all volume 1.25e-10
+  32000 settings made for volume
+
+velocity        all set 0.0 0.0 0.0 sum no units box
+
+fix             F1 all nve
+
+compute         C1 all damage/atom
+
+velocity 	all ramp vx -10.0 10.0 x ${myxmin} ${myxmax} units box
+velocity 	all ramp vx -10.0 10.0 x 0 ${myxmax} units box
+velocity 	all ramp vx -10.0 10.0 x 0 0.01975 units box
+
+variable	mystep equal 		0.8*sqrt((2.0*${mydensity})/(512*(${myc}/$h)*${myvolume}))
+variable	mystep equal 		0.8*sqrt((2.0*2440)/(512*(${myc}/$h)*${myvolume}))
+variable	mystep equal 		0.8*sqrt((2.0*2440)/(512*(5.43248872420337e+22/$h)*${myvolume}))
+variable	mystep equal 		0.8*sqrt((2.0*2440)/(512*(5.43248872420337e+22/0.0005)*${myvolume}))
+variable	mystep equal 		0.8*sqrt((2.0*2440)/(512*(5.43248872420337e+22/0.0005)*1.25e-10))
+timestep        ${mystep}
+timestep        2.11931492396226e-08
+thermo		20
+
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 0.002515
+  ghost atom cutoff = 0.002515
+  binsize = 0.0012575, bins = 16 13 10
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair peri/pmb, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix PERI_NEIGH, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Peridynamic bonds:
+  total # of bonds = 3457032
+  bonds/atom = 108.032
+Per MPI rank memory allocation (min/avg/max) = 133.6 | 133.6 | 133.6 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume 
+       0 2.0134233e+27            0            0 1.3342785e+09 2.4509971e+14 3.6292128e-06 
+      20 1.7695805e+27 1.6163291e+08            0 1.3343188e+09 2.1541601e+14 3.6292128e-06 
+      40 1.3041477e+27 4.6848143e+08            0 1.332729e+09 1.5875756e+14 3.6292128e-06 
+      60 9.8975313e+26 5.7284448e+08            0 1.2287455e+09 1.2048543e+14 3.6292128e-06 
+      80 9.3888573e+26 4.0928092e+08            0 1.0314725e+09 1.1429321e+14 3.6292128e-06 
+     100 8.3930314e+26 3.8522361e+08            0 9.4142265e+08 1.0217075e+14 3.6292128e-06 
+Loop time of 11.0398 on 1 procs for 100 steps with 32000 atoms
+
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 11.005     | 11.005     | 11.005     |   0.0 | 99.68
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 6.6042e-05 | 6.6042e-05 | 6.6042e-05 |   0.0 |  0.00
+Output  | 0.00057292 | 0.00057292 | 0.00057292 |   0.0 |  0.01
+Modify  | 0.0256     | 0.0256     | 0.0256     |   0.0 |  0.23
+Other   |            | 0.008592   |            |       |  0.08
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    6.74442e+06 ave 6.74442e+06 max 6.74442e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  1.34888e+07 ave 1.34888e+07 max 1.34888e+07 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 13488836
+Ave neighs/atom = 421.526
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:11

bench/POTENTIALS/log.16Mar18.peri.4

@@ -0,0 +1,217 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# Crack growth in notched 3D Peridynamic block
+
+# Mesh spacing
+variable    	h equal 5.00e-4
+# Peridynamic horizon
+variable    	delta equal 3.0*${h}
+variable    	delta equal 3.0*0.0005
+# Height of plate (meters)
+variable    	height equal 31.5*${h}
+variable    	height equal 31.5*0.0005
+# Width of plate (meters)
+variable    	width equal 39.5*${h}
+variable    	width equal 39.5*0.0005
+# Thickness of plate (meters)
+variable    	depth equal 24.5*${h}
+variable    	depth equal 24.5*0.0005
+# Height of notch
+variable	crackheight equal 10*${h}
+variable	crackheight equal 10*0.0005
+# Density of plate
+variable	mydensity equal 2440.0
+# Elastic modulus of material
+variable	myE equal 72.0e9
+# Strain energy release rate at branching
+variable	myG equal 135.0
+# constant, but define it as a variable here
+variable    	pi equal 3.14159265358979323846
+
+units 		si
+boundary        s s s
+atom_style      peri
+atom_modify	map array
+variable 	myskin equal 2.0*${h}
+variable 	myskin equal 2.0*0.0005
+neighbor	${myskin} bin
+neighbor	0.001 bin
+
+lattice         sc $h
+lattice         sc 0.0005
+Lattice spacing in x,y,z = 0.0005 0.0005 0.0005
+variable	myxmin equal 0.0
+variable	myxmax equal ${width}
+variable	myxmax equal 0.01975
+variable	myymin equal 0.0
+variable	myymax equal ${height}
+variable	myymax equal 0.01575
+variable	myzmin equal 0.0
+variable	myzmax equal ${depth}
+variable	myzmax equal 0.01225
+region          plate block 		${myxmin} ${myxmax} ${myymin} ${myymax} ${myzmin} ${myzmax} 		units box
+region          plate block 		0 ${myxmax} ${myymin} ${myymax} ${myzmin} ${myzmax} 		units box
+region          plate block 		0 0.01975 ${myymin} ${myymax} ${myzmin} ${myzmax} 		units box
+region          plate block 		0 0.01975 0 ${myymax} ${myzmin} ${myzmax} 		units box
+region          plate block 		0 0.01975 0 0.01575 ${myzmin} ${myzmax} 		units box
+region          plate block 		0 0.01975 0 0.01575 0 ${myzmax} 		units box
+region          plate block 		0 0.01975 0 0.01575 0 0.01225 		units box
+create_box      3 plate
+Created orthogonal box = (0 0 0) to (0.01975 0.01575 0.01225)
+  2 by 2 by 1 MPI processor grid
+create_atoms    1 region plate
+Created 32000 atoms
+  Time spent = 0.0011344 secs
+
+
+pair_style      peri/pmb
+variable	myk equal (2.0/3.0)*${myE}
+variable	myk equal (2.0/3.0)*72000000000
+
+variable	myc equal ((18.0*${myk})/(${pi}*(${delta}^4)))
+variable	myc equal ((18.0*48000000000)/(${pi}*(${delta}^4)))
+variable	myc equal ((18.0*48000000000)/(3.14159265358979*(${delta}^4)))
+variable	myc equal ((18.0*48000000000)/(3.14159265358979*(0.0015^4)))
+variable	mydelta equal (${delta}+(${delta}/100.0))
+variable	mydelta equal (0.0015+(${delta}/100.0))
+variable	mydelta equal (0.0015+(0.0015/100.0))
+variable	mys0 equal sqrt((5.0*${myG})/(9.0*${myk}*${delta}))
+variable	mys0 equal sqrt((5.0*135)/(9.0*${myk}*${delta}))
+variable	mys0 equal sqrt((5.0*135)/(9.0*48000000000*${delta}))
+variable	mys0 equal sqrt((5.0*135)/(9.0*48000000000*0.0015))
+
+variable	tmpvar1 equal ${myymax}-${crackheight}
+variable	tmpvar1 equal 0.01575-${crackheight}
+variable	tmpvar1 equal 0.01575-0.005
+variable	tmpvar2 equal 0.5*${width}
+variable	tmpvar2 equal 0.5*0.01975
+
+region		topleft  block 		0.0 ${tmpvar2} ${tmpvar1} ${myymax} ${myzmin} ${myzmax} 		units box
+region		topleft  block 		0.0 0.009875 ${tmpvar1} ${myymax} ${myzmin} ${myzmax} 		units box
+region		topleft  block 		0.0 0.009875 0.01075 ${myymax} ${myzmin} ${myzmax} 		units box
+region		topleft  block 		0.0 0.009875 0.01075 0.01575 ${myzmin} ${myzmax} 		units box
+region		topleft  block 		0.0 0.009875 0.01075 0.01575 0 ${myzmax} 		units box
+region		topleft  block 		0.0 0.009875 0.01075 0.01575 0 0.01225 		units box
+region		topright block 		${tmpvar2} ${myxmax} ${tmpvar1} ${myymax} ${myzmin} ${myzmax} 		units box
+region		topright block 		0.009875 ${myxmax} ${tmpvar1} ${myymax} ${myzmin} ${myzmax} 		units box
+region		topright block 		0.009875 0.01975 ${tmpvar1} ${myymax} ${myzmin} ${myzmax} 		units box
+region		topright block 		0.009875 0.01975 0.01075 ${myymax} ${myzmin} ${myzmax} 		units box
+region		topright block 		0.009875 0.01975 0.01075 0.01575 ${myzmin} ${myzmax} 		units box
+region		topright block 		0.009875 0.01975 0.01075 0.01575 0 ${myzmax} 		units box
+region		topright block 		0.009875 0.01975 0.01075 0.01575 0 0.01225 		units box
+set 		region topleft  type 2
+  5000 settings made for type
+set 		region topright type 3
+  5000 settings made for type
+pair_coeff      1 1 ${myc} ${mydelta} ${mys0} 0.0
+pair_coeff      1 1 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
+pair_coeff      1 1 5.43248872420337e+22 0.001515 ${mys0} 0.0
+pair_coeff      1 1 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
+pair_coeff      2 2 ${myc} ${mydelta} ${mys0} 0.0
+pair_coeff      2 2 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
+pair_coeff      2 2 5.43248872420337e+22 0.001515 ${mys0} 0.0
+pair_coeff      2 2 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
+pair_coeff      3 3 ${myc} ${mydelta} ${mys0} 0.0
+pair_coeff      3 3 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
+pair_coeff      3 3 5.43248872420337e+22 0.001515 ${mys0} 0.0
+pair_coeff      3 3 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
+pair_coeff      2 3 ${myc}        0.0 ${mys0} 0.0
+pair_coeff      2 3 5.43248872420337e+22        0.0 ${mys0} 0.0
+pair_coeff      2 3 5.43248872420337e+22        0.0 0.00102062072615966 0.0
+pair_coeff      1 2 ${myc} ${mydelta} ${mys0} 0.0
+pair_coeff      1 2 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
+pair_coeff      1 2 5.43248872420337e+22 0.001515 ${mys0} 0.0
+pair_coeff      1 2 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
+pair_coeff      1 3 ${myc} ${mydelta} ${mys0} 0.0
+pair_coeff      1 3 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
+pair_coeff      1 3 5.43248872420337e+22 0.001515 ${mys0} 0.0
+pair_coeff      1 3 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
+set             group all density ${mydensity}
+set             group all density 2440
+  32000 settings made for density
+variable	myvolume equal ($h)^3
+variable	myvolume equal (0.0005)^3
+set             group all volume ${myvolume}
+set             group all volume 1.25e-10
+  32000 settings made for volume
+
+velocity        all set 0.0 0.0 0.0 sum no units box
+
+fix             F1 all nve
+
+compute         C1 all damage/atom
+
+velocity 	all ramp vx -10.0 10.0 x ${myxmin} ${myxmax} units box
+velocity 	all ramp vx -10.0 10.0 x 0 ${myxmax} units box
+velocity 	all ramp vx -10.0 10.0 x 0 0.01975 units box
+
+variable	mystep equal 		0.8*sqrt((2.0*${mydensity})/(512*(${myc}/$h)*${myvolume}))
+variable	mystep equal 		0.8*sqrt((2.0*2440)/(512*(${myc}/$h)*${myvolume}))
+variable	mystep equal 		0.8*sqrt((2.0*2440)/(512*(5.43248872420337e+22/$h)*${myvolume}))
+variable	mystep equal 		0.8*sqrt((2.0*2440)/(512*(5.43248872420337e+22/0.0005)*${myvolume}))
+variable	mystep equal 		0.8*sqrt((2.0*2440)/(512*(5.43248872420337e+22/0.0005)*1.25e-10))
+timestep        ${mystep}
+timestep        2.11931492396226e-08
+thermo		20
+
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 0.002515
+  ghost atom cutoff = 0.002515
+  binsize = 0.0012575, bins = 16 13 10
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair peri/pmb, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix PERI_NEIGH, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Peridynamic bonds:
+  total # of bonds = 3457032
+  bonds/atom = 108.032
+Per MPI rank memory allocation (min/avg/max) = 47.63 | 48.11 | 48.78 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume 
+       0 2.0134233e+27            0            0 1.3342785e+09 2.4509971e+14 3.6292128e-06 
+      20 1.7695805e+27 1.6163291e+08            0 1.3343188e+09 2.1541601e+14 3.6292128e-06 
+      40 1.3041477e+27 4.6848143e+08            0 1.332729e+09 1.5875756e+14 3.6292128e-06 
+      60 9.8975313e+26 5.7284448e+08            0 1.2287455e+09 1.2048543e+14 3.6292128e-06 
+      80 9.3888573e+26 4.0928092e+08            0 1.0314725e+09 1.1429321e+14 3.6292128e-06 
+     100 8.3930314e+26 3.8522361e+08            0 9.4142265e+08 1.0217075e+14 3.6292128e-06 
+Loop time of 2.8928 on 4 procs for 100 steps with 32000 atoms
+
+99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.7472     | 2.7951     | 2.8585     |   2.9 | 96.62
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.019592   | 0.083156   | 0.13278    |  17.0 |  2.87
+Output  | 0.00022125 | 0.00034326 | 0.00058961 |   0.0 |  0.01
+Modify  | 0.0083542  | 0.0089623  | 0.0095983  |   0.5 |  0.31
+Other   |            | 0.005276   |            |       |  0.18
+
+Nlocal:    8000 ave 8000 max 8000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    5125 ave 5125 max 5125 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    1.6861e+06 ave 1.77502e+06 max 1.60625e+06 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+FullNghs:  3.37221e+06 ave 3.41832e+06 max 3.3261e+06 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 13488836
+Ave neighs/atom = 421.526
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:03

bench/POTENTIALS/log.16Mar18.protein.1

@@ -0,0 +1,123 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# Rhodopsin model
+
+units           real
+neighbor	2.0 bin
+neigh_modify    delay 5 every 1
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+pair_style      lj/charmm/coul/long 8.0 10.0
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data       data.protein
+  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  8 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  27723 bonds
+  reading angles ...
+  40467 angles
+  reading dihedrals ...
+  56829 dihedrals
+  reading impropers ...
+  1034 impropers
+  4 = max # of 1-2 neighbors
+  12 = max # of 1-3 neighbors
+  24 = max # of 1-4 neighbors
+  26 = max # of special neighbors
+
+fix             1 all shake 0.0001 5 0 m 1.0 a 232
+  1617 = # of size 2 clusters
+  3633 = # of size 3 clusters
+  747 = # of size 4 clusters
+  4233 = # of frozen angles
+fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
+
+special_bonds   charmm
+
+thermo_style    multi
+timestep        2.0
+
+run		100
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.248835
+  grid = 25 32 32
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0355478
+  estimated relative force accuracy = 0.000107051
+  using double precision FFTs
+  3d grid and FFT values/proc = 41070 25600
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 10 13 13
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 140 | 140 | 140 Mbytes
+---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
+TotEng   =    -25356.2064 KinEng   =     21444.8313 Temp     =       299.0397 
+PotEng   =    -46801.0377 E_bond   =      2537.9940 E_angle  =     10921.3742 
+E_dihed  =      5211.7865 E_impro  =       213.5116 E_vdwl   =     -2307.8634 
+E_coul   =    207025.8927 E_long   =   -270403.7333 Press    =      -149.3301 
+Volume   =    307995.0335 
+---------------- Step      100 ----- CPU =     23.7567 (sec) ----------------
+TotEng   =    -25290.7386 KinEng   =     21591.9096 Temp     =       301.0906 
+PotEng   =    -46882.6482 E_bond   =      2567.9789 E_angle  =     10781.9556 
+E_dihed  =      5198.7493 E_impro  =       216.7863 E_vdwl   =     -1902.6458 
+E_coul   =    206659.5007 E_long   =   -270404.9733 Press    =         6.7898 
+Volume   =    308133.9933 
+Loop time of 23.7568 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 0.727 ns/day, 32.995 hours/ns, 4.209 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 17.905     | 17.905     | 17.905     |   0.0 | 75.37
+Bond    | 0.73417    | 0.73417    | 0.73417    |   0.0 |  3.09
+Kspace  | 1.4676     | 1.4676     | 1.4676     |   0.0 |  6.18
+Neigh   | 2.9907     | 2.9907     | 2.9907     |   0.0 | 12.59
+Comm    | 0.037427   | 0.037427   | 0.037427   |   0.0 |  0.16
+Output  | 0.00011754 | 0.00011754 | 0.00011754 |   0.0 |  0.00
+Modify  | 0.60985    | 0.60985    | 0.60985    |   0.0 |  2.57
+Other   |            | 0.01201    |            |       |  0.05
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    47958 ave 47958 max 47958 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 12028098
+Ave neighs/atom = 375.878
+Ave special neighs/atom = 7.43187
+Neighbor list builds = 11
+Dangerous builds = 0
+Total wall time: 0:00:24

bench/POTENTIALS/log.16Mar18.protein.4

@@ -0,0 +1,123 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# Rhodopsin model
+
+units           real
+neighbor	2.0 bin
+neigh_modify    delay 5 every 1
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+pair_style      lj/charmm/coul/long 8.0 10.0
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data       data.protein
+  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  8 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  27723 bonds
+  reading angles ...
+  40467 angles
+  reading dihedrals ...
+  56829 dihedrals
+  reading impropers ...
+  1034 impropers
+  4 = max # of 1-2 neighbors
+  12 = max # of 1-3 neighbors
+  24 = max # of 1-4 neighbors
+  26 = max # of special neighbors
+
+fix             1 all shake 0.0001 5 0 m 1.0 a 232
+  1617 = # of size 2 clusters
+  3633 = # of size 3 clusters
+  747 = # of size 4 clusters
+  4233 = # of frozen angles
+fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
+
+special_bonds   charmm
+
+thermo_style    multi
+timestep        2.0
+
+run		100
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.248835
+  grid = 25 32 32
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0355478
+  estimated relative force accuracy = 0.000107051
+  using double precision FFTs
+  3d grid and FFT values/proc = 13230 6400
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 10 13 13
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 49.07 | 49.17 | 49.46 Mbytes
+---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
+TotEng   =    -25356.2064 KinEng   =     21444.8313 Temp     =       299.0397 
+PotEng   =    -46801.0377 E_bond   =      2537.9940 E_angle  =     10921.3742 
+E_dihed  =      5211.7865 E_impro  =       213.5116 E_vdwl   =     -2307.8634 
+E_coul   =    207025.8927 E_long   =   -270403.7333 Press    =      -149.3301 
+Volume   =    307995.0335 
+---------------- Step      100 ----- CPU =      6.3997 (sec) ----------------
+TotEng   =    -25290.7386 KinEng   =     21591.9096 Temp     =       301.0906 
+PotEng   =    -46882.6483 E_bond   =      2567.9789 E_angle  =     10781.9556 
+E_dihed  =      5198.7493 E_impro  =       216.7863 E_vdwl   =     -1902.6458 
+E_coul   =    206659.5007 E_long   =   -270404.9733 Press    =         6.7898 
+Volume   =    308133.9933 
+Loop time of 6.39977 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 2.700 ns/day, 8.889 hours/ns, 15.626 timesteps/s
+98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.4434     | 4.5321     | 4.6846     |   4.3 | 70.82
+Bond    | 0.17894    | 0.18568    | 0.19951    |   1.9 |  2.90
+Kspace  | 0.4651     | 0.61064    | 0.69123    |  11.1 |  9.54
+Neigh   | 0.7739     | 0.77394    | 0.774      |   0.0 | 12.09
+Comm    | 0.057676   | 0.069183   | 0.07901    |   3.0 |  1.08
+Output  | 5.6505e-05 | 6.6578e-05 | 9.4414e-05 |   0.0 |  0.00
+Modify  | 0.21444    | 0.21866    | 0.22524    |   0.9 |  3.42
+Other   |            | 0.009451   |            |       |  0.15
+
+Nlocal:    8000 ave 8143 max 7933 min
+Histogram: 1 2 0 0 0 0 0 0 0 1
+Nghost:    22733.5 ave 22769 max 22693 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Neighs:    3.00702e+06 ave 3.0975e+06 max 2.96492e+06 min
+Histogram: 1 2 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 12028098
+Ave neighs/atom = 375.878
+Ave special neighs/atom = 7.43187
+Neighbor list builds = 11
+Dangerous builds = 0
+Total wall time: 0:00:06

bench/POTENTIALS/log.16Mar18.reaxc.1

@@ -0,0 +1,93 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
+
+units		real
+atom_style	charge
+
+read_data	data.reax
+  orthogonal box = (0 0 0) to (9.49107 9.49107 6.99123)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  58 atoms
+
+replicate	7 8 10
+  orthogonal box = (0 0 0) to (66.4375 75.9285 69.9123)
+  1 by 1 by 1 MPI processor grid
+  32480 atoms
+  Time spent = 0.00162625 secs
+
+velocity	all create 300.0 9999
+
+pair_style	reax/c NULL
+pair_coeff      * * ffield.reax C H O N
+
+timestep	0.1
+fix		1 all nve
+fix             2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
+
+thermo		10
+thermo_style	custom step temp ke pe pxx pyy pzz etotal
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 12 13 12
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair reax/c, perpetual
+      attributes: half, newton off, ghost
+      pair build: half/bin/newtoff/ghost
+      stencil: half/ghost/bin/3d/newtoff
+      bin: standard
+  (2) fix qeq/reax, perpetual, copy from (1)
+      attributes: half, newton off, ghost
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 1727 | 1727 | 1727 Mbytes
+Step Temp KinEng PotEng Pxx Pyy Pzz TotEng 
+       0          300    29044.119   -3232140.8    22804.879   -29365.593    6302.5637   -3203096.6 
+      10    299.37479     28983.59   -3232075.2    21746.778    -23987.41    7610.2967   -3203091.6 
+      20     295.5855    28616.735   -3231710.1    18178.568   -10871.882    10603.247   -3203093.3 
+      30    289.48845    28026.457   -3231123.2    12146.362    4985.5572    13364.455   -3203096.8 
+      40    282.66404     27365.76   -3230467.5    4284.2794    18132.771    14133.719   -3203101.7 
+      50    274.97005    26620.876   -3229730.4     -3719.11    25519.692    12551.708   -3203109.5 
+      60    266.11301    25763.393   -3228883.8   -9271.4049    27307.216    9753.2509   -3203120.4 
+      70     259.3263    25106.346   -3228237.2   -11150.726    24238.382    6578.5306   -3203130.8 
+      80    260.33956    25204.444   -3228344.2   -9576.6006     16737.65    3454.5747   -3203139.7 
+      90    269.90199    26130.219   -3229275.5    -5906.376    5246.1572    467.31789   -3203145.3 
+     100    280.76717    27182.117   -3230330.6   -1363.8281   -8133.2509   -1689.7711   -3203148.5 
+Loop time of 437.886 on 1 procs for 100 steps with 32480 atoms
+
+Performance: 0.002 ns/day, 12163.512 hours/ns, 0.228 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 350.29     | 350.29     | 350.29     |   0.0 | 80.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.026264   | 0.026264   | 0.026264   |   0.0 |  0.01
+Output  | 0.0024614  | 0.0024614  | 0.0024614  |   0.0 |  0.00
+Modify  | 87.55      | 87.55      | 87.55      |   0.0 | 19.99
+Other   |            | 0.01296    |            |       |  0.00
+
+Nlocal:    32480 ave 32480 max 32480 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    45128 ave 45128 max 45128 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.27781e+07 ave 1.27781e+07 max 1.27781e+07 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 12778082
+Ave neighs/atom = 393.414
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:07:24

bench/POTENTIALS/log.16Mar18.reaxc.4

@@ -0,0 +1,93 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
+
+units		real
+atom_style	charge
+
+read_data	data.reax
+  orthogonal box = (0 0 0) to (9.49107 9.49107 6.99123)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  58 atoms
+
+replicate	7 8 10
+  orthogonal box = (0 0 0) to (66.4375 75.9285 69.9123)
+  1 by 2 by 2 MPI processor grid
+  32480 atoms
+  Time spent = 0.000803709 secs
+
+velocity	all create 300.0 9999
+
+pair_style	reax/c NULL
+pair_coeff      * * ffield.reax C H O N
+
+timestep	0.1
+fix		1 all nve
+fix             2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
+
+thermo		10
+thermo_style	custom step temp ke pe pxx pyy pzz etotal
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 12 13 12
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair reax/c, perpetual
+      attributes: half, newton off, ghost
+      pair build: half/bin/newtoff/ghost
+      stencil: half/ghost/bin/3d/newtoff
+      bin: standard
+  (2) fix qeq/reax, perpetual, copy from (1)
+      attributes: half, newton off, ghost
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 647 | 647 | 647 Mbytes
+Step Temp KinEng PotEng Pxx Pyy Pzz TotEng 
+       0          300    29044.119   -3232140.8    22804.879   -29365.593    6302.5638   -3203096.6 
+      10    299.37479     28983.59   -3232075.2    21746.773   -23987.409    7610.2911   -3203091.6 
+      20    295.58552    28616.737   -3231710.1    18178.576   -10871.874    10603.421   -3203093.3 
+      30    289.48843    28026.455   -3231123.3    12146.158    4985.3436    13364.461   -3203096.8 
+      40    282.66409    27365.764   -3230467.5    4284.5077    18133.151    14133.949   -3203101.7 
+      50    274.97008    26620.879   -3229730.3    -3718.536    25520.328    12552.195   -3203109.5 
+      60    266.11301    25763.393   -3228883.7   -9271.0381    27307.591    9753.5339   -3203120.4 
+      70    259.32631    25106.348   -3228237.1   -11150.314    24238.962    6578.8636   -3203130.8 
+      80    260.33966    25204.453   -3228344.1   -9575.5709    16738.467    3455.2525   -3203139.7 
+      90    269.90213    26130.231   -3229275.5   -5906.0456    5246.2122    467.43473   -3203145.2 
+     100    280.76727    27182.127   -3230330.6   -1363.1733   -8132.8726   -1689.3275   -3203148.4 
+Loop time of 128.275 on 4 procs for 100 steps with 32480 atoms
+
+Performance: 0.007 ns/day, 3563.196 hours/ns, 0.780 timesteps/s
+99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 92.314     | 97.932     | 103.53     |  44.1 | 76.34
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.039458   | 5.6409     | 11.263     | 184.0 |  4.40
+Output  | 0.00086117 | 0.0010868  | 0.0016167  |   0.9 |  0.00
+Modify  | 24.687     | 24.688     | 24.69      |   0.0 | 19.25
+Other   |            | 0.01323    |            |       |  0.01
+
+Nlocal:    8120 ave 8120 max 8120 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    21992 ave 21992 max 21992 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    3.48274e+06 ave 3.48274e+06 max 3.48274e+06 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 13930976
+Ave neighs/atom = 428.909
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:02:10

bench/POTENTIALS/log.16Mar18.rebo.1

@@ -0,0 +1,87 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# REBO polyethelene benchmark
+
+units		    metal
+atom_style	    atomic
+
+read_data	    data.rebo
+  orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  60 atoms
+
+replicate	    17 16 2
+  orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
+  1 by 1 by 1 MPI processor grid
+  32640 atoms
+  Time spent = 0.00151849 secs
+
+neighbor	    0.5 bin
+neigh_modify	    delay 5 every 1
+
+pair_style	    rebo
+pair_coeff	    * * CH.airebo C H
+
+velocity	    all create 300.0 761341
+
+fix		    1 all nve
+timestep	    0.0005
+
+thermo		    10
+run		    100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.5
+  ghost atom cutoff = 6.5
+  binsize = 3.25, bins = 22 21 16
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair rebo, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 34.21 | 34.21 | 34.21 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          300   -138442.48            0    -137176.8    2464.5258 
+      10    179.38052   -137930.92            0   -137174.12     15656.95 
+      20    206.87725   -138046.63            0   -137173.83   -24042.005 
+      30    150.80048   -137807.07            0   -137170.86   -16524.069 
+      40    173.25027      -137902            0   -137171.07   -5716.7297 
+      50    151.80552   -137812.01            0   -137171.55    3481.1096 
+      60    199.08762   -138013.46            0   -137173.53    17882.906 
+      70     217.8592   -138093.51            0   -137174.38   -12269.648 
+      80    202.37612   -138029.05            0   -137175.24   -7622.1573 
+      90      194.905   -137996.68            0    -137174.4   -32267.297 
+     100    185.17966   -137954.16            0    -137172.9   -6902.1493 
+Loop time of 5.17257 on 1 procs for 100 steps with 32640 atoms
+
+Performance: 0.835 ns/day, 28.737 hours/ns, 19.333 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.3427     | 3.3427     | 3.3427     |   0.0 | 64.62
+Neigh   | 1.7764     | 1.7764     | 1.7764     |   0.0 | 34.34
+Comm    | 0.017914   | 0.017914   | 0.017914   |   0.0 |  0.35
+Output  | 0.0011199  | 0.0011199  | 0.0011199  |   0.0 |  0.02
+Modify  | 0.024357   | 0.024357   | 0.024357   |   0.0 |  0.47
+Other   |            | 0.01004    |            |       |  0.19
+
+Nlocal:    32640 ave 32640 max 32640 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    26460 ave 26460 max 26460 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  4.90213e+06 ave 4.90213e+06 max 4.90213e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 4902132
+Ave neighs/atom = 150.188
+Neighbor list builds = 9
+Dangerous builds = 0
+Total wall time: 0:00:05

bench/POTENTIALS/log.16Mar18.rebo.4

@@ -0,0 +1,87 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# REBO polyethelene benchmark
+
+units		    metal
+atom_style	    atomic
+
+read_data	    data.rebo
+  orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
+  1 by 1 by 4 MPI processor grid
+  reading atoms ...
+  60 atoms
+
+replicate	    17 16 2
+  orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
+  2 by 2 by 1 MPI processor grid
+  32640 atoms
+  Time spent = 0.000838995 secs
+
+neighbor	    0.5 bin
+neigh_modify	    delay 5 every 1
+
+pair_style	    rebo
+pair_coeff	    * * CH.airebo C H
+
+velocity	    all create 300.0 761341
+
+fix		    1 all nve
+timestep	    0.0005
+
+thermo		    10
+run		    100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.5
+  ghost atom cutoff = 6.5
+  binsize = 3.25, bins = 22 21 16
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair rebo, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 11.75 | 11.94 | 12.13 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          300   -138442.48            0    -137176.8    2464.5258 
+      10    179.38052   -137930.92            0   -137174.12     15656.95 
+      20    206.87725   -138046.63            0   -137173.83   -24042.005 
+      30    150.80048   -137807.07            0   -137170.86   -16524.069 
+      40    173.25027      -137902            0   -137171.07   -5716.7297 
+      50    151.80552   -137812.01            0   -137171.55    3481.1096 
+      60    199.08762   -138013.46            0   -137173.53    17882.906 
+      70     217.8592   -138093.51            0   -137174.38   -12269.648 
+      80    202.37612   -138029.05            0   -137175.24   -7622.1573 
+      90      194.905   -137996.68            0    -137174.4   -32267.297 
+     100    185.17966   -137954.16            0    -137172.9   -6902.1493 
+Loop time of 1.52214 on 4 procs for 100 steps with 32640 atoms
+
+Performance: 2.838 ns/day, 8.456 hours/ns, 65.697 timesteps/s
+98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.88531    | 0.90632    | 0.92546    |   1.6 | 59.54
+Neigh   | 0.53954    | 0.54258    | 0.54621    |   0.3 | 35.65
+Comm    | 0.035654   | 0.058364   | 0.079543   |   7.0 |  3.83
+Output  | 0.00048494 | 0.00065351 | 0.0011017  |   0.0 |  0.04
+Modify  | 0.0090034  | 0.0090633  | 0.0091114  |   0.0 |  0.60
+Other   |            | 0.005168   |            |       |  0.34
+
+Nlocal:    8160 ave 8163 max 8157 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Nghost:    11605.8 ave 11615 max 11593 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  1.22553e+06 ave 1.22734e+06 max 1.22455e+06 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+
+Total # of neighbors = 4902132
+Ave neighs/atom = 150.188
+Neighbor list builds = 9
+Dangerous builds = 0
+Total wall time: 0:00:01

bench/POTENTIALS/log.16Mar18.spce.1

@@ -0,0 +1,132 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# SPC/E water box benchmark
+
+units		real
+atom_style	full
+
+read_data	data.spce
+  orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  4500 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  3000 bonds
+  reading angles ...
+  1500 angles
+  2 = max # of 1-2 neighbors
+  1 = max # of 1-3 neighbors
+  1 = max # of 1-4 neighbors
+  2 = max # of special neighbors
+
+replicate	2 4 1
+  orthogonal box = (0.02645 0.02645 0.02641) to (71.0392 142.052 35.4736)
+  1 by 1 by 1 MPI processor grid
+  36000 atoms
+  24000 bonds
+  12000 angles
+  2 = max # of 1-2 neighbors
+  1 = max # of 1-3 neighbors
+  1 = max # of 1-4 neighbors
+  2 = max # of special neighbors
+  Time spent = 0.0105426 secs
+
+pair_style	lj/cut/coul/long 9.8 9.8
+kspace_style	pppm 1.0e-4
+
+pair_coeff	1 1 0.15535 3.166
+pair_coeff	* 2 0.0000 0.0000
+
+bond_style	harmonic
+angle_style	harmonic
+dihedral_style	none
+improper_style	none
+
+bond_coeff	1 1000.00 1.000
+angle_coeff	1 100.0 109.47
+
+special_bonds   lj/coul 0.0 0.0 0.5
+  2 = max # of 1-2 neighbors
+  1 = max # of 1-3 neighbors
+  1 = max # of 1-4 neighbors
+  2 = max # of special neighbors
+
+neighbor        2.0 bin
+neigh_modify	every 1 delay 10 check yes
+
+fix		1 all shake 0.0001 20 0 b 1 a 1
+  0 = # of size 2 clusters
+  0 = # of size 3 clusters
+  0 = # of size 4 clusters
+  12000 = # of frozen angles
+fix		2 all nvt temp 300.0 300.0 100.0
+
+velocity	all create 300 432567 dist uniform
+
+timestep	2.0
+
+thermo_style    one
+thermo		50
+
+run		100
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.268801
+  grid = 36 64 24
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0331015
+  estimated relative force accuracy = 9.96841e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 91977 55296
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 11.8
+  ghost atom cutoff = 11.8
+  binsize = 5.9, bins = 13 25 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 105.1 | 105.1 | 105.1 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          300   -133281.51            0   -111820.57    516.17807 
+      50    264.98553   -136986.74            0   -118030.61   -440.29256 
+     100    274.45966   -136364.57            0   -116730.69   -128.61949 
+Loop time of 20.172 on 1 procs for 100 steps with 36000 atoms
+
+Performance: 0.857 ns/day, 28.017 hours/ns, 4.957 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 15.818     | 15.818     | 15.818     |   0.0 | 78.41
+Bond    | 7.8201e-05 | 7.8201e-05 | 7.8201e-05 |   0.0 |  0.00
+Kspace  | 1.966      | 1.966      | 1.966      |   0.0 |  9.75
+Neigh   | 2.0639     | 2.0639     | 2.0639     |   0.0 | 10.23
+Comm    | 0.043918   | 0.043918   | 0.043918   |   0.0 |  0.22
+Output  | 0.00025153 | 0.00025153 | 0.00025153 |   0.0 |  0.00
+Modify  | 0.27056    | 0.27056    | 0.27056    |   0.0 |  1.34
+Other   |            | 0.009522   |            |       |  0.05
+
+Nlocal:    36000 ave 36000 max 36000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    56963 ave 56963 max 56963 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.24625e+07 ave 1.24625e+07 max 1.24625e+07 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 12462451
+Ave neighs/atom = 346.179
+Ave special neighs/atom = 2
+Neighbor list builds = 9
+Dangerous builds = 6
+Total wall time: 0:00:20

bench/POTENTIALS/log.16Mar18.spce.4

@@ -0,0 +1,132 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# SPC/E water box benchmark
+
+units		real
+atom_style	full
+
+read_data	data.spce
+  orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  4500 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  3000 bonds
+  reading angles ...
+  1500 angles
+  2 = max # of 1-2 neighbors
+  1 = max # of 1-3 neighbors
+  1 = max # of 1-4 neighbors
+  2 = max # of special neighbors
+
+replicate	2 4 1
+  orthogonal box = (0.02645 0.02645 0.02641) to (71.0392 142.052 35.4736)
+  1 by 4 by 1 MPI processor grid
+  36000 atoms
+  24000 bonds
+  12000 angles
+  2 = max # of 1-2 neighbors
+  1 = max # of 1-3 neighbors
+  1 = max # of 1-4 neighbors
+  2 = max # of special neighbors
+  Time spent = 0.00535488 secs
+
+pair_style	lj/cut/coul/long 9.8 9.8
+kspace_style	pppm 1.0e-4
+
+pair_coeff	1 1 0.15535 3.166
+pair_coeff	* 2 0.0000 0.0000
+
+bond_style	harmonic
+angle_style	harmonic
+dihedral_style	none
+improper_style	none
+
+bond_coeff	1 1000.00 1.000
+angle_coeff	1 100.0 109.47
+
+special_bonds   lj/coul 0.0 0.0 0.5
+  2 = max # of 1-2 neighbors
+  1 = max # of 1-3 neighbors
+  1 = max # of 1-4 neighbors
+  2 = max # of special neighbors
+
+neighbor        2.0 bin
+neigh_modify	every 1 delay 10 check yes
+
+fix		1 all shake 0.0001 20 0 b 1 a 1
+  0 = # of size 2 clusters
+  0 = # of size 3 clusters
+  0 = # of size 4 clusters
+  12000 = # of frozen angles
+fix		2 all nvt temp 300.0 300.0 100.0
+
+velocity	all create 300 432567 dist uniform
+
+timestep	2.0
+
+thermo_style    one
+thermo		50
+
+run		100
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.268801
+  grid = 36 64 24
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0331015
+  estimated relative force accuracy = 9.96841e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 27993 13824
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 11.8
+  ghost atom cutoff = 11.8
+  binsize = 5.9, bins = 13 25 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 37.74 | 37.74 | 37.74 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          300   -133281.51            0   -111820.57    516.17807 
+      50    264.98553   -136986.74            0   -118030.61   -440.29256 
+     100    274.45966   -136364.57            0   -116730.69   -128.61949 
+Loop time of 5.43807 on 4 procs for 100 steps with 36000 atoms
+
+Performance: 3.178 ns/day, 7.553 hours/ns, 18.389 timesteps/s
+99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.0016     | 4.0968     | 4.1706     |   3.3 | 75.34
+Bond    | 7.1049e-05 | 8.5771e-05 | 0.00010586 |   0.0 |  0.00
+Kspace  | 0.56386    | 0.63614    | 0.73036    |   8.3 | 11.70
+Neigh   | 0.52575    | 0.52587    | 0.52594    |   0.0 |  9.67
+Comm    | 0.045847   | 0.047308   | 0.048331   |   0.4 |  0.87
+Output  | 9.1314e-05 | 0.00012183 | 0.00021172 |   0.0 |  0.00
+Modify  | 0.12561    | 0.1258     | 0.12605    |   0.1 |  2.31
+Other   |            | 0.005944   |            |       |  0.11
+
+Nlocal:    9000 ave 9002 max 8998 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    24134.2 ave 24184 max 24062 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+Neighs:    3.11561e+06 ave 3.11676e+06 max 3.11446e+06 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+
+Total # of neighbors = 12462451
+Ave neighs/atom = 346.179
+Ave special neighs/atom = 2
+Neighbor list builds = 9
+Dangerous builds = 6
+Total wall time: 0:00:05

bench/POTENTIALS/log.16Mar18.sw.1

@@ -0,0 +1,77 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# bulk Si via Stillinger-Weber
+
+units		metal
+atom_style	atomic
+
+lattice		diamond 5.431
+Lattice spacing in x,y,z = 5.431 5.431 5.431
+region		box block 0 20 0 20 0 10
+create_box	1 box
+Created orthogonal box = (0 0 0) to (108.62 108.62 54.31)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  Time spent = 0.00191712 secs
+
+pair_style	sw
+pair_coeff	* * Si.sw Si
+mass            1 28.06
+
+velocity	all create 1000.0 376847 loop geom
+
+neighbor	1.0 bin
+neigh_modify    delay 5 every 1
+
+fix		1 all nve
+
+timestep	0.001
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.77118
+  ghost atom cutoff = 4.77118
+  binsize = 2.38559, bins = 46 46 23
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair sw, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 12.52 | 12.52 | 12.52 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1000    -138771.2            0      -134635    6866.6499 
+     100    508.80533   -136736.12            0    -134631.6    6361.7858 
+Loop time of 5.66634 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 1.525 ns/day, 15.740 hours/ns, 17.648 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.5464     | 5.5464     | 5.5464     |   0.0 | 97.88
+Neigh   | 0.075834   | 0.075834   | 0.075834   |   0.0 |  1.34
+Comm    | 0.0092049  | 0.0092049  | 0.0092049  |   0.0 |  0.16
+Output  | 0.00010991 | 0.00010991 | 0.00010991 |   0.0 |  0.00
+Modify  | 0.024666   | 0.024666   | 0.024666   |   0.0 |  0.44
+Other   |            | 0.01014    |            |       |  0.18
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    12495 ave 12495 max 12495 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  894818 ave 894818 max 894818 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 894818
+Ave neighs/atom = 27.9631
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:05

bench/POTENTIALS/log.16Mar18.sw.4

@@ -0,0 +1,77 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# bulk Si via Stillinger-Weber
+
+units		metal
+atom_style	atomic
+
+lattice		diamond 5.431
+Lattice spacing in x,y,z = 5.431 5.431 5.431
+region		box block 0 20 0 20 0 10
+create_box	1 box
+Created orthogonal box = (0 0 0) to (108.62 108.62 54.31)
+  2 by 2 by 1 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  Time spent = 0.000604153 secs
+
+pair_style	sw
+pair_coeff	* * Si.sw Si
+mass            1 28.06
+
+velocity	all create 1000.0 376847 loop geom
+
+neighbor	1.0 bin
+neigh_modify    delay 5 every 1
+
+fix		1 all nve
+
+timestep	0.001
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.77118
+  ghost atom cutoff = 4.77118
+  binsize = 2.38559, bins = 46 46 23
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair sw, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.104 | 4.104 | 4.104 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1000    -138771.2            0      -134635    6866.6499 
+     100    508.80533   -136736.12            0    -134631.6    6361.7858 
+Loop time of 1.47105 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 5.873 ns/day, 4.086 hours/ns, 67.978 timesteps/s
+98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.3788     | 1.3929     | 1.4053     |   0.8 | 94.69
+Neigh   | 0.019134   | 0.019502   | 0.019816   |   0.2 |  1.33
+Comm    | 0.024183   | 0.035734   | 0.049122   |   4.7 |  2.43
+Output  | 5.1975e-05 | 6.6102e-05 | 0.00010204 |   0.0 |  0.00
+Modify  | 0.0063825  | 0.0064374  | 0.0064764  |   0.0 |  0.44
+Other   |            | 0.01638    |            |       |  1.11
+
+Nlocal:    8000 ave 8015 max 7978 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+Nghost:    4995 ave 5017 max 4980 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  223704 ave 224108 max 223131 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+
+Total # of neighbors = 894818
+Ave neighs/atom = 27.9631
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:01

bench/POTENTIALS/log.16Mar18.tersoff.1

@@ -0,0 +1,77 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# bulk Si via Tersoff
+
+units		metal
+atom_style	atomic
+
+lattice		diamond 5.431
+Lattice spacing in x,y,z = 5.431 5.431 5.431
+region		box block 0 20 0 20 0 10
+create_box	1 box
+Created orthogonal box = (0 0 0) to (108.62 108.62 54.31)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  Time spent = 0.0019412 secs
+
+pair_style	tersoff
+pair_coeff	* * Si.tersoff Si
+mass            1 28.06
+
+velocity	all create 1000.0 376847 loop geom
+
+neighbor	1.0 bin
+neigh_modify    delay 5 every 1
+
+fix		1 all nve
+
+timestep	0.001
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.2
+  ghost atom cutoff = 4.2
+  binsize = 2.1, bins = 52 52 26
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair tersoff, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 11.1 | 11.1 | 11.1 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1000   -148173.19            0   -144036.99    7019.4434 
+     100    430.57813   -145815.61            0   -144034.65   -14550.734 
+Loop time of 8.53088 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 1.013 ns/day, 23.697 hours/ns, 11.722 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 8.4236     | 8.4236     | 8.4236     |   0.0 | 98.74
+Neigh   | 0.065852   | 0.065852   | 0.065852   |   0.0 |  0.77
+Comm    | 0.0078607  | 0.0078607  | 0.0078607  |   0.0 |  0.09
+Output  | 0.00010872 | 0.00010872 | 0.00010872 |   0.0 |  0.00
+Modify  | 0.023968   | 0.023968   | 0.023968   |   0.0 |  0.28
+Other   |            | 0.009521   |            |       |  0.11
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    11537 ave 11537 max 11537 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  530500 ave 530500 max 530500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 530500
+Ave neighs/atom = 16.5781
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:08

bench/POTENTIALS/log.16Mar18.tersoff.4

@@ -0,0 +1,77 @@
+LAMMPS (16 Mar 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# bulk Si via Tersoff
+
+units		metal
+atom_style	atomic
+
+lattice		diamond 5.431
+Lattice spacing in x,y,z = 5.431 5.431 5.431
+region		box block 0 20 0 20 0 10
+create_box	1 box
+Created orthogonal box = (0 0 0) to (108.62 108.62 54.31)
+  2 by 2 by 1 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  Time spent = 0.000605822 secs
+
+pair_style	tersoff
+pair_coeff	* * Si.tersoff Si
+mass            1 28.06
+
+velocity	all create 1000.0 376847 loop geom
+
+neighbor	1.0 bin
+neigh_modify    delay 5 every 1
+
+fix		1 all nve
+
+timestep	0.001
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.2
+  ghost atom cutoff = 4.2
+  binsize = 2.1, bins = 52 52 26
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair tersoff, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.753 | 3.753 | 3.753 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1000   -148173.19            0   -144036.99    7019.4434 
+     100    430.57813   -145815.61            0   -144034.65   -14550.734 
+Loop time of 2.16161 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 3.997 ns/day, 6.004 hours/ns, 46.262 timesteps/s
+99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.1122     | 2.1165     | 2.122      |   0.2 | 97.91
+Neigh   | 0.016894   | 0.016915   | 0.016955   |   0.0 |  0.78
+Comm    | 0.012348   | 0.017858   | 0.022105   |   2.7 |  0.83
+Output  | 4.7684e-05 | 6.2048e-05 | 9.9421e-05 |   0.0 |  0.00
+Modify  | 0.0064063  | 0.0064579  | 0.0065169  |   0.0 |  0.30
+Other   |            | 0.003793   |            |       |  0.18
+
+Nlocal:    8000 ave 8005 max 7993 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+Nghost:    4580.25 ave 4593 max 4567 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  132625 ave 132785 max 132562 min
+Histogram: 2 1 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 530500
+Ave neighs/atom = 16.5781
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:02

bench/POTENTIALS/log.26Jun12.adp.1

@@ -1,52 +0,0 @@
-LAMMPS (29 Jun 2012)
-# bulk Ni in ADP
-
-units		metal
-atom_style	atomic
-
-lattice		fcc 3.52
-Lattice spacing in x,y,z = 3.52 3.52 3.52
-region		box block 0 20 0 20 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
-  1 by 1 by 1 MPI processor grid
-create_atoms	1 box
-Created 32000 atoms
-
-pair_style	adp
-pair_coeff	* * Ni.adp Ni
-
-velocity	all create 1600.0 376847 loop geom
-
-neighbor	1.0 bin
-neigh_modify    delay 5 every 1
-
-fix		1 all nve
-
-timestep	0.005
-
-run		100
-Memory usage per processor = 25.3022 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1600      -142400            0   -135782.09    20259.105 
-     100    793.05485   -139023.13            0    -135742.9    32175.694 
-Loop time of 17.8688 on 1 procs for 100 steps with 32000 atoms
-
-Pair  time (%) = 17.078 (95.5745)
-Neigh time (%) = 0.677115 (3.78937)
-Comm  time (%) = 0.0346231 (0.193763)
-Outpt time (%) = 0.000118971 (0.000665802)
-Other time (%) = 0.0789182 (0.441653)
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    19911 ave 19911 max 19911 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    1.33704e+06 ave 1.33704e+06 max 1.33704e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1337035
-Ave neighs/atom = 41.7823
-Neighbor list builds = 13
-Dangerous builds = 0
-