git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@16053 f3b2605a-c512-4ea7-a41b-209d697bcdaa

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@16051 f3b2605a-c512-4ea7-a41b-209d697bcdaa

.gitattributes

@@ -1,11 +0,0 @@
-.gitattributes export-ignore
-.gitignore export-ignore
-.github export-ignore
-.lgtm.yml export-ignore
-SECURITY.md export-ignore
-*       text=auto
-*.jpg   -text
-*.pdf   -text
-*.gz    -text
-*.png   -text
-*.ps    -text

.github/CODEOWNERS

@@ -1,159 +0,0 @@
-# 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/*        @rbberger
-src/GPU/*             @ndtrung81
-src/KOKKOS/*          @stanmoore1
-src/KIM/*             @ellio167
-src/LATTE/*           @cnegre
-src/MESSAGE/*         @sjplimp
-src/MLIAP/*           @athomps
-src/SNAP/*            @athomps
-src/SPIN/*            @julient31
-src/BROWNIAN/*        @samueljmcameron
-src/CG-DNA/*          @ohenrich
-src/CG-SDK/*          @akohlmey
-src/COLVARS/*         @giacomofiorin
-src/DIELECTRIC/*      @ndtrung81
-src/FEP/*             @agiliopadua
-src/ML-HDNNP/*        @singraber
-src/INTEL/*           @wmbrownintel
-src/MANIFOLD/*        @Pakketeretet2
-src/MDI/*             @taylor-a-barnes
-src/MEAM/*            @martok
-src/MESONT/*          @iafoss
-src/MOFFF/*           @hheenen
-src/MOLFILE/*         @akohlmey
-src/NETCDF/*          @pastewka
-src/ML-PACE/*         @yury-lysogorskiy
-src/PLUMED/*          @gtribello
-src/PHONON/*          @lingtikong
-src/PTM/*             @pmla
-src/OPENMP/*          @akohlmey
-src/QMMM/*            @akohlmey
-src/REAXFF/*          @hasanmetin @stanmoore1
-src/REACTION/*        @jrgissing
-src/SCAFACOS/*        @rhalver
-src/TALLY/*           @akohlmey
-src/UEF/*             @danicholson
-src/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/REPLICA/*_grem.*                @dstelter92
-src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
-src/MISC/*_tracker.*                @jtclemm
-
-# 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/min_*.*               @sjplimp
-src/memory.*              @sjplimp
-src/modify.*              @sjplimp @stanmoore1
-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/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
-src/verlet.*              @sjplimp @stanmoore1
-src/math_eigen_impl.h     @jewettaij
-
-# tools
-tools/msi2lmp/*       @akohlmey
-tools/emacs/*         @HaoZeke
-tools/singularity/*   @akohlmey @rbberger
-tools/coding_standard/* @rbberger
-tools/valgrind/*      @akohlmey
-tools/swig/*          @akohlmey
-tools/offline/*       @rbberger
-
-# tests
-unittest/*            @akohlmey @rbberger
-
-# cmake
-cmake/*               @junghans @rbberger
-cmake/Modules/Packages/COLVARS.cmake @junghans @rbberger @giacomofiorin
-cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
-cmake/presets/*.cmake @akohlmey
-
-# python
-python/*              @rbberger
-
-# fortran
-fortran/*             @akohlmey
-
-# docs
-doc/utils/*/*         @rbberger
-doc/Makefile          @rbberger
-doc/README            @rbberger
-examples/plugin/*     @akohlmey
-
-# for releases
-src/version.h         @sjplimp

.github/CODE_OF_CONDUCT.md

@@ -1,67 +0,0 @@
-# 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

@@ -1,94 +0,0 @@
-# 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 guide for submitting new features in the LAMMPS manual](https://www.lammps.org/doc/Modify_contribute.html)
-* [The guide on programming style and requirement in the LAMMPS manual](https://www.lammps.org/doc/Modify_style.html)
-* [The GitHub tutorial in the LAMMPS 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 either the ['lammps-users' mailing list](https://lammps.sandia.gov/mail.html) or the [LAMMPS Material Science Discourse forum](https://matsci.org/lammps). You do not need to be subscribed to post to the list (but a mailing list subscription avoids having your post delayed until it is approved by a mailing list moderator). Most posts to the mailing list receive a response within less than 24 hours. Before posting to the mailing list, please read the [mailing list guidelines](https://lammps.sandia.gov/guidelines.html). Following those guidelines will help greatly to get a helpful response. Always mention which LAMMPS version you are using. The LAMMPS forum was recently created as part of a larger effort to build a materials science community and have discussions not just about using LAMMPS. Thus the forum may be also used for discussions that would be off-topic for the mailing list. Those will just have to be posted to a more general category.
-
-## How Can I Contribute?
-
-There are several ways how you can actively contribute to the LAMMPS project: you can discuss compiling and using LAMMPS, and solving LAMMPS related problems with other LAMMPS users on the lammps-users mailing list or the forum, you can report bugs or suggest enhancements by creating issues on GitHub (or posting them to the lammps-users mailing list or posting in the LAMMPS Materials Science Discourse forum), and you can contribute by submitting pull requests on GitHub or e-mail your code
-to one of the [LAMMPS core developers](https://lammps.sandia.gov/authors.html). As you may see from the aforementioned developer page, the LAMMPS software package includes the efforts of a very large number of contributors beyond the principal authors and maintainers.
-
-### 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.
-
-The LAMMPS Materials Science Discourse forum was created recently to facilitate discussion not just about LAMMPS and as part of a larger effort  towards building a materials science community. The forum contains a read-only sub-category with the continually updated mailing list archive, so you won't miss anything by joining only the forum and not the mailing list.
-
-### 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. Instructions, guidelines, requirements,
-and recommendations are in the following sections of the LAMMPS manual:
-* [The guide for submitting new features in the LAMMPS manual](https://lammps.sandia.gov/doc/Modify_contribute.html)
-* [The guide on programming style and requirement in the LAMMPS manual](https://lammps.sandia.gov/doc/Modify_contribute.html)
-* [The GitHub tutorial in the LAMMPS manual](http://lammps.sandia.gov/doc/Howto_github.html)
-
-
-## 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 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. Feature requests may be labeled with `volunteer_needed` if none of the LAMMPS developers has the time and the required knowledge implement the feature.
-
-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. Otherwise the `unconfirmed` label will be applied and some comment about what was tried to confirm the bug added. 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 will 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
-
-Pull requests are the **only** way that changes get made to the LAMMPS distribution.  So also the LAMMPS core developers will submit pull requests for their own changes and discuss them on GitHub.  Thus if you submit a pull request it will be treated in a similar fashion. When you submit a pull request you may opt to submit a "Draft" pull request.  That means your changes are visible and will be subject to testing, but reviewers will not be (auto-)assigned and comments will take into account that this is not complete. On the other hand, this is a perfect way to ask the LAMMPS developers for comments on non-obvious changes and get feedback and possible suggestions for improvements or recommendations about what to avoid.
-Immediately after the submission, the LAMMPS continuing integration server at ci.lammps.org will download your submitted branch and perform a number of tests: it will tests whether it compiles cleanly under various conditions, it will also do a check on whether your included documentation translates cleanly and run some unit tests and other checks. Whether these tests are successful or fail will be recorded.  If a test fails, please inspect the corresponding output on the CI server and take the necessary steps, if needed, so that the code can compile cleanly again.  The test will be re-run each time the pull request is updated with a push to the remote branch on GitHub.  If you are unsure about what you need to change, ask a question in the discussion area of the pull request.
-Next a LAMMPS core developer will self-assign and do an overall technical assessment of the submission.  If you submitted a draft pull request, this will not happen unless you mark it "ready for review".  If you are not yet invited as a LAMMPS collaborator, and your contribution seems significant, you may also receive an invitation for collaboration on the LAMMPS repository.  As part of the assessment, the pull request will be categorized with labels. There are two special labels: `needs_work` (indicates that work from the submitter of the pull request is needed) and `work_in_progress` (indicates, that the assigned LAMMPS developer will make changes, if not done by the contributor who made the submit). 
-You may also receive comments and suggestions on the overall submission or specific details and on occasion specific requests for changes as part of the review. If permitted, also additional changes may be pushed into your pull request branch or a pull request may be filed in your LAMMPS fork on GitHub to include those changes.
-The LAMMPS developer may then decide to assign the pull request to another developer (e.g. when that developer is more knowledgeable about the submitted feature or enhancement or has written the modified code). It may also happen, that additional developers are requested to provide a review and approve the changes. For submissions, that may change the general behavior of LAMMPS, or where a possibility of unwanted side effects exists, additional tests may be requested by the assigned developer.
-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.  The minimum requirement to merge a pull request is that all automated tests have to pass and at least one LAMMPS developer has approved integrating the submitted code. Since the approver will not be the person merging a pull request, you will have at least two LAMMPS developers that looked at your contribution.
-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 work flow may be adjusted.
-

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,32 +0,0 @@
----
-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

@@ -1,20 +0,0 @@
----
-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

@@ -1,21 +0,0 @@
----
-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

@@ -1,15 +0,0 @@
----
-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

@@ -1,45 +0,0 @@
-**Summary**
-
-<!--Briefly describe the new feature(s), enhancement(s), or bugfix(es) included in this pull request.-->
-
-**Related Issue(s)**
-
-<!--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

@@ -1,45 +0,0 @@
----
-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(s) that are eliminated by this pull request.-->
-
-**Related Issue(s)**
-
-<!--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-->
-
-**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 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
-- [ ] 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.
-

.github/PULL_REQUEST_TEMPLATE/maintenance_refactoring.md

@@ -1,43 +0,0 @@
----
-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 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-->
-
-**Detailed Description**
-
-<!--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 is submitted-->
-- [ ] The pull request is complete
-- [ ] The source code follows the LAMMPS formatting guidelines
-- [ ] 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.
-
-

.github/PULL_REQUEST_TEMPLATE/new_feature.md

@@ -1,54 +0,0 @@
----
-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 Issue(s)**
-
-<!--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 new feature(s) 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/update_enhancement.md

@@ -1,54 +0,0 @@
----
-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.-->
-
-**Related Issue(s)**
-
-<!--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-->
-
-**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 updates to the existing docs are included
-- [ ] The 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 updated or added to the unittest tree.
-- [ ] A package specific README file has been 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/codecov.yml

@@ -1,29 +0,0 @@
-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

.github/codeql/cpp.yml

@@ -1,4 +0,0 @@
-paths:
- - src
- - lib
- - tools

.github/codeql/python.yml

@@ -1,5 +0,0 @@
-paths:
- - python/lammps
-
-queries:
- - uses: security-and-quality

.github/dependabot.yml

@@ -1,6 +0,0 @@
-version: 2
-updates:
-  - package-ecosystem: "github-actions"
-    directory: "/"
-    schedule:
-      interval: "weekly"

.github/workflows/codeql-analysis.yml

@@ -1,56 +0,0 @@
-# GitHub action to run static code analysis on C++ and Python code
-name: "CodeQL Code Analysis"
-
-on:
-  push:
-    branches: [develop]
-
-  workflow_dispatch:
-
-jobs:
-  analyze:
-    name: Analyze
-    if: ${{ github.repository == 'lammps/lammps' }}
-    runs-on: ubuntu-latest
-
-    permissions:
-      security-events: write
-      actions: read
-      contents: read
-
-    strategy:
-      fail-fast: false
-      matrix:
-        language: ['cpp', 'python']
-
-    steps:
-    - name: Checkout repository
-      uses: actions/checkout@v3
-      with:
-        fetch-depth: 2
-
-    - name: Setup Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: '3.x'
-
-    - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
-      with:
-        languages: ${{ matrix.language }}
-        config-file: ./.github/codeql/${{ matrix.language }}.yml
-
-    - name: Create Build Environment
-      if: ${{ matrix.language == 'cpp' }}
-      run: mkdir build
-
-    - name: Building LAMMPS via CMake
-      if: ${{ matrix.language == 'cpp' }}
-      shell: bash
-      working-directory: build
-      run: |
-        cmake -C ../cmake/presets/most.cmake ../cmake
-        cmake --build . --parallel 2
-
-    - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2

.github/workflows/compile-msvc.yml

@@ -1,49 +0,0 @@
-# GitHub action to build LAMMPS on Windows with Visual C++
-name: "Native Windows Compilation and Unit Tests"
-
-on:
-  push:
-    branches: [develop]
-
-  workflow_dispatch:
-
-jobs:
-  build:
-    name: Windows Compilation Test
-    if: ${{ github.repository == 'lammps/lammps' }}
-    runs-on: windows-latest
-
-    steps:
-    - name: Checkout repository
-      uses: actions/checkout@v3
-      with:
-        fetch-depth: 2
-
-    - name: Select Python version
-      uses: actions/setup-python@v4
-      with:
-        python-version: '3.10'
-
-    - name: Building LAMMPS via CMake
-      shell: bash
-      run: |
-        python3 -m pip install numpy
-        python3 -m pip install pyyaml
-        cmake -C cmake/presets/windows.cmake \
-              -D PKG_PYTHON=on \
-              -S cmake -B build \
-              -D BUILD_SHARED_LIBS=on \
-              -D LAMMPS_EXCEPTIONS=on \
-              -D ENABLE_TESTING=on
-        cmake --build build --config Release
-
-    - name: Run LAMMPS executable
-      shell: bash
-      run: |
-        ./build/Release/lmp.exe -h
-        ./build/Release/lmp.exe -in bench/in.lj
-
-    - name: Run Unit Tests
-      working-directory: build
-      shell: bash
-      run: ctest -V -C Release

.github/workflows/unittest-macos.yml

@@ -1,57 +0,0 @@
-# GitHub action to build LAMMPS on MacOS and run unit tests
-name: "Unittest for MacOS"
-
-on:
-  push:
-    branches: [develop]
-
-  workflow_dispatch:
-
-jobs:
-  build:
-    name: MacOS Unit Test
-    if: ${{ github.repository == 'lammps/lammps' }}
-    runs-on: macos-latest
-    env:
-      CCACHE_DIR: ${{ github.workspace }}/.ccache
-
-    steps:
-    - name: Checkout repository
-      uses: actions/checkout@v3
-      with:
-        fetch-depth: 2
-
-    - name: Install ccache
-      run: brew install ccache
-
-    - name: Create Build Environment
-      run: mkdir build
-
-    - name: Set up ccache
-      uses: actions/cache@v3
-      with:
-        path: ${{ env.CCACHE_DIR }}
-        key: macos-ccache-${{ github.sha }}
-        restore-keys: macos-ccache-
-
-    - name: Building LAMMPS via CMake
-      shell: bash
-      working-directory: build
-      run: |
-        ccache -z
-        python3 -m pip install pyyaml
-        cmake -C ../cmake/presets/clang.cmake \
-              -C ../cmake/presets/most.cmake \
-              -D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-              -D CMAKE_C_COMPILER_LAUNCHER=ccache \
-              -D ENABLE_TESTING=on \
-              -D BUILD_SHARED_LIBS=on \
-              -D LAMMPS_EXCEPTIONS=on \
-              ../cmake
-        cmake --build . --parallel 2
-        ccache -s
-
-    - name: Run Tests
-      working-directory: build
-      shell: bash
-      run: ctest -V

.gitignore

@@ -1,57 +0,0 @@
-*~
-*.o
-*.so
-*.lo
-*.cu_o
-*.ptx
-*_ptx.h
-*.a
-*.d
-*.x
-*.exe
-*.sif
-*.dll
-*.pyc
-*.whl
-a.out
-__pycache__
-
-Obj_*
-log.lammps
-log.cite
-*.bz2
-*.gz
-*.tar
-.*.swp
-*.orig
-*.rej
-vgcore.*
-.vagrant
-\#*#
-.#*
-.vscode
-
-.DS_Store
-.DS_Store?
-._*
-.Spotlight-V100
-.Trashes
-ehthumbs.db
-Thumbs.db
-.lammps_history
-.vs
-
-#cmake
-/build*
-/CMakeCache.txt
-/CMakeFiles/
-/Testing
-/Makefile
-/Testing
-/cmake_install.cmake
-/lmp
-out/Debug
-out/RelWithDebInfo
-out/Release
-out/x86
-out/x64

.lgtm.yml

@@ -1,14 +0,0 @@
-extraction:
-  cpp:
-    configure:
-      command:
-      - "mkdir build"
-      - "cd build"
-      - "cmake -G Ninja -C ../cmake/presets/most.cmake ../cmake"
-    index:
-      build_command:
-      - "cd build"
-      - "ninja"
-  python:
-    python_setup:
-      version: 3

LICENSE

@@ -1,9 +1,9 @@
 GNU GENERAL PUBLIC LICENSE
 
-Version 2, June 1991
+Version 2, June 1991 
 
 Copyright (C) 1989, 1991 Free Software Foundation, Inc.  
-51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+59 Temple Place - Suite 330, Boston, MA  02111-1307, USA
 
 Everyone is permitted to copy and distribute verbatim copies of this
 license document, but changing it is not allowed.
@@ -301,8 +301,9 @@ one line to give the program's name and an idea of what it does.
 Copyright (C) yyyy  name of author
 
 This program is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License version 2 as
-published by the Free Software Foundation.
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or (at
+your option) any later version.
 
 This program is distributed in the hope that it will be useful, but
 WITHOUT ANY WARRANTY; without even the implied warranty of

README

@@ -14,40 +14,29 @@ LAMMPS is a classical molecular dynamics simulation code designed to
 run efficiently on parallel computers.  It was developed at Sandia
 National Laboratories, a US Department of Energy facility, with
 funding from the DOE.  It is an open-source code, distributed freely
-under the terms of the GNU Public License (GPL) version 2.
+under the terms of the GNU Public License (GPL).
 
 The primary author of the code is Steve Plimpton, who can be emailed
-at sjplimp@sandia.gov.  The LAMMPS WWW Site at www.lammps.org has
+at sjplimp@sandia.gov.  The LAMMPS WWW Site at lammps.sandia.gov has
 more information about the code and its uses.
 
 The LAMMPS distribution includes the following files and directories:
 
-README                     this file
-LICENSE                    the GNU General Public License (GPL)
-bench                      benchmark problems
-cmake                      CMake build files
-doc                        documentation
-examples                   simple test problems
-fortran                    Fortran wrapper for LAMMPS
-lib                        additional provided or external libraries
-potentials                 interatomic potential files
-python                     Python wrappers for LAMMPS
-src                        source files
-tools                      pre- and post-processing tools
+README			   this file
+LICENSE			   the GNU General Public License (GPL)
+bench			   benchmark problems
+couple			   code coupling examples using LAMMPS as a library
+doc			   documentation
+examples		   simple test problems
+lib			   libraries LAMMPS can be linked with
+potentials		   interatomic potential files
+python			   Python wrapper on LAMMPS as a library
+src			   source files
+tools			   pre- and post-processing tools
 
 Point your browser at any of these files to get started:
 
-https://docs.lammps.org/Manual.html         LAMMPS manual
-https://docs.lammps.org/Intro.html          hi-level introduction
-https://docs.lammps.org/Build.html          how to build LAMMPS
-https://docs.lammps.org/Run_head.html       how to run LAMMPS
-https://docs.lammps.org/Commands_all.html   Table of available commands
-https://docs.lammps.org/Library.html        LAMMPS library interfaces
-https://docs.lammps.org/Modify.html         how to modify and extend LAMMPS
-https://docs.lammps.org/Developer.html      LAMMPS developer info
-
-You can also create these doc pages locally:
-
-% cd doc
-% make html                # creates HTML pages in doc/html
-% make pdf                 # creates Manual.pdf
+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

SECURITY.md

@@ -1,39 +0,0 @@
-# Security Policy
-
-LAMMPS is designed as a user-level application to conduct computer
-simulations for research using classical mechanics.  As such LAMMPS
-depends to some degrees on users providing correctly formatted input and
-LAMMPS needs to read and write files based on uncontrolled user input.
-As a parallel application for use in high-performance computing
-environments, performance critical steps are also done without checking
-data.
-
-LAMMPS also is interfaced to a number of external libraries, including
-libraries with experimental research software, that are not validated
-and tested by the LAMMPS developers, so it is easy to import bad
-behavior from calling functions in one of those libraries.
-
-Thus is is quite easy to crash LAMMPS through malicious input and do all
-kinds of filesystem manipulations.  And because of that LAMMPS should
-**NEVER** be compiled or **run** as superuser, either from a "root" or
-"administrator" account directly or indirectly via "sudo" or "su".
-
-Therefore what could be seen as a security vulnerability is usually
-either a user mistake or a bug in the code.  Bugs can be reported in
-the LAMMPS project
-[issue tracker on GitHub](https://github.com/lammps/lammps/issues).
-
-To mitigate issues with using homoglyphs or bidirectional reordering in
-unicode, which have been demonstrated as a vector to obfuscate and hide
-malicious changes to the source code, all LAMMPS submissions are checked
-for unicode characters and only all-ASCII source code is accepted.
-
-# Version Updates
-
-LAMMPS follows continuous release development model.  We aim to keep all
-release versions (stable or patch) fully functional and employ a variety
-of automatic testing procedures to detect failures of existing
-functionality from adding new features before releases are made.  Thus
-bugfixes and updates are only integrated into the current development
-branch and thus the next (patch) release and users are recommended to
-update regularly.

bench/FERMI/README

@@ -0,0 +1,103 @@
+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

@@ -0,0 +1,24 @@
+# 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

@@ -0,0 +1,37 @@
+# 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

@@ -0,0 +1,22 @@
+# 3d Lennard-Jones melt
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 $x 0 $y 0 $z
+create_box	1 box
+create_atoms	1 box
+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 0 every 20 check no
+
+fix		1 all nve
+
+run		$t

bench/FERMI/in.lj.titan

@@ -0,0 +1,35 @@
+# 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

@@ -0,0 +1,30 @@
+# 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

@@ -0,0 +1,39 @@
+# 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

@@ -0,0 +1,42 @@
+# 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/KEPLER/Makefile.cpu

@@ -0,0 +1,108 @@
+# linux = Shannon Linux box, Intel icc, OpenMPI, KISS FFTW
+
+SHELL = /bin/sh
+
+# ---------------------------------------------------------------------
+# compiler/linker settings
+# specify flags and libraries needed for your compiler
+
+CC =		icc
+CCFLAGS =	-O
+SHFLAGS =	-fPIC
+DEPFLAGS =	-M
+
+LINK =		icc
+LINKFLAGS =	-O
+LIB =           -lstdc++
+SIZE =		size
+
+ARCHIVE =	ar
+ARFLAGS =	-rc
+SHLIBFLAGS =	-shared
+
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+# if you change any -D setting, do full re-compile after "make clean"
+
+# LAMMPS ifdef settings, OPTIONAL
+# see possible settings in doc/Section_start.html#2_2 (step 4)
+
+LMP_INC =
+
+# MPI library, REQUIRED
+# see discussion in doc/Section_start.html#2_2 (step 5)
+# can point to dummy MPI library in src/STUBS as in Makefile.serial
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC =       -I/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/include/
+MPI_PATH =      -L/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/lib
+MPI_LIB =	-lmpi
+
+# FFT library, OPTIONAL
+# see discussion in doc/Section_start.html#2_2 (step 6)
+# can be left blank to use provided KISS FFT library
+# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC =
+FFT_PATH = 
+FFT_LIB =
+
+# JPEG and/or PNG library, OPTIONAL
+# see discussion in doc/Section_start.html#2_2 (step 7)
+# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
+# INC = path(s) for jpeglib.h and/or png.h
+# PATH = path(s) for JPEG library and/or PNG library
+# LIB = name(s) of JPEG library and/or PNG library
+
+JPG_INC =       
+JPG_PATH = 	
+JPG_LIB =	-ljpeg
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include	Makefile.package.settings
+include	Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
+
+# Path to src files
+
+vpath %.cpp ..
+vpath %.h ..
+
+# Link target
+
+$(EXE):	$(OBJ)
+	$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
+	$(SIZE) $(EXE)
+
+# Library targets
+
+lib:	$(OBJ)
+	$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
+
+shlib:	$(OBJ)
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
+        $(OBJ) $(EXTRA_LIB) $(LIB)
+
+# Compilation rules
+
+%.o:%.cpp
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
+
+%.d:%.cpp
+	$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
+
+# Individual dependencies
+
+DEPENDS = $(OBJ:.o=.d)
+sinclude $(DEPENDS)

bench/KEPLER/Makefile.cuda

@@ -0,0 +1,108 @@
+# linux = Shannon Linux box, Intel icc, OpenMPI, KISS FFTW
+
+SHELL = /bin/sh
+
+# ---------------------------------------------------------------------
+# compiler/linker settings
+# specify flags and libraries needed for your compiler
+
+CC =		icc
+CCFLAGS =	-O
+SHFLAGS =	-fPIC
+DEPFLAGS =	-M
+
+LINK =		icc
+LINKFLAGS =	-O
+LIB =           -lstdc++
+SIZE =		size
+
+ARCHIVE =	ar
+ARFLAGS =	-rc
+SHLIBFLAGS =	-shared
+
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+# if you change any -D setting, do full re-compile after "make clean"
+
+# LAMMPS ifdef settings, OPTIONAL
+# see possible settings in doc/Section_start.html#2_2 (step 4)
+
+LMP_INC =
+
+# MPI library, REQUIRED
+# see discussion in doc/Section_start.html#2_2 (step 5)
+# can point to dummy MPI library in src/STUBS as in Makefile.serial
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC =       -I/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/include/
+MPI_PATH =      -L/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/lib
+MPI_LIB =	-lmpi
+
+# FFT library, OPTIONAL
+# see discussion in doc/Section_start.html#2_2 (step 6)
+# can be left blank to use provided KISS FFT library
+# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC =
+FFT_PATH = 
+FFT_LIB =
+
+# JPEG and/or PNG library, OPTIONAL
+# see discussion in doc/Section_start.html#2_2 (step 7)
+# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
+# INC = path(s) for jpeglib.h and/or png.h
+# PATH = path(s) for JPEG library and/or PNG library
+# LIB = name(s) of JPEG library and/or PNG library
+
+JPG_INC =       
+JPG_PATH = 	
+JPG_LIB =	-ljpeg
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include	Makefile.package.settings
+include	Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
+
+# Path to src files
+
+vpath %.cpp ..
+vpath %.h ..
+
+# Link target
+
+$(EXE):	$(OBJ)
+	$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
+	$(SIZE) $(EXE)
+
+# Library targets
+
+lib:	$(OBJ)
+	$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
+
+shlib:	$(OBJ)
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
+        $(OBJ) $(EXTRA_LIB) $(LIB)
+
+# Compilation rules
+
+%.o:%.cpp
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
+
+%.d:%.cpp
+	$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
+
+# Individual dependencies
+
+DEPENDS = $(OBJ:.o=.d)
+sinclude $(DEPENDS)

bench/KEPLER/Makefile.gpu

@@ -0,0 +1,108 @@
+# linux = Shannon Linux box, Intel icc, OpenMPI, KISS FFTW
+
+SHELL = /bin/sh
+
+# ---------------------------------------------------------------------
+# compiler/linker settings
+# specify flags and libraries needed for your compiler
+
+CC =		icc
+CCFLAGS =	-O
+SHFLAGS =	-fPIC
+DEPFLAGS =	-M
+
+LINK =		icc
+LINKFLAGS =	-O
+LIB =           -lstdc++
+SIZE =		size
+
+ARCHIVE =	ar
+ARFLAGS =	-rc
+SHLIBFLAGS =	-shared
+
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+# if you change any -D setting, do full re-compile after "make clean"
+
+# LAMMPS ifdef settings, OPTIONAL
+# see possible settings in doc/Section_start.html#2_2 (step 4)
+
+LMP_INC =
+
+# MPI library, REQUIRED
+# see discussion in doc/Section_start.html#2_2 (step 5)
+# can point to dummy MPI library in src/STUBS as in Makefile.serial
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC =       -I/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/include/
+MPI_PATH =      -L/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/lib
+MPI_LIB =	-lmpi
+
+# FFT library, OPTIONAL
+# see discussion in doc/Section_start.html#2_2 (step 6)
+# can be left blank to use provided KISS FFT library
+# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC =
+FFT_PATH = 
+FFT_LIB =
+
+# JPEG and/or PNG library, OPTIONAL
+# see discussion in doc/Section_start.html#2_2 (step 7)
+# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
+# INC = path(s) for jpeglib.h and/or png.h
+# PATH = path(s) for JPEG library and/or PNG library
+# LIB = name(s) of JPEG library and/or PNG library
+
+JPG_INC =       
+JPG_PATH = 	
+JPG_LIB =	-ljpeg
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include	Makefile.package.settings
+include	Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
+
+# Path to src files
+
+vpath %.cpp ..
+vpath %.h ..
+
+# Link target
+
+$(EXE):	$(OBJ)
+	$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
+	$(SIZE) $(EXE)
+
+# Library targets
+
+lib:	$(OBJ)
+	$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
+
+shlib:	$(OBJ)
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
+        $(OBJ) $(EXTRA_LIB) $(LIB)
+
+# Compilation rules
+
+%.o:%.cpp
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
+
+%.d:%.cpp
+	$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
+
+# Individual dependencies
+
+DEPENDS = $(OBJ:.o=.d)
+sinclude $(DEPENDS)

bench/KEPLER/Makefile.gpu.double

@@ -0,0 +1,50 @@
+# /* ----------------------------------------------------------------------   
+#  Generic Linux Makefile for CUDA 
+#     - Change CUDA_ARCH for your GPU
+# ------------------------------------------------------------------------- */
+
+# which file will be copied to Makefile.lammps
+
+EXTRAMAKE = Makefile.lammps.standard
+
+CUDA_HOME = /home/projects/cuda/6.0.37
+NVCC = nvcc
+
+# Kepler CUDA
+CUDA_ARCH = -arch=sm_35
+# Tesla CUDA
+#CUDA_ARCH = -arch=sm_21
+# newer CUDA
+#CUDA_ARCH = -arch=sm_13
+# older CUDA
+#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
+
+# this setting should match LAMMPS Makefile
+# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
+
+LMP_INC = -DLAMMPS_SMALLBIG
+
+# precision for GPU calculations
+# -D_SINGLE_SINGLE  # Single precision for all calculations
+# -D_DOUBLE_DOUBLE  # Double precision for all calculations
+# -D_SINGLE_DOUBLE  # Accumulation of forces, etc. in double
+
+CUDA_PRECISION = -D_DOUBLE_DOUBLE
+
+CUDA_INCLUDE = -I$(CUDA_HOME)/include
+CUDA_LIB = -L$(CUDA_HOME)/lib64
+CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math
+
+CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
+CUDR_OPTS = -O2 # -xHost -no-prec-div -ansi-alias
+
+BIN_DIR = ./
+OBJ_DIR = ./
+LIB_DIR = ./
+AR = ar
+BSH = /bin/sh
+
+CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini
+
+include Nvidia.makefile
+

bench/KEPLER/Makefile.gpu.mixed

@@ -0,0 +1,50 @@
+# /* ----------------------------------------------------------------------   
+#  Generic Linux Makefile for CUDA 
+#     - Change CUDA_ARCH for your GPU
+# ------------------------------------------------------------------------- */
+
+# which file will be copied to Makefile.lammps
+
+EXTRAMAKE = Makefile.lammps.standard
+
+CUDA_HOME = /home/projects/cuda/6.0.37
+NVCC = nvcc
+
+# Kepler CUDA
+CUDA_ARCH = -arch=sm_35
+# Tesla CUDA
+#CUDA_ARCH = -arch=sm_21
+# newer CUDA
+#CUDA_ARCH = -arch=sm_13
+# older CUDA
+#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
+
+# this setting should match LAMMPS Makefile
+# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
+
+LMP_INC = -DLAMMPS_SMALLBIG
+
+# precision for GPU calculations
+# -D_SINGLE_SINGLE  # Single precision for all calculations
+# -D_DOUBLE_DOUBLE  # Double precision for all calculations
+# -D_SINGLE_DOUBLE  # Accumulation of forces, etc. in double
+
+CUDA_PRECISION = -D_SINGLE_DOUBLE
+
+CUDA_INCLUDE = -I$(CUDA_HOME)/include
+CUDA_LIB = -L$(CUDA_HOME)/lib64
+CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math
+
+CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
+CUDR_OPTS = -O2 # -xHost -no-prec-div -ansi-alias
+
+BIN_DIR = ./
+OBJ_DIR = ./
+LIB_DIR = ./
+AR = ar
+BSH = /bin/sh
+
+CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini
+
+include Nvidia.makefile
+

bench/KEPLER/Makefile.gpu.single

@@ -0,0 +1,50 @@
+# /* ----------------------------------------------------------------------   
+#  Generic Linux Makefile for CUDA 
+#     - Change CUDA_ARCH for your GPU
+# ------------------------------------------------------------------------- */
+
+# which file will be copied to Makefile.lammps
+
+EXTRAMAKE = Makefile.lammps.standard
+
+CUDA_HOME = /home/projects/cuda/6.0.37
+NVCC = nvcc
+
+# Kepler CUDA
+CUDA_ARCH = -arch=sm_35
+# Tesla CUDA
+#CUDA_ARCH = -arch=sm_21
+# newer CUDA
+#CUDA_ARCH = -arch=sm_13
+# older CUDA
+#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
+
+# this setting should match LAMMPS Makefile
+# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
+
+LMP_INC = -DLAMMPS_SMALLBIG
+
+# precision for GPU calculations
+# -D_SINGLE_SINGLE  # Single precision for all calculations
+# -D_DOUBLE_DOUBLE  # Double precision for all calculations
+# -D_SINGLE_DOUBLE  # Accumulation of forces, etc. in double
+
+CUDA_PRECISION = -D_SINGLE_SINGLE
+
+CUDA_INCLUDE = -I$(CUDA_HOME)/include
+CUDA_LIB = -L$(CUDA_HOME)/lib64
+CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math
+
+CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
+CUDR_OPTS = -O2 # -xHost -no-prec-div -ansi-alias
+
+BIN_DIR = ./
+OBJ_DIR = ./
+LIB_DIR = ./
+AR = ar
+BSH = /bin/sh
+
+CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini
+
+include Nvidia.makefile
+

bench/KEPLER/Makefile.intel.cpu

@@ -0,0 +1,109 @@
+# linux = Shannon Linux box, Intel icc, OpenMPI, KISS FFTW
+
+SHELL = /bin/sh
+
+# ---------------------------------------------------------------------
+# compiler/linker settings
+# specify flags and libraries needed for your compiler
+
+CC =		icc
+CCFLAGS =	-O3 -openmp -DLAMMPS_MEMALIGN=64 -no-offload \
+                -xHost -fno-alias -ansi-alias -restrict -override-limits
+SHFLAGS =	-fPIC
+DEPFLAGS =	-M
+
+LINK =		icc
+LINKFLAGS =	-O -openmp
+LIB =           -lstdc++
+SIZE =		size
+
+ARCHIVE =	ar
+ARFLAGS =	-rc
+SHLIBFLAGS =	-shared
+
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+# if you change any -D setting, do full re-compile after "make clean"
+
+# LAMMPS ifdef settings, OPTIONAL
+# see possible settings in doc/Section_start.html#2_2 (step 4)
+
+LMP_INC =	-DLAMMPS_GZIP -DLAMMPS_JPEG
+
+# MPI library, REQUIRED
+# see discussion in doc/Section_start.html#2_2 (step 5)
+# can point to dummy MPI library in src/STUBS as in Makefile.serial
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC =       -I/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/include/
+MPI_PATH =      -L/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/lib
+MPI_LIB =	-lmpi
+
+# FFT library, OPTIONAL
+# see discussion in doc/Section_start.html#2_2 (step 6)
+# can be left blank to use provided KISS FFT library
+# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC =
+FFT_PATH = 
+FFT_LIB =
+
+# JPEG and/or PNG library, OPTIONAL
+# see discussion in doc/Section_start.html#2_2 (step 7)
+# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
+# INC = path(s) for jpeglib.h and/or png.h
+# PATH = path(s) for JPEG library and/or PNG library
+# LIB = name(s) of JPEG library and/or PNG library
+
+JPG_INC =       
+JPG_PATH = 	
+JPG_LIB =	-ljpeg
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include	Makefile.package.settings
+include	Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
+
+# Path to src files
+
+vpath %.cpp ..
+vpath %.h ..
+
+# Link target
+
+$(EXE):	$(OBJ)
+	$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
+	$(SIZE) $(EXE)
+
+# Library targets
+
+lib:	$(OBJ)
+	$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
+
+shlib:	$(OBJ)
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
+        $(OBJ) $(EXTRA_LIB) $(LIB)
+
+# Compilation rules
+
+%.o:%.cpp
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
+
+%.d:%.cpp
+	$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
+
+# Individual dependencies
+
+DEPENDS = $(OBJ:.o=.d)
+sinclude $(DEPENDS)

bench/KEPLER/Makefile.kokkos.cuda

@@ -0,0 +1,113 @@
+# linux = Shannon Linux box, Intel icc, OpenMPI, KISS FFTW
+
+SHELL = /bin/sh
+
+# ---------------------------------------------------------------------
+# compiler/linker settings
+# specify flags and libraries needed for your compiler
+
+CC =		nvcc
+CCFLAGS =	-O3 -arch=sm_35
+SHFLAGS =	-fPIC
+DEPFLAGS =	-M
+
+LINK =		mpicxx
+LINKFLAGS =	-O
+LIB =           -lstdc++
+SIZE =		size
+
+ARCHIVE =	ar
+ARFLAGS =	-rc
+SHLIBFLAGS =	-shared
+
+OMP = yes
+CUDA = yes
+
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+# if you change any -D setting, do full re-compile after "make clean"
+
+# LAMMPS ifdef settings, OPTIONAL
+# see possible settings in doc/Section_start.html#2_2 (step 4)
+
+LMP_INC =
+
+# MPI library, REQUIRED
+# see discussion in doc/Section_start.html#2_2 (step 5)
+# can point to dummy MPI library in src/STUBS as in Makefile.serial
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC =       -I/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/include/
+MPI_PATH =      -L/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/lib
+MPI_LIB =	-lmpi
+
+# FFT library, OPTIONAL
+# see discussion in doc/Section_start.html#2_2 (step 6)
+# can be left blank to use provided KISS FFT library
+# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC =
+FFT_PATH = 
+FFT_LIB =
+
+# JPEG and/or PNG library, OPTIONAL
+# see discussion in doc/Section_start.html#2_2 (step 7)
+# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
+# INC = path(s) for jpeglib.h and/or png.h
+# PATH = path(s) for JPEG library and/or PNG library
+# LIB = name(s) of JPEG library and/or PNG library
+
+JPG_INC =       
+JPG_PATH = 	
+JPG_LIB =	-ljpeg
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include	Makefile.package.settings
+include	Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
+
+# Path to src files
+
+vpath %.cpp ..
+vpath %.h ..
+
+# Link target
+
+$(EXE):	$(OBJ)
+	$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
+	$(SIZE) $(EXE)
+
+# Library targets
+
+lib:	$(OBJ)
+	$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
+
+shlib:	$(OBJ)
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
+        $(OBJ) $(EXTRA_LIB) $(LIB)
+
+# Compilation rules
+%.o:%.cu
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
+
+%.o:%.cpp
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
+
+%.d:%.cpp
+	$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
+
+# Individual dependencies
+
+DEPENDS = $(OBJ:.o=.d)
+sinclude $(DEPENDS)

bench/KEPLER/Makefile.kokkos.omp

@@ -0,0 +1,110 @@
+# linux = Shannon Linux box, Intel icc, OpenMPI, KISS FFTW
+
+SHELL = /bin/sh
+
+# ---------------------------------------------------------------------
+# compiler/linker settings
+# specify flags and libraries needed for your compiler
+
+CC =		icc
+CCFLAGS =	-O
+SHFLAGS =	-fPIC
+DEPFLAGS =	-M
+
+LINK =		icc
+LINKFLAGS =	-O
+LIB =           -lstdc++
+SIZE =		size
+
+ARCHIVE =	ar
+ARFLAGS =	-rc
+SHLIBFLAGS =	-shared
+
+OMP = yes
+
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+# if you change any -D setting, do full re-compile after "make clean"
+
+# LAMMPS ifdef settings, OPTIONAL
+# see possible settings in doc/Section_start.html#2_2 (step 4)
+
+LMP_INC =
+
+# MPI library, REQUIRED
+# see discussion in doc/Section_start.html#2_2 (step 5)
+# can point to dummy MPI library in src/STUBS as in Makefile.serial
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC =       -I/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/include/
+MPI_PATH =      -L/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/lib
+MPI_LIB =	-lmpi
+
+# FFT library, OPTIONAL
+# see discussion in doc/Section_start.html#2_2 (step 6)
+# can be left blank to use provided KISS FFT library
+# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC =
+FFT_PATH = 
+FFT_LIB =
+
+# JPEG and/or PNG library, OPTIONAL
+# see discussion in doc/Section_start.html#2_2 (step 7)
+# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
+# INC = path(s) for jpeglib.h and/or png.h
+# PATH = path(s) for JPEG library and/or PNG library
+# LIB = name(s) of JPEG library and/or PNG library
+
+JPG_INC =       
+JPG_PATH = 	
+JPG_LIB =	-ljpeg
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include	Makefile.package.settings
+include	Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
+
+# Path to src files
+
+vpath %.cpp ..
+vpath %.h ..
+
+# Link target
+
+$(EXE):	$(OBJ)
+	$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
+	$(SIZE) $(EXE)
+
+# Library targets
+
+lib:	$(OBJ)
+	$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
+
+shlib:	$(OBJ)
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
+        $(OBJ) $(EXTRA_LIB) $(LIB)
+
+# Compilation rules
+
+%.o:%.cpp
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
+
+%.d:%.cpp
+	$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
+
+# Individual dependencies
+
+DEPENDS = $(OBJ:.o=.d)
+sinclude $(DEPENDS)

bench/KEPLER/Makefile.omp

@@ -0,0 +1,108 @@
+# linux = Shannon Linux box, Intel icc, OpenMPI, KISS FFTW
+
+SHELL = /bin/sh
+
+# ---------------------------------------------------------------------
+# compiler/linker settings
+# specify flags and libraries needed for your compiler
+
+CC =		icc
+CCFLAGS =	-O3 -openmp -restrict -ansi-alias
+SHFLAGS =	-fPIC
+DEPFLAGS =	-M
+
+LINK =		icc
+LINKFLAGS =	-O -openmp
+LIB =           -lstdc++
+SIZE =		size
+
+ARCHIVE =	ar
+ARFLAGS =	-rc
+SHLIBFLAGS =	-shared
+
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+# if you change any -D setting, do full re-compile after "make clean"
+
+# LAMMPS ifdef settings, OPTIONAL
+# see possible settings in doc/Section_start.html#2_2 (step 4)
+
+LMP_INC =
+
+# MPI library, REQUIRED
+# see discussion in doc/Section_start.html#2_2 (step 5)
+# can point to dummy MPI library in src/STUBS as in Makefile.serial
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC =       -I/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/include/
+MPI_PATH =      -L/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/lib
+MPI_LIB =	-lmpi
+
+# FFT library, OPTIONAL
+# see discussion in doc/Section_start.html#2_2 (step 6)
+# can be left blank to use provided KISS FFT library
+# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC =
+FFT_PATH = 
+FFT_LIB =
+
+# JPEG and/or PNG library, OPTIONAL
+# see discussion in doc/Section_start.html#2_2 (step 7)
+# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
+# INC = path(s) for jpeglib.h and/or png.h
+# PATH = path(s) for JPEG library and/or PNG library
+# LIB = name(s) of JPEG library and/or PNG library
+
+JPG_INC =       
+JPG_PATH = 	
+JPG_LIB =	-ljpeg
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include	Makefile.package.settings
+include	Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
+
+# Path to src files
+
+vpath %.cpp ..
+vpath %.h ..
+
+# Link target
+
+$(EXE):	$(OBJ)
+	$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
+	$(SIZE) $(EXE)
+
+# Library targets
+
+lib:	$(OBJ)
+	$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
+
+shlib:	$(OBJ)
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
+        $(OBJ) $(EXTRA_LIB) $(LIB)
+
+# Compilation rules
+
+%.o:%.cpp
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
+
+%.d:%.cpp
+	$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
+
+# Individual dependencies
+
+DEPENDS = $(OBJ:.o=.d)
+sinclude $(DEPENDS)

bench/KEPLER/Makefile.opt

@@ -0,0 +1,108 @@
+# linux = Shannon Linux box, Intel icc, OpenMPI, KISS FFTW
+
+SHELL = /bin/sh
+
+# ---------------------------------------------------------------------
+# compiler/linker settings
+# specify flags and libraries needed for your compiler
+
+CC =		icc
+CCFLAGS =	-O -restrict
+SHFLAGS =	-fPIC
+DEPFLAGS =	-M
+
+LINK =		icc
+LINKFLAGS =	-O
+LIB =           -lstdc++
+SIZE =		size
+
+ARCHIVE =	ar
+ARFLAGS =	-rc
+SHLIBFLAGS =	-shared
+
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings
+# specify settings for LAMMPS features you will use
+# if you change any -D setting, do full re-compile after "make clean"
+
+# LAMMPS ifdef settings, OPTIONAL
+# see possible settings in doc/Section_start.html#2_2 (step 4)
+
+LMP_INC =
+
+# MPI library, REQUIRED
+# see discussion in doc/Section_start.html#2_2 (step 5)
+# can point to dummy MPI library in src/STUBS as in Makefile.serial
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC =       -I/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/include/
+MPI_PATH =      -L/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/lib
+MPI_LIB =	-lmpi
+
+# FFT library, OPTIONAL
+# see discussion in doc/Section_start.html#2_2 (step 6)
+# can be left blank to use provided KISS FFT library
+# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC =
+FFT_PATH = 
+FFT_LIB =
+
+# JPEG and/or PNG library, OPTIONAL
+# see discussion in doc/Section_start.html#2_2 (step 7)
+# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
+# INC = path(s) for jpeglib.h and/or png.h
+# PATH = path(s) for JPEG library and/or PNG library
+# LIB = name(s) of JPEG library and/or PNG library
+
+JPG_INC =       
+JPG_PATH = 	
+JPG_LIB =	-ljpeg
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include	Makefile.package.settings
+include	Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
+
+# Path to src files
+
+vpath %.cpp ..
+vpath %.h ..
+
+# Link target
+
+$(EXE):	$(OBJ)
+	$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
+	$(SIZE) $(EXE)
+
+# Library targets
+
+lib:	$(OBJ)
+	$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
+
+shlib:	$(OBJ)
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
+        $(OBJ) $(EXTRA_LIB) $(LIB)
+
+# Compilation rules
+
+%.o:%.cpp
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
+
+%.d:%.cpp
+	$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
+
+# Individual dependencies
+
+DEPENDS = $(OBJ:.o=.d)
+sinclude $(DEPENDS)

bench/KEPLER/README

@@ -0,0 +1,68 @@
+These are build and input and run scripts used to run the LJ benchmark
+in the top-level bench directory using all the various accelerator
+packages currently available in LAMMPS.  The results of running these
+benchmarks on a GPU cluster with Kepler GPUs are shown on the "GPU
+(Kepler)" section of the Benchmark page of the LAMMPS WWW site:
+lammps.sandia.gov/bench.
+
+The specifics of the benchmark machine are as follows:
+
+It is a small GPU cluster at Sandia National Labs called "shannon". It
+has 32 nodes, each with two 8-core Sandy Bridge Xeon CPUs (E5-2670,
+2.6GHz, HT deactivated), for a total of 512 cores.  Twenty-four of the
+nodes have two NVIDIA Kepler GPUs (K20x, 2688 732 MHz cores).  LAMMPS
+was compiled with the Intel icc compiler, using module
+openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37.
+
+------------------------------------------------------------------------
+
+You can, of course, build LAMMPS yourself with any of the accelerator
+packages installed for your platform.
+
+The build.py script will build LAMMPS for the various accelerlator
+packages using the Makefile.* files in this dir, which you can edit if
+necessary for your platform.  You must set the "lmpdir" variable at
+the top of build.py to the home directory of LAMMPS as installed on
+your system.  Note that the build.py script hardcodes the arch setting
+for the USER-CUDA package, which should be matched to the GPUs on your
+system, e.g. sm_35 for Kepler GPUs.  For the GPU package, this setting
+is in the Makefile.gpu.* files, as is the CUDA_HOME variable which
+should point to where NVIDIA Cuda software is installed on your
+system.
+
+Once the Makefiles are in place, then typing, for example,
+
+python build.py cpu gpu
+
+will build executables for the CPU (no accelerators), and 3 variants
+(double, mixed, single precision) of the GPU package.  See the list of
+possible targets at the top of the build.py script.
+
+Note that the build.py script will un-install all packages in your
+LAMMPS directory, then only install the ones needed for the benchmark.
+The Makefile.* files in this dir are copied into lammps/src/MAKE, as a
+dummy Makefile.foo, so they will not conflict with makefiles that may
+already be there.  The build.py script also builds the auxiliary GPU
+and USER-CUDA library as needed.
+
+LAMMPS executables that are generated by build.py are copied into this
+directory when the script finishes each build.
+
+------------------------------------------------------------------------
+
+The in.* files can be run with any of the accelerator packages,
+if you specify the appropriate command-line switches.  These
+include switches to set the problem size and number of timesteps
+to run.
+
+The run*.sh scripts have sample mpirun commands for running the input
+scripts on a single node or on multiple nodes for the strong and weak
+scaling results shown on the benchmark web page.  These scripts are
+provided for illustration purposes, to show what command-line
+arguments are used with each accelerator package.
+
+Note that we generate these run scripts, either for interactive or
+batch submission, via Python scripts which often produces a long list
+of runs to exercise a combination of options.  To perform a quick
+benchmark calculation on your platform, you will typically only want
+to run a few commands out of any of the run*.sh scripts.

bench/KEPLER/build.py

@@ -0,0 +1,187 @@
+#!/usr/local/bin/python
+
+# Syntax: build.py target1 target2 ...
+#         targets:
+#         cpu, opt, omp,
+#         gpu/double, gpu/mixed, gpu/single,
+#         cuda/double, cuda/mixed, cuda/single,
+#         intel/cpu, intel/phi,
+#         kokkos/omp, kokkos/phi, kokkos/cuda
+#         gpu = gpu/double + gpu/mixed + gpu/single
+#         cuda = cuda/double + cuda/mixed + cuda/single
+#         intel = intel/cpu + intel/phi
+#         kokkos = kokkos/omp + kokkos/phi + kokkos/cuda
+#         all = cpu + opt + omp + gpu + cuda + intel + kokkos
+
+# create exectuables for different packages
+# MUST set lmpdir to path of LAMMPS home directory
+
+import sys,commands,os
+
+lmpdir = "~/lammps"
+
+# build LAMMPS
+# copy makefile into src/MAKE as Makefile.foo, then remove it
+
+def build_lammps(makefile,pkg):
+  print "Building LAMMPS with %s and %s packages ..." % (makefile,pkg)
+  commands.getoutput("cp %s %s/src/MAKE/Makefile.foo" % (makefile,lmpdir))
+  cwd = os.getcwd()
+  os.chdir(os.path.expanduser(lmpdir + "/src"))
+  str = "make clean-foo"
+  txt = commands.getoutput(str)
+  str = "make no-all"
+  txt = commands.getoutput(str)
+  for package in pkg:
+    str = "make yes-%s" % package
+    txt = commands.getoutput(str)
+    print txt
+  str = "make -j 16 foo"
+  txt = commands.getoutput(str)
+  os.remove("MAKE/Makefile.foo")
+  os.chdir(cwd)
+
+# build GPU library in LAMMPS
+# copy makefile into lib/gpu as Makefile.foo, then remove it
+  
+def build_gpu(makefile):
+  print "Building GPU lib with %s ..." % makefile
+  commands.getoutput("cp %s %s/lib/gpu/Makefile.foo" % (makefile,lmpdir))
+  cwd = os.getcwd()
+  os.chdir(os.path.expanduser(lmpdir + "/lib/gpu"))
+  str = "make -f Makefile.foo clean"
+  txt = commands.getoutput(str)
+  str = "make -j 16 -f Makefile.foo"
+  txt = commands.getoutput(str)
+  os.remove("Makefile.foo")
+  os.chdir(cwd)
+
+# build CUDA library in LAMMPS
+# set precision and arch explicitly as options to make in lib/cuda
+  
+def build_cuda(precision,arch):
+  print "Building USER-CUDA lib with %s and arch sm_%d ..." % (precision,arch)
+  cwd = os.getcwd()
+  os.chdir(os.path.expanduser(lmpdir + "/lib/cuda"))
+  str = "make clean"
+  txt = commands.getoutput(str)
+  if precision == "double": pflag = 2
+  elif precision == "mixed": pflag = 4
+  elif precision == "single": pflag = 1
+  str = "make -j 16 precision=%d arch=%s" % (pflag,arch)
+  txt = commands.getoutput(str)
+
+  os.chdir(cwd)
+
+# main program
+# convert target keywords into target flags
+
+  cpu = opt = omp = 0
+gpu = gpu_double = gpu_mixed = gpu_single = 0
+cuda = cuda_double = cuda_mixed = cuda_single = 0
+intel = intel_cpu = intel_phi = 0
+kokkos = kokkos_omp = kokkos_phi = kokkos_cuda = 0
+  
+targets = sys.argv[1:]
+for target in targets:
+  if target == "cpu": cpu = 1
+  elif target == "opt": opt = 1
+  elif target == "omp": omp = 1
+  elif target == "gpu/double": gpu_double = 1
+  elif target == "gpu/mixed": gpu_mixed = 1
+  elif target == "gpu/single": gpu_single = 1
+  elif target == "gpu": gpu = 1
+  elif target == "cuda/double": cuda_double = 1
+  elif target == "cuda/mixed": cuda_mixed = 1
+  elif target == "cuda/single": cuda_single = 1
+  elif target == "cuda": cuda = 1
+  elif target == "intel/cpu": intel_cpu = 1
+  elif target == "intel/phi": intel_phi = 1
+  elif target == "intel": intel = 1
+  elif target == "kokkos/omp": kokkos_omp = 1
+  elif target == "kokkos/phi": kokkos_phi = 1
+  elif target == "kokkos/cuda": kokkos_cuda = 1
+  elif target == "kokkos": kokkos = 1
+  elif target == "all": cpu = omp = gpu = cuda = intel = kokkos = 1
+  else: print "Target",target,"is unknown"
+
+if gpu: gpu_double = gpu_mixed = gpu_single = 1
+if cuda: cuda_double = cuda_mixed = cuda_single = 1
+if intel: intel_cpu = intel_phi = 1
+if kokkos: kokkos_omp = kokkos_phi = kokkos_cuda = 1
+
+# CPU
+
+if cpu:
+  build_lammps(makefile = "Makefile.cpu", pkg = [])
+  print commands.getoutput("mv %s/src/lmp_foo ./lmp_cpu" % lmpdir)
+
+# OPT
+
+if opt:
+  build_lammps(makefile = "Makefile.opt", pkg = ["opt"])
+  print commands.getoutput("mv %s/src/lmp_foo ./lmp_opt" % lmpdir)
+
+# OMP
+
+if omp:
+  build_lammps(makefile = "Makefile.omp", pkg = ["user-omp"])
+  print commands.getoutput("mv %s/src/lmp_foo ./lmp_omp" % lmpdir)
+
+# GPU, 3 precisions
+
+if gpu_double:
+  build_gpu(makefile = "Makefile.gpu.double")
+  build_lammps(makefile = "Makefile.gpu", pkg = ["gpu"])
+  print commands.getoutput("mv %s/src/lmp_foo ./lmp_gpu_double" % lmpdir)
+
+if gpu_mixed:
+  build_gpu(makefile = "Makefile.gpu.mixed")
+  build_lammps(makefile = "Makefile.gpu", pkg = ["gpu"])
+  print commands.getoutput("mv %s/src/lmp_foo ./lmp_gpu_mixed" % lmpdir)
+
+if gpu_single:
+  build_gpu(makefile = "Makefile.gpu.single")
+  build_lammps(makefile = "Makefile.gpu", pkg = ["gpu"])
+  print commands.getoutput("mv %s/src/lmp_foo ./lmp_gpu_single" % lmpdir)
+
+# CUDA, 3 precisions
+
+if cuda_double:
+  build_cuda(precision = "double", arch = 35)
+  build_lammps(makefile = "Makefile.cuda", pkg = ["kspace","user-cuda"])
+  print commands.getoutput("mv %s/src/lmp_foo ./lmp_cuda_double" % lmpdir)
+
+if cuda_mixed:
+  build_cuda(precision = "mixed", arch = 35)
+  build_lammps(makefile = "Makefile.cuda", pkg = ["kspace","user-cuda"])
+  print commands.getoutput("mv %s/src/lmp_foo ./lmp_cuda_mixed" % lmpdir)
+
+if cuda_single:
+  build_cuda(precision = "single", arch = 35)
+  build_lammps(makefile = "Makefile.cuda", pkg = ["kspace","user-cuda"])
+  print commands.getoutput("mv %s/src/lmp_foo ./lmp_cuda_single" % lmpdir)
+
+# INTEL, CPU and Phi
+
+if intel_cpu:
+  build_lammps(makefile = "Makefile.intel.cpu", pkg = ["user-intel"])
+  print commands.getoutput("mv %s/src/lmp_foo ./lmp_intel_cpu" % lmpdir)
+
+if intel_phi:
+  build_lammps(makefile = "Makefile.intel.phi", pkg = ["user-intel","user-omp"])
+  print commands.getoutput("mv %s/src/lmp_foo ./lmp_intel_phi" % lmpdir)
+
+# KOKKOS, all variants
+
+if kokkos_omp:
+  build_lammps(makefile = "Makefile.kokkos.omp", pkg = ["kokkos"])
+  print commands.getoutput("mv %s/src/lmp_foo ./lmp_kokkos_omp" % lmpdir)
+
+if kokkos_phi:
+  build_lammps(makefile = "Makefile.kokkos.phi", pkg = ["kokkos"])
+  print commands.getoutput("mv %s/src/lmp_foo ./lmp_kokkos_phi" % lmpdir)
+
+if kokkos_cuda:
+  build_lammps(makefile = "Makefile.kokkos.cuda", pkg = ["kokkos"])
+  print commands.getoutput("mv %s/src/lmp_foo ./lmp_kokkos_cuda" % lmpdir)

bench/KEPLER/in.lj

@@ -0,0 +1,22 @@
+# 3d Lennard-Jones melt
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 $x 0 $y 0 $z
+create_box	1 box
+create_atoms	1 box
+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 0 every 20 check no
+
+fix		1 all nve
+
+run		$t

bench/KEPLER/run_cpu.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+#SBATCH -N 1 --time=12:00:00
+
+mpirun -np 1 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cpu.128K.1
+
+mpirun -np 2 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cpu.128K.2
+
+mpirun -np 4 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cpu.128K.4
+
+mpirun -np 6 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cpu.128K.6
+
+mpirun -np 8 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cpu.128K.8
+
+mpirun -np 10 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cpu.128K.10
+
+mpirun -np 12 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cpu.128K.12
+
+mpirun -np 14 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cpu.128K.14
+
+mpirun -np 16 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cpu.128K.16

bench/KEPLER/run_cuda.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+#SBATCH -N 1 --time=12:00:00
+
+mpirun -N 1 lmp_cuda_double -c on -sf cuda -pk cuda 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cuda.double.128K.1
+
+mpirun -N 2 lmp_cuda_double -c on -sf cuda -pk cuda 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cuda.double.128K.2
+
+mpirun -N 1 lmp_cuda_mixed -c on -sf cuda -pk cuda 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cuda.mixed.128K.1
+
+mpirun -N 2 lmp_cuda_mixed -c on -sf cuda -pk cuda 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cuda.mixed.128K.2
+
+mpirun -N 1 lmp_cuda_single -c on -sf cuda -pk cuda 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cuda.single.128K.1
+
+mpirun -N 2 lmp_cuda_single -c on -sf cuda -pk cuda 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.cuda.single.128K.2

bench/KEPLER/run_gpu.sh

@@ -0,0 +1,155 @@
+#!/bin/bash
+#SBATCH -N 1 --time=12:00:00
+
+mpirun -np 1 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.single.128K.1.1
+
+mpirun -np 2 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.single.128K.2.1
+
+mpirun -np 2 lmp_gpu_single -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.single.128K.2.2
+
+mpirun -np 4 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.single.128K.4.1
+
+mpirun -np 4 lmp_gpu_single -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.single.128K.4.2
+
+mpirun -np 6 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.single.128K.6.1
+
+mpirun -np 6 lmp_gpu_single -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.single.128K.6.2
+
+mpirun -np 8 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.single.128K.8.1
+
+mpirun -np 8 lmp_gpu_single -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.single.128K.8.2
+
+mpirun -np 10 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.single.128K.10.1
+
+mpirun -np 10 lmp_gpu_single -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.single.128K.10.2
+
+mpirun -np 12 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.single.128K.12.1
+
+mpirun -np 12 lmp_gpu_single -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.single.128K.12.2
+
+mpirun -np 14 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.single.128K.14.1
+
+mpirun -np 14 lmp_gpu_single -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.single.128K.14.2
+
+mpirun -np 16 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.single.128K.16.1
+
+mpirun -np 16 lmp_gpu_single -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.single.128K.16.2
+
+mpirun -np 1 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.mixed.128K.1.1
+
+mpirun -np 2 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.mixed.128K.2.1
+
+mpirun -np 2 lmp_gpu_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.mixed.128K.2.2
+
+mpirun -np 4 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.mixed.128K.4.1
+
+mpirun -np 4 lmp_gpu_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.mixed.128K.4.2
+
+mpirun -np 6 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.mixed.128K.6.1
+
+mpirun -np 6 lmp_gpu_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.mixed.128K.6.2
+
+mpirun -np 8 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.mixed.128K.8.1
+
+mpirun -np 8 lmp_gpu_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.mixed.128K.8.2
+
+mpirun -np 10 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.mixed.128K.10.1
+
+mpirun -np 10 lmp_gpu_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.mixed.128K.10.2
+
+mpirun -np 12 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.mixed.128K.12.1
+
+mpirun -np 12 lmp_gpu_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.mixed.128K.12.2
+
+mpirun -np 14 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.mixed.128K.14.1
+
+mpirun -np 14 lmp_gpu_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.mixed.128K.14.2
+
+mpirun -np 16 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.mixed.128K.16.1
+
+mpirun -np 16 lmp_gpu_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.mixed.128K.16.2
+
+mpirun -np 1 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.double.128K.1.1
+
+mpirun -np 2 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.double.128K.2.1
+
+mpirun -np 2 lmp_gpu_double -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.double.128K.2.2
+
+mpirun -np 4 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.double.128K.4.1
+
+mpirun -np 4 lmp_gpu_double -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.double.128K.4.2
+
+mpirun -np 6 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.double.128K.6.1
+
+mpirun -np 6 lmp_gpu_double -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.double.128K.6.2
+
+mpirun -np 8 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.double.128K.8.1
+
+mpirun -np 8 lmp_gpu_double -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.double.128K.8.2
+
+mpirun -np 10 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.double.128K.10.1
+
+mpirun -np 10 lmp_gpu_double -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.double.128K.10.2
+
+mpirun -np 12 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.double.128K.12.1
+
+mpirun -np 12 lmp_gpu_double -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.double.128K.12.2
+
+mpirun -np 14 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.double.128K.14.1
+
+mpirun -np 14 lmp_gpu_double -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.double.128K.14.2
+
+mpirun -np 16 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.double.128K.16.1
+
+mpirun -np 16 lmp_gpu_double -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.gpu.double.128K.16.2

bench/KEPLER/run_intel_cpu.sh

@@ -0,0 +1,83 @@
+#!/bin/bash
+#SBATCH -N 1 --time=12:00:00
+
+mpirun -np 1 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.1
+
+mpirun -np 2 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.2
+
+mpirun -np 4 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.4
+
+mpirun -np 6 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.6
+
+mpirun -np 8 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.8
+
+mpirun -np 10 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.10
+
+mpirun -np 12 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.12
+
+mpirun -np 14 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.14
+
+mpirun -np 16 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.16
+
+mpirun -np 1 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.1
+
+mpirun -np 2 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.2
+
+mpirun -np 4 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.4
+
+mpirun -np 6 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.6
+
+mpirun -np 8 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.8
+
+mpirun -np 10 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.10
+
+mpirun -np 12 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.12
+
+mpirun -np 14 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.14
+
+mpirun -np 16 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.16
+
+mpirun -np 1 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.1
+
+mpirun -np 2 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.2
+
+mpirun -np 4 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.4
+
+mpirun -np 6 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.6
+
+mpirun -np 8 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.8
+
+mpirun -np 10 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.10
+
+mpirun -np 12 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.12
+
+mpirun -np 14 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.14
+
+mpirun -np 16 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.16

bench/KEPLER/run_kokkos_cuda.sh

@@ -0,0 +1,74 @@
+#!/bin/bash
+#SBATCH -N 1 --time=12:00:00
+
+mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 1 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.1
+
+mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 2 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.2
+
+mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 3 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.3
+
+mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 4 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.4
+
+mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 5 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.5
+
+mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 6 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.6
+
+mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 7 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.7
+
+mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 8 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.8
+
+mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 9 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.9
+
+mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 10 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.10
+
+mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 11 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.11
+
+mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 12 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.12
+
+mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 13 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.13
+
+mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 14 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.14
+
+mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 15 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.15
+
+mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 16 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.16
+
+mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 1 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.1
+
+mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 2 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.2
+
+mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 3 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.3
+
+mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 4 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.4
+
+mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 5 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.5
+
+mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 6 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.6
+
+mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 7 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.7
+
+mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 8 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.8

bench/KEPLER/run_kokkos_omp.sh

@@ -0,0 +1,17 @@
+#!/bin/bash
+#SBATCH -N 1 --time=12:00:00
+
+mpirun -np full -bind-to socket -map-by socket -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 16 -sf kk -pk kokkos neigh full newton off comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.omp.128K.1.16
+
+mpirun -np full -bind-to socket -map-by socket -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 8 -sf kk -pk kokkos neigh full newton off comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.omp.128K.2.8
+
+mpirun -np full -bind-to socket -map-by socket -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 4 -sf kk -pk kokkos neigh full newton off comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.omp.128K.4.4
+
+mpirun -np full -bind-to socket -map-by socket -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 2 -sf kk -pk kokkos neigh full newton off comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.omp.128K.8.2
+
+mpirun -np half -bind-to socket -map-by socket -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 1 -sf kk -pk kokkos neigh half newton on comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.kokkos.omp.128K.16.1

bench/KEPLER/run_omp.sh

@@ -0,0 +1,17 @@
+#!/bin/bash
+#SBATCH -N 1 --time=12:00:00
+
+mpirun -np 1 lmp_omp -sf omp -pk omp 16 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.omp.128K.1.16
+
+mpirun -np 2 lmp_omp -sf omp -pk omp 8 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.omp.128K.2.8
+
+mpirun -np 4 lmp_omp -sf omp -pk omp 4 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.omp.128K.4.4
+
+mpirun -np 8 lmp_omp -sf omp -pk omp 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.omp.128K.8.2
+
+mpirun -np 16 lmp_omp -sf omp -pk omp 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.omp.128K.16.1

bench/KEPLER/run_opt.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+#SBATCH -N 1 --time=12:00:00
+
+mpirun -np 1 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.opt.128K.1
+
+mpirun -np 2 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.opt.128K.2
+
+mpirun -np 4 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.opt.128K.4
+
+mpirun -np 6 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.opt.128K.6
+
+mpirun -np 8 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.opt.128K.8
+
+mpirun -np 10 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.opt.128K.10
+
+mpirun -np 12 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.opt.128K.12
+
+mpirun -np 14 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.opt.128K.14
+
+mpirun -np 16 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
+mv log.lammps log.10Sep14.lj.opt.128K.16

bench/KEPLER/run_strong.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+#SBATCH -N 16 --time=12:00:00
+
+mpirun -npernode 16 lmp_cpu -v x 64 -v y 64 -v z 128 -v t 100 < in.lj
+mv log.lammps log.28Jun14.lj.cpu.2048K.16.16
+
+mpirun -npernode 16 lmp_omp -sf omp -pk omp 1 -v x 64 -v y 64 -v z 128 -v t 100 < in.lj
+mv log.lammps log.28Jun14.lj.omp.2048K.16.1.16
+
+mpirun -npernode 2 lmp_cuda -c on -sf cuda -pk cuda 2 -v x 64 -v y 64 -v z 128 -v t 100 < in.lj
+mv log.lammps log.28Jun14.lj.cuda.2048K.2.16
+
+mpirun -npernode 14 lmp_gpu -sf gpu -pk gpu 2 -v x 64 -v y 64 -v z 128 -v t 100 < in.lj
+mv log.lammps log.28Jun14.lj.gpu.2048K.2.14.16
+
+mpirun -npernode 2 lmp_kokkos_cuda -k on g 2 t 1 -sf kk -pk kokkos comm device -v x 64 -v y 64 -v z 128 -v t 100 < in.lj
+mv log.lammps log.28Jun14.lj.kokkos.cuda.2048K.2.1.16
+
+mpirun -np 256 -bind-to core -map-by core -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 1 -sf kk -pk kokkos comm device -v x 64 -v y 64 -v z 128 -v t 100 < in.lj
+mv log.lammps log.28Jun14.lj.kokkos.omp.2048K.16.1.16

bench/KEPLER/run_weak.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+#SBATCH -N 16 --time=12:00:00
+
+mpirun -npernode 16 lmp_cpu -v x 128 -v y 128 -v z 128 -v t 100 < in.lj
+mv log.lammps log.28Jun14.lj.cpu.512K.16.16
+
+mpirun -npernode 16 lmp_omp -sf omp -pk omp 1 -v x 128 -v y 128 -v z 128 -v t 100 < in.lj
+mv log.lammps log.28Jun14.lj.omp.512K.16.1.16
+
+mpirun -npernode 2 lmp_cuda -c on -sf cuda -pk cuda 2 -v x 128 -v y 128 -v z 128 -v t 100 < in.lj
+mv log.lammps log.28Jun14.lj.cuda.512K.2.16
+
+mpirun -npernode 14 lmp_gpu -sf gpu -pk gpu 2 -v x 128 -v y 128 -v z 128 -v t 100 < in.lj
+mv log.lammps log.28Jun14.lj.gpu.512K.2.14.16
+
+mpirun -npernode 2 lmp_kokkos_cuda -k on g 2 t 1 -sf kk -pk kokkos comm device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj
+mv log.lammps log.28Jun14.lj.kokkos.cuda.512K.2.1.16
+
+mpirun -np 256 -bind-to core -map-by core -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 1 -sf kk -pk kokkos comm device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj
+mv log.lammps log.28Jun14.lj.kokkos.omp.512K.16.1.16

bench/POTENTIALS/CH.airebo

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

bench/POTENTIALS/CH.rebo

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

bench/POTENTIALS/CdTe.bop

@@ -0,0 +1,44 @@
+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
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+  6.314400e-01   8.252896e-01   3.174259e-02
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+  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

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

bench/POTENTIALS/Cu_u3.eam

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

bench/POTENTIALS/Cu_u3.eam

@@ -0,0 +1,305 @@
+Cu functions (universal 3), SM Foiles et al, PRB, 33, 7983 (1986)
+   29     63.550         3.6150    FCC
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+  5.2756517056398833e-02  5.0571572648238083e-02  4.8513378601664936e-02  4.6573934725081756e-02  4.4745722480991068e-02
+  4.3021679522073253e-02  4.1395175224364866e-02  3.9859987214311721e-02  3.8410278881708670e-02  3.7040577866510604e-02
+  3.5745755503880039e-02  3.4521007208912380e-02  3.3361833779917971e-02  3.2264023597108116e-02  3.1223635691821294e-02
+  3.0236983660070216e-02  2.9300620393215571e-02  2.8411323597772320e-02  2.7566082075896281e-02  2.6762082737777249e-02
+  2.5996698317105604e-02  2.5267475760840985e-02  2.4572125264713973e-02  2.3908509926274246e-02  2.3274635987705516e-02
+  2.2668643641204911e-02  2.2088798370316409e-02  2.1533482801290083e-02  2.1001189039288493e-02  2.0490511464994254e-02
+  2.0000139967999431e-02  1.9528853594166895e-02  1.9075514584991349e-02  1.8639062787818239e-02  1.8218510416650235e-02
+  1.7812937144080498e-02  1.7421485505751177e-02  1.7043356599549031e-02  1.6677806062561751e-02  1.6324140309613155e-02
+  1.5981713017976018e-02  1.5649921843605585e-02  1.5328205354974755e-02  1.5016040171312250e-02  1.4712938292708366e-02
+  1.4418444610242331e-02  1.4132134584901757e-02  1.3853612084676337e-02  1.3582507369821917e-02  1.3318475216818060e-02
+  1.3061193172097418e-02  1.2810359927147186e-02  1.2565693807050415e-02  1.2326931365025051e-02  1.2093826075940506e-02
+  1.1866147122233661e-02  1.1643678266026136e-02  1.1426216801644407e-02  1.1213572583084475e-02  1.1005567121320226e-02
+  1.0802032746662471e-02  1.0602811831688208e-02  1.0407756070544782e-02  1.0216725810699157e-02  1.0029589433467268e-02
+  9.8462227798860602e-03  9.6665086187306404e-03  9.4903361536790021e-03  9.3176005668363371e-03  9.1482025960089031e-03
+  8.9820481433065535e-03  8.8190479128032462e-03  8.6591170751522117e-03  8.5021749571883021e-03  8.3481447546937537e-03
+  8.1969532666261724e-03  8.0485306492223962e-03  7.9028101885199598e-03  7.7597280899136256e-03  7.6192232834934315e-03
+  7.4812372439735375e-03  7.3457138241272979e-03  7.2125991007052359e-03  7.0818412319012813e-03  6.9533903254870300e-03
+  6.8271983168139705e-03  6.7032188559211503e-03  6.5814072030662141e-03  6.4617201320263939e-03  6.3441158405819764e-03
+  6.2285538676237207e-03  6.1149950163802147e-03  6.0034012832899109e-03  5.8937357920846312e-03  5.7859627326801166e-03
+  5.6800473044990030e-03  5.5759556638887986e-03  5.4736548753111791e-03  5.3731128660109428e-03  5.2742983838981461e-03
+  5.1771809583849582e-03  5.0817308639591330e-03  4.9879190862693046e-03  4.8957172905357560e-03  4.8050977921015592e-03
+  4.7160335289582467e-03  4.6284980360953021e-03  4.5424654215287241e-03  4.4579103438822931e-03  4.3748079913988880e-03
+  4.2931340622749670e-03  4.2128647462132407e-03  4.1339767071033873e-03  4.0564470667446839e-03  3.9802533895282599e-03
+  3.9053736680121076e-03  3.8317863093158128e-03  3.7594701222811860e-03  3.6884043053326127e-03  3.6185684349951674e-03
+  3.5499424550168301e-03  3.4825066660512660e-03  3.4162417158645347e-03  3.3511285900229004e-03  3.2871486030347646e-03
+  3.2242833899080170e-03  3.1625148980992668e-03  3.1018253798278661e-03  3.0421973847258310e-03  2.9836137528083811e-03
+  2.9260576077371064e-03  2.8695123503632708e-03  2.8139616525287708e-03  2.7593894511106498e-03  2.7057799422959966e-03
+  2.6531175760685227e-03  2.6013870509009052e-03  2.5505733086344240e-03  2.5006615295404683e-03  2.4516371275501436e-03
+  2.4034857456453340e-03  2.3561932514012535e-03  2.3097457326723414e-03  2.2641294934160616e-03  2.2193310496436136e-03
+  2.1753371254977782e-03  2.1321346494441173e-03  2.0897107505768314e-03  2.0480527550303662e-03  2.0071481824917164e-03
+  1.9669847428123305e-03  1.9275503327108034e-03  1.8888330325659355e-03  1.8508211032951805e-03  1.8135029833145980e-03
+  1.7768672855772646e-03  1.7409027946878666e-03  1.7055984640891586e-03  1.6709434133182904e-03  1.6369269253308227e-03
+  1.6035384438881917e-03  1.5707675710093030e-03  1.5386040644797400e-03  1.5070378354209296e-03  1.4760589459142243e-03
+  1.4456576066784674e-03  1.4158241748004133e-03  1.3865491515145517e-03  1.3578231800324136e-03  1.3296370434173130e-03
+  1.3019816625059188e-03  1.2748480938728074e-03  1.2482275278369870e-03  1.2221112865106742e-03  1.1964908218862064e-03
+  1.1713577139624703e-03  1.1467036689077198e-03  1.1225205172586891e-03  1.0988002121543120e-03  1.0755348276031765e-03
+  1.0527165567835728e-03  1.0303377103750150e-03  1.0083907149206553e-03  9.8686811121878604e-04  9.6576255274356815e-04
+  9.4506680409354657e-04  9.2477373946662708e-04  9.0487634116191706e-04  8.8536769810608137e-04  8.6624100440530968e-04
+  8.4748955791986991e-04  8.2910675886310736e-04  8.1108610842155551e-04  7.9342120739794852e-04  7.7610575487466887e-04
+  7.5913354689786591e-04  7.4249847518158968e-04  7.2619452583109687e-04  7.1021577808524222e-04  6.9455640307671332e-04
+  6.7921066261025093e-04  6.6417290795844214e-04  6.4943757867335500e-04  6.3499920141575628e-04  6.2085238879914031e-04
+  6.0699183824991856e-04  5.9341233088238896e-04  5.8010873038847818e-04  5.6707598194186137e-04  5.5430911111587280e-04
+  5.4180322281523891e-04  5.2955350022104025e-04  5.1755520374872563e-04  5.0580367001857793e-04  4.9429431083891986e-04
+  4.8302261220136561e-04  4.7198413328763435e-04  4.6117450548847222e-04  4.5058943143359842e-04  4.4022468403297037e-04
+  4.3007610552883886e-04  4.2013960655883260e-04  4.1041116522908330e-04  4.0088682619821882e-04  3.9156269977118005e-04
+  3.8243496100300207e-04  3.7349984881274514e-04  3.6475366510662147e-04  3.5619277391102898e-04  3.4781360051482253e-04
+  3.3961263062063513e-04  3.3158640950565685e-04  3.2373154119109092e-04  3.1604468762060252e-04  3.0852256784754707e-04
+  3.0116195723081836e-04  2.9395968663908575e-04  2.8691264166377101e-04  2.8001776184017647e-04  2.7327203987681688e-04
+  2.6667252089326854e-04  2.6021630166557681e-04  2.5390052988028163e-04  2.4772240339593181e-04  2.4167916951265550e-04
+  2.3576812424967210e-04  2.2998661163024531e-04  2.2433202297460642e-04  2.1880179620031078e-04  2.1339341513026532e-04
+  2.0810440880823181e-04  2.0293235082175821e-04  1.9787485863260665e-04  1.9292959291436311e-04  1.8809425689761319e-04
+  1.8336659572205580e-04  1.7874439579616125e-04  1.7422548416372047e-04  1.6980772787763936e-04  1.6548903338088530e-04
+  1.6126734589430591e-04  1.5714064881157744e-04  1.5310696310104604e-04  1.4916434671449329e-04  1.4531089400280153e-04
+  1.4154473513841234e-04  1.3786403554466153e-04  1.3426699533172857e-04  1.3075184873951283e-04  1.2731686358694039e-04
+  1.2396034072819674e-04  1.2068061351527565e-04  1.1747604726729168e-04  1.1434503874632306e-04  1.1128601563955686e-04
+  1.0829743604811193e-04  1.0537778798212988e-04  1.0252558886227753e-04  9.9739385027582898e-05  9.7017751249615057e-05
+  9.4359290252773662e-05  9.1762632240957511e-05  8.9226434430383569e-05  8.6749380588361721e-05  8.4330180578390864e-05
+  8.1967569911181246e-05  7.9660309301724484e-05  7.7407184232279429e-05  7.5207004521348451e-05  7.3058603898526649e-05
+  7.0960839585107720e-05  6.8912591880629977e-05  6.6912763755002085e-05  6.4960280446513426e-05  6.3054089065330086e-05
+  6.1193158202771814e-05  5.9376477546041213e-05  5.7603057498502742e-05  5.5871928805544500e-05  5.4182142185708361e-05
+  5.2532767967318744e-05  5.0922895730446966e-05  4.9351633954125953e-05  4.7818109668823321e-05  4.6321468114150300e-05
+  4.4860872401664663e-05  4.3435503182825573e-05  4.2044558321957873e-05  4.0687252574273750e-05  3.9362817268785450e-05
+  3.8070499996214428e-05  3.6809564301621984e-05  3.5579289382025496e-05  3.4378969788611451e-05  3.3207915133769052e-05
+  3.2065449802711312e-05  3.0950912669766876e-05  2.9863656819185611e-05  2.8803049270468119e-05  2.7768470708167169e-05
+  2.6759315216115260e-05  2.5774990015931323e-05  2.4814915209964844e-05  2.3878523528387922e-05  2.2965260080560611e-05
+  2.2074582110528148e-05  2.1205958756658535e-05  2.0358870815317476e-05  1.9532810508535560e-05  1.8727281255713447e-05
+  1.7941797449145505e-05  1.7175884233475961e-05  1.6429077288930018e-05  1.5700922618341645e-05  1.4990976337865471e-05
+  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
+  5.7821158571569505e-06  5.3226559136389283e-06  4.8749262408651290e-06  4.4386399401326240e-06  4.0135167480073166e-06
+  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/Ni.adp

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

bench/POTENTIALS/Ni.meam

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

bench/POTENTIALS/Ni.meam

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

bench/POTENTIALS/README

@@ -1,11 +1,11 @@
 These are input scripts used to run benchmark tests for many of the
 interatomic potentials in LAMMPS.  The results of running these
 scripts on different machines are shown on the Potentials section of
-the Benchmark page of the LAMMPS WWW site (https://www.lammps.org/bench.html).
+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_mpi has been built
+directory.  This assumes that the executable lmp_linux 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
@@ -15,10 +15,18 @@ 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_mpi -in in.fene
-lmp_mpi -in in.tersoff
+lmp_linux < in.fene
+lmp_linux < in.tersoff
 
-mpirun -np 4 lmp_mpi -in in.fene
-mpirun -np 4 lmp_mpi -in in.protein
+mpirun -np 4 lmp_linux < in.fene
+mpirun -np 4 lmp_linux < in.protein

bench/POTENTIALS/Si.sw

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

bench/POTENTIALS/Si.sw

@@ -0,0 +1,17 @@
+# 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.tersoff

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

bench/POTENTIALS/Si.tersoff

@@ -0,0 +1,16 @@
+# 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/data.airebo

@@ -1,78 +0,0 @@
-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

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

bench/POTENTIALS/data.reax

@@ -1,77 +0,0 @@
-# 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

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

bench/POTENTIALS/ffield.comb

@@ -1,98 +1,98 @@
-# COMB parameters for various elements (Si, Cu, Hf, Ti, Zr, U, O) and mixtures (their oxides and alloys)
-# Edited by Tzu-Ray Shan from MSE, Univ. FL in Apr 2010
-#
-# Elements currently available: Si, Cu, Hf, Ti, Zr, U, O
-# Oxides   currently available: Si-O, Cu-O, Hf-O, Ti-O
-#
-# Si parameter set from (JG Yu, SB Sinnott, SR Phillpot, Phys. Rev. B 75 085311 2007)
-# 		   ,and (TR Shan, BD Devine, SR Phillpot, SB Sinnott, to be sub to Phys. Rev. B)
-# O  parameter set from (TR Shan, BD Devine, SB Sinnott, SR Phillpot, Phys. Rev. B 81 125328 2010)
-# Cu parameter set from (BD Devine, TR Shan, SB Sinnott, SR Phillpot, to be sub to Phys. Rev. B)
-# Hf parameter set from (TR Shan, BD Devine, SB Sinnott, SR Phillpot, Phys. Rev. B 81 125328 2010)
-# Ti parameter set from (TR Shan, SR Phillpot, SB Sinnott, in preparation)
-# U  parameter set from (Y Li, TR Shan, SB Sinnott, SR Phillpot, in preparation)
-# Zr parameter set from (T Iwasaki, J. Mater. Res. 20 5 1300 2005)
-#
-# Multiple entries can be added to this file, LAMMPS reads the ones it needs
-# Only M-O are added in the potential table, using mixing rules to generate desired alloy (A-B) parameters
-# 8  entries for a desired A-B type: AAA, BBB, AAB, ABA, ABB, BAA, BBA, BBA
-# 27 entries for a system containing three elements A, B and C
-# These entries are in LAMMPS "metal" units
-#
-Hf Hf Hf 1 0 1 0 1.011011 0.046511 0.959614 0.959614 55.9421 55.9421 3.90 0.10 2.069563 2.069563 707.53 707.53 0 0 0.008 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 0.26152 -0.25918 0 3.139520d0 0 0.009410d0 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12  0.0
-Ti Ti Ti 1 0 1 0 1.255016 0.089078 1.226342 1.226342 99.3916 99.3916 3.40 0.10 2.082408 2.082408 546.386 546.386 0 0 0.0084 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -4 4 2.508854 -2.511416 0 2.46820415900968 0 0.151351003255176 0 0.873685 0.392632 0.392632 1.78349 1.78349 12  0.0
-O O O 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 2.8 0.2 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12  0.0
-Cu Cu Cu 1 0 1 0 1 0.140835 1.681711 1.681711 146.987 146.987 2.95 0.05 2.794608 2.794608 952.693 952.693 0.077 0.0095 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -6 2 0.1677645 -0.161007 0 5.946437 0 0 0 0.454784 0.72571 0.72571 0.274649 0.274649 12  -2.0
-Si Si Si 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.7322 471.18 471.18 2.90 0.10 2.4799 2.4799 1830.8 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 1.651725 -1.658949 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -0.499378 2.999911 2.999911 12  0.0
-Zr Zr Zr 1 0 1 0 1 0 0.929 0.929 39.9454 39.9454 3.8 0.31 1.857 1.857 382.6 382.6 0 0 0 0 0 0 1 1 1 1 -4 4 1.64 -1.5 -4 4 1.64 -1.5 0 3.139520d0 0 0.009410d0 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12  0.0
-U U U 1 0 1 0 4.346966 0.77617 0.832 0.832 162.6 162.6 3.9 0.15 1.835 1.835 795.6 795.6 0 0 0 0 0 0 1 1 1 1 -4 4 2 -2 -4 4 2 -2 0 3.139520d0 0 0.009410d0 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12  0.0
-#                                               
-Si O O 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 2.68 471.18 260.893 2.80 0.25 2.4799 5.36 1830.8 3326.69 0 0 0 109.47 0.3122 0 1 1 1 1 -4 4 1.651725 -1.658949 -1.8349 5.5046 0.00148 -0.00112 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.922011 2.999911 0.971086 12 0
-O Si Si 1 6.6 1 -0.229 1 2 2.68 1.7322 260.893 471.18 2.80 0.25 5.36 2.4799 3326.69 1830.8 0 0 0 143.73 2.6 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 1.651725 -1.658949 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -0.499378 0.971086 2.999911 12 0
-Si O Si 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 2.68 471.18 260.893 2.80 0.25 2.4799 5.36 1830.8 3326.69 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -1.8349 5.5046 0.00148 -0.00112 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.922011 2.999911 0.971086 12 0
-O Si O 1 6.6 1 -0.229 1 2 2.68 1.7322 260.893 471.18 3.20 0.25 5.36 2.4799 3326.69 1830.8 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 1.651725 -1.658949 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -0.499378 0.971086 2.999911 12 0
-Si Si O 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.7322 471.18 471.18 2.80 0.25 2.4799 2.4799 1830.8 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 1.651725 -1.658949 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -0.499378 2.999911 2.999911 12 0
-O O Si 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 2.80 0.25 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12 0
-#
-Si Cu Cu 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.681711 471.18 146.987 2.70 0.10 2.4799 2.794608 1830.8 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -6 2 0.1677645 -0.161007 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 0.72571 2.999911 0.274649 12   0
-Cu Si Si 1 0 1 0 1 0.140835 1.681711 1.7322 146.987 471.18 2.70 0.10 2.794608 2.4799 952.693 1830.8 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 1.651725 -1.658949 0 5.946437 0 0 0 0.454784 0.72571 -0.499378 0.274649 2.999911 12   0
-Si Cu Si 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.681711 471.18 146.987 2.70 0.10 2.4799 2.794608 1830.8 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -6 2 0.1677645 -0.161007 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 0.72571 2.999911 0.274649 12   0
-Cu Si Cu 1 0 1 0 1 0.140835 1.681711 1.7322 146.987 471.18 2.70 0.10 2.794608 2.4799 952.693 1830.8 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 1.651725 -1.658949 0 5.946437 0 0 0 0.454784 0.72571 -0.499378 0.274649 2.999911 12   0
-Si Si Cu 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.7322 471.18 471.18 2.70 0.10 2.4799 2.4799 1830.8 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 1.651725 -1.658949 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -0.499378 2.999911 2.999911 12   0
-Cu Cu Si 1 0 1 0 1 0.140835 1.681711 1.681711 146.987 146.987 2.70 0.10 2.794608 2.794608 952.693 952.693 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -6 2 0.1677645 -0.161007 0 5.946437 0 0 0 0.454784 0.72571 0.72571 0.274649 0.274649 12   0
-#                                                
-Si O Cu 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 2.68 471.18 260.893 2.80 0.10 2.4799 5.36 1830.8 3326.69 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -1.8349 5.5046 0.00148 -0.00112 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.922011 2.999911 0.971086 12   0
-Cu O Si 1 0 1 0 1 0.140835 1.681711 2.68 146.987 260.893 2.40 0.10 2.794608 5.36 952.693 3326.69 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -6 2 0.1677645 -0.161007 -1.8349 5.5046 0.00148 -0.00112 0 5.946437 0 0 0 0.454784 0.72571 -3.922011 0.274649 0.971086 12  0
-Si Cu O 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.681711 471.18 146.987 2.70 0.10 2.4799 2.794608 1830.8 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -6 2 0.1677645 -0.161007 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 0.72571 2.999911 0.274649 12   0
-Cu Si O 1 0 1 0 1 0.140835 1.681711 1.7322 146.987 471.18 2.70 0.10 2.794608 2.4799 952.693 1830.8 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 1.651725 -1.658949 0 5.946437 0 0 0 0.454784 0.72571 -0.499378 0.274649 2.999911 12   0
-O Si Cu 1 6.6 1 -0.229 1 2 2.68 1.7322 260.893 471.18 2.80 0.10 5.36 2.4799 3326.69 1830.8 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 1.651725 -1.658949 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -0.499378 0.971086 2.999911 12   0
-O Cu Si 1 6.6 1 -0.229 1 2 2.68 1.681711 260.893 146.987 2.40 0.10 5.36 2.794608 3326.69 952.693 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -1.8349 5.5046 0.00148 -0.00112 -6 2 0.1677645 -0.161007 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.72571 0.971086 0.274649 12  0
-#
-Cu O O 1 0 1 0 1 0.140835 1.681711 2.68 146.987 260.893 2.40 0.110 2.794608 5.36 952.693 3326.69 0 0 0 360 3.0 0 0.15867 1.106214 0.533319 1.857837 -6 2 0.1677645 -0.161007 -1.8349 5.5046 0.00148 -0.00112 0 5.946437 0 0 0 0.454784 0.72571 -3.922011 0.274649 0.971086 12  -1.0
-O Cu Cu 1 6.6 1 -0.229 1 2 2.68 1.681711 260.893 146.987 2.40 0.110 5.36 2.794608 3326.69 952.693 0 0 0 109.47 2.98 0 0.15867 1.106214 0.533319 1.857837 -1.8349 5.5046 0.00148 -0.00112 -6 2 0.1677645 -0.161007 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.72571 0.971086 0.274649 12  0
-Cu O Cu 1 0 1 0 1 0.140835 1.681711 2.68 146.987 260.893 2.40 0.110 2.794608 5.36 952.693 3326.69 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -6 2 0.1677645 -0.161007 -1.8349 5.5046 0.00148 -0.00112 0 5.946437 0 0 0 0.454784 0.72571 -3.922011 0.274649 0.971086 12  0
-O Cu O 1 6.6 1 -0.229 1 2 2.68 1.681711 260.893 146.987 2.40 0.110 5.36 2.794608 3326.69 952.693 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -1.8349 5.5046 0.00148 -0.00112 -6 2 0.1677645 -0.161007 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.72571 0.971086 0.274649 12  0
-Cu Cu O 1 0 1 0 1 0.140835 1.681711 1.681711 146.987 146.987 2.90 0.05 2.794608 2.794608 952.693 952.693 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -6 2 0.1677645 -0.161007 0 5.946437 0 0 0 0.454784 0.72571 0.72571 0.274649 0.274649 12  0
-O O Cu 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 2.80 0.20 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12  0
-#
-Si Hf Hf 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 0.959614 471.18 55.9421 3.26 0.15 2.4799 2.069563 1830.8 707.53 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 0.26152 -0.25918 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.92875 2.999911 4.83958 12 0
-Hf Si Si 1 0 1 0 1.011011 0.046511 0.959614 1.7322 55.9421 471.18 3.26 0.15 2.069563 2.4799 707.53 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 1.651725 -1.658949 0 3.13952 0 0.00941 0 0.719131 -3.92875 -0.499378 4.83958 2.999911 12 0
-Si Hf Si 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 0.959614 471.18 55.9421 3.26 0.15 2.4799 2.069563 1830.8 707.53 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 0.26152 -0.25918 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.92875 2.999911 4.83958 12 0
-Hf Si Hf 1 0 1 0 1.011011 0.046511 0.959614 1.7322 55.9421 471.18 3.26 0.15 2.069563 2.4799 707.53 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 1.651725 -1.658949 0 3.13952 0 0.00941 0 0.719131 -3.92875 -0.499378 4.83958 2.999911 12 0
-Si Si Hf 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.7322 471.18 471.18 3.26 0.15 2.4799 2.4799 1830.8 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 1.651725 -1.658949 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -0.499378 2.999911 2.999911 12 0
-Hf Hf Si 1 0 1 0 1.011011 0.046511 0.959614 0.959614 55.9421 55.9421 3.26 0.15 2.069563 2.069563 707.53 707.53 0 0 0 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 0.26152 -0.25918 0 3.13952 0 0.00941 0 0.719131 -3.92875 -3.92875 4.83958 4.83958 12 0
-#
-Si O Hf 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 2.68 471.18 260.893 3.196 0.21 2.4799 5.36 1830.8 3326.69 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -1.8349 5.5046 0.00148 -0.00112 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.922011 2.999911 0.971086 12 0
-Hf O Si 1 0 1 0 1.011011 0.046511 0.959614 2.68 55.9421 260.893 3.196 0.21 2.069563 5.36 707.53 3326.69 0 0 0 0 0 0.14 1 1 1 1 -4 4 0.26152 -0.25918 -1.8349 5.5046 0.00148 -0.00112 0 3.13952 0 0.00941 0 0.719131 -3.92875 -3.922011 4.83958 0.971086 12  0.16
-Si Hf O 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 0.959614 471.18 55.9421 3.26 0.15 2.4799 2.069563 1830.8 707.53 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 0.26152 -0.25918 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.92875 2.999911 4.83958 12 0
-Hf Si O 1 0 1 0 1.011011 0.046511 0.959614 1.7322 55.9421 471.18 3.26 0.15 2.069563 2.4799 707.53 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 1.651725 -1.658949 0 3.13952 0 0.00941 0 0.719131 -3.92875 -0.499378 4.83958 2.999911 12 0
-O Si Hf 1 6.6 1 -0.229 1 2 2.68 1.7322 260.893 471.18 3.196 0.21 5.36 2.4799 3326.69 1830.8 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 1.651725 -1.658949 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -0.499378 0.971086 2.999911 12 0
-O Hf Si 1 6.6 1 -0.229 1 2 2.68 0.959614 260.893 55.9421 3.196 0.21 5.36 2.069563 3326.69 707.53 0 0 0 0 0 0.14 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 0.26152 -0.25918 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.92875 0.971086 4.83958 12 0.16
-#
-Hf O O 1 0 1 0 1.011011 0.046511 0.959614 2.68 55.9421 260.893 3.29 0.12 2.069563 5.36 707.53 3326.69 0 0 0 0 0 0.14 1 1 1 1 -4 4 0.26152 -0.25918 -1.8349 5.5046 0.00148 -0.00112 0 3.13952 0 0.00941 0 0.679131 -3.92875 -3.922011 4.83958 0.971086 12  0.30
-O Hf Hf 1 6.6 1 -0.229 1 2 2.68 0.959614 260.893 55.9421 3.29 0.12 5.36 2.069563 3326.69 707.53 0 0 0 0 0 0.14 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 0.26152 -0.25918 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.92875 0.971086 4.83958 12  0.30
-Hf O Hf 1 0 1 0 1.011011 0.046511 0.959614 2.68 55.9421 260.893 3.29 0.12 2.069563 5.36 707.53 3326.69 0 0 0 0 0 0.14 1 1 1 1 -4 4 0.26152 -0.25918 -1.8349 5.5046 0.00148 -0.00112 0 3.13952 0 0.00941 0 0.679131 -3.92875 -3.922011 4.83958 0.971086 12  0.30
-O Hf O 1 6.6 1 -0.229 1 2 2.68 0.959614 260.893 55.9421 3.29 0.12 5.36 2.069563 3326.69 707.53 0 0 0 0 0 0.14 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 0.26152 -0.25918 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.92875 0.971086 4.83958 12  0.30
-Hf Hf O 1 0 1 0 1.011011 0.046511 0.959614 0.959614 55.9421 55.9421 3.29 0.12 2.069563 2.069563 707.53 707.53 0 0 0 0 0 0.0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 0.26152 -0.25918 0 3.13952 0 0.00941 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12  0.30
-O O Hf 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 3.29 0.12 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0.0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12  0.30
-#
-Ti O O 1 0 1 0 1.255016 0.089078 1.226342 2.68 99.3916 260.893 3.25 0.10 2.082408 5.36 546.386 3326.69 0 0 0 90 0.403105 8.45  0.088406 0.969934 0.296577 1.326746 -4 4 2.508854 -2.511416 -1.8349 5.5046 0.00148 -0.00112 0 1.943430774 0 0.254695274 0 0.873685 0.392632 -3.922011 1.78349 0.971086 12  0.0
-O Ti Ti 1 6.6 1 -0.229 1 2 2.68 1.226342 260.893 99.3916 3.25 0.10 5.36 2.082408 3326.69 546.386 0 0 0 130.54 0.202777 8.45  0.088406 0.969934 0.296577 1.326746 -1.8349 5.5046 0.00148 -0.00112 -4 4 2.508854 -2.511416 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.392632 0.971086 1.78349 12  0.0
-Ti O Ti 1 0 1 0 1.255016 0.089078 1.226342 2.68 99.3916 260.893 3.25 0.10 2.082408 5.36 546.386 3326.69 0 0 0 0 0 8.45  0.088406 0.969934 0.296577 1.326746 -4 4 2.508854 -2.511416 -1.8349 5.5046 0.00148 -0.00112 0 1.943430774 0 0.254695274 0 0.873685 0.392632 -3.922011 1.78349 0.971086 12  0.0
-O Ti O 1 6.6 1 -0.229 1 2 2.68 1.226342 260.893 99.3916 3.25 0.10 5.36 2.082408 3326.69 546.386 0 0 0 0 0 8.45  0.088406 0.969934 0.296577 1.326746 -1.8349 5.5046 0.00148 -0.00112 -4 4 2.508854 -2.511416 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.392632 0.971086 1.78349 12  0.0
-Ti Ti O 1 0 1 0 1.255016 0.089078 1.226342 1.226342 99.3916 99.3916 3.25 0.10 2.082408 2.082408 546.386 546.386 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -4 4 2.508854 -2.511416 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.392632 1.78349 1.78349 12  0.0
-O O Ti 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 2.80 0.20 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12  0.0
-#
-Ti Cu Cu 1 0 1 0 1.255016 0.089078 1.226342 1.681711 99.3916 146.987 3.40 0.15 2.082408 2.794608 546.386 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -6 2 0.1677645 -0.161007 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.72571 1.78349 0.274649 12 0
-Cu Ti Ti 1 0 1 0 1 0.140835 1.681711 1.226342 146.987 99.3916 3.40 0.15 2.794608 2.082408 952.693 546.386 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 2.508854 -2.511416 0 5.946437 0 0 0 0.454784 0.72571 0.392632 0.274649 1.78349 12 0
-Ti Cu Ti 1 0 1 0 1.255016 0.089078 1.226342 1.681711 99.3916 146.987 3.40 0.15 2.082408 2.794608 546.386 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -6 2 0.1677645 -0.161007 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.72571 1.78349 0.274649 12 0
-Cu Ti Cu 1 0 1 0 1 0.140835 1.681711 1.226342 146.987 99.3916 3.40 0.15 2.794608 2.082408 952.693 546.386 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 2.508854 -2.511416 0 5.946437 0 0 0 0.454784 0.72571 0.392632 0.274649 1.78349 12 0
-Ti Ti Cu 1 0 1 0 1.255016 0.089078 1.226342 1.226342 99.3916 99.3916 3.40 0.10 2.082408 2.082408 546.386 546.386 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -4 4 2.508854 -2.511416 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.392632 1.78349 1.78349 12 0
-Cu Cu Ti 1 0 1 0 1 0.140835 1.681711 1.681711 146.987 146.987 2.90 0.05 2.794608 2.794608 952.693 952.693 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -6 2 0.1677645 -0.161007 0 5.946437 0 0 0 0.454784 0.72571 0.72571 0.274649 0.274649 12 0
-#                                                
-Ti O Cu 1 0 1 0 1.255016 0.089078 1.226342 2.68 99.3916 260.893 3.25 0.10 2.082408 5.36 546.386 3326.69 0 0 0 0 0  8.45  0.088406 0.969934 0.296577 1.326746 -4 4 2.508854 -2.511416 -1.8349 5.5046 0.00148 -0.00112 0 1.943430774 0 0.254695274 0 0.873685 0.392632 -3.922011 1.78349 0.971086 12 0
-Cu O Ti 1 0 1 0 1 0.140835 1.681711 2.68 146.987 260.893 2.40 0.10 2.794608 5.36 952.693 3326.69 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -6 2 0.1677645 -0.161007 -1.8349 5.5046 0.00148 -0.00112 0 5.946437 0 0 0 0.454784 0.72571 -3.922011 0.274649 0.971086 12  0
-Ti Cu O 1 0 1 0 1.255016 0.089078 1.226342 1.681711 99.3916 146.987 3.40 0.15 2.082408 2.794608 546.386 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -6 2 0.1677645 -0.161007 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.72571 1.78349 0.274649 12 0
-Cu Ti O 1 0 1 0 1 0.140835 1.681711 1.226342 146.987 99.3916 3.40 0.15 2.794608 2.082408 952.693 546.386 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 2.508854 -2.511416 0 5.946437 0 0 0 0.454784 0.72571 0.392632 0.274649 1.78349 12 0
-O Ti Cu 1 6.6 1 -0.229 1 2 2.68 1.226342 260.893 99.3916 3.25 0.10 5.36 2.082408 3326.69 546.386 0 0 0 0 0  8.45  0.088406 0.969934 0.296577 1.326746 -1.8349 5.5046 0.00148 -0.00112 -4 4 2.508854 -2.511416 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.392632 0.971086 1.78349 12 0
-O Cu Ti 1 6.6 1 -0.229 1 2 2.68 1.681711 260.893 146.987 2.40 0.10 5.36 2.794608 3326.69 952.693 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -1.8349 5.5046 0.00148 -0.00112 -6 2 0.1677645 -0.161007 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.72571 0.971086 0.274649 12  0
+# COMB parameters for various elements (Si, Cu, Hf, Ti, Zr, U, O) and mixtures (their oxides and alloys)
+# Edited by Tzu-Ray Shan from MSE, Univ. FL in Apr 2010
+#
+# Elements currently available: Si, Cu, Hf, Ti, Zr, U, O
+# Oxides   currently available: Si-O, Cu-O, Hf-O, Ti-O
+#
+# Si parameter set from (JG Yu, SB Sinnott, SR Phillpot, Phys. Rev. B 75 085311 2007)
+# 		   ,and (TR Shan, BD Devine, SR Phillpot, SB Sinnott, to be sub to Phys. Rev. B)
+# O  parameter set from (TR Shan, BD Devine, SB Sinnott, SR Phillpot, Phys. Rev. B 81 125328 2010)
+# Cu parameter set from (BD Devine, TR Shan, SB Sinnott, SR Phillpot, to be sub to Phys. Rev. B)
+# Hf parameter set from (TR Shan, BD Devine, SB Sinnott, SR Phillpot, Phys. Rev. B 81 125328 2010)
+# Ti parameter set from (TR Shan, SR Phillpot, SB Sinnott, in preparation)
+# U  parameter set from (Y Li, TR Shan, SB Sinnott, SR Phillpot, in preparation)
+# Zr parameter set from (T Iwasaki, J. Mater. Res. 20 5 1300 2005)
+#
+# Multiple entries can be added to this file, LAMMPS reads the ones it needs
+# Only M-O are added in the potential table, using mixing rules to generate desired alloy (A-B) parameters
+# 8  entries for a desired A-B type: AAA, BBB, AAB, ABA, ABB, BAA, BBA, BBA
+# 27 entries for a system containing three elements A, B and C
+# These entries are in LAMMPS "metal" units
+#
+Hf Hf Hf 1 0 1 0 1.011011 0.046511 0.959614 0.959614 55.9421 55.9421 3.90 0.10 2.069563 2.069563 707.53 707.53 0 0 0.008 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 0.26152 -0.25918 0 3.139520d0 0 0.009410d0 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12  0.0
+Ti Ti Ti 1 0 1 0 1.255016 0.089078 1.226342 1.226342 99.3916 99.3916 3.40 0.10 2.082408 2.082408 546.386 546.386 0 0 0.0084 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -4 4 2.508854 -2.511416 0 2.46820415900968 0 0.151351003255176 0 0.873685 0.392632 0.392632 1.78349 1.78349 12  0.0
+O O O 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 2.8 0.2 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12  0.0
+Cu Cu Cu 1 0 1 0 1 0.140835 1.681711 1.681711 146.987 146.987 2.95 0.05 2.794608 2.794608 952.693 952.693 0.077 0.0095 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -6 2 0.1677645 -0.161007 0 5.946437 0 0 0 0.454784 0.72571 0.72571 0.274649 0.274649 12  -2.0
+Si Si Si 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.7322 471.18 471.18 2.90 0.10 2.4799 2.4799 1830.8 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 1.651725 -1.658949 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -0.499378 2.999911 2.999911 12  0.0
+Zr Zr Zr 1 0 1 0 1 0 0.929 0.929 39.9454 39.9454 3.8 0.31 1.857 1.857 382.6 382.6 0 0 0 0 0 0 1 1 1 1 -4 4 1.64 -1.5 -4 4 1.64 -1.5 0 3.139520d0 0 0.009410d0 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12  0.0
+U U U 1 0 1 0 4.346966 0.77617 0.832 0.832 162.6 162.6 3.9 0.15 1.835 1.835 795.6 795.6 0 0 0 0 0 0 1 1 1 1 -4 4 2 -2 -4 4 2 -2 0 3.139520d0 0 0.009410d0 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12  0.0
+#                                               
+Si O O 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 2.68 471.18 260.893 2.80 0.25 2.4799 5.36 1830.8 3326.69 0 0 0 109.47 0.3122 0 1 1 1 1 -4 4 1.651725 -1.658949 -1.8349 5.5046 0.00148 -0.00112 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.922011 2.999911 0.971086 12 0
+O Si Si 1 6.6 1 -0.229 1 2 2.68 1.7322 260.893 471.18 2.80 0.25 5.36 2.4799 3326.69 1830.8 0 0 0 143.73 2.6 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 1.651725 -1.658949 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -0.499378 0.971086 2.999911 12 0
+Si O Si 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 2.68 471.18 260.893 2.80 0.25 2.4799 5.36 1830.8 3326.69 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -1.8349 5.5046 0.00148 -0.00112 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.922011 2.999911 0.971086 12 0
+O Si O 1 6.6 1 -0.229 1 2 2.68 1.7322 260.893 471.18 3.20 0.25 5.36 2.4799 3326.69 1830.8 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 1.651725 -1.658949 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -0.499378 0.971086 2.999911 12 0
+Si Si O 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.7322 471.18 471.18 2.80 0.25 2.4799 2.4799 1830.8 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 1.651725 -1.658949 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -0.499378 2.999911 2.999911 12 0
+O O Si 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 2.80 0.25 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12 0
+#
+Si Cu Cu 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.681711 471.18 146.987 2.70 0.10 2.4799 2.794608 1830.8 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -6 2 0.1677645 -0.161007 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 0.72571 2.999911 0.274649 12   0
+Cu Si Si 1 0 1 0 1 0.140835 1.681711 1.7322 146.987 471.18 2.70 0.10 2.794608 2.4799 952.693 1830.8 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 1.651725 -1.658949 0 5.946437 0 0 0 0.454784 0.72571 -0.499378 0.274649 2.999911 12   0
+Si Cu Si 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.681711 471.18 146.987 2.70 0.10 2.4799 2.794608 1830.8 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -6 2 0.1677645 -0.161007 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 0.72571 2.999911 0.274649 12   0
+Cu Si Cu 1 0 1 0 1 0.140835 1.681711 1.7322 146.987 471.18 2.70 0.10 2.794608 2.4799 952.693 1830.8 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 1.651725 -1.658949 0 5.946437 0 0 0 0.454784 0.72571 -0.499378 0.274649 2.999911 12   0
+Si Si Cu 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.7322 471.18 471.18 2.70 0.10 2.4799 2.4799 1830.8 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 1.651725 -1.658949 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -0.499378 2.999911 2.999911 12   0
+Cu Cu Si 1 0 1 0 1 0.140835 1.681711 1.681711 146.987 146.987 2.70 0.10 2.794608 2.794608 952.693 952.693 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -6 2 0.1677645 -0.161007 0 5.946437 0 0 0 0.454784 0.72571 0.72571 0.274649 0.274649 12   0
+#                                                
+Si O Cu 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 2.68 471.18 260.893 2.80 0.10 2.4799 5.36 1830.8 3326.69 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -1.8349 5.5046 0.00148 -0.00112 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.922011 2.999911 0.971086 12   0
+Cu O Si 1 0 1 0 1 0.140835 1.681711 2.68 146.987 260.893 2.40 0.10 2.794608 5.36 952.693 3326.69 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -6 2 0.1677645 -0.161007 -1.8349 5.5046 0.00148 -0.00112 0 5.946437 0 0 0 0.454784 0.72571 -3.922011 0.274649 0.971086 12  0
+Si Cu O 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.681711 471.18 146.987 2.70 0.10 2.4799 2.794608 1830.8 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -6 2 0.1677645 -0.161007 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 0.72571 2.999911 0.274649 12   0
+Cu Si O 1 0 1 0 1 0.140835 1.681711 1.7322 146.987 471.18 2.70 0.10 2.794608 2.4799 952.693 1830.8 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 1.651725 -1.658949 0 5.946437 0 0 0 0.454784 0.72571 -0.499378 0.274649 2.999911 12   0
+O Si Cu 1 6.6 1 -0.229 1 2 2.68 1.7322 260.893 471.18 2.80 0.10 5.36 2.4799 3326.69 1830.8 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 1.651725 -1.658949 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -0.499378 0.971086 2.999911 12   0
+O Cu Si 1 6.6 1 -0.229 1 2 2.68 1.681711 260.893 146.987 2.40 0.10 5.36 2.794608 3326.69 952.693 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -1.8349 5.5046 0.00148 -0.00112 -6 2 0.1677645 -0.161007 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.72571 0.971086 0.274649 12  0
+#
+Cu O O 1 0 1 0 1 0.140835 1.681711 2.68 146.987 260.893 2.40 0.110 2.794608 5.36 952.693 3326.69 0 0 0 360 3.0 0 0.15867 1.106214 0.533319 1.857837 -6 2 0.1677645 -0.161007 -1.8349 5.5046 0.00148 -0.00112 0 5.946437 0 0 0 0.454784 0.72571 -3.922011 0.274649 0.971086 12  -1.0
+O Cu Cu 1 6.6 1 -0.229 1 2 2.68 1.681711 260.893 146.987 2.40 0.110 5.36 2.794608 3326.69 952.693 0 0 0 109.47 2.98 0 0.15867 1.106214 0.533319 1.857837 -1.8349 5.5046 0.00148 -0.00112 -6 2 0.1677645 -0.161007 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.72571 0.971086 0.274649 12  0
+Cu O Cu 1 0 1 0 1 0.140835 1.681711 2.68 146.987 260.893 2.40 0.110 2.794608 5.36 952.693 3326.69 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -6 2 0.1677645 -0.161007 -1.8349 5.5046 0.00148 -0.00112 0 5.946437 0 0 0 0.454784 0.72571 -3.922011 0.274649 0.971086 12  0
+O Cu O 1 6.6 1 -0.229 1 2 2.68 1.681711 260.893 146.987 2.40 0.110 5.36 2.794608 3326.69 952.693 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -1.8349 5.5046 0.00148 -0.00112 -6 2 0.1677645 -0.161007 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.72571 0.971086 0.274649 12  0
+Cu Cu O 1 0 1 0 1 0.140835 1.681711 1.681711 146.987 146.987 2.90 0.05 2.794608 2.794608 952.693 952.693 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -6 2 0.1677645 -0.161007 0 5.946437 0 0 0 0.454784 0.72571 0.72571 0.274649 0.274649 12  0
+O O Cu 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 2.80 0.20 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12  0
+#
+Si Hf Hf 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 0.959614 471.18 55.9421 3.26 0.15 2.4799 2.069563 1830.8 707.53 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 0.26152 -0.25918 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.92875 2.999911 4.83958 12 0
+Hf Si Si 1 0 1 0 1.011011 0.046511 0.959614 1.7322 55.9421 471.18 3.26 0.15 2.069563 2.4799 707.53 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 1.651725 -1.658949 0 3.13952 0 0.00941 0 0.719131 -3.92875 -0.499378 4.83958 2.999911 12 0
+Si Hf Si 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 0.959614 471.18 55.9421 3.26 0.15 2.4799 2.069563 1830.8 707.53 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 0.26152 -0.25918 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.92875 2.999911 4.83958 12 0
+Hf Si Hf 1 0 1 0 1.011011 0.046511 0.959614 1.7322 55.9421 471.18 3.26 0.15 2.069563 2.4799 707.53 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 1.651725 -1.658949 0 3.13952 0 0.00941 0 0.719131 -3.92875 -0.499378 4.83958 2.999911 12 0
+Si Si Hf 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.7322 471.18 471.18 3.26 0.15 2.4799 2.4799 1830.8 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 1.651725 -1.658949 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -0.499378 2.999911 2.999911 12 0
+Hf Hf Si 1 0 1 0 1.011011 0.046511 0.959614 0.959614 55.9421 55.9421 3.26 0.15 2.069563 2.069563 707.53 707.53 0 0 0 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 0.26152 -0.25918 0 3.13952 0 0.00941 0 0.719131 -3.92875 -3.92875 4.83958 4.83958 12 0
+#
+Si O Hf 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 2.68 471.18 260.893 3.196 0.21 2.4799 5.36 1830.8 3326.69 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -1.8349 5.5046 0.00148 -0.00112 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.922011 2.999911 0.971086 12 0
+Hf O Si 1 0 1 0 1.011011 0.046511 0.959614 2.68 55.9421 260.893 3.196 0.21 2.069563 5.36 707.53 3326.69 0 0 0 0 0 0.14 1 1 1 1 -4 4 0.26152 -0.25918 -1.8349 5.5046 0.00148 -0.00112 0 3.13952 0 0.00941 0 0.719131 -3.92875 -3.922011 4.83958 0.971086 12  0.16
+Si Hf O 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 0.959614 471.18 55.9421 3.26 0.15 2.4799 2.069563 1830.8 707.53 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 0.26152 -0.25918 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.92875 2.999911 4.83958 12 0
+Hf Si O 1 0 1 0 1.011011 0.046511 0.959614 1.7322 55.9421 471.18 3.26 0.15 2.069563 2.4799 707.53 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 1.651725 -1.658949 0 3.13952 0 0.00941 0 0.719131 -3.92875 -0.499378 4.83958 2.999911 12 0
+O Si Hf 1 6.6 1 -0.229 1 2 2.68 1.7322 260.893 471.18 3.196 0.21 5.36 2.4799 3326.69 1830.8 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 1.651725 -1.658949 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -0.499378 0.971086 2.999911 12 0
+O Hf Si 1 6.6 1 -0.229 1 2 2.68 0.959614 260.893 55.9421 3.196 0.21 5.36 2.069563 3326.69 707.53 0 0 0 0 0 0.14 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 0.26152 -0.25918 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.92875 0.971086 4.83958 12 0.16
+#
+Hf O O 1 0 1 0 1.011011 0.046511 0.959614 2.68 55.9421 260.893 3.29 0.12 2.069563 5.36 707.53 3326.69 0 0 0 0 0 0.14 1 1 1 1 -4 4 0.26152 -0.25918 -1.8349 5.5046 0.00148 -0.00112 0 3.13952 0 0.00941 0 0.679131 -3.92875 -3.922011 4.83958 0.971086 12  0.30
+O Hf Hf 1 6.6 1 -0.229 1 2 2.68 0.959614 260.893 55.9421 3.29 0.12 5.36 2.069563 3326.69 707.53 0 0 0 0 0 0.14 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 0.26152 -0.25918 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.92875 0.971086 4.83958 12  0.30
+Hf O Hf 1 0 1 0 1.011011 0.046511 0.959614 2.68 55.9421 260.893 3.29 0.12 2.069563 5.36 707.53 3326.69 0 0 0 0 0 0.14 1 1 1 1 -4 4 0.26152 -0.25918 -1.8349 5.5046 0.00148 -0.00112 0 3.13952 0 0.00941 0 0.679131 -3.92875 -3.922011 4.83958 0.971086 12  0.30
+O Hf O 1 6.6 1 -0.229 1 2 2.68 0.959614 260.893 55.9421 3.29 0.12 5.36 2.069563 3326.69 707.53 0 0 0 0 0 0.14 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 0.26152 -0.25918 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.92875 0.971086 4.83958 12  0.30
+Hf Hf O 1 0 1 0 1.011011 0.046511 0.959614 0.959614 55.9421 55.9421 3.29 0.12 2.069563 2.069563 707.53 707.53 0 0 0 0 0 0.0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 0.26152 -0.25918 0 3.13952 0 0.00941 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12  0.30
+O O Hf 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 3.29 0.12 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0.0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12  0.30
+#
+Ti O O 1 0 1 0 1.255016 0.089078 1.226342 2.68 99.3916 260.893 3.25 0.10 2.082408 5.36 546.386 3326.69 0 0 0 90 0.403105 8.45  0.088406 0.969934 0.296577 1.326746 -4 4 2.508854 -2.511416 -1.8349 5.5046 0.00148 -0.00112 0 1.943430774 0 0.254695274 0 0.873685 0.392632 -3.922011 1.78349 0.971086 12  0.0
+O Ti Ti 1 6.6 1 -0.229 1 2 2.68 1.226342 260.893 99.3916 3.25 0.10 5.36 2.082408 3326.69 546.386 0 0 0 130.54 0.202777 8.45  0.088406 0.969934 0.296577 1.326746 -1.8349 5.5046 0.00148 -0.00112 -4 4 2.508854 -2.511416 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.392632 0.971086 1.78349 12  0.0
+Ti O Ti 1 0 1 0 1.255016 0.089078 1.226342 2.68 99.3916 260.893 3.25 0.10 2.082408 5.36 546.386 3326.69 0 0 0 0 0 8.45  0.088406 0.969934 0.296577 1.326746 -4 4 2.508854 -2.511416 -1.8349 5.5046 0.00148 -0.00112 0 1.943430774 0 0.254695274 0 0.873685 0.392632 -3.922011 1.78349 0.971086 12  0.0
+O Ti O 1 6.6 1 -0.229 1 2 2.68 1.226342 260.893 99.3916 3.25 0.10 5.36 2.082408 3326.69 546.386 0 0 0 0 0 8.45  0.088406 0.969934 0.296577 1.326746 -1.8349 5.5046 0.00148 -0.00112 -4 4 2.508854 -2.511416 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.392632 0.971086 1.78349 12  0.0
+Ti Ti O 1 0 1 0 1.255016 0.089078 1.226342 1.226342 99.3916 99.3916 3.25 0.10 2.082408 2.082408 546.386 546.386 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -4 4 2.508854 -2.511416 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.392632 1.78349 1.78349 12  0.0
+O O Ti 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 2.80 0.20 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12  0.0
+#
+Ti Cu Cu 1 0 1 0 1.255016 0.089078 1.226342 1.681711 99.3916 146.987 3.40 0.15 2.082408 2.794608 546.386 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -6 2 0.1677645 -0.161007 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.72571 1.78349 0.274649 12 0
+Cu Ti Ti 1 0 1 0 1 0.140835 1.681711 1.226342 146.987 99.3916 3.40 0.15 2.794608 2.082408 952.693 546.386 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 2.508854 -2.511416 0 5.946437 0 0 0 0.454784 0.72571 0.392632 0.274649 1.78349 12 0
+Ti Cu Ti 1 0 1 0 1.255016 0.089078 1.226342 1.681711 99.3916 146.987 3.40 0.15 2.082408 2.794608 546.386 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -6 2 0.1677645 -0.161007 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.72571 1.78349 0.274649 12 0
+Cu Ti Cu 1 0 1 0 1 0.140835 1.681711 1.226342 146.987 99.3916 3.40 0.15 2.794608 2.082408 952.693 546.386 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 2.508854 -2.511416 0 5.946437 0 0 0 0.454784 0.72571 0.392632 0.274649 1.78349 12 0
+Ti Ti Cu 1 0 1 0 1.255016 0.089078 1.226342 1.226342 99.3916 99.3916 3.40 0.10 2.082408 2.082408 546.386 546.386 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -4 4 2.508854 -2.511416 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.392632 1.78349 1.78349 12 0
+Cu Cu Ti 1 0 1 0 1 0.140835 1.681711 1.681711 146.987 146.987 2.90 0.05 2.794608 2.794608 952.693 952.693 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -6 2 0.1677645 -0.161007 0 5.946437 0 0 0 0.454784 0.72571 0.72571 0.274649 0.274649 12 0
+#                                                
+Ti O Cu 1 0 1 0 1.255016 0.089078 1.226342 2.68 99.3916 260.893 3.25 0.10 2.082408 5.36 546.386 3326.69 0 0 0 0 0  8.45  0.088406 0.969934 0.296577 1.326746 -4 4 2.508854 -2.511416 -1.8349 5.5046 0.00148 -0.00112 0 1.943430774 0 0.254695274 0 0.873685 0.392632 -3.922011 1.78349 0.971086 12 0
+Cu O Ti 1 0 1 0 1 0.140835 1.681711 2.68 146.987 260.893 2.40 0.10 2.794608 5.36 952.693 3326.69 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -6 2 0.1677645 -0.161007 -1.8349 5.5046 0.00148 -0.00112 0 5.946437 0 0 0 0.454784 0.72571 -3.922011 0.274649 0.971086 12  0
+Ti Cu O 1 0 1 0 1.255016 0.089078 1.226342 1.681711 99.3916 146.987 3.40 0.15 2.082408 2.794608 546.386 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -6 2 0.1677645 -0.161007 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.72571 1.78349 0.274649 12 0
+Cu Ti O 1 0 1 0 1 0.140835 1.681711 1.226342 146.987 99.3916 3.40 0.15 2.794608 2.082408 952.693 546.386 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 2.508854 -2.511416 0 5.946437 0 0 0 0.454784 0.72571 0.392632 0.274649 1.78349 12 0
+O Ti Cu 1 6.6 1 -0.229 1 2 2.68 1.226342 260.893 99.3916 3.25 0.10 5.36 2.082408 3326.69 546.386 0 0 0 0 0  8.45  0.088406 0.969934 0.296577 1.326746 -1.8349 5.5046 0.00148 -0.00112 -4 4 2.508854 -2.511416 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.392632 0.971086 1.78349 12 0
+O Cu Ti 1 6.6 1 -0.229 1 2 2.68 1.681711 260.893 146.987 2.40 0.10 5.36 2.794608 3326.69 952.693 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -1.8349 5.5046 0.00148 -0.00112 -6 2 0.1677645 -0.161007 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.72571 0.971086 0.274649 12  0

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.table Cd Te
+pair_coeff	* * CdTe.bop Cd Te
 mass		1 112.4
 mass		2 127.6
 
-comm_modify	cutoff 14.7
+communicate	single 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
 
-comm_modify	vel yes
+communicate	single 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
-comm_modify	vel yes
+communicate	single vel yes
 
 read_data	data.granular
 

bench/POTENTIALS/in.reax

@@ -0,0 +1,22 @@
+# 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 C H O N
+pair_coeff      * * ffield.reax 1 2 3 4
 
 timestep	0.1
 fix		1 all nve 

bench/POTENTIALS/in.rebo

@@ -11,7 +11,7 @@ neighbor	    0.5 bin
 neigh_modify	    delay 5 every 1
 
 pair_style	    rebo
-pair_coeff	    * * CH.rebo C H
+pair_coeff	    * * CH.airebo C H
 
 velocity	    all create 300.0 761341
 

bench/POTENTIALS/library.meam

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

bench/POTENTIALS/library.meam

@@ -0,0 +1,162 @@
+# 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/log.26Jun12.adp.1

@@ -0,0 +1,52 @@
+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
+

bench/POTENTIALS/log.26Jun12.adp.4

@@ -0,0 +1,52 @@
+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 2 by 2 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 = 8.14011 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 4.95441 on 4 procs for 100 steps with 32000 atoms
+
+Pair  time (%) = 4.6421 (93.6964)
+Neigh time (%) = 0.176992 (3.57242)
+Comm  time (%) = 0.110454 (2.22941)
+Outpt time (%) = 7.62939e-05 (0.00153992)
+Other time (%) = 0.0247837 (0.500235)
+
+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
+

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

@@ -0,0 +1,63 @@
+LAMMPS (29 Jun 2012)
+# 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
+  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
+
+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
+Memory usage per processor = 105.507 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          300    -139299.7            0   -138034.03    8830.3329 
+      10    143.00954   -138633.58            0   -138030.23    32329.276 
+      20    219.32814   -138956.58            0   -138031.25   -3487.5421 
+      30    120.47567   -138535.14            0   -138026.86    11367.446 
+      40    158.54609    -138696.2            0   -138027.31    13272.949 
+      50    92.336357   -138415.63            0   -138026.07    23805.366 
+      60    182.26046   -138797.42            0   -138028.48    33008.508 
+      70    153.25324   -138676.08            0   -138029.52    3951.7505 
+      80    173.39519   -138762.84            0    -138031.3    20742.112 
+      90    193.98121   -138849.35            0   -138030.96   -10033.519 
+     100    193.18028   -138846.08            0   -138031.07    31990.015 
+Loop time of 106.235 on 1 procs for 100 steps with 32640 atoms
+
+Pair  time (%) = 97.6504 (91.919)
+Neigh time (%) = 8.44267 (7.94714)
+Comm  time (%) = 0.0546622 (0.0514539)
+Outpt time (%) = 0.00114608 (0.00107881)
+Other time (%) = 0.0864127 (0.0813409)
+
+Nlocal:    32640 ave 32640 max 32640 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    48220 ave 48220 max 48220 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:  2.22341e+07 ave 2.22341e+07 max 2.22341e+07 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 22234140
+Ave neighs/atom = 681.193
+Neighbor list builds = 8
+Dangerous builds = 0

bench/POTENTIALS/log.26Jun12.airebo.4

@@ -0,0 +1,63 @@
+LAMMPS (29 Jun 2012)
+# 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
+  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
+
+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
+Memory usage per processor = 29.8097 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          300    -139299.7            0   -138034.03    8830.3329 
+      10    143.00954   -138633.58            0   -138030.23    32329.276 
+      20    219.32814   -138956.58            0   -138031.25   -3487.5421 
+      30    120.47567   -138535.14            0   -138026.86    11367.446 
+      40    158.54609    -138696.2            0   -138027.31    13272.949 
+      50    92.336357   -138415.63            0   -138026.07    23805.366 
+      60    182.26046   -138797.42            0   -138028.48    33008.508 
+      70    153.25324   -138676.08            0   -138029.52    3951.7505 
+      80    173.39519   -138762.84            0    -138031.3    20742.112 
+      90    193.98121   -138849.35            0   -138030.96   -10033.519 
+     100    193.18028   -138846.08            0   -138031.07    31990.015 
+Loop time of 29.0637 on 4 procs for 100 steps with 32640 atoms
+
+Pair  time (%) = 25.1182 (86.4249)
+Neigh time (%) = 2.97429 (10.2337)
+Comm  time (%) = 0.940242 (3.23511)
+Outpt time (%) = 0.000824273 (0.00283609)
+Other time (%) = 0.0300676 (0.103454)
+
+Nlocal:    8160 ave 8177 max 8143 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Nghost:    22625.5 ave 22644 max 22608 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  5.55854e+06 ave 5.57118e+06 max 5.54428e+06 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+
+Total # of neighbors = 22234140
+Ave neighs/atom = 681.193
+Neighbor list builds = 8
+Dangerous builds = 0

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

@@ -0,0 +1,57 @@
+LAMMPS (29 Jun 2012)
+# 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
+
+pair_style	bop 4.9
+pair_coeff	* * CdTe.bop Cd Te
+mass		1 112.4
+mass		2 127.6
+
+communicate	single 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
+Memory usage per processor = 73.7078 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1000    -69539.48            0   -65403.285    3468.3799 
+     100    572.83068    -67772.68            0    -65403.34    1847.9403 
+Loop time of 80.268 on 1 procs for 100 steps with 32000 atoms
+
+Pair  time (%) = 79.1627 (98.623)
+Neigh time (%) = 0.973292 (1.21255)
+Comm  time (%) = 0.051837 (0.0645799)
+Outpt time (%) = 0.000120163 (0.000149702)
+Other time (%) = 0.0800123 (0.0996815)
+
+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:  141090 ave 141090 max 141090 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 141090
+Ave neighs/atom = 4.40906
+Neighbor list builds = 14
+Dangerous builds = 0

bench/POTENTIALS/log.26Jun12.bop.4

@@ -0,0 +1,57 @@
+LAMMPS (29 Jun 2012)
+# 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
+
+pair_style	bop 4.9
+pair_coeff	* * CdTe.bop Cd Te
+mass		1 112.4
+mass		2 127.6
+
+communicate	single 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
+Memory usage per processor = 26.6187 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1000    -69539.48            0   -65403.285    3468.3799 
+     100    572.83068    -67772.68            0    -65403.34    1847.9403 
+Loop time of 20.6725 on 4 procs for 100 steps with 32000 atoms
+
+Pair  time (%) = 19.6654 (95.1287)
+Neigh time (%) = 0.355175 (1.71811)
+Comm  time (%) = 0.625993 (3.02815)
+Outpt time (%) = 7.26581e-05 (0.000351473)
+Other time (%) = 0.025782 (0.124717)
+
+Nlocal:    8000 ave 8005 max 7996 min
+Histogram: 1 0 1 0 0 1 0 0 0 1
+Nghost:    15171 ave 15175 max 15166 min
+Histogram: 1 0 0 0 1 0 0 1 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  35272.5 ave 35327 max 35221 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+
+Total # of neighbors = 141090
+Ave neighs/atom = 4.40906
+Neighbor list builds = 14
+Dangerous builds = 0

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

@@ -0,0 +1,71 @@
+LAMMPS (29 Jun 2012)
+# 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
+  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
+Memory usage per processor = 95.0552 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Press Volume 
+       0          300    -6.800513   -6.8392899    4.6301362   -11.469426    2.8887101    -1.444355    14558.344    462016.62 
+      10    271.62515   -6.8007192   -6.8358285    4.6332165   -11.469045    2.8882392   -1.4441196    14514.953    462016.62 
+      20    238.98408   -6.8009297   -6.8318199    4.6310324   -11.462852    2.8879087   -1.4439543    13651.411    462016.62 
+      30     210.3787   -6.8010518   -6.8282445    4.6294419   -11.457686    2.8878659   -1.4439329    12043.903    462016.62 
+      40     193.1516   -6.8010917   -6.8260577    4.6290792   -11.455137    2.8882154   -1.4441076    9835.5857    462016.62 
+      50    191.94742   -6.8010622   -6.8258726     4.630419   -11.456292    2.8890872   -1.4445436    6942.5175    462016.62 
+      60    207.61185    -6.800982   -6.8278171      4.63437   -11.462187    2.8904146   -1.4452072    3246.4843    462016.62 
+      70    236.98233   -6.8008686      -6.8315    4.6406466   -11.472147    2.8920875   -1.4460437    -1291.732    462016.62 
+      80    273.85158    -6.800735   -6.8361321    4.6488576    -11.48499     2.894141   -1.4470705   -6592.9936    462016.62 
+      90    310.76808   -6.8006054   -6.8407741    4.6597903   -11.500564    2.8962597   -1.4481298   -12439.324    462016.62 
+     100    340.98434   -6.8004987    -6.844573      4.67158   -11.516153    2.8982813   -1.4491406   -18618.072    462016.62 
+Loop time of 648.075 on 1 procs for 100 steps with 32400 atoms
+
+Pair  time (%) = 151.932 (23.4435)
+Neigh time (%) = 0 (0)
+Comm  time (%) = 0.0529873 (0.00817611)
+Outpt time (%) = 0.0037415 (0.000577325)
+Other time (%) = 496.087 (76.5477)
+
+Nlocal:    32400 ave 32400 max 32400 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    42400 ave 42400 max 42400 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:  1.85289e+07 ave 1.85289e+07 max 1.85289e+07 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18528904
+Ave neighs/atom = 571.88
+Neighbor list builds = 0
+Dangerous builds = 0

bench/POTENTIALS/log.26Jun12.comb.4

@@ -0,0 +1,71 @@
+LAMMPS (29 Jun 2012)
+# 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
+  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
+Memory usage per processor = 26.6527 Mbytes
+Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Press Volume 
+       0          300    -6.800513   -6.8392899    4.6301362   -11.469426    2.8887101    -1.444355    14558.344    462016.62 
+      10    271.62515   -6.8007192   -6.8358285    4.6332165   -11.469045    2.8882392   -1.4441196    14514.953    462016.62 
+      20    238.98408   -6.8009297   -6.8318199    4.6310324   -11.462852    2.8879087   -1.4439543    13651.411    462016.62 
+      30     210.3787   -6.8010518   -6.8282445    4.6294419   -11.457686    2.8878659   -1.4439329    12043.903    462016.62 
+      40     193.1516   -6.8010917   -6.8260577    4.6290792   -11.455137    2.8882154   -1.4441076    9835.5857    462016.62 
+      50    191.94742   -6.8010622   -6.8258726     4.630419   -11.456292    2.8890872   -1.4445436    6942.5175    462016.62 
+      60    207.61185    -6.800982   -6.8278171      4.63437   -11.462187    2.8904146   -1.4452072    3246.4843    462016.62 
+      70    236.98233   -6.8008686      -6.8315    4.6406466   -11.472147    2.8920875   -1.4460437    -1291.732    462016.62 
+      80    273.85158    -6.800735   -6.8361321    4.6488576    -11.48499     2.894141   -1.4470705   -6592.9936    462016.62 
+      90    310.76808   -6.8006054   -6.8407741    4.6597903   -11.500564    2.8962597   -1.4481298   -12439.324    462016.62 
+     100    340.98434   -6.8004987    -6.844573      4.67158   -11.516153    2.8982813   -1.4491406   -18618.072    462016.62 
+Loop time of 166.681 on 4 procs for 100 steps with 32400 atoms
+
+Pair  time (%) = 38.5193 (23.1097)
+Neigh time (%) = 0 (0)
+Comm  time (%) = 0.700634 (0.420345)
+Outpt time (%) = 0.00150448 (0.000902613)
+Other time (%) = 127.459 (76.4691)
+
+Nlocal:    8100 ave 8106 max 8094 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    20650 ave 20686 max 20614 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  4.63223e+06 ave 4.63577e+06 max 4.62881e+06 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 18528904
+Ave neighs/atom = 571.88
+Neighbor list builds = 0
+Dangerous builds = 0