patch 8Mar18

allow for mpi4py version 2 or 3 in Python wrapper

.github/CODEOWNERS

@@ -0,0 +1,21 @@
+# 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
+
+# packages
+src/KOKKOS            @stanmoore1
+src/USER-CGSDK        @akohlmey
+src/USER-COLVARS      @giacomofiorin
+src/USER-OMP          @akohlmey
+src/USER-QMMM         @akohlmey
+
+# tools
+tools/msi2lmp/*       @akohlmey

.github/CONTRIBUTING.md

@@ -0,0 +1,112 @@
+# 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 workflows for contributing to the LAMMPS molecular dynamics software project. These guidelines focus on submitting issues or pull requests on the LAMMPS GitHub project.
+
+Thus please also have a look at:
+* [The Section on submitting new features for inclusion in LAMMPS of the Manual](http://lammps.sandia.gov/doc/Section_modify.html#mod-15)
+* [The LAMMPS GitHub Tutorial in the Manual](http://lammps.sandia.gov/doc/tutorial_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 Workflows](#github-workflows)
+* [Issues](#issues)
+* [Pull Requests](#pull-requests)
+
+__
+
+## I don't want to read this whole thing I just have a question!
+
+> **Note:** Please do not file an issue to ask a general question about LAMMPS, its features, how to use specific commands, or how perform simulations or analysis in LAMMPS. Instead post your question to the ['lammps-users' mailing list](http://lammps.sandia.gov/mail.html). You do not need to be subscribed to post to the list (but a mailing list subscription avoids having your post delayed until it is approved by a mailing list moderator). Most posts to the mailing list receive a response within less than 24 hours. Before posting to the mailing list, please read the [mailing list guidelines](http://lammps.sandia.gov/guidelines.html). Following those guidelines will help greatly to get a helpful response. Always mention which LAMMPS version you are using.
+
+## How Can I Contribute?
+
+There are several ways how you can actively contribute to the LAMMPS project: you can discuss compiling and using LAMMPS, and solving LAMMPS related problems with other LAMMPS users on the lammps-users mailing list, you can report bugs or suggest enhancements by creating issues on GitHub (or posting them to the lammps-users mailing list), and you can contribute by submitting pull requests on GitHub or e-mail your code
+to one of the [LAMMPS core developers](http://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](http://lammps.sandia.gov/guidelines.html) to maximize your chances to receive a helpful response.
+
+Anyone can browse/search previous questions/answers in the archives. You do not have to subscribe to the list to post questions, receive answers (to your questions), or browse/search the archives. You **do** need to subscribe to the list if you want emails for **all** the posts (as individual messages or in digest form), or to answer questions yourself. Feel free to sign up and help us out! Answering questions from fellow LAMMPS users is a great way to pay back the community for providing you a useful tool for free, and to pass on the advice you have received yourself to others. It improves your karma and helps you understand your own research better.
+
+If you post a message and you are a subscriber, your message will appear immediately. If you are not a subscriber, your message will be moderated, which typically takes one business day. Either way, when someone replies the reply will usually be sent to both, your personal email address and the mailing list. When replying to people, that responded to your post to the list, please always included the mailing list in your replies (i.e. use "Reply All" and **not** "Reply"). Responses will appear on the list in a few minutes, but it can take a few hours for postings and replies to show up in the SourceForge archive. Sending replies also to the mailing list is important, so that responses are archived and people with a similar issue can search for possible solutions in the mailing list archive.
+
+### Reporting Bugs
+
+While developers writing code for LAMMPS are careful to test their code, LAMMPS is such a large and complex software, that it is impossible to test for all combinations of features under all normal and not so normal circumstances. Thus bugs do happen, and if you suspect, that you have encountered one, please try to document it and report it as an [Issue](https://github.com/lammps/lammps/issues) on the LAMMPS GitHub project web page. However, before reporting a bug, you need to check whether this is something that may have already been corrected. The [Latest Features and Bug Fixes in LAMMPS](http://lammps.sandia.gov/bug.html) web page lists all significant changes to LAMMPS over the years. It also tells you what the current latest development version of LAMMPS is, and you should test whether your issue still applies to that version.
+
+When you click on the green "New Issue" button, you will be provided with a text field, where you can enter your message. That text field with contain a template with several headlines and some descriptions. Keep the headlines that are relevant to your reported potential bug and replace the descriptions with the information as suggested by the descriptions.
+You can also attach small text files (please add the file name extension `.txt` or it will be rejected), images, or small compressed text files (using gzip, do not use RAR or 7-ZIP or similar tools that are uncommon outside of Windows machines). In many cases, bugs are best illustrated by providing a small input deck (do **not** attach your entire production input, but remove everything that is not required to reproduce the issue, and scale down your system size, that the resulting calculation runs fast and can be run on small desktop quickly).
+
+To be able to submit an issue on GitHub, you have to register for an account (for GitHub in general). If you do not want to do that, or have other reservations against submitting an issue there, you can - as an alternative and in decreasing preference - either send an e-mail to the lammps-users mailing list, the original authors of the feature that you suspect to be affected, or one or more of the core LAMMPS developers.
+
+### Suggesting Enhancements
+
+The LAMMPS developers welcome suggestions for enhancements or new features. These should be submitted using the [GitHub Issue Tracker](https://github.com/lammps/lammps/issues) of the LAMMPS project. This is particularly recommended, when you plan to implement the feature or enhancement yourself, as this allows to coordinate in case there are other similar or conflicting ongoing developments.
+The LAMMPS developers will review your submission and consider implementing it. Whether this will actually happen depends on many factors: how difficult it would be, how much effort it would take, how many users would benefit from it, how well the individual developer would understand the underlying physics of the feature, and whether this is a feature that would fit into a software like LAMMPS, or would be better implemented as a separate tool. Because of these factors, it matters how well the suggested enhancement is formulated and the overall benefit is argued convincingly.
+
+To be able to submit an issue on GitHub, you have to register for an account (for GitHub in general). If you do not want to do that, or have other reservations against submitting an issue there, you can - as an alternative - send an e-mail to the lammps-users mailing list.
+
+### Contributing Code
+
+We encourage users to submit new features or modifications for LAMMPS to the core developers so they can be added to the LAMMPS distribution. The preferred way to manage and coordinate this is by submitting a pull request at the LAMMPS project on GitHub. For any larger modifications or programming project, you are encouraged to contact the LAMMPS developers ahead of time, in order to discuss implementation strategies and coding guidelines, that will make it easier to integrate your contribution and result in less work for everybody involved. You are also encouraged to search through the list of open issues on GitHub and submit a new issue for a planned feature, so you would not duplicate the work of others (and possibly get scooped by them) or have your work duplicated by others.
+
+How quickly your contribution will be integrated depends largely on how much effort it will cause to integrate and test it, how much it requires changes to the core code base, and of how much interest it is to the larger LAMMPS community. Please see below for a checklist of typical requirements. Once you have prepared everything, see [this tutorial](http://lammps.sandia.gov/doc/tutorial_github.html)
+ for instructions on how to submit your changes or new files through a GitHub pull request
+
+Here is a checklist of steps you need to follow to submit a single file or user package for our consideration. Following these steps will save both you and us time. See existing files in packages in the source directory for examples. If you are uncertain, please ask on the lammps-users mailing list.
+
+* All source files you provide must compile with the most current version of LAMMPS with multiple configurations. In particular you need to test compiling LAMMPS from scratch with `-DLAMMPS_BIGBIG` set in addition to the default `-DLAMMPS_SMALLBIG` setting. Your code will need to work correctly in serial and in parallel using MPI.
+* For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no lines over 80 characters. I/O is done via the C-style stdio library, class header files should not import any system headers outside <stdio.h>, STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. Header files must not import namespaces with using. This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages.
+* If you want your contribution to be added as a user-contributed feature, and it is a single file (actually a `<name>.cpp` and `<name>.h` file) it can be rapidly added to the USER-MISC directory. Include the one-line entry to add to the USER-MISC/README file in that directory, along with the 2 source files. You can do this multiple times if you wish to contribute several individual features.
+* If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like USER-FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this USER-FOO directory.
+* Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code.
+* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are simple text files with a specific markup language, that are then auto-converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.txt` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. A description of the markup can also be found in `lammps/doc/utils/txt2html/README.html` As appropriate, the text files can include links to equations (see doc/Eqs/*.tex for examples, we auto-create the associated JPG files), or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.txt for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv, the requirement for generating the PDF format manual is the htmldoc software. Please run at least "make html" and carefully inspect and proofread the resulting HTML format doc page before submitting your code.
+* For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/USER for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind
+* If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the *.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide.
+
+Finally, as a general rule-of-thumb, the more clear and self-explanatory you make your documentation and README files, and the easier you make it for people to get started, e.g. by providing example scripts, the more likely it is that users will try out your new feature.
+
+If the new features/files are broadly useful we may add them as core files to LAMMPS or as part of a standard package. Else we will add them as a user-contributed file or package. Examples of user packages are in src sub-directories that start with USER. The USER-MISC package is simply a collection of (mostly) unrelated single files, which is the simplest way to have your contribution quickly added to the LAMMPS distribution. You can see a list of the both standard and user packages by typing "make package" in the LAMMPS src directory.
+
+Note that by providing us files to release, you are agreeing to make them open-source, i.e. we can release them under the terms of the GPL, used as a license for the rest of LAMMPS. See Section 1.4 for details.
+
+With user packages and files, all we are really providing (aside from the fame and fortune that accompanies having your name in the source code and on the Authors page of the LAMMPS WWW site), is a means for you to distribute your work to the LAMMPS user community, and a mechanism for others to easily try out your new feature. This may help you find bugs or make contact with new collaborators. Note that you are also implicitly agreeing to support your code which means answer questions, fix bugs, and maintain it if LAMMPS changes in some way that breaks it (an unusual event).
+
+To be able to submit an issue on GitHub, you have to register for an account (for GitHub in general). If you do not want to do that, or have other reservations or difficulties to submit a pull request, you can - as an alternative - contact one or more of the core LAMMPS developers and ask if one of them would be interested in manually merging your code into LAMMPS and send them your source code. Since the effort to merge a pull request is a small fraction of the effort of integrating source code manually (which would usually be done by converting the contribution into a pull request), your chances to have your new code included quickly are the best with a pull request.
+
+If you prefer to submit patches or full files, you should first make certain, that your code works correctly with the latest patch-level version of LAMMPS and contains all bug fixes from it. Then create a gzipped tar file of all changed or added files or a corresponding patch file using 'diff -u' or 'diff -c' and compress it with gzip. Please only use gzip compression, as this works well on all platforms.
+
+## GitHub Workflows
+
+This section briefly summarizes the steps that will happen **after** you have submitted either an issue or a pull request on the LAMMPS GitHub project page. 
+
+### Issues
+
+After submitting an issue, one or more of the LAMMPS developers will review it and categorize it by assigning labels. Confirmed bug reports will be labeled `bug`; if the bug report also contains a suggestion for how to fix it, it will be labeled `bugfix`; if the issue is a feature request, it will be labeled `enhancement`. Other labels may be attached as well, depending on which parts of the LAMMPS code are affected. If the assessment is, that the issue does not warrant any changes, the `wontfix` label will be applied and if the submission is incorrect or something that should not be submitted as an issue, the `invalid` label will be applied. In both of the last two cases, the issue will then be closed without further action.
+
+For feature requests, what happens next is that developers may comment on the viability or relevance of the request, discuss and make suggestions for how to implement it. If a LAMMPS developer or user is planning to implement the feature, the issue will be assigned to that developer. For developers, that are not yet listed as LAMMPS project collaborators, they will receive an invitation to be added to the LAMMPS project as a collaborator so they can get assigned. If the requested feature or enhancement is implemented, it will usually be submitted as a pull request, which will contain a reference to the issue number. And once the pull request is reviewed and accepted for inclusion into LAMMPS, the issue will be closed. For details on how pull requests are processed, please see below.
+
+For bug reports, the next step is that one of the core LAMMPS developers will self-assign to the issue and try to confirm the bug. If confirmed, the `bug` label and potentially other labels are added to classify the issue and its impact to LAMMPS. Before confirming, further questions may be asked or requests for providing additional input files or details about the steps required to reproduce the issue. Any bugfix is likely to be submitted as a pull request (more about that below) and since most bugs require only local changes, the bugfix may be included in a pull request specifically set up to collect such local bugfixes or small enhancements. Once the bugfix is included in the master branch, the issue will be closed.
+
+### Pull Requests
+
+For submitting pull requests, there is a [detailed tutorial](http://lammps.sandia.gov/doc/tutorial_github.html) in the LAMMPS manual. Thus only a brief breakdown of the steps is presented here.
+Immediately after the submission, the LAMMPS continuing integration server at ci.lammps.org will download your submitted branch and perform a simple compilation test, i.e. will test whether your submitted code can be compiled under various conditions. It will also do a check on whether your included documentation translates cleanly. Whether these tests are successful or fail will be recorded. If a test fails, please inspect the corresponding output on the CI server and take the necessary steps, if needed, so that the code can compile cleanly again. The test will be re-run each the pull request is updated with a push to the remote branch on GitHub.
+Next a LAMMPS core developer will self-assign and do an overall technical assessment of the submission. If you are not yet registered as a LAMMPS collaborator, you will receive an invitation for that.
+You may also receive comments and suggestions on the overall submission or specific details. If permitted, 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 be assigned to the LAMMPS lead developer, Steve Plimpton (@sjplimp), who will then have the final decision on whether the submission will be included, additional changes are required or it will be ultimately rejected. After the pull request is merged, you may delete the pull request branch in your personal LAMMPS fork.
+Since the learning curve for git is quite steep for efficiently managing remote repositories, local and remote branches, pull requests and more, do not hesitate to ask questions, if you are not sure about how to do certain steps that are asked of you. Even if the changes asked of you do not make sense to you, they may be important for the LAMMPS developers. Please also note, that these all are guidelines and not set in stone.
+

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,31 @@
+## Summary
+
+_Please provide a brief description of the issue_
+
+## Type of Issue
+
+_Is this a 'Bug Report' or a 'Suggestion for an Enhancement'?_
+
+## Detailed Description (Enhancement Suggestion)
+
+_Explain how you would like to see LAMMPS enhanced, what feature(s) you are looking for, provide references to relevant background information, and whether you are willing to implement the enhancement yourself or would like to participate in the implementation_
+
+## LAMMPS Version (Bug Report)
+
+_Please specify which LAMMPS version this issue was detected with. If this is not the latest development version, please stop and test that version, too, and report it here if the bug persists_
+
+## Expected Behavior (Bug Report)
+
+_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 (Bug Report)
+
+_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 research._
+
+## Steps to Reproduce (Bug Report)
+
+_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 input that are as small as possible and run as fast as possible. NOTE: the less effort and time it takes to reproduce your issue, the more likely, that somebody will look into it._
+
+## 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/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,29 @@
+## Purpose
+
+_Briefly describe the new feature(s), enhancement(s), or bugfix(es) included in this pull request. If this addresses an open GitHub Issue, mention the issue number, e.g. with `fixes #221` or `closes #135`, so that issue will 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_
+
+## Backward Compatibility
+
+_Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why_
+
+## Implementation Notes
+
+_Provide any relevant details about how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected_
+
+## Post Submission Checklist
+
+_Please check the fields below as they are completed_
+- [ ] The feature or features in this pull request is complete
+- [ ] Suitable new documentation files and/or updates to the existing docs are included
+- [ ] One or more example input decks are included
+- [ ] The source code follows the LAMMPS formatting guidelines
+
+## Further Information, Files, and Links
+
+_Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)_
+
+

.gitignore

@@ -0,0 +1,42 @@
+*~
+*.o
+*.so
+*.cu_o
+*.ptx
+*_ptx.h
+*.a
+*.d
+*.x
+*.exe
+*.dll
+*.pyc
+__pycache__
+
+Obj_*
+log.lammps
+log.cite
+*.bz2
+*.gz
+*.tar
+.*.swp
+*.orig
+*.rej
+.vagrant
+\#*#
+.#*
+
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+#cmake
+/build*
+/CMakeCache.txt
+/CMakeFiles/
+/Makefile
+/cmake_install.cmake
+/lmp

LICENSE

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

bench/Cu_u3.eam

@@ -1,4 +1,4 @@
-Cu functions (universal 3)
+DATE: 2007-06-11 CONTRIBUTOR: Stephen Foiles, foiles@sandia.gov CITATION: Foiles et al, Phys Rev B, 33, 7983 (1986) COMMENT: Cu functions (universal 3), SM Foiles et al, PRB, 33, 7983 (1986)
    29     63.550         3.6150    FCC
   500  5.0100200400801306e-04  500  1.0000000000000009e-02  4.9499999999999886e+00
   0.                     -3.1561636903424350e-01 -5.2324876182494506e-01 -6.9740831416804383e-01 -8.5202525457518519e-01

bench/FERMI/README

@@ -1,55 +1,21 @@
 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.
+benchmarks in the top-level bench directory using the GPU accelerator
+package.  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
+you have built 3 executables with the GPU package
 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 exe
-Make.py -d ~/lammps -j 16 -p #all opt orig -m linux -o opt exe
-Make.py -d ~/lammps -j 16 -p #all omp orig -m linux -o omp exe
-Make.py -d ~/lammps -j 16 -p #all gpu orig -m linux \
-        -gpu mode=double arch=20 -o gpu_double libs exe
-Make.py -d ~/lammps -j 16 -p #all gpu orig -m linux \
-        -gpu mode=mixed arch=20 -o gpu_mixed libs exe
-Make.py -d ~/lammps -j 16 -p #all gpu orig -m linux \
-        -gpu mode=single arch=20 -o gpu_single libs exe
-Make.py -d ~/lammps -j 16 -p #all cuda orig -m linux \
-        -cuda mode=double arch=20 -o cuda_double libs exe
-Make.py -d ~/lammps -j 16 -p #all cuda orig -m linux \
-        -cuda mode=mixed arch=20 -o cuda_mixed libs exe
-Make.py -d ~/lammps -j 16 -p #all cuda orig -m linux \
-        -cuda mode=single arch=20 -o cuda_single libs exe
-Make.py -d ~/lammps -j 16 -p #all intel orig -m linux -o intel_cpu exe
-Make.py -d ~/lammps -j 16 -p #all kokkos orig -m linux -o kokkos_omp exe
-Make.py -d ~/lammps -j 16 -p #all kokkos orig -kokkos cuda arch=20 \
-        -m cuda -o kokkos_cuda 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 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 libs exe
-
 ------------------------------------------------------------------------
 
-To run on just CPUs (without using the GPU or USER-CUDA styles),
+To run on just CPUs (without using the GPU 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
@@ -81,23 +47,5 @@ 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/POTENTIALS/in.dpd

@@ -2,7 +2,7 @@
 
 units		lj
 atom_style	atomic
-communicate	single vel yes
+comm_modify     mode single vel yes
 
 lattice		fcc 3.0
 region		box block 0 20 0 20 0 20

bench/README

@@ -71,49 +71,33 @@ integration
 
 ----------------------------------------------------------------------
 
-Here is a src/Make.py command which will perform a parallel build of a
-LAMMPS executable "lmp_mpi" with all the packages needed by all the
-examples.  This assumes you have an MPI installed on your machine so
-that "mpicxx" can be used as the wrapper compiler.  It also assumes
-you have an Intel compiler to use as the base compiler.  You can leave
-off the "-cc mpi wrap=icc" switch if that is not the case.  You can
-also leave off the "-fft fftw3" switch if you do not have the FFTW
-(v3) installed as an FFT package, in which case the default KISS FFT
-library will be used.
-
-cd src
-Make.py -j 16 -p none molecule manybody kspace granular orig \
-  -cc mpi wrap=icc -fft fftw3 -a file mpi
-
-----------------------------------------------------------------------
-
 Here is how to run each problem, assuming the LAMMPS executable is
 named lmp_mpi, and you are using the mpirun command to launch parallel
 runs:
 
 Serial (one processor runs):
 
-lmp_mpi < in.lj
-lmp_mpi < in.chain
-lmp_mpi < in.eam
-lmp_mpi < in.chute
-lmp_mpi < in.rhodo
+lmp_mpi -in in.lj
+lmp_mpi -in in.chain
+lmp_mpi -in in.eam
+lmp_mpi -in in.chute
+lmp_mpi -in in.rhodo
 
 Parallel fixed-size runs (on 8 procs in this case):
 
-mpirun -np 8 lmp_mpi < in.lj
-mpirun -np 8 lmp_mpi < in.chain
-mpirun -np 8 lmp_mpi < in.eam
-mpirun -np 8 lmp_mpi < in.chute
-mpirun -np 8 lmp_mpi < in.rhodo
+mpirun -np 8 lmp_mpi -in in.lj
+mpirun -np 8 lmp_mpi -in in.chain
+mpirun -np 8 lmp_mpi -in in.eam
+mpirun -np 8 lmp_mpi -in in.chute
+mpirun -np 8 lmp_mpi -in in.rhodo
 
 Parallel scaled-size runs (on 16 procs in this case):
 
-mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 < in.lj
-mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 < in.chain.scaled
-mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 < in.eam
-mpirun -np 16 lmp_mpi -var x 4 -var y 4 < in.chute.scaled
-mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 < in.rhodo.scaled
+mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 -in in.lj
+mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 -in in.chain.scaled
+mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 -in in.eam
+mpirun -np 16 lmp_mpi -var x 4 -var y 4 -in in.chute.scaled
+mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 -in in.rhodo.scaled
 
 For each of the scaled-size runs you must set 3 variables as -var
 command line switches.  The variables x,y,z are used in the input

bench/in.chute

@@ -5,7 +5,7 @@ units		lj
 atom_style	sphere
 boundary	p p fs
 newton		off
-communicate	single vel yes
+comm_modify	vel yes
 
 read_data	data.chute
 

bench/in.chute.scaled

@@ -8,7 +8,7 @@ units		lj
 atom_style	sphere
 boundary	p p fs
 newton		off
-communicate	single vel yes
+comm_modify	vel yes
 
 read_data	data.chute
 

bench/log.1Feb14.chain.fixed.linux.1

@@ -1,63 +0,0 @@
-LAMMPS (1 Feb 2014)
-# FENE beadspring benchmark
-
-units		lj
-atom_style	bond
-special_bonds   fene
-
-read_data	data.chain
-  orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-  scanning bonds ...
-  1 = max bonds/atom
-  reading bonds ...
-  31680 bonds
-  2 = max # of 1-2 neighbors
-  2 = max # of special neighbors
-
-neighbor	0.4 bin
-neigh_modify	every 1 delay 1
-
-bond_style      fene
-bond_coeff	1 30.0 1.5 1.0 1.0
-
-pair_style	lj/cut 1.12
-pair_modify	shift yes
-pair_coeff	1 1 1.0 1.0 1.12
-
-fix		1 all nve
-fix		2 all langevin 1.0 1.0 10.0 904297
-
-thermo          100
-timestep	0.012
-
-run		100
-Memory usage per processor = 11.5156 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0   0.97029772   0.44484087    20.494523    22.394765    4.6721833 
-     100    0.9729966    0.4361122    20.507698     22.40326    4.6548819 
-Loop time of 1.00129 on 1 procs for 100 steps with 32000 atoms
-
-Pair  time (%) = 0.201344 (20.1083)
-Bond  time (%) = 0.0870376 (8.69251)
-Neigh time (%) = 0.45714 (45.6549)
-Comm  time (%) = 0.0338521 (3.38083)
-Outpt time (%) = 0.000102043 (0.0101911)
-Other time (%) = 0.221819 (22.1532)
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    9493 ave 9493 max 9493 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    155873 ave 155873 max 155873 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 155873
-Ave neighs/atom = 4.87103
-Ave special neighs/atom = 1.98
-Neighbor list builds = 25
-Dangerous builds = 0

bench/log.1Feb14.chain.fixed.linux.4

@@ -1,63 +0,0 @@
-LAMMPS (1 Feb 2014)
-# FENE beadspring benchmark
-
-units		lj
-atom_style	bond
-special_bonds   fene
-
-read_data	data.chain
-  orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-  scanning bonds ...
-  1 = max bonds/atom
-  reading bonds ...
-  31680 bonds
-  2 = max # of 1-2 neighbors
-  2 = max # of special neighbors
-
-neighbor	0.4 bin
-neigh_modify	every 1 delay 1
-
-bond_style      fene
-bond_coeff	1 30.0 1.5 1.0 1.0
-
-pair_style	lj/cut 1.12
-pair_modify	shift yes
-pair_coeff	1 1 1.0 1.0 1.12
-
-fix		1 all nve
-fix		2 all langevin 1.0 1.0 10.0 904297
-
-thermo          100
-timestep	0.012
-
-run		100
-Memory usage per processor = 4.85536 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0   0.97029772   0.44484087    20.494523    22.394765    4.6721833 
-     100   0.97145835   0.43803883    20.502691    22.397872     4.626988 
-Loop time of 0.274804 on 4 procs for 100 steps with 32000 atoms
-
-Pair  time (%) = 0.0507675 (18.4741)
-Bond  time (%) = 0.0225385 (8.20169)
-Neigh time (%) = 0.121537 (44.2269)
-Comm  time (%) = 0.0207262 (7.54219)
-Outpt time (%) = 8.74996e-05 (0.0318408)
-Other time (%) = 0.0591468 (21.5233)
-
-Nlocal:    8000 ave 8030 max 7974 min
-Histogram: 1 0 0 1 0 1 0 0 0 1
-Nghost:    4177 ave 4191 max 4160 min
-Histogram: 1 0 0 0 1 0 0 1 0 1
-Neighs:    38995.8 ave 39169 max 38852 min
-Histogram: 1 0 0 1 1 0 0 0 0 1
-
-Total # of neighbors = 155983
-Ave neighs/atom = 4.87447
-Ave special neighs/atom = 1.98
-Neighbor list builds = 25
-Dangerous builds = 0

bench/log.1Feb14.chain.scaled.linux.4

@@ -1,79 +0,0 @@
-LAMMPS (1 Feb 2014)
-# FENE beadspring benchmark
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-units		lj
-atom_style	bond
-atom_modify	map hash
-special_bonds   fene
-
-read_data	data.chain
-  orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-  scanning bonds ...
-  1 = max bonds/atom
-  reading bonds ...
-  31680 bonds
-  2 = max # of 1-2 neighbors
-  2 = max # of special neighbors
-
-replicate	$x $y $z
-replicate	2 $y $z
-replicate	2 2 $z
-replicate	2 2 1
-  orthogonal box = (-16.796 -16.796 -16.796) to (50.388 50.388 16.796)
-  2 by 2 by 1 MPI processor grid
-  128000 atoms
-  126720 bonds
-  2 = max # of 1-2 neighbors
-  2 = max # of special neighbors
-
-neighbor	0.4 bin
-neigh_modify	every 1 delay 1
-
-bond_style      fene
-bond_coeff	1 30.0 1.5 1.0 1.0
-
-pair_style	lj/cut 1.12
-pair_modify	shift yes
-pair_coeff	1 1 1.0 1.0 1.12
-
-fix		1 all nve
-fix		2 all langevin 1.0 1.0 10.0 904297
-
-thermo          100
-timestep	0.012
-
-run		100
-Memory usage per processor = 13.4806 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0   0.97027498   0.44484087    20.494523    22.394765    4.6721833 
-     100   0.97682955   0.44239968    20.500229    22.407862    4.6527025 
-Loop time of 1.16627 on 4 procs for 100 steps with 128000 atoms
-
-Pair  time (%) = 0.224354 (19.2369)
-Bond  time (%) = 0.0961447 (8.24378)
-Neigh time (%) = 0.510646 (43.7846)
-Comm  time (%) = 0.0876382 (7.5144)
-Outpt time (%) = 0.000156462 (0.0134156)
-Other time (%) = 0.24733 (21.207)
-
-Nlocal:    32000 ave 32015 max 31983 min
-Histogram: 1 0 1 0 0 0 0 0 1 1
-Nghost:    9492 ave 9522 max 9432 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-Neighs:    155837 ave 156079 max 155506 min
-Histogram: 1 0 0 0 0 1 0 0 1 1
-
-Total # of neighbors = 623349
-Ave neighs/atom = 4.86991
-Ave special neighs/atom = 1.98
-Neighbor list builds = 25
-Dangerous builds = 0

bench/log.1Feb14.chute.fixed.linux.1

@@ -1,65 +0,0 @@
-LAMMPS (1 Feb 2014)
-# LAMMPS benchmark of granular flow
-# chute flow of 32000 atoms with frozen base at 26 degrees
-
-units		lj
-atom_style	sphere
-boundary	p p fs
-newton		off
-communicate	single vel yes
-
-read_data	data.chute
-  orthogonal box = (0 0 0) to (40 20 37.2886)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-
-pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
-pair_coeff	* *
-
-neighbor	0.1 bin
-neigh_modify	every 1 delay 0
-
-timestep	0.0001
-
-group		bottom type 2
-912 atoms in group bottom
-group		active subtract all bottom
-31088 atoms in group active
-neigh_modify	exclude group bottom bottom
-
-fix		1 all gravity 1.0 chute 26.0
-fix		2 bottom freeze
-fix		3 active nve/sphere
-
-compute		1 all erotate/sphere
-thermo_style	custom step atoms ke c_1 vol
-thermo_modify	norm no
-thermo		100
-
-run		100
-Memory usage per processor = 21.4184 Mbytes
-Step Atoms KinEng 1 Volume 
-       0    32000    784139.13    1601.1263    29833.783 
-     100    32000    784292.08    1571.0968    29834.707 
-Loop time of 0.540977 on 1 procs for 100 steps with 32000 atoms
-
-Pair  time (%) = 0.330571 (61.1064)
-Neigh time (%) = 0.0416589 (7.70067)
-Comm  time (%) = 0.018239 (3.3715)
-Outpt time (%) = 0.000189066 (0.034949)
-Other time (%) = 0.150319 (27.7865)
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    5463 ave 5463 max 5463 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    115133 ave 115133 max 115133 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 115133
-Ave neighs/atom = 3.59791
-Neighbor list builds = 2
-Dangerous builds = 0

bench/log.1Feb14.chute.fixed.linux.4

@@ -1,65 +0,0 @@
-LAMMPS (1 Feb 2014)
-# LAMMPS benchmark of granular flow
-# chute flow of 32000 atoms with frozen base at 26 degrees
-
-units		lj
-atom_style	sphere
-boundary	p p fs
-newton		off
-communicate	single vel yes
-
-read_data	data.chute
-  orthogonal box = (0 0 0) to (40 20 37.2886)
-  2 by 1 by 2 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-
-pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
-pair_coeff	* *
-
-neighbor	0.1 bin
-neigh_modify	every 1 delay 0
-
-timestep	0.0001
-
-group		bottom type 2
-912 atoms in group bottom
-group		active subtract all bottom
-31088 atoms in group active
-neigh_modify	exclude group bottom bottom
-
-fix		1 all gravity 1.0 chute 26.0
-fix		2 bottom freeze
-fix		3 active nve/sphere
-
-compute		1 all erotate/sphere
-thermo_style	custom step atoms ke c_1 vol
-thermo_modify	norm no
-thermo		100
-
-run		100
-Memory usage per processor = 10.7034 Mbytes
-Step Atoms KinEng 1 Volume 
-       0    32000    784139.13    1601.1263    29833.783 
-     100    32000    784292.08    1571.0968    29834.707 
-Loop time of 0.133553 on 4 procs for 100 steps with 32000 atoms
-
-Pair  time (%) = 0.0669281 (50.1135)
-Neigh time (%) = 0.01061 (7.9444)
-Comm  time (%) = 0.0142241 (10.6505)
-Outpt time (%) = 9.28044e-05 (0.0694888)
-Other time (%) = 0.041698 (31.2221)
-
-Nlocal:    8000 ave 8008 max 7992 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost:    2439 ave 2450 max 2428 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs:    29500.5 ave 30488 max 28513 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 118002
-Ave neighs/atom = 3.68756
-Neighbor list builds = 2
-Dangerous builds = 0

bench/log.1Feb14.chute.scaled.linux.4

@@ -1,75 +0,0 @@
-LAMMPS (1 Feb 2014)
-# LAMMPS benchmark of granular flow
-# chute flow of 32000 atoms with frozen base at 26 degrees
-
-variable	x index 1
-variable	y index 1
-
-units		lj
-atom_style	sphere
-boundary	p p fs
-newton		off
-communicate	single vel yes
-
-read_data	data.chute
-  orthogonal box = (0 0 0) to (40 20 37.2886)
-  2 by 1 by 2 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-
-replicate	$x $y 1
-replicate	2 $y 1
-replicate	2 2 1
-  orthogonal box = (0 0 0) to (80 40 37.2923)
-  2 by 2 by 1 MPI processor grid
-  128000 atoms
-
-pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
-pair_coeff	* *
-
-neighbor	0.1 bin
-neigh_modify	every 1 delay 0
-
-timestep	0.0001
-
-group		bottom type 2
-3648 atoms in group bottom
-group		active subtract all bottom
-124352 atoms in group active
-neigh_modify	exclude group bottom bottom
-
-fix		1 all gravity 1.0 chute 26.0
-fix		2 bottom freeze
-fix		3 active nve/sphere
-
-compute		1 all erotate/sphere
-thermo_style	custom step atoms ke c_1 vol
-thermo_modify	norm no
-thermo		100
-
-run		100
-Memory usage per processor = 22.3334 Mbytes
-Step Atoms KinEng 1 Volume 
-       0   128000    3136556.5    6404.5051    119335.13 
-     100   128000    3137168.3    6284.3873    119338.83 
-Loop time of 0.862817 on 4 procs for 100 steps with 128000 atoms
-
-Pair  time (%) = 0.518524 (60.0966)
-Neigh time (%) = 0.0441293 (5.11455)
-Comm  time (%) = 0.057479 (6.66178)
-Outpt time (%) = 0.000286222 (0.0331729)
-Other time (%) = 0.242399 (28.0939)
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Nghost:    5463 ave 5463 max 5463 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Neighs:    115133 ave 115133 max 115133 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 460532
-Ave neighs/atom = 3.59791
-Neighbor list builds = 2
-Dangerous builds = 0

bench/log.1Feb14.eam.fixed.linux.1

@@ -1,67 +0,0 @@
-LAMMPS (1 Feb 2014)
-# bulk Cu lattice
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	xx equal 20*1
-variable	yy equal 20*$y
-variable	yy equal 20*1
-variable	zz equal 20*$z
-variable	zz equal 20*1
-
-units		metal
-atom_style	atomic
-
-lattice		fcc 3.615
-Lattice spacing in x,y,z = 3.615 3.615 3.615
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-region		box block 0 20 0 ${yy} 0 ${zz}
-region		box block 0 20 0 20 0 ${zz}
-region		box block 0 20 0 20 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
-  1 by 1 by 1 MPI processor grid
-create_atoms	1 box
-Created 32000 atoms
-
-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		100
-Memory usage per processor = 15.3727 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1600      -113280            0   -106662.09    18703.573 
-      50    781.69049   -109873.35            0   -106640.13    52273.088 
-     100      801.832    -109957.3            0   -106640.77    51322.821 
-Loop time of 5.93175 on 1 procs for 100 steps with 32000 atoms
-
-Pair  time (%) = 5.20741 (87.7887)
-Neigh time (%) = 0.618579 (10.4283)
-Comm  time (%) = 0.0310862 (0.524064)
-Outpt time (%) = 0.000214815 (0.00362144)
-Other time (%) = 0.0744634 (1.25533)
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    19909 ave 19909 max 19909 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    1.20778e+06 ave 1.20778e+06 max 1.20778e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1207784
-Ave neighs/atom = 37.7433
-Neighbor list builds = 13
-Dangerous builds = 0

bench/log.1Feb14.eam.fixed.linux.4

@@ -1,67 +0,0 @@
-LAMMPS (1 Feb 2014)
-# bulk Cu lattice
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	xx equal 20*1
-variable	yy equal 20*$y
-variable	yy equal 20*1
-variable	zz equal 20*$z
-variable	zz equal 20*1
-
-units		metal
-atom_style	atomic
-
-lattice		fcc 3.615
-Lattice spacing in x,y,z = 3.615 3.615 3.615
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-region		box block 0 20 0 ${yy} 0 ${zz}
-region		box block 0 20 0 20 0 ${zz}
-region		box block 0 20 0 20 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
-  1 by 2 by 2 MPI processor grid
-create_atoms	1 box
-Created 32000 atoms
-
-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		100
-Memory usage per processor = 4.92441 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1600      -113280            0   -106662.09    18703.573 
-      50    781.69049   -109873.35            0   -106640.13    52273.088 
-     100      801.832    -109957.3            0   -106640.77    51322.821 
-Loop time of 1.57335 on 4 procs for 100 steps with 32000 atoms
-
-Pair  time (%) = 1.35199 (85.9304)
-Neigh time (%) = 0.160176 (10.1806)
-Comm  time (%) = 0.0413526 (2.62832)
-Outpt time (%) = 0.000119448 (0.00759193)
-Other time (%) = 0.0197157 (1.2531)
-
-Nlocal:    8000 ave 8008 max 7993 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Nghost:    9130.25 ave 9138 max 9122 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs:    301946 ave 302392 max 301360 min
-Histogram: 1 0 0 0 1 0 0 0 1 1
-
-Total # of neighbors = 1207784
-Ave neighs/atom = 37.7433
-Neighbor list builds = 13
-Dangerous builds = 0

bench/log.1Feb14.eam.scaled.linux.4

@@ -1,67 +0,0 @@
-LAMMPS (1 Feb 2014)
-# bulk Cu lattice
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	xx equal 20*2
-variable	yy equal 20*$y
-variable	yy equal 20*2
-variable	zz equal 20*$z
-variable	zz equal 20*1
-
-units		metal
-atom_style	atomic
-
-lattice		fcc 3.615
-Lattice spacing in x,y,z = 3.615 3.615 3.615
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-region		box block 0 40 0 ${yy} 0 ${zz}
-region		box block 0 40 0 40 0 ${zz}
-region		box block 0 40 0 40 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (144.6 144.6 72.3)
-  2 by 2 by 1 MPI processor grid
-create_atoms	1 box
-Created 128000 atoms
-
-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		100
-Memory usage per processor = 15.2891 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1600      -453120            0   -426647.73    18704.012 
-      50    779.50001   -439457.02            0   -426560.06    52355.276 
-     100    797.97828   -439764.76            0   -426562.07     51474.74 
-Loop time of 6.55459 on 4 procs for 100 steps with 128000 atoms
-
-Pair  time (%) = 5.63064 (85.9037)
-Neigh time (%) = 0.698691 (10.6596)
-Comm  time (%) = 0.123277 (1.88077)
-Outpt time (%) = 0.000314116 (0.00479231)
-Other time (%) = 0.101672 (1.55115)
-
-Nlocal:    32000 ave 32092 max 31914 min
-Histogram: 1 0 0 1 0 1 0 0 0 1
-Nghost:    19910 ave 19997 max 19818 min
-Histogram: 1 0 0 0 1 0 1 0 0 1
-Neighs:    1.20728e+06 ave 1.21142e+06 max 1.2036e+06 min
-Histogram: 1 0 0 1 1 0 0 0 0 1
-
-Total # of neighbors = 4829126
-Ave neighs/atom = 37.7275
-Neighbor list builds = 14
-Dangerous builds = 0

bench/log.1Feb14.lj.fixed.linux.1

@@ -1,64 +0,0 @@
-LAMMPS (1 Feb 2014)
-# 3d Lennard-Jones melt
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	xx equal 20*1
-variable	yy equal 20*$y
-variable	yy equal 20*1
-variable	zz equal 20*$z
-variable	zz equal 20*1
-
-units		lj
-atom_style	atomic
-
-lattice		fcc 0.8442
-Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-region		box block 0 20 0 ${yy} 0 ${zz}
-region		box block 0 20 0 20 0 ${zz}
-region		box block 0 20 0 20 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
-  1 by 1 by 1 MPI processor grid
-create_atoms	1 box
-Created 32000 atoms
-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		100
-Memory usage per processor = 13.2266 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
-     100    0.7574531   -5.7585055            0   -4.6223613   0.20726105 
-Loop time of 2.26599 on 1 procs for 100 steps with 32000 atoms
-
-Pair  time (%) = 1.92891 (85.1244)
-Neigh time (%) = 0.252641 (11.1493)
-Comm  time (%) = 0.0243704 (1.07549)
-Outpt time (%) = 0.000110865 (0.00489256)
-Other time (%) = 0.059957 (2.64596)
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    19657 ave 19657 max 19657 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    1.20283e+06 ave 1.20283e+06 max 1.20283e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1202833
-Ave neighs/atom = 37.5885
-Neighbor list builds = 5
-Dangerous builds = 0

bench/log.1Feb14.lj.fixed.linux.4

@@ -1,64 +0,0 @@
-LAMMPS (1 Feb 2014)
-# 3d Lennard-Jones melt
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	xx equal 20*1
-variable	yy equal 20*$y
-variable	yy equal 20*1
-variable	zz equal 20*$z
-variable	zz equal 20*1
-
-units		lj
-atom_style	atomic
-
-lattice		fcc 0.8442
-Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-region		box block 0 20 0 ${yy} 0 ${zz}
-region		box block 0 20 0 20 0 ${zz}
-region		box block 0 20 0 20 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
-  1 by 2 by 2 MPI processor grid
-create_atoms	1 box
-Created 32000 atoms
-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		100
-Memory usage per processor = 4.31282 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
-     100    0.7574531   -5.7585055            0   -4.6223613   0.20726105 
-Loop time of 0.628341 on 4 procs for 100 steps with 32000 atoms
-
-Pair  time (%) = 0.505093 (80.3851)
-Neigh time (%) = 0.0659957 (10.5032)
-Comm  time (%) = 0.0406293 (6.46611)
-Outpt time (%) = 8.43406e-05 (0.0134227)
-Other time (%) = 0.016539 (2.63216)
-
-Nlocal:    8000 ave 8037 max 7964 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Nghost:    9007.5 ave 9050 max 8968 min
-Histogram: 1 1 0 0 0 0 0 1 0 1
-Neighs:    300708 ave 305113 max 297203 min
-Histogram: 1 0 0 1 1 0 0 0 0 1
-
-Total # of neighbors = 1202833
-Ave neighs/atom = 37.5885
-Neighbor list builds = 5
-Dangerous builds = 0

bench/log.1Feb14.lj.scaled.linux.4

@@ -1,64 +0,0 @@
-LAMMPS (1 Feb 2014)
-# 3d Lennard-Jones melt
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	xx equal 20*2
-variable	yy equal 20*$y
-variable	yy equal 20*2
-variable	zz equal 20*$z
-variable	zz equal 20*1
-
-units		lj
-atom_style	atomic
-
-lattice		fcc 0.8442
-Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-region		box block 0 40 0 ${yy} 0 ${zz}
-region		box block 0 40 0 40 0 ${zz}
-region		box block 0 40 0 40 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (67.1838 67.1838 33.5919)
-  2 by 2 by 1 MPI processor grid
-create_atoms	1 box
-Created 128000 atoms
-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		100
-Memory usage per processor = 13.1495 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1.44   -6.7733681            0   -4.6133849   -5.0196788 
-     100   0.75841891    -5.759957            0   -4.6223375   0.20008866 
-Loop time of 2.54147 on 4 procs for 100 steps with 128000 atoms
-
-Pair  time (%) = 2.08305 (81.9623)
-Neigh time (%) = 0.258072 (10.1545)
-Comm  time (%) = 0.116279 (4.57528)
-Outpt time (%) = 0.000139415 (0.00548562)
-Other time (%) = 0.0839326 (3.30252)
-
-Nlocal:    32000 ave 32060 max 31939 min
-Histogram: 1 0 1 0 0 0 0 1 0 1
-Nghost:    19630.8 ave 19681 max 19562 min
-Histogram: 1 0 0 0 1 0 0 0 1 1
-Neighs:    1.20195e+06 ave 1.20354e+06 max 1.19931e+06 min
-Histogram: 1 0 0 0 0 0 0 2 0 1
-
-Total # of neighbors = 4807797
-Ave neighs/atom = 37.5609
-Neighbor list builds = 5
-Dangerous builds = 0

bench/log.1Feb14.rhodo.fixed.linux.1

@@ -1,109 +0,0 @@
-LAMMPS (1 Feb 2014)
-# Rhodopsin model
-
-units           real
-neigh_modify    delay 5 every 1
-
-atom_style      full
-bond_style      harmonic
-angle_style     charmm
-dihedral_style  charmm
-improper_style  harmonic
-pair_style      lj/charmm/coul/long 8.0 10.0
-pair_modify     mix arithmetic
-kspace_style    pppm 1e-4
-
-read_data       data.rhodo
-  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-  scanning bonds ...
-  4 = max bonds/atom
-  scanning angles ...
-  8 = max angles/atom
-  scanning dihedrals ...
-  18 = max dihedrals/atom
-  scanning impropers ...
-  2 = max impropers/atom
-  reading bonds ...
-  27723 bonds
-  reading angles ...
-  40467 angles
-  reading dihedrals ...
-  56829 dihedrals
-  reading impropers ...
-  1034 impropers
-  4 = max # of 1-2 neighbors
-  12 = max # of 1-3 neighbors
-  24 = max # of 1-4 neighbors
-  26 = max # of special neighbors
-
-fix             1 all shake 0.0001 5 0 m 1.0 a 232
-  1617 = # of size 2 clusters
-  3633 = # of size 3 clusters
-  747 = # of size 4 clusters
-  4233 = # of frozen angles
-fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
-
-special_bonds   charmm
-
-thermo          50
-thermo_style    multi
-timestep        2.0
-
-run		100
-PPPM initialization ...
-  G vector (1/distance) = 0.248835
-  grid = 25 32 32
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0355478
-  estimated relative force accuracy = 0.000107051
-  using double precision FFTs
-  3d grid and FFT values/proc = 41070 25600
-Memory usage per processor = 139.238 Mbytes
----------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
-TotEng   =    -25356.2064 KinEng   =     21444.8313 Temp     =       299.0397 
-PotEng   =    -46801.0377 E_bond   =      2537.9940 E_angle  =     10921.3742 
-E_dihed  =      5211.7865 E_impro  =       213.5116 E_vdwl   =     -2307.8634 
-E_coul   =    207025.8927 E_long   =   -270403.7333 Press    =      -142.6035 
-Volume   =    307995.0335 
----------------- Step       50 ----- CPU =     17.8100 (sec) ----------------
-TotEng   =    -25330.0828 KinEng   =     21501.0029 Temp     =       299.8230 
-PotEng   =    -46831.0857 E_bond   =      2471.7004 E_angle  =     10836.4975 
-E_dihed  =      5239.6299 E_impro  =       227.1218 E_vdwl   =     -1993.2754 
-E_coul   =    206797.6331 E_long   =   -270410.3930 Press    =       237.6701 
-Volume   =    308031.5639 
----------------- Step      100 ----- CPU =     36.2348 (sec) ----------------
-TotEng   =    -25290.7592 KinEng   =     21592.0117 Temp     =       301.0920 
-PotEng   =    -46882.7709 E_bond   =      2567.9807 E_angle  =     10781.9408 
-E_dihed  =      5198.7432 E_impro  =       216.7834 E_vdwl   =     -1902.4783 
-E_coul   =    206659.2327 E_long   =   -270404.9733 Press    =         6.9960 
-Volume   =    308133.9888 
-Loop time of 36.2348 on 1 procs for 100 steps with 32000 atoms
-
-Pair  time (%) = 26.0418 (71.8696)
-Bond  time (%) = 1.26644 (3.4951)
-Kspce time (%) = 3.24933 (8.96742)
-Neigh time (%) = 4.47968 (12.3629)
-Comm  time (%) = 0.0700378 (0.193289)
-Outpt time (%) = 0.000230074 (0.000634953)
-Other time (%) = 1.12729 (3.11108)
-
-FFT time (% of Kspce) = 0.276809 (8.51896)
-FFT Gflps 3d (1d only) = 1.87746 3.23903
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    47958 ave 47958 max 47958 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 12028107
-Ave neighs/atom = 375.878
-Ave special neighs/atom = 7.43187
-Neighbor list builds = 11
-Dangerous builds = 0

bench/log.1Feb14.rhodo.fixed.linux.4

@@ -1,109 +0,0 @@
-LAMMPS (1 Feb 2014)
-# Rhodopsin model
-
-units           real
-neigh_modify    delay 5 every 1
-
-atom_style      full
-bond_style      harmonic
-angle_style     charmm
-dihedral_style  charmm
-improper_style  harmonic
-pair_style      lj/charmm/coul/long 8.0 10.0
-pair_modify     mix arithmetic
-kspace_style    pppm 1e-4
-
-read_data       data.rhodo
-  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-  scanning bonds ...
-  4 = max bonds/atom
-  scanning angles ...
-  8 = max angles/atom
-  scanning dihedrals ...
-  18 = max dihedrals/atom
-  scanning impropers ...
-  2 = max impropers/atom
-  reading bonds ...
-  27723 bonds
-  reading angles ...
-  40467 angles
-  reading dihedrals ...
-  56829 dihedrals
-  reading impropers ...
-  1034 impropers
-  4 = max # of 1-2 neighbors
-  12 = max # of 1-3 neighbors
-  24 = max # of 1-4 neighbors
-  26 = max # of special neighbors
-
-fix             1 all shake 0.0001 5 0 m 1.0 a 232
-  1617 = # of size 2 clusters
-  3633 = # of size 3 clusters
-  747 = # of size 4 clusters
-  4233 = # of frozen angles
-fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
-
-special_bonds   charmm
-
-thermo          50
-thermo_style    multi
-timestep        2.0
-
-run		100
-PPPM initialization ...
-  G vector (1/distance) = 0.248835
-  grid = 25 32 32
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0355478
-  estimated relative force accuracy = 0.000107051
-  using double precision FFTs
-  3d grid and FFT values/proc = 13230 6400
-Memory usage per processor = 54.595 Mbytes
----------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
-TotEng   =    -25356.2064 KinEng   =     21444.8313 Temp     =       299.0397 
-PotEng   =    -46801.0377 E_bond   =      2537.9940 E_angle  =     10921.3742 
-E_dihed  =      5211.7865 E_impro  =       213.5116 E_vdwl   =     -2307.8634 
-E_coul   =    207025.8927 E_long   =   -270403.7333 Press    =      -142.6035 
-Volume   =    307995.0335 
----------------- Step       50 ----- CPU =      4.7061 (sec) ----------------
-TotEng   =    -25330.0829 KinEng   =     21501.0029 Temp     =       299.8230 
-PotEng   =    -46831.0857 E_bond   =      2471.7004 E_angle  =     10836.4975 
-E_dihed  =      5239.6299 E_impro  =       227.1218 E_vdwl   =     -1993.2754 
-E_coul   =    206797.6331 E_long   =   -270410.3930 Press    =       237.6701 
-Volume   =    308031.5639 
----------------- Step      100 ----- CPU =      9.5889 (sec) ----------------
-TotEng   =    -25290.7592 KinEng   =     21592.0117 Temp     =       301.0920 
-PotEng   =    -46882.7709 E_bond   =      2567.9807 E_angle  =     10781.9408 
-E_dihed  =      5198.7432 E_impro  =       216.7834 E_vdwl   =     -1902.4783 
-E_coul   =    206659.2327 E_long   =   -270404.9733 Press    =         6.9960 
-Volume   =    308133.9888 
-Loop time of 9.58898 on 4 procs for 100 steps with 32000 atoms
-
-Pair  time (%) = 6.62576 (69.0976)
-Bond  time (%) = 0.317414 (3.31019)
-Kspce time (%) = 1.04771 (10.9262)
-Neigh time (%) = 1.15891 (12.0859)
-Comm  time (%) = 0.0844751 (0.88096)
-Outpt time (%) = 0.00015074 (0.00157201)
-Other time (%) = 0.354558 (3.69756)
-
-FFT time (% of Kspce) = 0.0967343 (9.23289)
-FFT Gflps 3d (1d only) = 5.37243 12.7459
-
-Nlocal:    8000 ave 8143 max 7933 min
-Histogram: 1 2 0 0 0 0 0 0 0 1
-Nghost:    22733.5 ave 22769 max 22693 min
-Histogram: 1 0 0 0 0 2 0 0 0 1
-Neighs:    3.00703e+06 ave 3.0975e+06 max 2.96493e+06 min
-Histogram: 1 2 0 0 0 0 0 0 0 1
-
-Total # of neighbors = 12028107
-Ave neighs/atom = 375.878
-Ave special neighs/atom = 7.43187
-Neighbor list builds = 11
-Dangerous builds = 0

bench/log.1Feb14.rhodo.scaled.linux.4

@@ -1,130 +0,0 @@
-LAMMPS (1 Feb 2014)
-# Rhodopsin model
-
-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 8.0 10.0
-pair_modify     mix arithmetic
-kspace_style    pppm 1e-4
-
-read_data       data.rhodo
-  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  32000 atoms
-  reading velocities ...
-  32000 velocities
-  scanning bonds ...
-  4 = max bonds/atom
-  scanning angles ...
-  8 = max angles/atom
-  scanning dihedrals ...
-  18 = max dihedrals/atom
-  scanning impropers ...
-  2 = max impropers/atom
-  reading bonds ...
-  27723 bonds
-  reading angles ...
-  40467 angles
-  reading dihedrals ...
-  56829 dihedrals
-  reading impropers ...
-  1034 impropers
-  4 = max # of 1-2 neighbors
-  12 = max # of 1-3 neighbors
-  24 = max # of 1-4 neighbors
-  26 = max # of special neighbors
-
-replicate	$x $y $z
-replicate	2 $y $z
-replicate	2 2 $z
-replicate	2 2 1
-  orthogonal box = (-27.5 -38.5 -36.3646) to (82.5 115.5 36.3615)
-  2 by 2 by 1 MPI processor grid
-  128000 atoms
-  110892 bonds
-  161868 angles
-  227316 dihedrals
-  4136 impropers
-  4 = max # of 1-2 neighbors
-  12 = max # of 1-3 neighbors
-  24 = max # of 1-4 neighbors
-  26 = max # of special neighbors
-
-fix             1 all shake 0.0001 5 0 m 1.0 a 232
-  6468 = # of size 2 clusters
-  14532 = # of size 3 clusters
-  2988 = # of size 4 clusters
-  16932 = # of frozen angles
-fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
-
-special_bonds   charmm
-
-thermo          50
-thermo_style    multi
-timestep        2.0
-
-run		100
-PPPM initialization ...
-  G vector (1/distance) = 0.248593
-  grid = 48 60 36
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0359793
-  estimated relative force accuracy = 0.00010835
-  using double precision FFTs
-  3d grid and FFT values/proc = 41615 25920
-Memory usage per processor = 146.358 Mbytes
----------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
-TotEng   =   -101425.4887 KinEng   =     85779.3251 Temp     =       299.0304 
-PotEng   =   -187204.8138 E_bond   =     10151.9760 E_angle  =     43685.4968 
-E_dihed  =     20847.1460 E_impro  =       854.0463 E_vdwl   =     -9231.4537 
-E_coul   =    827053.5824 E_long   =  -1080565.6077 Press    =      -142.3092 
-Volume   =   1231980.1340 
----------------- Step       50 ----- CPU =     18.9852 (sec) ----------------
-TotEng   =   -101320.2676 KinEng   =     86003.4837 Temp     =       299.8118 
-PotEng   =   -187323.7514 E_bond   =      9887.1072 E_angle  =     43346.7922 
-E_dihed  =     20958.7032 E_impro  =       908.4715 E_vdwl   =     -7973.4457 
-E_coul   =    826141.3831 E_long   =  -1080592.7629 Press    =       238.0161 
-Volume   =   1232126.1855 
----------------- Step      100 ----- CPU =     38.9161 (sec) ----------------
-TotEng   =   -101158.1853 KinEng   =     86355.6148 Temp     =       301.0393 
-PotEng   =   -187513.8001 E_bond   =     10272.0693 E_angle  =     43128.6453 
-E_dihed  =     20793.9759 E_impro  =       867.0826 E_vdwl   =     -7586.7186 
-E_coul   =    825583.7120 E_long   =  -1080572.5667 Press    =        15.2151 
-Volume   =   1232535.8423 
-Loop time of 38.9162 on 4 procs for 100 steps with 128000 atoms
-
-Pair  time (%) = 27.1908 (69.8701)
-Bond  time (%) = 1.30758 (3.35999)
-Kspce time (%) = 3.99359 (10.262)
-Neigh time (%) = 4.65272 (11.9557)
-Comm  time (%) = 0.216829 (0.557168)
-Outpt time (%) = 0.000280738 (0.000721391)
-Other time (%) = 1.55441 (3.99426)
-
-FFT time (% of Kspce) = 0.448314 (11.2258)
-FFT Gflps 3d (1d only) = 5.34183 11.5795
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Nghost:    47957 ave 47957 max 47957 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Neighs:    1.20281e+07 ave 1.20572e+07 max 1.1999e+07 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 48112472
-Ave neighs/atom = 375.879
-Ave special neighs/atom = 7.43187
-Neighbor list builds = 11
-Dangerous builds = 0

bench/log.6Oct16.chain.fixed.icc.1

@@ -0,0 +1,78 @@
+LAMMPS (6 Oct 2016)
+# FENE beadspring benchmark
+
+units		lj
+atom_style	bond
+special_bonds   fene
+
+read_data	data.chain
+  orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  31680 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of special neighbors
+
+neighbor	0.4 bin
+neigh_modify	every 1 delay 1
+
+bond_style      fene
+bond_coeff	1 30.0 1.5 1.0 1.0
+
+pair_style	lj/cut 1.12
+pair_modify	shift yes
+pair_coeff	1 1 1.0 1.0 1.12
+
+fix		1 all nve
+fix		2 all langevin 1.0 1.0 10.0 904297
+
+thermo          100
+timestep	0.012
+
+run		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 1 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.52
+  ghost atom cutoff = 1.52
+  binsize = 0.76 -> bins = 45 45 45
+Memory usage per processor = 12.0423 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0   0.97029772   0.44484087    20.494523    22.394765    4.6721833 
+     100    0.9729966    0.4361122    20.507698     22.40326    4.6548819 
+Loop time of 0.977647 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 106050.541 tau/day, 102.286 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.19421    | 0.19421    | 0.19421    |   0.0 | 19.86
+Bond    | 0.08741    | 0.08741    | 0.08741    |   0.0 |  8.94
+Neigh   | 0.45791    | 0.45791    | 0.45791    |   0.0 | 46.84
+Comm    | 0.032649   | 0.032649   | 0.032649   |   0.0 |  3.34
+Output  | 0.00012207 | 0.00012207 | 0.00012207 |   0.0 |  0.01
+Modify  | 0.18071    | 0.18071    | 0.18071    |   0.0 | 18.48
+Other   |            | 0.02464    |            |       |  2.52
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    9493 ave 9493 max 9493 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    155873 ave 155873 max 155873 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 155873
+Ave neighs/atom = 4.87103
+Ave special neighs/atom = 1.98
+Neighbor list builds = 25
+Dangerous builds = 0
+Total wall time: 0:00:01

bench/log.6Oct16.chain.fixed.icc.4

@@ -0,0 +1,78 @@
+LAMMPS (6 Oct 2016)
+# FENE beadspring benchmark
+
+units		lj
+atom_style	bond
+special_bonds   fene
+
+read_data	data.chain
+  orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  31680 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of special neighbors
+
+neighbor	0.4 bin
+neigh_modify	every 1 delay 1
+
+bond_style      fene
+bond_coeff	1 30.0 1.5 1.0 1.0
+
+pair_style	lj/cut 1.12
+pair_modify	shift yes
+pair_coeff	1 1 1.0 1.0 1.12
+
+fix		1 all nve
+fix		2 all langevin 1.0 1.0 10.0 904297
+
+thermo          100
+timestep	0.012
+
+run		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 1 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.52
+  ghost atom cutoff = 1.52
+  binsize = 0.76 -> bins = 45 45 45
+Memory usage per processor = 4.14663 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0   0.97029772   0.44484087    20.494523    22.394765    4.6721833 
+     100   0.97145835   0.43803883    20.502691    22.397872     4.626988 
+Loop time of 0.269205 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 385133.446 tau/day, 371.464 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.049383   | 0.049756   | 0.049988   |   0.1 | 18.48
+Bond    | 0.022701   | 0.022813   | 0.022872   |   0.0 |  8.47
+Neigh   | 0.11982    | 0.12002    | 0.12018    |   0.0 | 44.58
+Comm    | 0.020274   | 0.021077   | 0.022348   |   0.5 |  7.83
+Output  | 5.3167e-05 | 5.6148e-05 | 6.3181e-05 |   0.1 |  0.02
+Modify  | 0.046276   | 0.046809   | 0.047016   |   0.1 | 17.39
+Other   |            | 0.008669   |            |       |  3.22
+
+Nlocal:    8000 ave 8030 max 7974 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Nghost:    4177 ave 4191 max 4160 min
+Histogram: 1 0 0 0 1 0 0 1 0 1
+Neighs:    38995.8 ave 39169 max 38852 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+
+Total # of neighbors = 155983
+Ave neighs/atom = 4.87447
+Ave special neighs/atom = 1.98
+Neighbor list builds = 25
+Dangerous builds = 0
+Total wall time: 0:00:00

bench/log.6Oct16.chain.scaled.icc.4

@@ -0,0 +1,94 @@
+LAMMPS (6 Oct 2016)
+# FENE beadspring benchmark
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+units		lj
+atom_style	bond
+atom_modify	map hash
+special_bonds   fene
+
+read_data	data.chain
+  orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  31680 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of special neighbors
+
+replicate	$x $y $z
+replicate	2 $y $z
+replicate	2 2 $z
+replicate	2 2 1
+  orthogonal box = (-16.796 -16.796 -16.796) to (50.388 50.388 16.796)
+  2 by 2 by 1 MPI processor grid
+  128000 atoms
+  126720 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of special neighbors
+
+neighbor	0.4 bin
+neigh_modify	every 1 delay 1
+
+bond_style      fene
+bond_coeff	1 30.0 1.5 1.0 1.0
+
+pair_style	lj/cut 1.12
+pair_modify	shift yes
+pair_coeff	1 1 1.0 1.0 1.12
+
+fix		1 all nve
+fix		2 all langevin 1.0 1.0 10.0 904297
+
+thermo          100
+timestep	0.012
+
+run		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 1 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.52
+  ghost atom cutoff = 1.52
+  binsize = 0.76 -> bins = 89 89 45
+Memory usage per processor = 13.2993 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0   0.97027498   0.44484087    20.494523    22.394765    4.6721833 
+     100   0.97682955   0.44239968    20.500229    22.407862    4.6527025 
+Loop time of 1.14845 on 4 procs for 100 steps with 128000 atoms
+
+Performance: 90277.919 tau/day, 87.074 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.2203     | 0.22207    | 0.22386    |   0.3 | 19.34
+Bond    | 0.094861   | 0.095302   | 0.095988   |   0.1 |  8.30
+Neigh   | 0.52127    | 0.5216     | 0.52189    |   0.0 | 45.42
+Comm    | 0.079585   | 0.082159   | 0.084366   |   0.7 |  7.15
+Output  | 0.00013304 | 0.00015306 | 0.00018501 |   0.2 |  0.01
+Modify  | 0.18351    | 0.18419    | 0.1856     |   0.2 | 16.04
+Other   |            | 0.04298    |            |       |  3.74
+
+Nlocal:    32000 ave 32015 max 31983 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+Nghost:    9492 ave 9522 max 9432 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Neighs:    155837 ave 156079 max 155506 min
+Histogram: 1 0 0 0 0 1 0 0 1 1
+
+Total # of neighbors = 623349
+Ave neighs/atom = 4.86991
+Ave special neighs/atom = 1.98
+Neighbor list builds = 25
+Dangerous builds = 0
+Total wall time: 0:00:01

bench/log.6Oct16.chute.fixed.icc.1

@@ -0,0 +1,80 @@
+LAMMPS (6 Oct 2016)
+# LAMMPS benchmark of granular flow
+# chute flow of 32000 atoms with frozen base at 26 degrees
+
+units		lj
+atom_style	sphere
+boundary	p p fs
+newton		off
+comm_modify	vel yes
+
+read_data	data.chute
+  orthogonal box = (0 0 0) to (40 20 37.2886)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+
+pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
+pair_coeff	* *
+
+neighbor	0.1 bin
+neigh_modify	every 1 delay 0
+
+timestep	0.0001
+
+group		bottom type 2
+912 atoms in group bottom
+group		active subtract all bottom
+31088 atoms in group active
+neigh_modify	exclude group bottom bottom
+
+fix		1 all gravity 1.0 chute 26.0
+fix		2 bottom freeze
+fix		3 active nve/sphere
+
+compute		1 all erotate/sphere
+thermo_style	custom step atoms ke c_1 vol
+thermo_modify	norm no
+thermo		100
+
+run		100
+Neighbor list info ...
+  2 neighbor list requests
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.1
+  ghost atom cutoff = 1.1
+  binsize = 0.55 -> bins = 73 37 68
+Memory usage per processor = 16.0904 Mbytes
+Step Atoms KinEng c_1 Volume 
+       0    32000    784139.13    1601.1263    29833.783 
+     100    32000    784292.08    1571.0968    29834.707 
+Loop time of 0.534174 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 1617.451 tau/day, 187.205 timesteps/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.33346    | 0.33346    | 0.33346    |   0.0 | 62.43
+Neigh   | 0.043902   | 0.043902   | 0.043902   |   0.0 |  8.22
+Comm    | 0.018391   | 0.018391   | 0.018391   |   0.0 |  3.44
+Output  | 0.00022411 | 0.00022411 | 0.00022411 |   0.0 |  0.04
+Modify  | 0.11666    | 0.11666    | 0.11666    |   0.0 | 21.84
+Other   |            | 0.02153    |            |       |  4.03
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    5463 ave 5463 max 5463 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    115133 ave 115133 max 115133 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 115133
+Ave neighs/atom = 3.59791
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:00

bench/log.6Oct16.chute.fixed.icc.4

@@ -0,0 +1,80 @@
+LAMMPS (6 Oct 2016)
+# LAMMPS benchmark of granular flow
+# chute flow of 32000 atoms with frozen base at 26 degrees
+
+units		lj
+atom_style	sphere
+boundary	p p fs
+newton		off
+comm_modify	vel yes
+
+read_data	data.chute
+  orthogonal box = (0 0 0) to (40 20 37.2886)
+  2 by 1 by 2 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+
+pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
+pair_coeff	* *
+
+neighbor	0.1 bin
+neigh_modify	every 1 delay 0
+
+timestep	0.0001
+
+group		bottom type 2
+912 atoms in group bottom
+group		active subtract all bottom
+31088 atoms in group active
+neigh_modify	exclude group bottom bottom
+
+fix		1 all gravity 1.0 chute 26.0
+fix		2 bottom freeze
+fix		3 active nve/sphere
+
+compute		1 all erotate/sphere
+thermo_style	custom step atoms ke c_1 vol
+thermo_modify	norm no
+thermo		100
+
+run		100
+Neighbor list info ...
+  2 neighbor list requests
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.1
+  ghost atom cutoff = 1.1
+  binsize = 0.55 -> bins = 73 37 68
+Memory usage per processor = 7.04927 Mbytes
+Step Atoms KinEng c_1 Volume 
+       0    32000    784139.13    1601.1263    29833.783 
+     100    32000    784292.08    1571.0968    29834.707 
+Loop time of 0.171815 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 5028.653 tau/day, 582.020 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.093691   | 0.096898   | 0.10005    |   0.8 | 56.40
+Neigh   | 0.011976   | 0.012059   | 0.012146   |   0.1 |  7.02
+Comm    | 0.016384   | 0.017418   | 0.018465   |   0.8 | 10.14
+Output  | 7.7963e-05 | 0.00010747 | 0.00013304 |   0.2 |  0.06
+Modify  | 0.031744   | 0.031943   | 0.032167   |   0.1 | 18.59
+Other   |            | 0.01339    |            |       |  7.79
+
+Nlocal:    8000 ave 8008 max 7992 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    2439 ave 2450 max 2428 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    29500.5 ave 30488 max 28513 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 118002
+Ave neighs/atom = 3.68756
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:00

bench/log.6Oct16.chute.scaled.icc.4

@@ -0,0 +1,90 @@
+LAMMPS (6 Oct 2016)
+# LAMMPS benchmark of granular flow
+# chute flow of 32000 atoms with frozen base at 26 degrees
+
+variable	x index 1
+variable	y index 1
+
+units		lj
+atom_style	sphere
+boundary	p p fs
+newton		off
+comm_modify	vel yes
+
+read_data	data.chute
+  orthogonal box = (0 0 0) to (40 20 37.2886)
+  2 by 1 by 2 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+
+replicate	$x $y 1
+replicate	2 $y 1
+replicate	2 2 1
+  orthogonal box = (0 0 0) to (80 40 37.2922)
+  2 by 2 by 1 MPI processor grid
+  128000 atoms
+
+pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
+pair_coeff	* *
+
+neighbor	0.1 bin
+neigh_modify	every 1 delay 0
+
+timestep	0.0001
+
+group		bottom type 2
+3648 atoms in group bottom
+group		active subtract all bottom
+124352 atoms in group active
+neigh_modify	exclude group bottom bottom
+
+fix		1 all gravity 1.0 chute 26.0
+fix		2 bottom freeze
+fix		3 active nve/sphere
+
+compute		1 all erotate/sphere
+thermo_style	custom step atoms ke c_1 vol
+thermo_modify	norm no
+thermo		100
+
+run		100
+Neighbor list info ...
+  2 neighbor list requests
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.1
+  ghost atom cutoff = 1.1
+  binsize = 0.55 -> bins = 146 73 68
+Memory usage per processor = 16.1265 Mbytes
+Step Atoms KinEng c_1 Volume 
+       0   128000    3136556.5    6404.5051    119335.13 
+     100   128000    3137168.3    6284.3873    119338.83 
+Loop time of 0.832365 on 4 procs for 100 steps with 128000 atoms
+
+Performance: 1038.006 tau/day, 120.140 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.5178     | 0.52208    | 0.52793    |   0.5 | 62.72
+Neigh   | 0.047003   | 0.047113   | 0.047224   |   0.0 |  5.66
+Comm    | 0.05233    | 0.052988   | 0.053722   |   0.2 |  6.37
+Output  | 0.00024986 | 0.00032717 | 0.00036693 |   0.3 |  0.04
+Modify  | 0.15517    | 0.15627    | 0.15808    |   0.3 | 18.77
+Other   |            | 0.0536     |            |       |  6.44
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    5463 ave 5463 max 5463 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    115133 ave 115133 max 115133 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 460532
+Ave neighs/atom = 3.59791
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:00

bench/log.6Oct16.eam.fixed.icc.1

@@ -0,0 +1,83 @@
+LAMMPS (6 Oct 2016)
+# bulk Cu lattice
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		metal
+atom_style	atomic
+
+lattice		fcc 3.615
+Lattice spacing in x,y,z = 3.615 3.615 3.615
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+
+pair_style	eam
+pair_coeff	1 1 Cu_u3.eam
+Reading potential file Cu_u3.eam with DATE: 2007-06-11
+
+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		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.95
+  ghost atom cutoff = 5.95
+  binsize = 2.975 -> bins = 25 25 25
+Memory usage per processor = 11.2238 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1600      -113280            0   -106662.09    18703.573 
+      50    781.69049   -109873.35            0   -106640.13    52273.088 
+     100      801.832    -109957.3            0   -106640.77    51322.821 
+Loop time of 5.96529 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 7.242 ns/day, 3.314 hours/ns, 16.764 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.2743     | 5.2743     | 5.2743     |   0.0 | 88.42
+Neigh   | 0.59212    | 0.59212    | 0.59212    |   0.0 |  9.93
+Comm    | 0.030399   | 0.030399   | 0.030399   |   0.0 |  0.51
+Output  | 0.00026202 | 0.00026202 | 0.00026202 |   0.0 |  0.00
+Modify  | 0.050487   | 0.050487   | 0.050487   |   0.0 |  0.85
+Other   |            | 0.01776    |            |       |  0.30
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    19909 ave 19909 max 19909 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.20778e+06 ave 1.20778e+06 max 1.20778e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1207784
+Ave neighs/atom = 37.7433
+Neighbor list builds = 13
+Dangerous builds = 0
+Total wall time: 0:00:06

bench/log.6Oct16.eam.fixed.icc.4

@@ -0,0 +1,83 @@
+LAMMPS (6 Oct 2016)
+# bulk Cu lattice
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		metal
+atom_style	atomic
+
+lattice		fcc 3.615
+Lattice spacing in x,y,z = 3.615 3.615 3.615
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+
+pair_style	eam
+pair_coeff	1 1 Cu_u3.eam
+Reading potential file Cu_u3.eam with DATE: 2007-06-11
+
+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		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.95
+  ghost atom cutoff = 5.95
+  binsize = 2.975 -> bins = 25 25 25
+Memory usage per processor = 5.59629 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1600      -113280            0   -106662.09    18703.573 
+      50    781.69049   -109873.35            0   -106640.13    52273.088 
+     100      801.832    -109957.3            0   -106640.77    51322.821 
+Loop time of 1.64562 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 26.252 ns/day, 0.914 hours/ns, 60.767 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.408      | 1.4175     | 1.4341     |   0.9 | 86.14
+Neigh   | 0.15512    | 0.15722    | 0.16112    |   0.6 |  9.55
+Comm    | 0.029105   | 0.049986   | 0.061822   |   5.8 |  3.04
+Output  | 0.00010991 | 0.00011539 | 0.00012302 |   0.0 |  0.01
+Modify  | 0.013383   | 0.013573   | 0.013883   |   0.2 |  0.82
+Other   |            | 0.007264   |            |       |  0.44
+
+Nlocal:    8000 ave 8008 max 7993 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost:    9130.25 ave 9138 max 9122 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    301946 ave 302392 max 301360 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+
+Total # of neighbors = 1207784
+Ave neighs/atom = 37.7433
+Neighbor list builds = 13
+Dangerous builds = 0
+Total wall time: 0:00:01

bench/log.6Oct16.eam.scaled.icc.4

@@ -0,0 +1,83 @@
+LAMMPS (6 Oct 2016)
+# bulk Cu lattice
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*2
+variable	yy equal 20*$y
+variable	yy equal 20*2
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		metal
+atom_style	atomic
+
+lattice		fcc 3.615
+Lattice spacing in x,y,z = 3.615 3.615 3.615
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 40 0 ${yy} 0 ${zz}
+region		box block 0 40 0 40 0 ${zz}
+region		box block 0 40 0 40 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (144.6 144.6 72.3)
+  2 by 2 by 1 MPI processor grid
+create_atoms	1 box
+Created 128000 atoms
+
+pair_style	eam
+pair_coeff	1 1 Cu_u3.eam
+Reading potential file Cu_u3.eam with DATE: 2007-06-11
+
+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		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.95
+  ghost atom cutoff = 5.95
+  binsize = 2.975 -> bins = 49 49 25
+Memory usage per processor = 11.1402 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1600      -453120            0   -426647.73    18704.012 
+      50    779.50001   -439457.02            0   -426560.06    52355.276 
+     100    797.97828   -439764.76            0   -426562.07     51474.74 
+Loop time of 6.60121 on 4 procs for 100 steps with 128000 atoms
+
+Performance: 6.544 ns/day, 3.667 hours/ns, 15.149 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.6676     | 5.7011     | 5.7469     |   1.3 | 86.36
+Neigh   | 0.66423    | 0.67119    | 0.68082    |   0.7 | 10.17
+Comm    | 0.079367   | 0.13668    | 0.1791     |  10.5 |  2.07
+Output  | 0.00026989 | 0.00028622 | 0.00031209 |   0.1 |  0.00
+Modify  | 0.060046   | 0.062203   | 0.065009   |   0.9 |  0.94
+Other   |            | 0.02974    |            |       |  0.45
+
+Nlocal:    32000 ave 32092 max 31914 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Nghost:    19910 ave 19997 max 19818 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+Neighs:    1.20728e+06 ave 1.21142e+06 max 1.2036e+06 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+
+Total # of neighbors = 4829126
+Ave neighs/atom = 37.7275
+Neighbor list builds = 14
+Dangerous builds = 0
+Total wall time: 0:00:06

bench/log.6Oct16.lj.fixed.icc.1

@@ -0,0 +1,79 @@
+LAMMPS (6 Oct 2016)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+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		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4 -> bins = 24 24 24
+Memory usage per processor = 8.21387 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
+     100    0.7574531   -5.7585055            0   -4.6223613   0.20726105 
+Loop time of 2.26185 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 19099.377 tau/day, 44.212 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.9328     | 1.9328     | 1.9328     |   0.0 | 85.45
+Neigh   | 0.2558     | 0.2558     | 0.2558     |   0.0 | 11.31
+Comm    | 0.024061   | 0.024061   | 0.024061   |   0.0 |  1.06
+Output  | 0.00012612 | 0.00012612 | 0.00012612 |   0.0 |  0.01
+Modify  | 0.040887   | 0.040887   | 0.040887   |   0.0 |  1.81
+Other   |            | 0.008214   |            |       |  0.36
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    19657 ave 19657 max 19657 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.20283e+06 ave 1.20283e+06 max 1.20283e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1202833
+Ave neighs/atom = 37.5885
+Neighbor list builds = 5
+Dangerous builds not checked
+Total wall time: 0:00:02

bench/log.6Oct16.lj.fixed.icc.4

@@ -0,0 +1,79 @@
+LAMMPS (6 Oct 2016)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+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		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4 -> bins = 24 24 24
+Memory usage per processor = 4.09506 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
+     100    0.7574531   -5.7585055            0   -4.6223613   0.20726105 
+Loop time of 0.635957 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 67929.172 tau/day, 157.243 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.51335    | 0.51822    | 0.52569    |   0.7 | 81.49
+Neigh   | 0.063695   | 0.064309   | 0.065397   |   0.3 | 10.11
+Comm    | 0.027525   | 0.03629    | 0.041959   |   3.1 |  5.71
+Output  | 6.3896e-05 | 6.6698e-05 | 7.081e-05  |   0.0 |  0.01
+Modify  | 0.012472   | 0.01254    | 0.012618   |   0.1 |  1.97
+Other   |            | 0.004529   |            |       |  0.71
+
+Nlocal:    8000 ave 8037 max 7964 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost:    9007.5 ave 9050 max 8968 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+Neighs:    300708 ave 305113 max 297203 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+
+Total # of neighbors = 1202833
+Ave neighs/atom = 37.5885
+Neighbor list builds = 5
+Dangerous builds not checked
+Total wall time: 0:00:00

bench/log.6Oct16.lj.scaled.icc.4

@@ -0,0 +1,79 @@
+LAMMPS (6 Oct 2016)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*2
+variable	yy equal 20*$y
+variable	yy equal 20*2
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 40 0 ${yy} 0 ${zz}
+region		box block 0 40 0 40 0 ${zz}
+region		box block 0 40 0 40 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (67.1838 67.1838 33.5919)
+  2 by 2 by 1 MPI processor grid
+create_atoms	1 box
+Created 128000 atoms
+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		100
+Neighbor list info ...
+  1 neighbor list requests
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4 -> bins = 48 48 24
+Memory usage per processor = 8.13678 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -6.7733681            0   -4.6133849   -5.0196788 
+     100   0.75841891    -5.759957            0   -4.6223375   0.20008866 
+Loop time of 2.55762 on 4 procs for 100 steps with 128000 atoms
+
+Performance: 16890.677 tau/day, 39.099 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.0583     | 2.0988     | 2.1594     |   2.6 | 82.06
+Neigh   | 0.24411    | 0.24838    | 0.25585    |   0.9 |  9.71
+Comm    | 0.066397   | 0.13872    | 0.1863     |  11.9 |  5.42
+Output  | 0.00012994 | 0.00021023 | 0.00025702 |   0.3 |  0.01
+Modify  | 0.055533   | 0.058343   | 0.061791   |   1.2 |  2.28
+Other   |            | 0.0132     |            |       |  0.52
+
+Nlocal:    32000 ave 32060 max 31939 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Nghost:    19630.8 ave 19681 max 19562 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Neighs:    1.20195e+06 ave 1.20354e+06 max 1.19931e+06 min
+Histogram: 1 0 0 0 0 0 0 2 0 1
+
+Total # of neighbors = 4807797
+Ave neighs/atom = 37.5609
+Neighbor list builds = 5
+Dangerous builds not checked
+Total wall time: 0:00:02

bench/log.6Oct16.rhodo.fixed.icc.1

@@ -0,0 +1,122 @@
+LAMMPS (6 Oct 2016)
+# Rhodopsin model
+
+units           real
+neigh_modify    delay 5 every 1
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+pair_style      lj/charmm/coul/long 8.0 10.0
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data       data.rhodo
+  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  8 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  27723 bonds
+  reading angles ...
+  40467 angles
+  reading dihedrals ...
+  56829 dihedrals
+  reading impropers ...
+  1034 impropers
+  4 = max # of 1-2 neighbors
+  12 = max # of 1-3 neighbors
+  24 = max # of 1-4 neighbors
+  26 = max # of special neighbors
+
+fix             1 all shake 0.0001 5 0 m 1.0 a 232
+  1617 = # of size 2 clusters
+  3633 = # of size 3 clusters
+  747 = # of size 4 clusters
+  4233 = # of frozen angles
+fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
+
+special_bonds   charmm
+
+thermo          50
+thermo_style    multi
+timestep        2.0
+
+run		100
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
+  G vector (1/distance) = 0.248835
+  grid = 25 32 32
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0355478
+  estimated relative force accuracy = 0.000107051
+  using double precision FFTs
+  3d grid and FFT values/proc = 41070 25600
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6 -> bins = 10 13 13
+Memory usage per processor = 93.2721 Mbytes
+---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
+TotEng   =    -25356.2064 KinEng   =     21444.8313 Temp     =       299.0397 
+PotEng   =    -46801.0377 E_bond   =      2537.9940 E_angle  =     10921.3742 
+E_dihed  =      5211.7865 E_impro  =       213.5116 E_vdwl   =     -2307.8634 
+E_coul   =    207025.8927 E_long   =   -270403.7333 Press    =      -149.3301 
+Volume   =    307995.0335 
+---------------- Step       50 ----- CPU =     17.2007 (sec) ----------------
+TotEng   =    -25330.0321 KinEng   =     21501.0036 Temp     =       299.8230 
+PotEng   =    -46831.0357 E_bond   =      2471.7033 E_angle  =     10836.5108 
+E_dihed  =      5239.6316 E_impro  =       227.1219 E_vdwl   =     -1993.2763 
+E_coul   =    206797.6655 E_long   =   -270410.3927 Press    =       237.6866 
+Volume   =    308031.5640 
+---------------- Step      100 ----- CPU =     35.0315 (sec) ----------------
+TotEng   =    -25290.7387 KinEng   =     21591.9096 Temp     =       301.0906 
+PotEng   =    -46882.6484 E_bond   =      2567.9789 E_angle  =     10781.9556 
+E_dihed  =      5198.7493 E_impro  =       216.7863 E_vdwl   =     -1902.6458 
+E_coul   =    206659.5006 E_long   =   -270404.9733 Press    =         6.7898 
+Volume   =    308133.9933 
+Loop time of 35.0316 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 0.493 ns/day, 48.655 hours/ns, 2.855 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 25.021     | 25.021     | 25.021     |   0.0 | 71.42
+Bond    | 1.2834     | 1.2834     | 1.2834     |   0.0 |  3.66
+Kspace  | 3.2116     | 3.2116     | 3.2116     |   0.0 |  9.17
+Neigh   | 4.2767     | 4.2767     | 4.2767     |   0.0 | 12.21
+Comm    | 0.069283   | 0.069283   | 0.069283   |   0.0 |  0.20
+Output  | 0.00028205 | 0.00028205 | 0.00028205 |   0.0 |  0.00
+Modify  | 1.14       | 1.14       | 1.14       |   0.0 |  3.25
+Other   |            | 0.02938    |            |       |  0.08
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    47958 ave 47958 max 47958 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 12028098
+Ave neighs/atom = 375.878
+Ave special neighs/atom = 7.43187
+Neighbor list builds = 11
+Dangerous builds = 0
+Total wall time: 0:00:36

bench/log.6Oct16.rhodo.fixed.icc.4

@@ -0,0 +1,122 @@
+LAMMPS (6 Oct 2016)
+# Rhodopsin model
+
+units           real
+neigh_modify    delay 5 every 1
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+pair_style      lj/charmm/coul/long 8.0 10.0
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data       data.rhodo
+  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  8 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  27723 bonds
+  reading angles ...
+  40467 angles
+  reading dihedrals ...
+  56829 dihedrals
+  reading impropers ...
+  1034 impropers
+  4 = max # of 1-2 neighbors
+  12 = max # of 1-3 neighbors
+  24 = max # of 1-4 neighbors
+  26 = max # of special neighbors
+
+fix             1 all shake 0.0001 5 0 m 1.0 a 232
+  1617 = # of size 2 clusters
+  3633 = # of size 3 clusters
+  747 = # of size 4 clusters
+  4233 = # of frozen angles
+fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
+
+special_bonds   charmm
+
+thermo          50
+thermo_style    multi
+timestep        2.0
+
+run		100
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
+  G vector (1/distance) = 0.248835
+  grid = 25 32 32
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0355478
+  estimated relative force accuracy = 0.000107051
+  using double precision FFTs
+  3d grid and FFT values/proc = 13230 6400
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6 -> bins = 10 13 13
+Memory usage per processor = 37.3604 Mbytes
+---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
+TotEng   =    -25356.2064 KinEng   =     21444.8313 Temp     =       299.0397 
+PotEng   =    -46801.0377 E_bond   =      2537.9940 E_angle  =     10921.3742 
+E_dihed  =      5211.7865 E_impro  =       213.5116 E_vdwl   =     -2307.8634 
+E_coul   =    207025.8927 E_long   =   -270403.7333 Press    =      -149.3301 
+Volume   =    307995.0335 
+---------------- Step       50 ----- CPU =      4.6056 (sec) ----------------
+TotEng   =    -25330.0321 KinEng   =     21501.0036 Temp     =       299.8230 
+PotEng   =    -46831.0357 E_bond   =      2471.7033 E_angle  =     10836.5108 
+E_dihed  =      5239.6316 E_impro  =       227.1219 E_vdwl   =     -1993.2763 
+E_coul   =    206797.6655 E_long   =   -270410.3927 Press    =       237.6866 
+Volume   =    308031.5640 
+---------------- Step      100 ----- CPU =      9.3910 (sec) ----------------
+TotEng   =    -25290.7386 KinEng   =     21591.9096 Temp     =       301.0906 
+PotEng   =    -46882.6482 E_bond   =      2567.9789 E_angle  =     10781.9556 
+E_dihed  =      5198.7493 E_impro  =       216.7863 E_vdwl   =     -1902.6458 
+E_coul   =    206659.5007 E_long   =   -270404.9733 Press    =         6.7898 
+Volume   =    308133.9933 
+Loop time of 9.39107 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 1.840 ns/day, 13.043 hours/ns, 10.648 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 6.2189     | 6.3266     | 6.6072     |   6.5 | 67.37
+Bond    | 0.30793    | 0.32122    | 0.3414     |   2.4 |  3.42
+Kspace  | 0.87994    | 1.1644     | 1.2855     |  15.3 | 12.40
+Neigh   | 1.1358     | 1.136      | 1.1362     |   0.0 | 12.10
+Comm    | 0.08292    | 0.084935   | 0.087077   |   0.5 |  0.90
+Output  | 0.00015712 | 0.00016558 | 0.00018501 |   0.1 |  0.00
+Modify  | 0.33717    | 0.34246    | 0.34794    |   0.7 |  3.65
+Other   |            | 0.01526    |            |       |  0.16
+
+Nlocal:    8000 ave 8143 max 7933 min
+Histogram: 1 2 0 0 0 0 0 0 0 1
+Nghost:    22733.5 ave 22769 max 22693 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Neighs:    3.00702e+06 ave 3.0975e+06 max 2.96492e+06 min
+Histogram: 1 2 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 12028098
+Ave neighs/atom = 375.878
+Ave special neighs/atom = 7.43187
+Neighbor list builds = 11
+Dangerous builds = 0
+Total wall time: 0:00:09

bench/log.6Oct16.rhodo.scaled.icc.4

@@ -0,0 +1,143 @@
+LAMMPS (6 Oct 2016)
+# Rhodopsin model
+
+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 8.0 10.0
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data       data.rhodo
+  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  8 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  27723 bonds
+  reading angles ...
+  40467 angles
+  reading dihedrals ...
+  56829 dihedrals
+  reading impropers ...
+  1034 impropers
+  4 = max # of 1-2 neighbors
+  12 = max # of 1-3 neighbors
+  24 = max # of 1-4 neighbors
+  26 = max # of special neighbors
+
+replicate	$x $y $z
+replicate	2 $y $z
+replicate	2 2 $z
+replicate	2 2 1
+  orthogonal box = (-27.5 -38.5 -36.3646) to (82.5 115.5 36.3615)
+  2 by 2 by 1 MPI processor grid
+  128000 atoms
+  110892 bonds
+  161868 angles
+  227316 dihedrals
+  4136 impropers
+  4 = max # of 1-2 neighbors
+  12 = max # of 1-3 neighbors
+  24 = max # of 1-4 neighbors
+  26 = max # of special neighbors
+
+fix             1 all shake 0.0001 5 0 m 1.0 a 232
+  6468 = # of size 2 clusters
+  14532 = # of size 3 clusters
+  2988 = # of size 4 clusters
+  16932 = # of frozen angles
+fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
+
+special_bonds   charmm
+
+thermo          50
+thermo_style    multi
+timestep        2.0
+
+run		100
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
+  G vector (1/distance) = 0.248593
+  grid = 48 60 36
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0359793
+  estimated relative force accuracy = 0.00010835
+  using double precision FFTs
+  3d grid and FFT values/proc = 41615 25920
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6 -> bins = 19 26 13
+Memory usage per processor = 96.9597 Mbytes
+---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
+TotEng   =   -101425.4887 KinEng   =     85779.3251 Temp     =       299.0304 
+PotEng   =   -187204.8138 E_bond   =     10151.9760 E_angle  =     43685.4968 
+E_dihed  =     20847.1460 E_impro  =       854.0463 E_vdwl   =     -9231.4537 
+E_coul   =    827053.5824 E_long   =  -1080565.6077 Press    =      -149.0358 
+Volume   =   1231980.1340 
+---------------- Step       50 ----- CPU =     18.1689 (sec) ----------------
+TotEng   =   -101320.0211 KinEng   =     86003.4933 Temp     =       299.8118 
+PotEng   =   -187323.5144 E_bond   =      9887.1189 E_angle  =     43346.8448 
+E_dihed  =     20958.7108 E_impro  =       908.4721 E_vdwl   =     -7973.4486 
+E_coul   =    826141.5493 E_long   =  -1080592.7617 Press    =       238.0404 
+Volume   =   1232126.1814 
+---------------- Step      100 ----- CPU =     37.2027 (sec) ----------------
+TotEng   =   -101157.9546 KinEng   =     86355.7413 Temp     =       301.0398 
+PotEng   =   -187513.6959 E_bond   =     10272.0456 E_angle  =     43128.7018 
+E_dihed  =     20794.0107 E_impro  =       867.0928 E_vdwl   =     -7587.2409 
+E_coul   =    825584.2416 E_long   =  -1080572.5474 Press    =        15.1729 
+Volume   =   1232535.8440 
+Loop time of 37.2028 on 4 procs for 100 steps with 128000 atoms
+
+Performance: 0.464 ns/day, 51.671 hours/ns, 2.688 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 25.431     | 25.738     | 25.984     |   4.0 | 69.18
+Bond    | 1.2966     | 1.3131     | 1.3226     |   0.9 |  3.53
+Kspace  | 3.7563     | 4.0123     | 4.3127     |  10.0 | 10.79
+Neigh   | 4.3778     | 4.378      | 4.3782     |   0.0 | 11.77
+Comm    | 0.1903     | 0.19549    | 0.20485    |   1.3 |  0.53
+Output  | 0.00031805 | 0.00037521 | 0.00039601 |   0.2 |  0.00
+Modify  | 1.4861     | 1.5051     | 1.5122     |   0.9 |  4.05
+Other   |            | 0.05992    |            |       |  0.16
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    47957 ave 47957 max 47957 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    1.20281e+07 ave 1.20572e+07 max 1.19991e+07 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 48112540
+Ave neighs/atom = 375.879
+Ave special neighs/atom = 7.43187
+Neighbor list builds = 11
+Dangerous builds = 0
+Total wall time: 0:00:38

cmake/CMakeLists.txt

@@ -0,0 +1,732 @@
+########################################
+# CMake build system
+# This file is part of LAMMPS
+# Created by Christoph Junghans and Richard Berger
+cmake_minimum_required(VERSION 3.1)
+
+project(lammps)
+set(SOVERSION 0)
+set(LAMMPS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../src)
+set(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib)
+set(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib)
+
+#To not conflict with old Makefile build system, we build everything here
+file(GLOB LIB_SOURCES ${LAMMPS_SOURCE_DIR}/*.cpp)
+file(GLOB LMP_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
+list(REMOVE_ITEM LIB_SOURCES ${LMP_SOURCES})
+
+# Cmake modules/macros are in a subdirectory to keep this file cleaner
+set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules)
+
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
+  #release comes with -O3 by default
+  set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
+endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
+
+# remove any style headers in the src dir
+file(GLOB SRC_STYLE_FILES ${LAMMPS_SOURCE_DIR}/style_*.h)
+if(SRC_STYLE_FILES)
+  file(REMOVE ${SRC_STYLE_FILES})
+endif()
+
+enable_language(CXX)
+
+######################################################################
+# compiler tests
+# these need ot be done early (before further tests).
+#####################################################################
+include(CheckCCompilerFlag)
+
+if (${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
+  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
+endif()
+
+########################################################################
+# User input options                                                   #
+########################################################################
+option(BUILD_SHARED_LIBS "Build shared libs" OFF)
+if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
+  set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+endif()
+include(GNUInstallDirs)
+
+set(LAMMPS_LINK_LIBS)
+set(LAMMPS_DEPS)
+set(LAMMPS_API_DEFINES)
+option(ENABLE_MPI "Build MPI version" OFF)
+if(ENABLE_MPI)
+  find_package(MPI REQUIRED)
+  include_directories(${MPI_C_INCLUDE_PATH})
+  list(APPEND LAMMPS_LINK_LIBS ${MPI_CXX_LIBRARIES})
+  option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
+  if(LAMMPS_LONGLONG_TO_LONG)
+    add_definitions(-DLAMMPS_LONGLONG_TO_LONG)
+  endif()
+else()
+  file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
+  add_library(mpi_stubs STATIC ${MPI_SOURCES})
+  include_directories(${LAMMPS_SOURCE_DIR}/STUBS)
+  list(APPEND LAMMPS_LINK_LIBS mpi_stubs)
+endif()
+
+set(LAMMPS_SIZE_LIMIT "LAMMPS_SMALLBIG" CACHE STRING "Lammps size limit")
+set_property(CACHE LAMMPS_SIZE_LIMIT PROPERTY STRINGS LAMMPS_SMALLBIG LAMMPS_BIGBIG LAMMPS_SMALLSMALL)
+add_definitions(-D${LAMMPS_SIZE_LIMIT})
+set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${LAMMPS_SIZE_LIMIT}")
+
+set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS")
+add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
+
+option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)
+if(LAMMPS_EXCEPTIONS)
+  add_definitions(-DLAMMPS_EXCEPTIONS)
+  set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -DLAMMPS_EXCEPTIONS")
+endif()
+
+set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary and liblammps (WON'T enable any features automatically")
+mark_as_advanced(LAMMPS_MACHINE)
+if(LAMMPS_MACHINE)
+  set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}")
+endif()
+
+option(CMAKE_VERBOSE_MAKEFILE "Verbose makefile" OFF)
+
+option(ENABLE_TESTING "Enable testing" OFF)
+if(ENABLE_TESTING)
+  enable_testing()
+endif(ENABLE_TESTING)
+
+option(ENABLE_ALL "Build all default packages" OFF)
+set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR
+  KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ
+  REAX REPLICA RIGID SHOCK SNAP SRD)
+set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE
+  USER-ATC USER-AWPMD USER-CGDNA USER-MESO
+  USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
+  USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
+  USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
+  USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
+set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
+foreach(PKG ${DEFAULT_PACKAGES})
+  option(ENABLE_${PKG} "Build ${PKG} Package" ${ENABLE_ALL})
+endforeach()
+foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
+  option(ENABLE_${PKG} "Build ${PKG} Package" OFF)
+endforeach()
+
+macro(pkg_depends PKG1 PKG2)
+  if(ENABLE_${PKG1} AND NOT ENABLE_${PKG2})
+    message(FATAL_ERROR "${PKG1} package needs LAMMPS to be build with ${PKG2}")
+  endif()
+endmacro()
+
+pkg_depends(MPIIO MPI)
+pkg_depends(QEQ MANYBODY)
+pkg_depends(USER-ATC MANYBODY)
+pkg_depends(USER-H5MD MPI)
+pkg_depends(USER-LB MPI)
+pkg_depends(USER-MISC MANYBODY)
+pkg_depends(USER-PHONON KSPACE)
+
+if(ENABLE_BODY AND ENABLE_POEMS)
+  message(FATAL_ERROR "BODY and POEMS cannot be enabled at the same time")
+endif()
+
+######################################################
+# packages with special compiler needs or external libs
+######################################################
+if(ENABLE_REAX OR ENABLE_MEAM OR ENABLE_USER-QUIP OR ENABLE_USER-QMMM OR ENABLE_LATTE)
+  enable_language(Fortran)
+  include(CheckFortranCompilerFlag)
+  check_Fortran_compiler_flag("-fno-second-underscore" FC_HAS_NO_SECOND_UNDERSCORE)
+endif()
+
+if(ENABLE_KOKKOS OR ENABLE_MSCG)
+  # starting with CMake 3.1 this is all you have to do to enforce C++11
+  set(CMAKE_CXX_STANDARD 11) # C++11...
+  set(CMAKE_CXX_STANDARD_REQUIRED ON) #...is required...
+  set(CMAKE_CXX_EXTENSIONS OFF) #...without compiler extensions like gnu++11
+endif()
+
+if(ENABLE_USER-OMP OR ENABLE_KOKKOS OR ENABLE_USER-INTEL)
+  find_package(OpenMP REQUIRED)
+  set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
+  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
+endif()
+
+if(ENABLE_KSPACE)
+  set(FFT "KISSFFT" CACHE STRING "FFT library for KSPACE package")
+  set_property(CACHE FFT PROPERTY STRINGS KISSFFT FFTW3 MKL FFTW2)
+  if(NOT FFT STREQUAL "KISSFFT")
+    find_package(${FFT} REQUIRED)
+    add_definitions(-DFFT_${FFT})
+    include_directories(${${FFT}_INCLUDE_DIRS})
+    list(APPEND LAMMPS_LINK_LIBS ${${FFT}_LIBRARIES})
+  endif()
+  set(PACK_OPTIMIZATION "PACK_ARRAY" CACHE STRING "Optimization for FFT")
+  set_property(CACHE PACK_OPTIMIZATION PROPERTY STRINGS PACK_ARRAY PACK_POINTER PACK_MEMCPY)
+  if(NOT PACK_OPTIMIZATION STREQUAL "PACK_ARRAY")
+    add_definitions(-D${PACK_OPTIMIZATION})
+  endif()
+endif()
+
+if(ENABLE_MSCG OR ENABLE_USER-ATC OR ENABLE_USER-AWPMD OR ENABLE_USER-QUIP OR ENABLE_LATTE)
+  find_package(LAPACK)
+  if(NOT LAPACK_FOUND)
+    enable_language(Fortran)
+    file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.f)
+    add_library(linalg STATIC ${LAPACK_SOURCES})
+    include(CheckFortranCompilerFlag)
+    check_Fortran_compiler_flag("-fno-second-underscore" FC_HAS_NO_SECOND_UNDERSCORE)
+    if(FC_HAS_NO_SECOND_UNDERSCORE)
+      target_compile_options(linalg PRIVATE -fno-second-underscore)
+    endif()
+    set(LAPACK_LIBRARIES linalg)
+  endif()
+endif()
+
+if(ENABLE_PYTHON)
+  find_package(PythonInterp REQUIRED)
+  find_package(PythonLibs REQUIRED)
+  add_definitions(-DLMP_PYTHON)
+  include_directories(${PYTHON_INCLUDE_DIR})
+  list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY})
+  if(BUILD_SHARED_LIBS)
+    if(NOT PYTHON_INSTDIR)
+      execute_process(COMMAND ${PYTHON_EXECUTABLE}
+        -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
+        OUTPUT_VARIABLE PYTHON_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
+    endif()
+    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})
+  endif()
+endif()
+
+find_package(JPEG)
+if(JPEG_FOUND)
+  add_definitions(-DLAMMPS_JPEG)
+  include_directories(${JPEG_INCLUDE_DIR})
+  list(APPEND LAMMPS_LINK_LIBS ${JPEG_LIBRARIES})
+endif()
+
+find_package(PNG)
+find_package(ZLIB)
+if(PNG_FOUND AND ZLIB_FOUND)
+  include_directories(${PNG_INCLUDE_DIRS} ${ZLIB_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS ${PNG_LIBRARIES} ${ZLIB_LIBRARIES})
+  add_definitions(-DLAMMPS_PNG)
+endif()
+
+find_program(GZIP_EXECUTABLE gzip)
+find_package_handle_standard_args(GZIP REQUIRED_VARS GZIP_EXECUTABLE)
+if(GZIP_FOUND)
+  add_definitions(-DLAMMPS_GZIP)
+endif()
+
+find_program(FFMPEG_EXECUTABLE ffmpeg)
+find_package_handle_standard_args(FFMPEG REQUIRED_VARS FFMPEG_EXECUTABLE)
+if(FFMPEG_FOUND)
+  add_definitions(-DLAMMPS_FFMPEG)
+endif()
+
+if(ENABLE_VORONOI)
+  find_package(VORO REQUIRED) #some distros
+  include_directories(${VORO_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS ${VORO_LIBRARIES})
+endif()
+
+if(ENABLE_LATTE)
+  find_package(LATTE QUIET)
+  if(NOT LATTE_FOUND)
+    message(STATUS "LATTE not found - we will build our own")
+    include(ExternalProject)
+    ExternalProject_Add(latte_build
+      URL https://github.com/lanl/LATTE/archive/v1.0.1.tar.gz
+      URL_MD5 5137e28cb1a64444bd571c98c98a6eee
+      SOURCE_SUBDIR cmake
+      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE}
+      )
+    ExternalProject_get_property(latte_build INSTALL_DIR)
+    set(LATTE_LIBRARIES ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/liblatte.a)
+    list(APPEND LAMMPS_DEPS latte_build)
+  endif()
+  list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+endif()
+
+if(ENABLE_USER-MOLFILE)
+  add_library(molfile INTERFACE)
+  target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile)
+  target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
+  list(APPEND LAMMPS_LINK_LIBS molfile)
+endif()
+
+if(ENABLE_USER-NETCDF)
+  find_package(NetCDF REQUIRED)
+  include_directories(NETCDF_INCLUDE_DIR)
+  list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARY})
+  add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
+endif()
+
+if(ENABLE_USER-SMD)
+  find_package(Eigen3 REQUIRED)
+  include_directories(${EIGEN3_INCLUDE_DIR})
+endif()
+
+if(ENABLE_USER-QUIP)
+  find_package(QUIP REQUIRED)
+  list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+endif()
+
+if(ENABLE_USER-QMMM)
+  find_package(QE REQUIRED)
+  include_directories(${QE_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+endif()
+
+if(ENABLE_USER-VTK)
+  find_package(VTK REQUIRED NO_MODULE)
+  include(${VTK_USE_FILE})
+  add_definitions(-DLAMMPS_VTK)
+  list(APPEND LAMMPS_LINK_LIBS ${VTK_LIBRARIES})
+endif()
+
+if(ENABLE_KIM)
+  find_package(KIM REQUIRED)
+  list(APPEND LAMMPS_LINK_LIBS ${KIM_LIBRARIES})
+  include_directories(${KIM_INCLUDE_DIRS})
+endif()
+
+if(ENABLE_MSCG)
+  find_package(GSL REQUIRED)
+  set(LAMMPS_LIB_MSCG_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/mscg)
+  set(MSCG_TARBALL ${LAMMPS_LIB_MSCG_BIN_DIR}/MS-CG-master.zip)
+  set(LAMMPS_LIB_MSCG_BIN_DIR ${LAMMPS_LIB_MSCG_BIN_DIR}/MSCG-release-master/src)
+  if(NOT EXISTS ${LAMMPS_LIB_MSCG_BIN_DIR})
+    if(NOT EXISTS ${MSCG_TARBALL})
+      message(STATUS "Downloading ${MSCG_TARBALL}")
+      file(DOWNLOAD
+        https://github.com/uchicago-voth/MSCG-release/archive/master.zip
+        ${MSCG_TARBALL} SHOW_PROGRESS) #EXPECTED_MD5 cannot be due due to master
+    endif()
+    message(STATUS "Unpacking ${MSCG_TARBALL}")
+    execute_process(COMMAND ${CMAKE_COMMAND} -E tar xvf ${MSCG_TARBALL}
+      WORKING_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/mscg)
+  endif()
+  file(GLOB MSCG_SOURCES ${LAMMPS_LIB_MSCG_BIN_DIR}/*.cpp)
+  add_library(mscg STATIC ${MSCG_SOURCES})
+  list(APPEND LAMMPS_LINK_LIBS mscg)
+  target_compile_options(mscg PRIVATE -DDIMENSION=3 -D_exclude_gromacs=1)
+  target_include_directories(mscg PUBLIC ${LAMMPS_LIB_MSCG_BIN_DIR})
+  target_link_libraries(mscg ${GSL_LIBRARIES} ${LAPACK_LIBRARIES})
+endif()
+
+########################################################################
+# Basic system tests (standard libraries, headers, functions, types)   #
+########################################################################
+include(CheckIncludeFile)
+foreach(HEADER math.h)
+  check_include_file(${HEADER} FOUND_${HEADER})
+  if(NOT FOUND_${HEADER})
+    message(FATAL_ERROR "Could not find needed header - ${HEADER}")
+  endif(NOT FOUND_${HEADER})
+endforeach(HEADER)
+
+set(MATH_LIBRARIES "m" CACHE STRING "math library")
+mark_as_advanced( MATH_LIBRARIES )
+include(CheckLibraryExists)
+foreach(FUNC sin cos)
+  check_library_exists(${MATH_LIBRARIES} ${FUNC} "" FOUND_${FUNC}_${MATH_LIBRARIES})
+  if(NOT FOUND_${FUNC}_${MATH_LIBRARIES})
+    message(FATAL_ERROR "Could not find needed math function - ${FUNC}")
+  endif(NOT FOUND_${FUNC}_${MATH_LIBRARIES})
+endforeach(FUNC)
+list(APPEND LAMMPS_LINK_LIBS ${MATH_LIBRARIES})
+
+######################################
+# Generate Basic Style files
+######################################
+include(StyleHeaderUtils)
+RegisterStyles(${LAMMPS_SOURCE_DIR})
+
+##############################################
+# add sources of enabled packages
+############################################
+foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES})
+  set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
+
+  # ignore PKG files which were manually installed in src folder
+  # headers are ignored during RegisterStyles
+  file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp)
+  file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/*.h)
+
+  foreach(PKG_FILE in ${${PKG}_SOURCES})
+      get_filename_component(FNAME ${PKG_FILE} NAME)
+      list(REMOVE_ITEM LIB_SOURCES ${LAMMPS_SOURCE_DIR}/${FNAME})
+  endforeach()
+
+  foreach(PKG_FILE in ${${PKG}_HEADERS})
+      get_filename_component(FNAME ${PKG_FILE} NAME)
+      DetectAndRemovePackageHeader(${LAMMPS_SOURCE_DIR}/${FNAME})
+  endforeach()
+
+  if(ENABLE_${PKG})
+    # detects styles in package and adds them to global list
+    RegisterStyles(${${PKG}_SOURCES_DIR})
+
+    list(APPEND LIB_SOURCES ${${PKG}_SOURCES})
+    include_directories(${${PKG}_SOURCES_DIR})
+  endif()
+endforeach()
+
+##############################################
+# add lib sources of (simple) enabled packages
+############################################
+foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
+  USER-QMMM)
+  if(ENABLE_${SIMPLE_LIB})
+    string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
+    string(TOLOWER "${PKG_LIB}" PKG_LIB)
+    file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.F
+      ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.c ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.cpp)
+    add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
+    list(APPEND LAMMPS_LINK_LIBS ${PKG_LIB})
+    if(PKG_LIB STREQUAL awpmd)
+      target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include)
+    elseif(PKG_LIB STREQUAL h5md)
+      target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include)
+    elseif(PKG_LIB STREQUAL colvars)
+      target_compile_options(colvars PRIVATE -DLEPTON)
+      target_include_directories(colvars PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton/include)
+      target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
+    else()
+      target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB})
+    endif()
+  endif()
+endforeach()
+
+if(ENABLE_USER-AWPMD)
+  target_link_libraries(awpmd ${LAPACK_LIBRARIES})
+endif()
+
+if(ENABLE_USER-ATC)
+  target_link_libraries(atc ${LAPACK_LIBRARIES})
+endif()
+
+if(ENABLE_USER-H5MD)
+  find_package(HDF5 REQUIRED)
+  target_link_libraries(h5md ${HDF5_LIBRARIES})
+  target_include_directories(h5md PRIVATE ${HDF5_INCLUDE_DIRS})
+endif()
+
+if(ENABLE_MEAM AND FC_HAS_NO_SECOND_UNDERSCORE)
+  foreach(FSRC ${meam_SOURCES})
+    string(REGEX REPLACE "^.*\\." "" FEXT "${FSRC}")
+    list(FIND CMAKE_Fortran_SOURCE_FILE_EXTENSIONS "${FEXT}" FINDEX)
+    if(FINDEX GREATER -1)
+      set_property(SOURCE ${FSRC} APPEND PROPERTY COMPILE_FLAGS "-fno-second-underscore")
+    endif()
+  endforeach()
+endif()
+
+if(ENABLE_REAX AND FC_HAS_NO_SECOND_UNDERSCORE)
+  target_compile_options(reax PRIVATE -fno-second-underscore)
+endif()
+
+
+######################################################################
+# packages which selectively include variants based on enabled styles
+# e.g. accelerator packages
+######################################################################
+if(ENABLE_USER-OMP)
+    set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP)
+    set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
+                         ${USER-OMP_SOURCES_DIR}/thr_omp.cpp
+                         ${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp
+                         ${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp)
+    set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}")
+
+    # detects styles which have USER-OMP version
+    RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
+
+    get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
+
+    list(APPEND LIB_SOURCES ${USER-OMP_SOURCES})
+    include_directories(${USER-OMP_SOURCES_DIR})
+endif()
+
+if(ENABLE_KOKKOS)
+  set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
+  set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
+  add_definitions(-DLMP_KOKKOS)
+  add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
+
+  set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
+                          ${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
+                          ${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src
+                          ${LAMMPS_LIB_KOKKOS_BIN_DIR})
+  include_directories(${Kokkos_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS kokkos)
+
+  set(KOKKOS_PKG_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/KOKKOS)
+  set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/atom_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/neighbor_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/neigh_list_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/neigh_bond_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/fix_nh_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
+  set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
+
+  # detects styles which have KOKKOS version
+  RegisterStylesExt(${KOKKOS_PKG_SOURCES_DIR} kokkos KOKKOS_PKG_SOURCES)
+
+  # register kokkos-only styles
+  RegisterNBinStyle(${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.h)
+  RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.h)
+
+  if(ENABLE_USER-DPD)
+    get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
+    list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.cpp)
+    RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.h)
+    set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
+  endif()
+
+  get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
+
+  list(APPEND LIB_SOURCES ${KOKKOS_PKG_SOURCES})
+  include_directories(${KOKKOS_PKG_SOURCES_DIR})
+endif()
+
+if(ENABLE_OPT)
+    set(OPT_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/OPT)
+    set(OPT_SOURCES)
+    set_property(GLOBAL PROPERTY "OPT_SOURCES" "${OPT_SOURCES}")
+
+    # detects styles which have OPT version
+    RegisterStylesExt(${OPT_SOURCES_DIR} opt OPT_SOURCES)
+
+    get_property(OPT_SOURCES GLOBAL PROPERTY OPT_SOURCES)
+
+    list(APPEND LIB_SOURCES ${OPT_SOURCES})
+    include_directories(${OPT_SOURCES_DIR})
+endif()
+
+if(ENABLE_USER-INTEL)
+    set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
+    set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/intel_preprocess.h
+                           ${USER-INTEL_SOURCES_DIR}/intel_buffers.h
+                           ${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp
+                           ${USER-INTEL_SOURCES_DIR}/math_extra_intel.h
+                           ${USER-INTEL_SOURCES_DIR}/nbin_intel.h
+                           ${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp
+                           ${USER-INTEL_SOURCES_DIR}/npair_intel.h
+                           ${USER-INTEL_SOURCES_DIR}/npair_intel.cpp
+                           ${USER-INTEL_SOURCES_DIR}/intel_simd.h
+                           ${USER-INTEL_SOURCES_DIR}/intel_intrinsics.h)
+
+    set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")
+
+    # detects styles which have USER-INTEL version
+    RegisterStylesExt(${USER-INTEL_SOURCES_DIR} opt USER-INTEL_SOURCES)
+
+    get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES)
+
+    list(APPEND LIB_SOURCES ${USER-INTEL_SOURCES})
+    include_directories(${USER-INTEL_SOURCES_DIR})
+endif()
+
+if(ENABLE_GPU)
+    set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
+    set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
+                    ${GPU_SOURCES_DIR}/fix_gpu.h
+                    ${GPU_SOURCES_DIR}/fix_gpu.cpp)
+
+    set(GPU_API "OpenCL" CACHE STRING "API used by GPU package")
+    set_property(CACHE GPU_API PROPERTY STRINGS OpenCL CUDA)
+
+    set(GPU_PREC "SINGLE_DOUBLE" CACHE STRING "LAMMPS GPU precision size")
+    set_property(CACHE GPU_PREC PROPERTY STRINGS SINGLE_DOUBLE SINGLE_SINGLE DOUBLE_DOUBLE)
+
+    file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cpp)
+    file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
+
+    if(GPU_API STREQUAL "CUDA")
+      find_package(CUDA REQUIRED)
+      find_program(BIN2C bin2c)
+      if(NOT BIN2C)
+        message(FATAL_ERROR "Couldn't find bin2c, use -DBIN2C helping cmake to find it.")
+      endif()
+      option(CUDPP_OPT "Enable CUDPP_OPT" ON)
+
+      set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM architecture")
+      set_property(CACHE GPU_ARCH PROPERTY STRINGS sm_10 sm_20 sm_30 sm_60)
+
+      file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/*.cu)
+      list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
+
+      cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
+
+      if(CUDPP_OPT)
+        cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
+        file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cpp)
+        file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cu)
+      endif()
+
+      cuda_compile_cubin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
+                   -DUNIX -O3 -Xptxas -v --use_fast_math -DNV_KERNEL -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC})
+
+      cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS $<$<BOOL:${BUILD_SHARED_LIBS}>:-Xcompiler=-fPIC>
+                   -DUNIX -O3 -Xptxas -v --use_fast_math -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC})
+
+      foreach(CU_OBJ ${GPU_GEN_OBJS})
+        get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
+        string(REGEX REPLACE "^.*_lal_" "" CU_NAME "${CU_NAME}")
+        add_custom_command(OUTPUT ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
+          COMMAND ${BIN2C} -c -n ${CU_NAME} ${CU_OBJ} > ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
+          DEPENDS ${CU_OBJ}
+          COMMENT "Generating ${CU_NAME}_cubin.h")
+        list(APPEND GPU_LIB_SOURCES ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h)
+      endforeach()
+      set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "${LAMMPS_LIB_BINARY_DIR}/gpu/*_cubin.h")
+
+
+      add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
+      target_link_libraries(gpu ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
+      target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
+      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC} -DMPI_GERYON -DUCL_NO_EXIT)
+      if(CUDPP_OPT)
+        target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
+        target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
+      endif()
+
+      list(APPEND LAMMPS_LINK_LIBS gpu)
+
+      add_executable(nvc_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
+      target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR)
+      target_link_libraries(nvc_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
+      target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
+
+
+    elseif(GPU_API STREQUAL "OpenCL")
+      find_package(OpenCL REQUIRED)
+      set(OCL_TUNE "GENERIC" CACHE STRING "OpenCL Device Tuning")
+      set_property(CACHE OCL_TUNE PROPERTY STRINGS INTEL FERMI KEPLER CYPRESS GENERIC)
+
+      include(OpenCLUtils)
+      set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
+
+      file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu)
+      list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu)
+
+      foreach(GPU_KERNEL ${GPU_LIB_CU})
+          get_filename_component(basename ${GPU_KERNEL} NAME_WE)
+          string(SUBSTRING ${basename} 4 -1 KERNEL_NAME)
+          GenerateOpenCLHeader(${KERNEL_NAME} ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h ${OCL_COMMON_HEADERS} ${GPU_KERNEL})
+          list(APPEND GPU_LIB_SOURCES ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h)
+      endforeach()
+
+      GenerateOpenCLHeader(gayberne ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu)
+      GenerateOpenCLHeader(gayberne_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu)
+      list(APPEND GPU_LIB_SOURCES ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h)
+
+      add_library(gpu STATIC ${GPU_LIB_SOURCES})
+      target_link_libraries(gpu ${OpenCL_LIBRARIES})
+      target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu ${OpenCL_INCLUDE_DIRS})
+      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC} -DMPI_GERYON -DUCL_NO_EXIT)
+      target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
+
+      list(APPEND LAMMPS_LINK_LIBS gpu)
+
+      add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
+      target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL)
+      target_link_libraries(ocl_get_devices PRIVATE ${OpenCL_LIBRARIES})
+      target_include_directories(ocl_get_devices PRIVATE ${OpenCL_INCLUDE_DIRS})
+    endif()
+
+    # GPU package
+    FindStyleHeaders(${GPU_SOURCES_DIR} FIX_CLASS fix_ FIX)
+
+    set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
+
+    # detects styles which have GPU version
+    RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)
+
+    get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
+
+    list(APPEND LIB_SOURCES ${GPU_SOURCES})
+    include_directories(${GPU_SOURCES_DIR})
+endif()
+
+######################################################
+# Generate style headers based on global list of
+# styles registered during package selection
+######################################################
+set(LAMMPS_STYLE_HEADERS_DIR ${CMAKE_CURRENT_BINARY_DIR}/styles)
+
+GenerateStyleHeaders(${LAMMPS_STYLE_HEADERS_DIR})
+
+include_directories(${LAMMPS_SOURCE_DIR})
+include_directories(${LAMMPS_STYLE_HEADERS_DIR})
+
+###########################################
+# Actually add executable and lib to build
+############################################
+add_library(lammps ${LIB_SOURCES})
+target_link_libraries(lammps ${LAMMPS_LINK_LIBS})
+if(LAMMPS_DEPS)
+  add_dependencies(lammps ${LAMMPS_DEPS})
+endif()
+set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
+if(BUILD_SHARED_LIBS)
+  set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
+  install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+  install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
+  configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
+  install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+endif()
+
+add_executable(lmp ${LMP_SOURCES})
+target_link_libraries(lmp lammps)
+set_target_properties(lmp PROPERTIES OUTPUT_NAME lmp${LAMMPS_MACHINE})
+install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
+if(ENABLE_TESTING)
+  add_test(ShowHelp lmp${LAMMPS_MACHINE} -help)
+endif()
+
+##################################
+# Print package summary
+##################################
+foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES} ${ACCEL_PACKAGES})
+  if(ENABLE_${PKG})
+    message(STATUS "Building package: ${PKG}")
+  endif()
+endforeach()
+
+string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
+message(STATUS "<<< Build configuration >>>
+   Build type       ${CMAKE_BUILD_TYPE}
+   Install path     ${CMAKE_INSTALL_PREFIX}
+   Compilers and Flags:
+   C++ Compiler     ${CMAKE_CXX_COMPILER}
+       Type         ${CMAKE_CXX_COMPILER_ID}
+   C++ Flags        ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
+get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
+if(LANGUAGES MATCHES ".*Fortran.*")
+  message(STATUS "Fortran Compiler ${CMAKE_Fortran_COMPILER} 
+           Type     ${CMAKE_Fortran_COMPILER_ID}
+   Fortran Flags    ${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}")
+endif()
+message(STATUS "Linker flags:
+   Executable      ${CMAKE_EXE_LINKER_FLAGS}")
+if(BUILD_SHARED_LIBS)
+  message(STATUS "Shared libries  ${CMAKE_SHARED_LINKER_FLAGS}")
+else()
+  message(STATUS "Static libries  ${CMAKE_STATIC_LINKER_FLAGS}")
+endif()
+message(STATUS "Link libraries: ${LAMMPS_LINK_LIBS}")
+

cmake/Modules/FindFFTW2.cmake

@@ -0,0 +1,22 @@
+# - Find fftw2
+# Find the native FFTW2 headers and libraries.
+#
+#  FFTW2_INCLUDE_DIRS - where to find fftw2.h, etc.
+#  FFTW2_LIBRARIES    - List of libraries when using fftw2.
+#  FFTW2_FOUND        - True if fftw2 found.
+#
+
+find_path(FFTW2_INCLUDE_DIR fftw.h)
+
+find_library(FFTW2_LIBRARY NAMES fftw)
+
+set(FFTW2_LIBRARIES ${FFTW2_LIBRARY})
+set(FFTW2_INCLUDE_DIRS ${FFTW2_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set FFTW2_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(FFTW2 DEFAULT_MSG FFTW2_LIBRARY FFTW2_INCLUDE_DIR)
+
+mark_as_advanced(FFTW2_INCLUDE_DIR FFTW2_LIBRARY )

cmake/Modules/FindFFTW3.cmake

@@ -0,0 +1,25 @@
+# - Find fftw3
+# Find the native FFTW3 headers and libraries.
+#
+#  FFTW3_INCLUDE_DIRS - where to find fftw3.h, etc.
+#  FFTW3_LIBRARIES    - List of libraries when using fftw3.
+#  FFTW3_FOUND        - True if fftw3 found.
+#
+
+find_package(PkgConfig)
+
+pkg_check_modules(PC_FFTW3 fftw3)
+find_path(FFTW3_INCLUDE_DIR fftw3.h HINTS ${PC_FFTW3_INCLUDE_DIRS})
+
+find_library(FFTW3_LIBRARY NAMES fftw3 HINTS ${PC_FFTW3_LIBRARY_DIRS})
+
+set(FFTW3_LIBRARIES ${FFTW3_LIBRARY})
+set(FFTW3_INCLUDE_DIRS ${FFTW3_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set FFTW3_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(FFTW3 DEFAULT_MSG FFTW3_LIBRARY FFTW3_INCLUDE_DIR)
+
+mark_as_advanced(FFTW3_INCLUDE_DIR FFTW3_LIBRARY )

cmake/Modules/FindKIM.cmake

@@ -0,0 +1,22 @@
+# - Find kim
+# Find the native KIM headers and libraries.
+#
+#  KIM_INCLUDE_DIRS - where to find kim.h, etc.
+#  KIM_LIBRARIES    - List of libraries when using kim.
+#  KIM_FOUND        - True if kim found.
+#
+
+find_path(KIM_INCLUDE_DIR KIM_API.h PATH_SUFFIXES kim-api-v1)
+
+find_library(KIM_LIBRARY NAMES kim-api-v1)
+
+set(KIM_LIBRARIES ${KIM_LIBRARY})
+set(KIM_INCLUDE_DIRS ${KIM_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set KIM_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(KIM DEFAULT_MSG KIM_LIBRARY KIM_INCLUDE_DIR)
+
+mark_as_advanced(KIM_INCLUDE_DIR KIM_LIBRARY )

cmake/Modules/FindLATTE.cmake

@@ -0,0 +1,18 @@
+# - Find latte
+# Find the native LATTE libraries.
+#
+#  LATTE_LIBRARIES    - List of libraries when using latte.
+#  LATTE_FOUND        - True if latte found.
+#
+
+find_library(LATTE_LIBRARY NAMES latte)
+
+set(LATTE_LIBRARIES ${LATTE_LIBRARY})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set LATTE_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(LATTE DEFAULT_MSG LATTE_LIBRARY)
+
+mark_as_advanced(LATTE_LIBRARY)

cmake/Modules/FindMKL.cmake

@@ -0,0 +1,22 @@
+# - Find mkl
+# Find the native MKL headers and libraries.
+#
+#  MKL_INCLUDE_DIRS - where to find mkl.h, etc.
+#  MKL_LIBRARIES    - List of libraries when using mkl.
+#  MKL_FOUND        - True if mkl found.
+#
+
+find_path(MKL_INCLUDE_DIR mkl_dfti.h HINTS $ENV{MKLROOT}/include)
+
+find_library(MKL_LIBRARY NAMES mkl_rt HINTS $ENV{MKLROOT}/lib $ENV{MKLROOT}/lib/intel64)
+
+set(MKL_LIBRARIES ${MKL_LIBRARY})
+set(MKL_INCLUDE_DIRS ${MKL_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set MKL_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(MKL DEFAULT_MSG MKL_LIBRARY MKL_INCLUDE_DIR)
+
+mark_as_advanced(MKL_INCLUDE_DIR MKL_LIBRARY )

cmake/Modules/FindNetCDF.cmake

@@ -0,0 +1,118 @@
+# - Find NetCDF
+# Find the native NetCDF includes and library
+#
+#  NETCDF_INCLUDE_DIR  - user modifiable choice of where netcdf headers are
+#  NETCDF_LIBRARY      - user modifiable choice of where netcdf libraries are
+#
+# Your package can require certain interfaces to be FOUND by setting these
+#
+#  NETCDF_CXX         - require the C++ interface and link the C++ library
+#  NETCDF_F77         - require the F77 interface and link the fortran library
+#  NETCDF_F90         - require the F90 interface and link the fortran library
+#
+# Or equivalently by calling FindNetCDF with a COMPONENTS argument containing one or
+# more of "CXX;F77;F90".
+#
+# When interfaces are requested the user has access to interface specific hints:
+#
+#  NETCDF_${LANG}_INCLUDE_DIR - where to search for interface header files
+#  NETCDF_${LANG}_LIBRARY     - where to search for interface libraries
+#
+# This module returns these variables for the rest of the project to use.
+#
+#  NETCDF_FOUND          - True if NetCDF found including required interfaces (see below)
+#  NETCDF_LIBRARIES      - All netcdf related libraries.
+#  NETCDF_INCLUDE_DIRS   - All directories to include.
+#  NETCDF_HAS_INTERFACES - Whether requested interfaces were found or not.
+#  NETCDF_${LANG}_INCLUDE_DIRS/NETCDF_${LANG}_LIBRARIES - C/C++/F70/F90 only interface
+#
+# Normal usage would be:
+#  set (NETCDF_F90 "YES")
+#  find_package (NetCDF REQUIRED)
+#  target_link_libraries (uses_everthing ${NETCDF_LIBRARIES})
+#  target_link_libraries (only_uses_f90 ${NETCDF_F90_LIBRARIES})
+
+#search starting from user editable cache var
+if (NETCDF_INCLUDE_DIR AND NETCDF_LIBRARY)
+  # Already in cache, be silent
+  set (NETCDF_FIND_QUIETLY TRUE)
+endif ()
+
+set(USE_DEFAULT_PATHS "NO_DEFAULT_PATH")
+if(NETCDF_USE_DEFAULT_PATHS)
+  set(USE_DEFAULT_PATHS "")
+endif()
+
+find_path (NETCDF_INCLUDE_DIR netcdf.h
+  HINTS "${NETCDF_DIR}/include")
+mark_as_advanced (NETCDF_INCLUDE_DIR)
+set (NETCDF_C_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR})
+
+find_library (NETCDF_LIBRARY NAMES netcdf
+  HINTS "${NETCDF_DIR}/lib")
+mark_as_advanced (NETCDF_LIBRARY)
+
+set (NETCDF_C_LIBRARIES ${NETCDF_LIBRARY})
+
+#start finding requested language components
+set (NetCDF_libs "")
+set (NetCDF_includes "${NETCDF_INCLUDE_DIR}")
+
+get_filename_component (NetCDF_lib_dirs "${NETCDF_LIBRARY}" PATH)
+set (NETCDF_HAS_INTERFACES "YES") # will be set to NO if we're missing any interfaces
+
+macro (NetCDF_check_interface lang header libs)
+  if (NETCDF_${lang})
+    #search starting from user modifiable cache var
+    find_path (NETCDF_${lang}_INCLUDE_DIR NAMES ${header}
+      HINTS "${NETCDF_INCLUDE_DIR}"
+      HINTS "${NETCDF_${lang}_ROOT}/include"
+      ${USE_DEFAULT_PATHS})
+
+    find_library (NETCDF_${lang}_LIBRARY NAMES ${libs}
+      HINTS "${NetCDF_lib_dirs}"
+      HINTS "${NETCDF_${lang}_ROOT}/lib"
+      ${USE_DEFAULT_PATHS})
+
+    mark_as_advanced (NETCDF_${lang}_INCLUDE_DIR NETCDF_${lang}_LIBRARY)
+
+    #export to internal varS that rest of project can use directly
+    set (NETCDF_${lang}_LIBRARIES ${NETCDF_${lang}_LIBRARY})
+    set (NETCDF_${lang}_INCLUDE_DIRS ${NETCDF_${lang}_INCLUDE_DIR})
+
+    if (NETCDF_${lang}_INCLUDE_DIR AND NETCDF_${lang}_LIBRARY)
+      list (APPEND NetCDF_libs ${NETCDF_${lang}_LIBRARY})
+      list (APPEND NetCDF_includes ${NETCDF_${lang}_INCLUDE_DIR})
+    else ()
+      set (NETCDF_HAS_INTERFACES "NO")
+      message (STATUS "Failed to find NetCDF interface for ${lang}")
+    endif ()
+  endif ()
+endmacro ()
+
+list (FIND NetCDF_FIND_COMPONENTS "CXX" _nextcomp)
+if (_nextcomp GREATER -1)
+  set (NETCDF_CXX 1)
+endif ()
+list (FIND NetCDF_FIND_COMPONENTS "F77" _nextcomp)
+if (_nextcomp GREATER -1)
+  set (NETCDF_F77 1)
+endif ()
+list (FIND NetCDF_FIND_COMPONENTS "F90" _nextcomp)
+if (_nextcomp GREATER -1)
+  set (NETCDF_F90 1)
+endif ()
+NetCDF_check_interface (CXX netcdfcpp.h netcdf_c++)
+NetCDF_check_interface (F77 netcdf.inc  netcdff)
+NetCDF_check_interface (F90 netcdf.mod  netcdff)
+
+#export accumulated results to internal varS that rest of project can depend on
+list (APPEND NetCDF_libs "${NETCDF_C_LIBRARIES}")
+set (NETCDF_LIBRARIES ${NetCDF_libs})
+set (NETCDF_INCLUDE_DIRS ${NetCDF_includes})
+
+# handle the QUIETLY and REQUIRED arguments and set NETCDF_FOUND to TRUE if
+# all listed variables are TRUE
+include (FindPackageHandleStandardArgs)
+find_package_handle_standard_args (NetCDF
+  DEFAULT_MSG NETCDF_LIBRARIES NETCDF_INCLUDE_DIRS NETCDF_HAS_INTERFACES)

cmake/Modules/FindQE.cmake

@@ -0,0 +1,29 @@
+# - Find quantum-espresso
+# Find the native QE headers and libraries.
+#
+#  QE_INCLUDE_DIRS - where to find quantum-espresso.h, etc.
+#  QE_LIBRARIES    - List of libraries when using quantum-espresso.
+#  QE_FOUND        - True if quantum-espresso found.
+#
+
+find_path(QE_INCLUDE_DIR libqecouple.h PATH_SUFFIXES COUPLE/include)
+
+find_library(QECOUPLE_LIBRARY NAMES qecouple)
+find_library(PW_LIBRARY NAMES pw)
+find_library(QEMOD_LIBRARY NAMES qemod)
+find_library(QEFFT_LIBRARY NAMES qefft)
+find_library(QELA_LIBRARY NAMES qela)
+find_library(CLIB_LIBRARY NAMES clib)
+find_library(IOTK_LIBRARY NAMES iotk)
+
+
+set(QE_LIBRARIES ${QECOUPLE_LIBRARY} ${PW_LIBRARY} ${QEMOD_LIBRARY} ${QEFFT_LIBRARY} ${QELA_LIBRARY} ${CLIB_LIBRARY} ${IOTK_LIBRARY})
+set(QE_INCLUDE_DIRS ${QE_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set QE_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(QE DEFAULT_MSG QECOUPLE_LIBRARY PW_LIBRARY QEMOD_LIBRARY QEFFT_LIBRARY QELA_LIBRARY CLIB_LIBRARY IOTK_LIBRARY QE_INCLUDE_DIR)
+
+mark_as_advanced(QE_INCLUDE_DIR QECOUPLE_LIBRARY PW_LIBRARY QEMOD_LIBRARY QEFFT_LIBRARY QELA_LIBRARY CLIB_LIBRARY IOTK_LIBRARY)

cmake/Modules/FindQUIP.cmake

@@ -0,0 +1,18 @@
+# - Find quip
+# Find the native QUIP libraries.
+#
+#  QUIP_LIBRARIES    - List of libraries when using fftw3.
+#  QUIP_FOUND        - True if fftw3 found.
+#
+
+find_library(QUIP_LIBRARY NAMES quip)
+
+set(QUIP_LIBRARIES ${QUIP_LIBRARY})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set QUIP_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(QUIP DEFAULT_MSG QUIP_LIBRARY)
+
+mark_as_advanced(QUIP_LIBRARY)

cmake/Modules/FindVORO.cmake

@@ -0,0 +1,22 @@
+# - Find voro++
+# Find the native VORO headers and libraries.
+#
+#  VORO_INCLUDE_DIRS - where to find voro++.hh, etc.
+#  VORO_LIBRARIES    - List of libraries when using voro++.
+#  VORO_FOUND        - True if voro++ found.
+#
+
+find_path(VORO_INCLUDE_DIR voro++.hh PATH_SUFFIXES voro++)
+
+find_library(VORO_LIBRARY NAMES voro++)
+
+set(VORO_LIBRARIES ${VORO_LIBRARY})
+set(VORO_INCLUDE_DIRS ${VORO_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set VORO_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(VORO DEFAULT_MSG VORO_LIBRARY VORO_INCLUDE_DIR)
+
+mark_as_advanced(VORO_INCLUDE_DIR VORO_LIBRARY )

cmake/Modules/OpenCLUtils.cmake

@@ -0,0 +1,18 @@
+function(GenerateOpenCLHeader varname outfile files)
+    message("Creating ${outfile}...")
+    file(WRITE ${outfile} "const char * ${varname} = \n")
+    math(EXPR ARG_END   "${ARGC}-1")
+
+    foreach(IDX RANGE 2 ${ARG_END})
+        list(GET ARGV ${IDX} filename)
+        file(READ ${filename} content)
+        string(REGEX REPLACE "\\s*//[^\n]*\n" "" content "${content}")
+        string(REGEX REPLACE "\\\\" "\\\\\\\\" content "${content}")
+        string(REGEX REPLACE "\"" "\\\\\"" content "${content}")
+        string(REGEX REPLACE "([^\n]+)\n" "\"\\1\\\\n\"\n" content "${content}")
+        string(REGEX REPLACE "\n+" "\n" content "${content}")
+        file(APPEND ${outfile} "${content}")
+    endforeach()
+
+    file(APPEND ${outfile} ";\n")
+endfunction(GenerateOpenCLHeader)

cmake/Modules/StyleHeaderUtils.cmake

@@ -0,0 +1,183 @@
+function(FindStyleHeaders path style_class file_pattern headers)
+    file(GLOB files "${path}/${file_pattern}*.h")
+    get_property(hlist GLOBAL PROPERTY ${headers})
+
+    foreach(file_name ${files})
+        file(STRINGS ${file_name} is_style LIMIT_COUNT 1 REGEX ${style_class})
+        if(is_style)
+            list(APPEND hlist ${file_name})
+        endif()
+    endforeach()
+    set_property(GLOBAL PROPERTY ${headers} "${hlist}")
+endfunction(FindStyleHeaders)
+
+function(AddStyleHeader path headers)
+    get_property(hlist GLOBAL PROPERTY ${headers})
+    list(APPEND hlist ${path})
+    set_property(GLOBAL PROPERTY ${headers} "${hlist}")
+endfunction(AddStyleHeader)
+
+function(FindStyleHeadersExt path style_class extension headers sources)
+    get_property(hlist GLOBAL PROPERTY ${headers})
+    get_property(slist GLOBAL PROPERTY ${sources})
+    set(ext_list)
+    get_filename_component(abs_path "${path}" ABSOLUTE)
+
+    foreach(file_name ${hlist})
+        get_filename_component(basename ${file_name} NAME_WE)
+        set(ext_file_name "${abs_path}/${basename}_${extension}.h")
+        if(EXISTS "${ext_file_name}")
+            file(STRINGS ${ext_file_name} is_style LIMIT_COUNT 1 REGEX ${style_class})
+            if(is_style)
+                list(APPEND ext_list ${ext_file_name})
+
+                set(source_file_name "${abs_path}/${basename}_${extension}.cpp")
+                if(EXISTS "${source_file_name}")
+                    list(APPEND slist ${source_file_name})
+                endif()
+            endif()
+        endif()
+    endforeach()
+
+    list(APPEND hlist ${ext_list})
+    set_property(GLOBAL PROPERTY ${headers} "${hlist}")
+    set_property(GLOBAL PROPERTY ${sources} "${slist}")
+endfunction(FindStyleHeadersExt)
+
+function(CreateStyleHeader path filename)
+    math(EXPR N "${ARGC}-2")
+
+    set(temp "")
+    if(N GREATER 0)
+        math(EXPR ARG_END   "${ARGC}-1")
+ 
+        foreach(IDX RANGE 2 ${ARG_END})
+            list(GET ARGV ${IDX} FNAME)
+            get_filename_component(FNAME ${FNAME} NAME)
+            set(temp "${temp}#include \"${FNAME}\"\n")
+        endforeach()
+    endif()
+    message(STATUS "Generating ${filename}...")
+    file(WRITE "${path}/${filename}.tmp" "${temp}" )
+    execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${path}/${filename}.tmp" "${path}/${filename}")
+endfunction(CreateStyleHeader)
+
+function(GenerateStyleHeader path property style)
+    get_property(files GLOBAL PROPERTY ${property})
+    #message("${property} = ${files}")
+    CreateStyleHeader("${path}" "style_${style}.h" ${files})
+endfunction(GenerateStyleHeader)
+
+function(RegisterNBinStyles search_path)
+    FindStyleHeaders(${search_path} NBIN_CLASS      nbin_      NBIN      ) # nbin      ) # neighbor
+endfunction(RegisterNBinStyles)
+
+function(RegisterNPairStyles search_path)
+    FindStyleHeaders(${search_path} NPAIR_CLASS     npair_     NPAIR     ) # npair     ) # neighbor
+endfunction(RegisterNPairStyles)
+
+function(RegisterNBinStyle path)
+    AddStyleHeader(${path} NBIN)
+endfunction(RegisterNBinStyle)
+
+function(RegisterNPairStyle path)
+    AddStyleHeader(${path} NPAIR)
+endfunction(RegisterNPairStyle)
+
+function(RegisterStyles search_path)
+    FindStyleHeaders(${search_path} ANGLE_CLASS     angle_     ANGLE     ) # angle     ) # force
+    FindStyleHeaders(${search_path} ATOM_CLASS      atom_vec_  ATOM_VEC  ) # atom      ) # atom      atom_vec_hybrid
+    FindStyleHeaders(${search_path} BODY_CLASS      body_      BODY      ) # body      ) # atom_vec_body
+    FindStyleHeaders(${search_path} BOND_CLASS      bond_      BOND      ) # bond      ) # force
+    FindStyleHeaders(${search_path} COMMAND_CLASS   ""         COMMAND   ) # command   ) # input
+    FindStyleHeaders(${search_path} COMPUTE_CLASS   compute_   COMPUTE   ) # compute   ) # modify
+    FindStyleHeaders(${search_path} DIHEDRAL_CLASS  dihedral_  DIHEDRAL  ) # dihedral  ) # force
+    FindStyleHeaders(${search_path} DUMP_CLASS      dump_      DUMP      ) # dump      ) # output    write_dump
+    FindStyleHeaders(${search_path} FIX_CLASS       fix_       FIX       ) # fix       ) # modify
+    FindStyleHeaders(${search_path} IMPROPER_CLASS  improper_  IMPROPER  ) # improper  ) # force
+    FindStyleHeaders(${search_path} INTEGRATE_CLASS ""         INTEGRATE ) # integrate ) # update
+    FindStyleHeaders(${search_path} KSPACE_CLASS    ""         KSPACE    ) # kspace    ) # force
+    FindStyleHeaders(${search_path} MINIMIZE_CLASS  min_       MINIMIZE  ) # minimize  ) # update
+    FindStyleHeaders(${search_path} NBIN_CLASS      nbin_      NBIN      ) # nbin      ) # neighbor
+    FindStyleHeaders(${search_path} NPAIR_CLASS     npair_     NPAIR     ) # npair     ) # neighbor
+    FindStyleHeaders(${search_path} NSTENCIL_CLASS  nstencil_  NSTENCIL  ) # nstencil  ) # neighbor
+    FindStyleHeaders(${search_path} NTOPO_CLASS     ntopo_     NTOPO     ) # ntopo     ) # neighbor
+    FindStyleHeaders(${search_path} PAIR_CLASS      pair_      PAIR      ) # pair      ) # force
+    FindStyleHeaders(${search_path} READER_CLASS    reader_    READER    ) # reader    ) # read_dump
+    FindStyleHeaders(${search_path} REGION_CLASS    region_    REGION    ) # region    ) # domain
+endfunction(RegisterStyles)
+
+function(RemovePackageHeader headers pkg_header)
+    get_property(hlist GLOBAL PROPERTY ${headers})
+    list(REMOVE_ITEM hlist ${pkg_header})
+    set_property(GLOBAL PROPERTY ${headers} "${hlist}")
+endfunction(RemovePackageHeader)
+
+function(DetectAndRemovePackageHeader fname)
+    RemovePackageHeader(ANGLE     ${fname})
+    RemovePackageHeader(ATOM_VEC  ${fname})
+    RemovePackageHeader(BODY      ${fname})
+    RemovePackageHeader(BOND      ${fname})
+    RemovePackageHeader(COMMAND   ${fname})
+    RemovePackageHeader(COMPUTE   ${fname})
+    RemovePackageHeader(DIHEDRAL  ${fname})
+    RemovePackageHeader(DUMP      ${fname})
+    RemovePackageHeader(FIX       ${fname})
+    RemovePackageHeader(IMPROPER  ${fname})
+    RemovePackageHeader(INTEGRATE ${fname})
+    RemovePackageHeader(KSPACE    ${fname})
+    RemovePackageHeader(MINIMIZE  ${fname})
+    RemovePackageHeader(NBIN      ${fname})
+    RemovePackageHeader(NPAIR     ${fname})
+    RemovePackageHeader(NSTENCIL  ${fname})
+    RemovePackageHeader(NTOPO     ${fname})
+    RemovePackageHeader(PAIR      ${fname})
+    RemovePackageHeader(READER    ${fname})
+    RemovePackageHeader(REGION    ${fname})
+endfunction(DetectAndRemovePackageHeader)
+
+function(RegisterStylesExt search_path extension sources)
+    FindStyleHeadersExt(${search_path} ANGLE_CLASS     ${extension}  ANGLE     ${sources})
+    FindStyleHeadersExt(${search_path} ATOM_CLASS      ${extension}  ATOM_VEC  ${sources})
+    FindStyleHeadersExt(${search_path} BODY_CLASS      ${extension}  BODY      ${sources})
+    FindStyleHeadersExt(${search_path} BOND_CLASS      ${extension}  BOND      ${sources})
+    FindStyleHeadersExt(${search_path} COMMAND_CLASS   ${extension}  COMMAND   ${sources})
+    FindStyleHeadersExt(${search_path} COMPUTE_CLASS   ${extension}  COMPUTE   ${sources})
+    FindStyleHeadersExt(${search_path} DIHEDRAL_CLASS  ${extension}  DIHEDRAL  ${sources})
+    FindStyleHeadersExt(${search_path} DUMP_CLASS      ${extension}  DUMP      ${sources})
+    FindStyleHeadersExt(${search_path} FIX_CLASS       ${extension}  FIX       ${sources})
+    FindStyleHeadersExt(${search_path} IMPROPER_CLASS  ${extension}  IMPROPER  ${sources})
+    FindStyleHeadersExt(${search_path} INTEGRATE_CLASS ${extension}  INTEGRATE ${sources})
+    FindStyleHeadersExt(${search_path} KSPACE_CLASS    ${extension}  KSPACE    ${sources})
+    FindStyleHeadersExt(${search_path} MINIMIZE_CLASS  ${extension}  MINIMIZE  ${sources})
+    FindStyleHeadersExt(${search_path} NBIN_CLASS      ${extension}  NBIN      ${sources})
+    FindStyleHeadersExt(${search_path} NPAIR_CLASS     ${extension}  NPAIR     ${sources})
+    FindStyleHeadersExt(${search_path} NSTENCIL_CLASS  ${extension}  NSTENCIL  ${sources})
+    FindStyleHeadersExt(${search_path} NTOPO_CLASS     ${extension}  NTOPO     ${sources})
+    FindStyleHeadersExt(${search_path} PAIR_CLASS      ${extension}  PAIR      ${sources})
+    FindStyleHeadersExt(${search_path} READER_CLASS    ${extension}  READER    ${sources})
+    FindStyleHeadersExt(${search_path} REGION_CLASS    ${extension}  REGION    ${sources})
+endfunction(RegisterStylesExt)
+
+function(GenerateStyleHeaders output_path)
+    GenerateStyleHeader(${output_path} ANGLE      angle     ) # force
+    GenerateStyleHeader(${output_path} ATOM_VEC   atom      ) # atom      atom_vec_hybrid
+    GenerateStyleHeader(${output_path} BODY       body      ) # atom_vec_body
+    GenerateStyleHeader(${output_path} BOND       bond      ) # force
+    GenerateStyleHeader(${output_path} COMMAND    command   ) # input
+    GenerateStyleHeader(${output_path} COMPUTE    compute   ) # modify
+    GenerateStyleHeader(${output_path} DIHEDRAL   dihedral  ) # force
+    GenerateStyleHeader(${output_path} DUMP       dump      ) # output    write_dump
+    GenerateStyleHeader(${output_path} FIX        fix       ) # modify
+    GenerateStyleHeader(${output_path} IMPROPER   improper  ) # force
+    GenerateStyleHeader(${output_path} INTEGRATE  integrate ) # update
+    GenerateStyleHeader(${output_path} KSPACE     kspace    ) # force
+    GenerateStyleHeader(${output_path} MINIMIZE   minimize  ) # update
+    GenerateStyleHeader(${output_path} NBIN       nbin      ) # neighbor
+    GenerateStyleHeader(${output_path} NPAIR      npair     ) # neighbor
+    GenerateStyleHeader(${output_path} NSTENCIL   nstencil  ) # neighbor
+    GenerateStyleHeader(${output_path} NTOPO      ntopo     ) # neighbor
+    GenerateStyleHeader(${output_path} PAIR       pair      ) # force
+    GenerateStyleHeader(${output_path} READER     reader    ) # read_dump
+    GenerateStyleHeader(${output_path} REGION     region    ) # domain
+endfunction(GenerateStyleHeaders)

cmake/README.md

@@ -0,0 +1,19 @@
+cmake-buildsystem
+-----------------
+
+To use the cmake build system instead of the make-driven one, do:
+```
+cmake /path/to/lammps/source/cmake
+```
+(please note the cmake directory as the very end)
+
+To enable package, e.g. GPU do
+```
+cmake /path/to/lammps/source/cmake -DENABLE_GPU=ON
+```
+
+cmake has many many options, do get an overview use the curses-based cmake interface, ccmake:
+```
+ccmake /path/to/lammps/source/cmake
+```
+(Don't forget to press "g" for generate once you are done with configuring)

cmake/gpu/lal_pppm_d.cu

@@ -0,0 +1,4 @@
+#define grdtyp double
+#define grdtyp4 double4
+
+#include "lal_pppm.cu"

cmake/gpu/lal_pppm_f.cu

@@ -0,0 +1,4 @@
+#define grdtyp float
+#define grdtyp4 float4
+
+#include "lal_pppm.cu"

cmake/pkgconfig/liblammps.pc.in

@@ -0,0 +1,18 @@
+# pkg-config file for lammps
+# https://people.freedesktop.org/~dbn/pkg-config-guide.html
+# Usage: cc `pkg-config --cflags --libs liblammps` -o myapp myapp.c
+# after you added @CMAKE_INSTALL_FULL_LIBDIR@/pkg-config to PKG_CONFIG_PATH,
+# e.g. export PKG_CONFIG_PATH=@CMAKE_INSTALL_FULL_LIBDIR@/pkgconfig
+
+prefix=@CMAKE_INSTALL_FULL_PREFIX@
+libdir=@CMAKE_INSTALL_FULL_LIBDIR@
+includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
+
+Name: liblammps@LAMMPS_MACHINE@
+Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library
+URL: http://lammps.sandia.gov
+Version:
+Requires:
+Libs: -L${libdir} -llammps@LAMMPS_MACHINE@
+Libs.private: -lm
+Cflags: -I${includedir} @LAMMPS_API_DEFINES@

doc/.gitignore

@@ -0,0 +1,6 @@
+/html
+/spelling
+/LAMMPS.epub
+/LAMMPS.mobi
+/Manual.pdf
+/Developer.pdf

doc/Eqs/fix_ti_rs_force.tex

@@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-
-\usepackage{amsmath}
-
-\begin{document}
-
-$$
-  F_{\text{total}} = \lambda F_{\text{int}}
-$$
-
-\end{document}

doc/Eqs/fix_ti_rs_function_1.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  \lambda(\tau) = \lambda_i + \tau \left( \lambda_f - \lambda_i \right)
-$$
-
-\end{document}

doc/Eqs/fix_ti_rs_function_2.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  \lambda(\tau) = \frac{\lambda_i}{1 + \tau \left( \frac{\lambda_i}{\lambda_f} - 1 \right)}
-$$
-
-\end{document}

doc/Eqs/fix_ti_rs_function_3.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  \lambda(\tau) = \frac{\lambda_i}{ 1 + \log_2(1+\tau) \left( \frac{\lambda_i}{\lambda_f} - 1 \right)}
-$$
-
-\end{document}

doc/Eqs/fix_ti_spring_force.tex

@@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-
-\usepackage{amsmath}
-
-\begin{document}
-
-$$
-  F_{\text{total}} = \left( 1-\lambda \right) F_{\text{solid}} + \lambda F_{\text{harm}}
-$$
-
-\end{document}

doc/Eqs/improper_umbrella.tex

@@ -1,13 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
-E=\frac{1}{2}K\left( \frac{1+cos\omega_0}{sin\omega_0}\right) ^2 \left( cos\omega - cos\omega_0\right) \qquad \omega_0 \neq 0^o
-$$
-
-$$
-E=K\left( 1-cos\omega\right)  \qquad \omega_0 = 0^o
-$$
-
-\end{document}

doc/Eqs/pair_lj_sf.tex

@@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
- F & = & F_{\mathrm{LJ}}(r) - F_{\mathrm{LJ}}(r_{\mathrm{c}}) \qquad r < r_{\mathrm{c}} \\
- E & = & E_{\mathrm{LJ}}(r) - E_{\mathrm{LJ}}(r_{\mathrm{c}}) + (r - r_{\mathrm{c}}) F_{\mathrm{LJ}}(r_{\mathrm{c}}) \qquad r < r_{\mathrm{c}} \\
- \mathrm{with} \qquad E_{\mathrm{LJ}}(r) & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \qquad \mathrm{and} \qquad F_{\mathrm{LJ}}(r) = - E^\prime_{\mathrm{LJ}}(r)
-\end{eqnarray*}                           
-
-\end{document}

doc/Eqs/pair_meam_spline.tex

@@ -1,13 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   E=\sum_{ij}\phi(r_{ij})+\sum_{i}U(\rho_{i}),
-$$
-
-$$
-   \rho_{i}=\sum_{j}\rho(r_{ij})+\sum_{jk}f(r_{ij})f(r_{ik})g[\cos(\theta_{jik})]
-$$
-
-\end{document}

doc/Eqs/pressure.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   P = \frac{N k_B T}{V} + \frac{\sum_{i}^{N} r_i \bullet f_i}{dV}
-$$
-
-\end{document}

doc/Makefile

@@ -0,0 +1,174 @@
+# Makefile for LAMMPS documentation
+
+SHELL 	      = /bin/bash
+SHA1          = $(shell echo $USER-$PWD | python utils/sha1sum.py)
+BUILDDIR      = /tmp/lammps-docs-$(SHA1)
+RSTDIR        = $(BUILDDIR)/rst
+VENV          = $(BUILDDIR)/docenv
+TXT2RST       = $(VENV)/bin/txt2rst
+ANCHORCHECK   = $(VENV)/bin/doc_anchor_check
+
+PYTHON        = $(shell which python3)
+HAS_PYTHON3    = NO
+HAS_VIRTUALENV = NO
+
+ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 0)
+HAS_PYTHON3 = YES
+endif
+
+ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 0)
+HAS_VIRTUALENV = YES
+endif
+
+SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
+SOURCES=$(filter-out src/lammps_commands.txt src/lammps_tutorials.txt,$(wildcard src/*.txt))
+OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
+
+.PHONY: help clean-all clean epub html pdf old venv spelling anchor_check
+
+# ------------------------------------------
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       create HTML doc pages in html dir"
+	@echo "  pdf        create Manual.pdf and Developer.pdf in this dir"
+	@echo "  old        create old-style HTML doc pages in old dir"
+	@echo "  fetch      fetch HTML and PDF files from LAMMPS web site"
+	@echo "  epub       create ePUB format manual for e-book readers"
+	@echo "  clean      remove all intermediate RST files"
+	@echo "  clean-all  reset the entire build environment"
+	@echo "  txt2html   build txt2html tool"
+	@echo "  anchor_check  scan for duplicate anchor labels"
+
+# ------------------------------------------
+
+clean-all:
+	rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe
+
+clean:
+	rm -rf $(RSTDIR) html
+	rm -rf spelling
+
+clean-spelling:
+	rm -rf spelling
+
+html: $(OBJECTS) $(ANCHORCHECK)
+	@(\
+		. $(VENV)/bin/activate ;\
+		cp -r src/* $(RSTDIR)/ ;\
+		sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
+		echo "############################################" ;\
+		doc_anchor_check src/*.txt ;\
+		echo "############################################" ;\
+		deactivate ;\
+	)
+	-rm html/searchindex.js
+	@rm -rf html/_sources
+	@rm -rf html/PDF
+	@rm -rf html/USER
+	@cp -r src/PDF html/PDF
+	@cp -r src/USER html/USER
+	@rm -rf html/PDF/.[sg]*
+	@rm -rf html/USER/.[sg]*
+	@rm -rf html/USER/*/.[sg]*
+	@rm -rf html/USER/*/*.[sg]*
+	@echo "Build finished. The HTML pages are in doc/html."
+
+spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt
+	@(\
+		. $(VENV)/bin/activate ;\
+		pip install sphinxcontrib-spelling ;\
+		cp -r src/* $(RSTDIR)/ ;\
+        cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ;\
+		sphinx-build -b spelling -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) spelling ;\
+		deactivate ;\
+	)
+	@echo "Spell check finished."
+
+epub: $(OBJECTS)
+	@mkdir -p epub
+	@rm -f LAMMPS.epub
+	@cp src/JPG/lammps-logo.png epub/
+	@(\
+		. $(VENV)/bin/activate ;\
+		cp -r src/* $(RSTDIR)/ ;\
+		sphinx-build $(SPHINXEXTRA) -b epub -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
+		deactivate ;\
+	)
+	@mv  epub/LAMMPS.epub .
+	@rm -rf epub
+	@echo "Build finished. The ePUB manual file is created."
+
+pdf: utils/txt2html/txt2html.exe
+	@(\
+		set -e; \
+		cd src; \
+		../utils/txt2html/txt2html.exe -b *.txt; \
+		htmldoc --batch lammps.book;          \
+		for s in `echo *.txt | sed -e 's,\.txt,\.html,g'` ; \
+			do grep -q $$s lammps.book || \
+			echo doc file $$s missing in src/lammps.book; done; \
+		rm *.html; \
+		cd Developer; \
+		pdflatex developer; \
+		pdflatex developer; \
+		mv developer.pdf ../../Developer.pdf; \
+	)
+
+old: utils/txt2html/txt2html.exe
+	@rm -rf old
+	@mkdir old; mkdir old/Eqs; mkdir old/JPG; mkdir old/PDF
+	@cd src; ../utils/txt2html/txt2html.exe -b *.txt; \
+	  mv *.html ../old; \
+	  cp Eqs/*.jpg ../old/Eqs; \
+	  cp JPG/* ../old/JPG; \
+	  cp PDF/* ../old/PDF;
+
+fetch:
+	@rm -rf html_www Manual_www.pdf Developer_www.pdf
+	@curl -s -o Manual_www.pdf http://lammps.sandia.gov/doc/Manual.pdf
+	@curl -s -o Developer_www.pdf http://lammps.sandia.gov/doc/Developer.pdf
+	@curl -s -o lammps-doc.tar.gz http://lammps.sandia.gov/tars/lammps-doc.tar.gz
+	@tar xzf lammps-doc.tar.gz
+	@rm -f lammps-doc.tar.gz
+
+txt2html: utils/txt2html/txt2html.exe
+
+anchor_check : $(ANCHORCHECK)
+	@(\
+		. $(VENV)/bin/activate ;\
+		doc_anchor_check src/*.txt ;\
+		deactivate ;\
+	)
+
+# ------------------------------------------
+
+utils/txt2html/txt2html.exe: utils/txt2html/txt2html.cpp
+	g++ -O -Wall -o $@ $<
+
+$(RSTDIR)/%.rst : src/%.txt $(TXT2RST)
+	@(\
+		mkdir -p $(RSTDIR) ; \
+		. $(VENV)/bin/activate ;\
+		txt2rst $< > $@ ;\
+		deactivate ;\
+	)
+
+$(VENV):
+	@if [ "$(HAS_PYTHON3)" == "NO" ] ; then echo "Python3 was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
+	@if [ "$(HAS_VIRTUALENV)" == "NO" ] ; then echo "virtualenv was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
+	@( \
+		virtualenv -p $(PYTHON) $(VENV); \
+		. $(VENV)/bin/activate; \
+		pip install Sphinx; \
+		pip install sphinxcontrib-images; \
+		deactivate;\
+	)
+
+$(TXT2RST) $(ANCHORCHECK): $(VENV)
+	@( \
+		. $(VENV)/bin/activate; \
+		(cd utils/converters;\
+		python setup.py develop);\
+		deactivate;\
+	)

doc/Manual.html

@@ -1,418 +0,0 @@
-<HTML>
-<HEAD>
-<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="30 Oct 2014 version">
-<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
-<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation.  This software and manual is distributed under the GNU General Public License.">
-</HEAD>
-
-<BODY>
-
-<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> 
-</CENTER>
-
-
-
-
-
-
-<HR>
-
-<H1></H1>
-
-<CENTER><H3>LAMMPS Documentation 
-</H3></CENTER>
-<CENTER><H4>30 Oct 2014 version 
-</H4></CENTER>
-<H4>Version info: 
-</H4>
-<P>The LAMMPS "version" is the date when it was released, such as 1 May
-2010. LAMMPS is updated continuously.  Whenever we fix a bug or add a
-feature, we release it immediately, and post a notice on <A HREF = "http://lammps.sandia.gov/bug.html">this page of
-the WWW site</A>.  Each dated copy of LAMMPS contains all the
-features and bug-fixes up to and including that version date. The
-version date is printed to the screen and logfile every time you run
-LAMMPS. It is also in the file src/version.h and in the LAMMPS
-directory name created when you unpack a tarball, and at the top of
-the first page of the manual (this page).
-</P>
-<UL><LI>If you browse the HTML doc pages on the LAMMPS WWW site, they always
-describe the most current version of LAMMPS. 
-
-<LI>If you browse the HTML doc pages included in your tarball, they
-describe the version you have. 
-
-<LI>The <A HREF = "Manual.pdf">PDF file</A> on the WWW site or in the tarball is updated
-about once per month.  This is because it is large, and we don't want
-it to be part of every patch. 
-
-<LI>There is also a <A HREF = "Developer.pdf">Developer.pdf</A> file in the doc
-directory, which describes the internal structure and algorithms of
-LAMMPS.  
-</UL>
-<P>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
-Simulator.
-</P>
-<P>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).
-</P>
-<P>The primary developers of LAMMPS are <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Aidan
-Thompson, and Paul Crozier who can be contacted at
-sjplimp,athomps,pscrozi at sandia.gov.  The <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> at
-http://lammps.sandia.gov has more information about the code and its
-uses.
-</P>
-
-
-
-
-<HR>
-
-<P>The LAMMPS documentation is organized into the following sections.  If
-you find errors or omissions in this manual or have suggestions for
-useful information to add, please send an email to the developers so
-we can improve the LAMMPS documentation.
-</P>
-<P>Once you are familiar with LAMMPS, you may want to bookmark <A HREF = "Section_commands.html#comm">this
-page</A> at Section_commands.html#comm since
-it gives quick access to documentation for all LAMMPS commands.
-</P>
-<P><A HREF = "Manual.pdf">PDF file</A> of the entire manual, generated by
-<A HREF = "http://freecode.com/projects/htmldoc">htmldoc</A>
-</P>
-<OL><LI><A HREF = "Section_intro.html">Introduction</A> 
-
-<UL>  1.1 <A HREF = "Section_intro.html#intro_1">What is LAMMPS</A> 
-<BR>
-  1.2 <A HREF = "Section_intro.html#intro_2">LAMMPS features</A> 
-<BR>
-  1.3 <A HREF = "Section_intro.html#intro_3">LAMMPS non-features</A> 
-<BR>
-  1.4 <A HREF = "Section_intro.html#intro_4">Open source distribution</A> 
-<BR>
-  1.5 <A HREF = "Section_intro.html#intro_5">Acknowledgments and citations</A> 
-<BR></UL>
-<LI><A HREF = "Section_start.html">Getting started</A> 
-
-<UL>  2.1 <A HREF = "Section_start.html#start_1">What's in the LAMMPS distribution</A> 
-<BR>
-  2.2 <A HREF = "Section_start.html#start_2">Making LAMMPS</A> 
-<BR>
-  2.3 <A HREF = "Section_start.html#start_3">Making LAMMPS with optional packages</A> 
-<BR>
-  2.4 <A HREF = "Section_start.html#start_4">Building LAMMPS via the Make.py script</A> 
-<BR>
-  2.5 <A HREF = "Section_start.html#start_5">Building LAMMPS as a library</A> 
-<BR>
-  2.6 <A HREF = "Section_start.html#start_6">Running LAMMPS</A> 
-<BR>
-  2.7 <A HREF = "Section_start.html#start_7">Command-line options</A> 
-<BR>
-  2.8 <A HREF = "Section_start.html#start_8">Screen output</A> 
-<BR>
-  2.9 <A HREF = "Section_start.html#start_9">Tips for users of previous versions</A> 
-<BR></UL>
-<LI><A HREF = "Section_commands.html">Commands</A> 
-
-<UL>  3.1 <A HREF = "Section_commands.html#cmd_1">LAMMPS input script</A> 
-<BR>
-  3.2 <A HREF = "Section_commands.html#cmd_2">Parsing rules</A> 
-<BR>
-  3.3 <A HREF = "Section_commands.html#cmd_3">Input script structure</A> 
-<BR>
-  3.4 <A HREF = "Section_commands.html#cmd_4">Commands listed by category</A> 
-<BR>
-  3.5 <A HREF = "Section_commands.html#cmd_5">Commands listed alphabetically</A> 
-<BR></UL>
-<LI><A HREF = "Section_packages.html">Packages</A> 
-
-<UL>  4.1 <A HREF = "Section_packages.html#pkg_1">Standard packages</A> 
-<BR>
-  4.2 <A HREF = "Section_packages.html#pkg_2">User packages</A> 
-<BR></UL>
-<LI><A HREF = "Section_accelerate.html">Accelerating LAMMPS performance</A> 
-
-<UL>  5.1 <A HREF = "Section_accelerate.html#acc_1">Measuring performance</A> 
-<BR>
-  5.2 <A HREF = "Section_accelerate.html#acc_2">Algorithms and code options to boost performace</A> 
-<BR>
-  5.3 <A HREF = "Section_accelerate.html#acc_3">Accelerator packages with optimized styles</A> 
-<BR>
-<UL>    5.3.1 <A HREF = "accelerate_cuda.html">USER-CUDA package</A> 
-<BR>
-    5.3.2 <A HREF = "accelerate_gpu.html">GPU package</A> 
-<BR>
-    5.3.3 <A HREF = "accelerate_intel.html">USER-INTEL package</A> 
-<BR>
-    5.3.4 <A HREF = "accelerate_kokkos.html">KOKKOS package</A> 
-<BR>
-    5.3.5 <A HREF = "accelerate_omp.html">USER-OMP package</A> 
-<BR>
-    5.3.6 <A HREF = "accelerate_opt.html">OPT package</A> 
-<BR></UL>
-  5.4 <A HREF = "Section_accelerate.html#acc_4">Comparison of various accelerator packages</A> 
-<BR></UL>
-<LI><A HREF = "Section_howto.html">How-to discussions</A> 
-
-<UL>  6.1 <A HREF = "Section_howto.html#howto_1">Restarting a simulation</A> 
-<BR>
-  6.2 <A HREF = "Section_howto.html#howto_2">2d simulations</A> 
-<BR>
-  6.3 <A HREF = "Section_howto.html#howto_3">CHARMM and AMBER force fields</A> 
-<BR>
-  6.4 <A HREF = "Section_howto.html#howto_4">Running multiple simulations from one input script</A> 
-<BR>
-  6.5 <A HREF = "Section_howto.html#howto_5">Multi-replica simulations</A> 
-<BR>
-  6.6 <A HREF = "Section_howto.html#howto_6">Granular models</A> 
-<BR>
-  6.7 <A HREF = "Section_howto.html#howto_7">TIP3P water model</A> 
-<BR>
-  6.8 <A HREF = "Section_howto.html#howto_8">TIP4P water model</A> 
-<BR>
-  6.9 <A HREF = "Section_howto.html#howto_9">SPC water model</A> 
-<BR>
-  6.10 <A HREF = "Section_howto.html#howto_10">Coupling LAMMPS to other codes</A> 
-<BR>
-  6.11 <A HREF = "Section_howto.html#howto_11">Visualizing LAMMPS snapshots</A> 
-<BR>
-  6.12 <A HREF = "Section_howto.html#howto_12">Triclinic (non-orthogonal) simulation boxes</A> 
-<BR>
-  6.13 <A HREF = "Section_howto.html#howto_13">NEMD simulations</A> 
-<BR>
-  6.14 <A HREF = "Section_howto.html#howto_14">Finite-size spherical and aspherical particles</A> 
-<BR>
-  6.15 <A HREF = "Section_howto.html#howto_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A> 
-<BR>
-  6.16 <A HREF = "Section_howto.html#howto_16">Thermostatting, barostatting, and compute temperature</A> 
-<BR>
-  6.17 <A HREF = "Section_howto.html#howto_17">Walls</A> 
-<BR>
-  6.18 <A HREF = "Section_howto.html#howto_18">Elastic constants</A> 
-<BR>
-  6.19 <A HREF = "Section_howto.html#howto_19">Library interface to LAMMPS</A> 
-<BR>
-  6.20 <A HREF = "Section_howto.html#howto_20">Calculating thermal conductivity</A> 
-<BR>
-  6.21 <A HREF = "Section_howto.html#howto_21">Calculating viscosity</A> 
-<BR>
-  6.22 <A HREF = "howto_22">Calculating a diffusion coefficient</A> 
-<BR></UL>
-<LI><A HREF = "Section_example.html">Example problems</A> 
-
-<LI><A HREF = "Section_perf.html">Performance & scalability</A> 
-
-<LI><A HREF = "Section_tools.html">Additional tools</A> 
-
-<LI><A HREF = "Section_modify.html">Modifying & extending LAMMPS</A> 
-
-<UL>  10.1 <A HREF = "Section_modify.html#mod_1">Atom styles</A> 
-<BR>
-  10.2 <A HREF = "Section_modify.html#mod_2">Bond, angle, dihedral, improper potentials</A> 
-<BR>
-  10.3 <A HREF = "Section_modify.html#mod_3">Compute styles</A> 
-<BR>
-  10.4 <A HREF = "Section_modify.html#mod_4">Dump styles</A> 
-<BR>
-  10.5 <A HREF = "Section_modify.html#mod_5">Dump custom output options</A> 
-<BR>
-  10.6 <A HREF = "Section_modify.html#mod_6">Fix styles</A> 
-<BR>
-  10.7 <A HREF = "Section_modify.html#mod_7">Input script commands</A> 
-<BR>
-  10.8 <A HREF = "Section_modify.html#mod_8">Kspace computations</A> 
-<BR>
-  10.9 <A HREF = "Section_modify.html#mod_9">Minimization styles</A> 
-<BR>
-  10.10 <A HREF = "Section_modify.html#mod_10">Pairwise potentials</A> 
-<BR>
-  10.11 <A HREF = "Section_modify.html#mod_11">Region styles</A> 
-<BR>
-  10.12 <A HREF = "Section_modify.html#mod_12">Body styles</A> 
-<BR>
-  10.13 <A HREF = "Section_modify.html#mod_13">Thermodynamic output options</A> 
-<BR>
-  10.14 <A HREF = "Section_modify.html#mod_14">Variable options</A> 
-<BR>
-  10.15 <A HREF = "Section_modify.html#mod_15">Submitting new features for inclusion in LAMMPS</A> 
-<BR></UL>
-<LI><A HREF = "Section_python.html">Python interface</A> 
-
-<UL>  11.1 <A HREF = "Section_python.html#py_1">Building LAMMPS as a shared library</A> 
-<BR>
-  11.2 <A HREF = "Section_python.html#py_2">Installing the Python wrapper into Python</A> 
-<BR>
-  11.3 <A HREF = "Section_python.html#py_3">Extending Python with MPI to run in parallel</A> 
-<BR>
-  11.4 <A HREF = "Section_python.html#py_4">Testing the Python-LAMMPS interface</A> 
-<BR>
-  11.5 <A HREF = "Section_python.html#py_5">Using LAMMPS from Python</A> 
-<BR>
-  11.6 <A HREF = "Section_python.html#py_6">Example Python scripts that use LAMMPS</A> 
-<BR></UL>
-<LI><A HREF = "Section_errors.html">Errors</A> 
-
-<UL>  12.1 <A HREF = "Section_errors.html#err_1">Common problems</A> 
-<BR>
-  12.2 <A HREF = "Section_errors.html#err_2">Reporting bugs</A> 
-<BR>
-  12.3 <A HREF = "Section_errors.html#err_3">Error & warning messages</A> 
-<BR></UL>
-<LI><A HREF = "Section_history.html">Future and history</A> 
-
-<UL>  13.1 <A HREF = "Section_history.html#hist_1">Coming attractions</A> 
-<BR>
-  13.2 <A HREF = "Section_history.html#hist_2">Past versions</A> 
-<BR></UL>
-
-</OL>
-
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doc/Manual.txt

@@ -1,257 +0,0 @@
-<HEAD>
-<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="30 Oct 2014 version">
-<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
-<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation.  This software and manual is distributed under the GNU General Public License.">
-</HEAD>
-
-<BODY>
-
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-<H1></H1>
-
-LAMMPS Documentation :c,h3
-30 Oct 2014 version :c,h4
-
-Version info: :h4
-
-The LAMMPS "version" is the date when it was released, such as 1 May
-2010. LAMMPS is updated continuously.  Whenever we fix a bug or add a
-feature, we release it immediately, and post a notice on "this page of
-the WWW site"_bug.  Each dated copy of LAMMPS contains all the
-features and bug-fixes up to and including that version date. The
-version date is printed to the screen and logfile every time you run
-LAMMPS. It is also in the file src/version.h and in the LAMMPS
-directory name created when you unpack a tarball, and at the top of
-the first page of the manual (this page).
-
-If you browse the HTML doc pages on the LAMMPS WWW site, they always
-describe the most current version of LAMMPS. :ulb,l
-
-If you browse the HTML doc pages included in your tarball, they
-describe the version you have. :l
-
-The "PDF file"_Manual.pdf on the WWW site or in the tarball is updated
-about once per month.  This is because it is large, and we don't want
-it to be part of every patch. :l
-
-There is also a "Developer.pdf"_Developer.pdf file in the doc
-directory, which describes the internal structure and algorithms of
-LAMMPS.  :ule,l
-
-LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
-Simulator.
-
-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).
-
-The primary developers of LAMMPS are "Steve Plimpton"_sjp, Aidan
-Thompson, and Paul Crozier who can be contacted at
-sjplimp,athomps,pscrozi at sandia.gov.  The "LAMMPS WWW Site"_lws at
-http://lammps.sandia.gov has more information about the code and its
-uses.
-
-:link(bug,http://lammps.sandia.gov/bug.html)
-:link(sjp,http://www.sandia.gov/~sjplimp)
-
-:line
-
-The LAMMPS documentation is organized into the following sections.  If
-you find errors or omissions in this manual or have suggestions for
-useful information to add, please send an email to the developers so
-we can improve the LAMMPS documentation.
-
-Once you are familiar with LAMMPS, you may want to bookmark "this
-page"_Section_commands.html#comm at Section_commands.html#comm since
-it gives quick access to documentation for all LAMMPS commands.
-
-"PDF file"_Manual.pdf of the entire manual, generated by
-"htmldoc"_http://freecode.com/projects/htmldoc
-
-"Introduction"_Section_intro.html :olb,l
-  1.1 "What is LAMMPS"_intro_1 :ulb,b
-  1.2 "LAMMPS features"_intro_2 :b
-  1.3 "LAMMPS non-features"_intro_3 :b
-  1.4 "Open source distribution"_intro_4 :b
-  1.5 "Acknowledgments and citations"_intro_5 :ule,b
-"Getting started"_Section_start.html :l
-  2.1 "What's in the LAMMPS distribution"_start_1 :ulb,b
-  2.2 "Making LAMMPS"_start_2 :b
-  2.3 "Making LAMMPS with optional packages"_start_3 :b
-  2.4 "Building LAMMPS via the Make.py script"_start_4 :b
-  2.5 "Building LAMMPS as a library"_start_5 :b
-  2.6 "Running LAMMPS"_start_6 :b
-  2.7 "Command-line options"_start_7 :b
-  2.8 "Screen output"_start_8 :b
-  2.9 "Tips for users of previous versions"_start_9 :ule,b
-"Commands"_Section_commands.html :l
-  3.1 "LAMMPS input script"_cmd_1 :ulb,b
-  3.2 "Parsing rules"_cmd_2 :b
-  3.3 "Input script structure"_cmd_3 :b
-  3.4 "Commands listed by category"_cmd_4 :b
-  3.5 "Commands listed alphabetically"_cmd_5 :ule,b
-"Packages"_Section_packages.html :l
-  4.1 "Standard packages"_pkg_1 :ulb,b
-  4.2 "User packages"_pkg_2 :ule,b
-"Accelerating LAMMPS performance"_Section_accelerate.html :l
-  5.1 "Measuring performance"_acc_1 :ulb,b
-  5.2 "Algorithms and code options to boost performace"_acc_2 :b
-  5.3 "Accelerator packages with optimized styles"_acc_3 :b
-    5.3.1 "USER-CUDA package"_accelerate_cuda.html :ulb,b
-    5.3.2 "GPU package"_accelerate_gpu.html :b
-    5.3.3 "USER-INTEL package"_accelerate_intel.html :b
-    5.3.4 "KOKKOS package"_accelerate_kokkos.html :b
-    5.3.5 "USER-OMP package"_accelerate_omp.html :b
-    5.3.6 "OPT package"_accelerate_opt.html :ule,b
-  5.4 "Comparison of various accelerator packages"_acc_4 :ule,b
-"How-to discussions"_Section_howto.html :l
-  6.1 "Restarting a simulation"_howto_1 :ulb,b
-  6.2 "2d simulations"_howto_2 :b
-  6.3 "CHARMM and AMBER force fields"_howto_3 :b
-  6.4 "Running multiple simulations from one input script"_howto_4 :b
-  6.5 "Multi-replica simulations"_howto_5 :b
-  6.6 "Granular models"_howto_6 :b
-  6.7 "TIP3P water model"_howto_7 :b
-  6.8 "TIP4P water model"_howto_8 :b
-  6.9 "SPC water model"_howto_9 :b
-  6.10 "Coupling LAMMPS to other codes"_howto_10 :b
-  6.11 "Visualizing LAMMPS snapshots"_howto_11 :b
-  6.12 "Triclinic (non-orthogonal) simulation boxes"_howto_12 :b
-  6.13 "NEMD simulations"_howto_13 :b
-  6.14 "Finite-size spherical and aspherical particles"_howto_14 :b
-  6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_howto_15 :b
-  6.16 "Thermostatting, barostatting, and compute temperature"_howto_16 :b
-  6.17 "Walls"_howto_17 :b
-  6.18 "Elastic constants"_howto_18 :b
-  6.19 "Library interface to LAMMPS"_howto_19 :b
-  6.20 "Calculating thermal conductivity"_howto_20 :b
-  6.21 "Calculating viscosity"_howto_21 :b
-  6.22 "Calculating a diffusion coefficient"_howto_22 :ule,b
-"Example problems"_Section_example.html :l
-"Performance & scalability"_Section_perf.html :l
-"Additional tools"_Section_tools.html :l
-"Modifying & extending LAMMPS"_Section_modify.html :l
-  10.1 "Atom styles"_mod_1 :ulb,b
-  10.2 "Bond, angle, dihedral, improper potentials"_mod_2 :b
-  10.3 "Compute styles"_mod_3 :b
-  10.4 "Dump styles"_mod_4 :b
-  10.5 "Dump custom output options"_mod_5 :b
-  10.6 "Fix styles"_mod_6 :b
-  10.7 "Input script commands"_mod_7 :b
-  10.8 "Kspace computations"_mod_8 :b
-  10.9 "Minimization styles"_mod_9 :b
-  10.10 "Pairwise potentials"_mod_10 :b
-  10.11 "Region styles"_mod_11 :b
-  10.12 "Body styles"_mod_12 :b
-  10.13 "Thermodynamic output options"_mod_13 :b
-  10.14 "Variable options"_mod_14 :b
-  10.15 "Submitting new features for inclusion in LAMMPS"_mod_15 :ule,b
-"Python interface"_Section_python.html :l
-  11.1 "Building LAMMPS as a shared library"_py_1 :ulb,b
-  11.2 "Installing the Python wrapper into Python"_py_2 :b
-  11.3 "Extending Python with MPI to run in parallel"_py_3 :b
-  11.4 "Testing the Python-LAMMPS interface"_py_4 :b
-  11.5 "Using LAMMPS from Python"_py_5 :b
-  11.6 "Example Python scripts that use LAMMPS"_py_6 :ule,b
-"Errors"_Section_errors.html :l
-  12.1 "Common problems"_err_1 :ulb,b
-  12.2 "Reporting bugs"_err_2 :b
-  12.3 "Error & warning messages"_err_3 :ule,b
-"Future and history"_Section_history.html :l
-  13.1 "Coming attractions"_hist_1 :ulb,b
-  13.2 "Past versions"_hist_2 :ule,b
-:ole
-
-:link(intro_1,Section_intro.html#intro_1)
-:link(intro_2,Section_intro.html#intro_2)
-:link(intro_3,Section_intro.html#intro_3)
-:link(intro_4,Section_intro.html#intro_4)
-:link(intro_5,Section_intro.html#intro_5)
-
-:link(start_1,Section_start.html#start_1)
-:link(start_2,Section_start.html#start_2)
-:link(start_3,Section_start.html#start_3)
-:link(start_4,Section_start.html#start_4)
-:link(start_5,Section_start.html#start_5)
-:link(start_6,Section_start.html#start_6)
-:link(start_7,Section_start.html#start_7)
-:link(start_8,Section_start.html#start_8)
-:link(start_9,Section_start.html#start_9)
-
-:link(cmd_1,Section_commands.html#cmd_1)
-:link(cmd_2,Section_commands.html#cmd_2)
-:link(cmd_3,Section_commands.html#cmd_3)
-:link(cmd_4,Section_commands.html#cmd_4)
-:link(cmd_5,Section_commands.html#cmd_5)
-
-:link(pkg_1,Section_packages.html#pkg_1)
-:link(pkg_2,Section_packages.html#pkg_2)
-
-:link(acc_1,Section_accelerate.html#acc_1)
-:link(acc_2,Section_accelerate.html#acc_2)
-:link(acc_3,Section_accelerate.html#acc_3)
-:link(acc_4,Section_accelerate.html#acc_4)
-
-:link(howto_1,Section_howto.html#howto_1)
-:link(howto_2,Section_howto.html#howto_2)
-:link(howto_3,Section_howto.html#howto_3)
-:link(howto_4,Section_howto.html#howto_4)
-:link(howto_5,Section_howto.html#howto_5)
-:link(howto_6,Section_howto.html#howto_6)
-:link(howto_7,Section_howto.html#howto_7)
-:link(howto_8,Section_howto.html#howto_8)
-:link(howto_9,Section_howto.html#howto_9)
-:link(howto_10,Section_howto.html#howto_10)
-:link(howto_11,Section_howto.html#howto_11)
-:link(howto_12,Section_howto.html#howto_12)
-:link(howto_13,Section_howto.html#howto_13)
-:link(howto_14,Section_howto.html#howto_14)
-:link(howto_15,Section_howto.html#howto_15)
-:link(howto_16,Section_howto.html#howto_16)
-:link(howto_17,Section_howto.html#howto_17)
-:link(howto_18,Section_howto.html#howto_18)
-:link(howto_19,Section_howto.html#howto_19)
-:link(howto_20,Section_howto.html#howto_20)
-:link(howto_21,Section_howto.html#howto_21)
-
-:link(mod_1,Section_modify.html#mod_1)
-:link(mod_2,Section_modify.html#mod_2)
-:link(mod_3,Section_modify.html#mod_3)
-:link(mod_4,Section_modify.html#mod_4)
-:link(mod_5,Section_modify.html#mod_5)
-:link(mod_6,Section_modify.html#mod_6)
-:link(mod_7,Section_modify.html#mod_7)
-:link(mod_8,Section_modify.html#mod_8)
-:link(mod_9,Section_modify.html#mod_9)
-:link(mod_10,Section_modify.html#mod_10)
-:link(mod_11,Section_modify.html#mod_11)
-:link(mod_12,Section_modify.html#mod_12)
-:link(mod_13,Section_modify.html#mod_13)
-:link(mod_14,Section_modify.html#mod_14)
-:link(mod_15,Section_modify.html#mod_15)
-
-:link(py_1,Section_python.html#py_1)
-:link(py_2,Section_python.html#py_2)
-:link(py_3,Section_python.html#py_3)
-:link(py_4,Section_python.html#py_4)
-:link(py_5,Section_python.html#py_5)
-:link(py_6,Section_python.html#py_6)
-
-:link(err_1,Section_errors.html#err_1)
-:link(err_2,Section_errors.html#err_2)
-:link(err_3,Section_errors.html#err_3)
-
-:link(hist_1,Section_history.html#hist_1)
-:link(hist_2,Section_history.html#hist_2)
-
-</BODY>

doc/README

@@ -0,0 +1,115 @@
+LAMMPS Documentation
+
+Depending on how you obtained LAMMPS, this directory has 2 or 3
+sub-directories and optionally 2 PDF files and an ePUB file:
+
+src             content files for LAMMPS documentation
+html            HTML version of the LAMMPS manual (see html/Manual.html)
+tools           tools and settings for building the documentation
+Manual.pdf      large PDF version of entire manual
+Developer.pdf   small PDF with info about how LAMMPS is structured
+LAMMPS.epub     Manual in ePUB format
+
+If you downloaded LAMMPS as a tarball from the web site, all these
+directories and files should be included.
+
+If you downloaded LAMMPS from the public SVN or Git repositories, then
+the HTML and PDF files are not included.  Instead you need to create
+them, in one of three ways:
+
+(a) You can "fetch" the current HTML and PDF files from the LAMMPS web
+site.  Just type "make fetch".  This should create a html_www dir and
+Manual_www.pdf/Developer_www.pdf files.  Note that if new LAMMPS
+features have been added more recently than the date of your version,
+the fetched documentation will include those changes (but your source
+code will not, unless you update your local repository).
+
+(b) You can build the HTML and PDF files yourself, by typing "make
+html" followed by "make pdf".  Note that the PDF make requires the
+HTML files already exist.  This requires various tools including
+Sphinx, which the build process will attempt to download and install
+on your system, if not already available.  See more details below.
+
+(c) You can genererate an older, simpler, less-fancy style of HTML
+documentation by typing "make old".  This will create an "old"
+directory.  This can be useful if (b) does not work on your box for
+some reason, or you want to quickly view the HTML version of a doc
+page you have created or edited yourself within the src directory.
+E.g. if you are planning to submit a new feature to LAMMPS.
+
+----------------
+
+The generation of all documentation is managed by the Makefile in this
+dir.
+
+Options:
+
+make html         # generate HTML in html dir using Sphinx
+make pdf          # generate 2 PDF files (Manual.pdf,Developer.pdf)
+                  #   in this dir via htmldoc and pdflatex
+make old          # generate old-style HTML pages in old dir via txt2html
+make fetch        # fetch HTML doc pages and 2 PDF files from web site
+                  #   as a tarball and unpack into html dir and 2 PDFs
+make epub         # generate LAMMPS.epub in ePUB format using Sphinx 
+make clean        # remove intermediate RST files created by HTML build
+make clean-all    # remove entire build folder and any cached data
+
+----------------
+
+Installing prerequisites for HTML build
+
+To run the HTML documention build toolchain, Python 3 and virtualenv
+have to be installed.  Here are instructions for common setups:
+
+# Ubuntu
+
+sudo apt-get install python-virtualenv
+
+# Fedora (up to version 21)
+# Red Hat Enterprise Linux or CentOS (up to version 7.x)
+
+sudo yum install python3-virtualenv
+
+# Fedora (since version 22)
+
+sudo dnf install python3-virtualenv
+
+# MacOS X
+
+## Python 3
+
+Download the latest Python 3 MacOS X package from
+https://www.python.org and install it.  This will install both Python
+3 and pip3.
+
+## virtualenv
+
+Once Python 3 is installed, open a Terminal and type
+
+pip3 install virtualenv
+
+This will install virtualenv from the Python Package Index.
+
+----------------
+
+Installing prerequisites for PDF build
+
+[TBA]
+
+----------------
+
+Installing prerequisites for epub build
+
+## ePUB
+
+Same as for HTML. This uses the same tools and configuration
+files as the HTML tree.
+
+For converting the generated ePUB file to a mobi format file
+(for e-book readers like Kindle, that cannot read ePUB), you
+also need to have the 'ebook-convert' tool from the "calibre"
+software installed. http://calibre-ebook.com/
+You first create the ePUB file with 'make epub' and then do:
+
+ebook-convert LAMMPS.epub LAMMPS.mobi
+

doc/Scripts/correlate.py

@@ -1,89 +0,0 @@
-#!/usr/bin/env python
-"""
-  function: 
-    parse the block of thermo data in a lammps logfile and perform auto- and 
-    cross correlation of the specified column data.  The total sum of the 
-    correlation is also computed which can be converted to an integral by 
-    multiplying by the timestep. 
-  output:
-    standard output contains column data for the auto- & cross correlations 
-    plus the total sum of each. Note, only the upper triangle of the 
-    correlation matrix is computed.
-  usage: 
-    correlate.py [-c col] <-c col2> <-s max_correlation_time>  [logfile] 
-"""
-import sys
-import re
-import array
-
-# parse command line
-
-maxCorrelationTime = 0
-cols = array.array("I")
-nCols = 0
-args = sys.argv[1:]
-index = 0
-while index < len(args):
-  arg = args[index]
-  index += 1
-  if   (arg == "-c"):
-    cols.append(int(args[index])-1)
-    nCols += 1
-    index += 1
-  elif (arg == "-s"):
-    maxCorrelationTime = int(args[index])
-    index += 1
-  else :
-    filename = arg
-if (nCols < 1): raise RuntimeError, 'no data columns requested'
-data = [array.array("d")]
-for s in range(1,nCols)  : data.append( array.array("d") )
-
-# read data block from log file
-
-start = False
-input = open(filename)
-nSamples = 0
-pattern = re.compile('\d')
-line = input.readline()
-while line :
-  columns = line.split()
-  if (columns and pattern.match(columns[0])) :
-    for i in range(nCols): 
-      data[i].append( float(columns[cols[i]]) )
-    nSamples += 1
-    start = True
-  else :
-     if (start) : break
-  line = input.readline()
-print "# read :",nSamples," samples of ", nCols," data"
-if( maxCorrelationTime < 1): maxCorrelationTime = int(nSamples/2);
- 
-# correlate and integrate
-
-correlationPairs = []
-for i in range(0,nCols):
-  for j in range(i,nCols): # note only upper triangle of the correlation matrix
-    correlationPairs.append([i,j])
-header = "# "
-for k in range(len(correlationPairs)):
-  i = str(correlationPairs[k][0]+1)
-  j = str(correlationPairs[k][1]+1)
-  header += " C"+i+j+" sum_C"+i+j
-print header
-nCorrelationPairs = len(correlationPairs)
-sum = [0.0] * nCorrelationPairs
-for s in range(maxCorrelationTime)  :
-  correlation = [0.0] * nCorrelationPairs
-  nt = nSamples-s
-  for t in range(0,nt)  :
-    for p in range(nCorrelationPairs):
-      i = correlationPairs[p][0]
-      j = correlationPairs[p][1]
-      correlation[p] += data[i][t]*data[j][s+t]
-  output = ""
-  for p in range(0,nCorrelationPairs):
-    correlation[p] /= nt
-    sum[p] += correlation[p]
-    output += str(correlation[p]) + " " + str(sum[p]) + " "
-  print output

doc/Section_accelerate.html

@@ -1,401 +0,0 @@
-<HTML>
-<CENTER><A HREF = "Section_packages.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
-<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_howto.html">Next
-Section</A> 
-</CENTER>
-
-
-
-
-
-
-<HR>
-
-<H3>5. Accelerating LAMMPS performance 
-</H3>
-<P>This section describes various methods for improving LAMMPS
-performance for different classes of problems running on different
-kinds of machines.
-</P>
-<P>There are two thrusts to the discussion that follows.  The
-first is using code options that implement alternate algorithms
-that can speed-up a simulation.  The second is to use one
-of the several accelerator packages provided with LAMMPS that
-contain code optimized for certain kinds of hardware, including
-multi-core CPUs, GPUs, and Intel Xeon Phi coprocessors.
-</P>
-<UL><LI>5.1 <A HREF = "#acc_1">Measuring performance</A> 
-
-<LI>5.2 <A HREF = "#acc_2">Algorithms and code options to boost performace</A> 
-
-<LI>5.3 <A HREF = "#acc_3">Accelerator packages with optimized styles</A> 
-
-<UL><LI>    5.3.1 <A HREF = "accelerate_cuda.html">USER-CUDA package</A> 
-
-<LI>    5.3.2 <A HREF = "accelerate_gpu.html">GPU package</A> 
-
-<LI>    5.3.3 <A HREF = "accelerate_intel.html">USER-INTEL package</A> 
-
-<LI>    5.3.4 <A HREF = "accelerate_kokkos.html">KOKKOS package</A> 
-
-<LI>    5.3.5 <A HREF = "accelerate_omp.html">USER-OMP package</A> 
-
-<LI>    5.3.6 <A HREF = "accelerate_opt.html">OPT package</A> 
-</UL>
-<LI>5.4 <A HREF = "#acc_4">Comparison of various accelerator packages</A> 
-</UL>
-<P>The <A HREF = "http://lammps.sandia.gov/bench.html">Benchmark page</A> of the LAMMPS
-web site gives performance results for the various accelerator
-packages discussed in Section 5.2, for several of the standard LAMMPS
-benchmark problems, as a function of problem size and number of
-compute nodes, on different hardware platforms.
-</P>
-<HR>
-
-<HR>
-
-<H4><A NAME = "acc_1"></A>5.1 Measuring performance 
-</H4>
-<P>Before trying to make your simulation run faster, you should
-understand how it currently performs and where the bottlenecks are.
-</P>
-<P>The best way to do this is run the your system (actual number of
-atoms) for a modest number of timesteps (say 100 steps) on several
-different processor counts, including a single processor if possible.
-Do this for an equilibrium version of your system, so that the
-100-step timings are representative of a much longer run.  There is
-typically no need to run for 1000s of timesteps to get accurate
-timings; you can simply extrapolate from short runs.
-</P>
-<P>For the set of runs, look at the timing data printed to the screen and
-log file at the end of each LAMMPS run.  <A HREF = "Section_start.html#start_8">This
-section</A> of the manual has an overview.
-</P>
-<P>Running on one (or a few processors) should give a good estimate of
-the serial performance and what portions of the timestep are taking
-the most time.  Running the same problem on a few different processor
-counts should give an estimate of parallel scalability.  I.e. if the
-simulation runs 16x faster on 16 processors, its 100% parallel
-efficient; if it runs 8x faster on 16 processors, it's 50% efficient.
-</P>
-<P>The most important data to look at in the timing info is the timing
-breakdown and relative percentages.  For example, trying different
-options for speeding up the long-range solvers will have little impact
-if they only consume 10% of the run time.  If the pairwise time is
-dominating, you may want to look at GPU or OMP versions of the pair
-style, as discussed below.  Comparing how the percentages change as
-you increase the processor count gives you a sense of how different
-operations within the timestep are scaling.  Note that if you are
-running with a Kspace solver, there is additional output on the
-breakdown of the Kspace time.  For PPPM, this includes the fraction
-spent on FFTs, which can be communication intensive.
-</P>
-<P>Another important detail in the timing info are the histograms of
-atoms counts and neighbor counts.  If these vary widely across
-processors, you have a load-imbalance issue.  This often results in
-inaccurate relative timing data, because processors have to wait when
-communication occurs for other processors to catch up.  Thus the
-reported times for "Communication" or "Other" may be higher than they
-really are, due to load-imbalance.  If this is an issue, you can
-uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile
-LAMMPS, to obtain synchronized timings.
-</P>
-<HR>
-
-<H4><A NAME = "acc_2"></A>5.2 General strategies 
-</H4>
-<P>NOTE: this section 5.2 is still a work in progress
-</P>
-<P>Here is a list of general ideas for improving simulation performance.
-Most of them are only applicable to certain models and certain
-bottlenecks in the current performance, so let the timing data you
-generate be your guide.  It is hard, if not impossible, to predict how
-much difference these options will make, since it is a function of
-problem size, number of processors used, and your machine.  There is
-no substitute for identifying performance bottlenecks, and trying out
-various options.
-</P>
-<UL><LI>rRESPA
-<LI>2-FFT PPPM
-<LI>Staggered PPPM
-<LI>single vs double PPPM
-<LI>partial charge PPPM
-<LI>verlet/split run style
-<LI>processor command for proc layout and numa layout
-<LI>load-balancing: balance and fix balance 
-</UL>
-<P>2-FFT PPPM, also called <I>analytic differentiation</I> or <I>ad</I> PPPM, uses
-2 FFTs instead of the 4 FFTs used by the default <I>ik differentiation</I>
-PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to
-achieve the same accuracy as 4-FFT PPPM. For problems where the FFT
-cost is the performance bottleneck (typically large problems running
-on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM.
-</P>
-<P>Staggered PPPM performs calculations using two different meshes, one
-shifted slightly with respect to the other.  This can reduce force
-aliasing errors and increase the accuracy of the method, but also
-doubles the amount of work required. For high relative accuracy, using
-staggered PPPM allows one to half the mesh size in each dimension as
-compared to regular PPPM, which can give around a 4x speedup in the
-kspace time. However, for low relative accuracy, using staggered PPPM
-gives little benefit and can be up to 2x slower in the kspace
-time. For example, the rhodopsin benchmark was run on a single
-processor, and results for kspace time vs. relative accuracy for the
-different methods are shown in the figure below.  For this system,
-staggered PPPM (using ik differentiation) becomes useful when using a
-relative accuracy of slightly greater than 1e-5 and above.
-</P>
-<CENTER><IMG SRC = "JPG/rhodo_staggered.jpg">
-</CENTER>
-<P>IMPORTANT NOTE: Using staggered PPPM may not give the same increase in
-accuracy of energy and pressure as it does in forces, so some caution
-must be used if energy and/or pressure are quantities of interest,
-such as when using a barostat.
-</P>
-<HR>
-
-<H4><A NAME = "acc_3"></A>5.3 Packages with optimized styles 
-</H4>
-<P>Accelerated versions of various <A HREF = "pair_style.html">pair_style</A>,
-<A HREF = "fix.html">fixes</A>, <A HREF = "compute.html">computes</A>, and other commands have
-been added to LAMMPS, which will typically run faster than the
-standard non-accelerated versions.  Some require appropriate hardware
-to be present on your system, e.g. GPUs or Intel Xeon Phi
-coprocessors.
-</P>
-<P>All of these commands are in packages provided with LAMMPS.  An
-overview of packages is give in <A HREF = "Section_packages.html">Section
-packages</A>.  These are the accelerator packages
-currently in LAMMPS, either as standard or user packages:
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR><TD ><A HREF = "accelerate_cuda.html">USER-CUDA</A> </TD><TD > for NVIDIA GPUs</TD></TR>
-<TR><TD ><A HREF = "accelerate_gpu.html">GPU</A> </TD><TD > for NVIDIA GPUs as well as OpenCL support</TD></TR>
-<TR><TD ><A HREF = "accelerate_intel.html">USER-INTEL</A> </TD><TD > for Intel CPUs and Intel Xeon Phi</TD></TR>
-<TR><TD ><A HREF = "accelerate_kokkos.html">KOKKOS</A> </TD><TD > for GPUs, Intel Xeon Phi, and OpenMP threading</TD></TR>
-<TR><TD ><A HREF = "accelerate_omp.html">USER-OMP</A> </TD><TD > for OpenMP threading</TD></TR>
-<TR><TD ><A HREF = "accelerate_opt.html">OPT</A> </TD><TD > generic CPU optimizations 
-</TD></TR></TABLE></DIV>
-
-<P>Any accelerated style has the same name as the corresponding standard
-style, except that a suffix is appended.  Otherwise, the syntax for
-the command that uses the style is identical, their functionality is
-the same, and the numerical results it produces should also be the
-same, except for precision and round-off effects.
-</P>
-<P>For example, all of these styles are accelerated variants of the
-Lennard-Jones <A HREF = "pair_lj.html">pair_style lj/cut</A>:
-</P>
-<UL><LI><A HREF = "pair_lj.html">pair_style lj/cut/cuda</A>
-<LI><A HREF = "pair_lj.html">pair_style lj/cut/gpu</A>
-<LI><A HREF = "pair_lj.html">pair_style lj/cut/intel</A>
-<LI><A HREF = "pair_lj.html">pair_style lj/cut/kk</A>
-<LI><A HREF = "pair_lj.html">pair_style lj/cut/omp</A>
-<LI><A HREF = "pair_lj.html">pair_style lj/cut/opt</A> 
-</UL>
-<P>To see what accelerate styles are currently available, see
-<A HREF = "Section_commands.html#cmd_5">Section_commands 5</A> of the manual.  The
-doc pages for individual commands (e.g. <A HREF = "pair_lj.html">pair lj/cut</A> or
-<A HREF = "fix_nve.html">fix nve</A>) also list any accelerated variants available
-for that style.
-</P>
-<P>To use an accelerator package in LAMMPS, and one or more of the styles
-it provides, follow these general steps.  Details vary from package to
-package and are explained in the individual accelerator doc pages,
-listed above:
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR><TD >build the accelerator library </TD><TD >  only for USER-CUDA and GPU packages </TD></TR>
-<TR><TD >install the accelerator package </TD><TD >  make yes-opt, make yes-user-intel, etc </TD></TR>
-<TR><TD >add compile/link flags to Makefile.machine </TD><TD >  in src/MAKE, <br>  only for USER-INTEL, KOKKOS, USER-OMP packages </TD></TR>
-<TR><TD >re-build LAMMPS </TD><TD >  make machine </TD></TR>
-<TR><TD >run a LAMMPS simulation </TD><TD >  lmp_machine < in.script </TD></TR>
-<TR><TD >enable the accelerator package </TD><TD >  via "-c on" and "-k on" <A HREF = "Section_start.html#start_7">command-line switches</A>, <br>  only for USER-CUDA and KOKKOS packages </TD></TR>
-<TR><TD >set any needed options for the package </TD><TD >  via "-pk" <A HREF = "Section_start.html#start_7">command-line switch</A> or  <A HREF = "package.html">package</A> command, <br>  only if defaults need to be changed </TD></TR>
-<TR><TD >use accelerated styles in your input script </TD><TD >  via "-sf" <A HREF = "Section_start.html#start_7">command-line switch</A> or  <A HREF = "suffix.html">suffix</A> command 
-</TD></TR></TABLE></DIV>
-
-<P>The first 4 steps can be done as a single command, using the
-src/Make.py tool.  The Make.py tool is discussed in <A HREF = "Section_start.html#start_4">Section
-2.4</A> of the manual, and its use is
-illustrated in the individual accelerator sections.  Typically these
-steps only need to be done once, to create an executable that uses one
-or more accelerator packages.
-</P>
-<P>The last 4 steps can all be done from the command-line when LAMMPS is
-launched, without changing your input script, as illustrated in the
-individual accelerator sections.  Or you can add
-<A HREF = "package.html">package</A> and <A HREF = "suffix.html">suffix</A> commands to your input
-script.
-</P>
-<P>IMPORTANT NOTE: With a few exceptions, you can build a single LAMMPS
-executable with all its accelerator packages installed.  Note that the
-USER-INTEL and KOKKOS packages require you to choose one of their
-options when building.  I.e. CPU or Phi for USER-INTEL.  OpenMP, Cuda,
-or Phi for KOKKOS.  Here are the exceptions; you cannot build a single
-executable with:
-</P>
-<UL><LI>both the USER-INTEL Phi and KOKKOS Phi options
-<LI>the USER-INTEL Phi or Kokkos Phi option, and either the USER-CUDA or GPU packages 
-</UL>
-<P>See the examples/accelerate/README and make.list files for sample
-Make.py commands that build LAMMPS with any or all of the accelerator
-packages.  As an example, here is a command that builds with all the
-GPU related packages installed (USER-CUDA, GPU, KOKKOS with Cuda),
-including settings to build the needed auxiliary USER-CUDA and GPU
-libraries for Kepler GPUs:
-</P>
-<PRE>Make.py -j 16 -p omp gpu cuda kokkos -cc nvcc wrap=mpi   -cuda mode=double arch=35 -gpu mode=double arch=35 \  -kokkos cuda arch=35 lib-all file mpi 
-</PRE>
-<P>The examples/accelerate directory also has input scripts that can be
-used with all of the accelerator packages.  See its README file for
-details.
-</P>
-<P>Likewise, the bench directory has FERMI and KEPLER and PHI
-sub-directories with Make.py commands and input scripts for using all
-the accelerator packages on various machines.  See the README files in
-those dirs.
-</P>
-<P>As mentioned above, the <A HREF = "http://lammps.sandia.gov/bench.html">Benchmark
-page</A> of the LAMMPS web site gives
-performance results for the various accelerator packages for several
-of the standard LAMMPS benchmark problems, as a function of problem
-size and number of compute nodes, on different hardware platforms.
-</P>
-<P>Here is a brief summary of what the various packages provide.  Details
-are in the individual accelerator sections.
-</P>
-<UL><LI>Styles with a "cuda" or "gpu" suffix are part of the USER-CUDA or GPU
-packages, and can be run on NVIDIA GPUs.  The speed-up on a GPU
-depends on a variety of factors, discussed in the accelerator
-sections. 
-
-<LI>Styles with an "intel" suffix are part of the USER-INTEL
-package. These styles support vectorized single and mixed precision
-calculations, in addition to full double precision.  In extreme cases,
-this can provide speedups over 3.5x on CPUs.  The package also
-supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM)
-coprocessors.  This can result in additional speedup over 2x depending
-on the hardware configuration. 
-
-<LI>Styles with a "kk" suffix are part of the KOKKOS package, and can be
-run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel
-Xeon Phi in "native" mode.  The speed-up depends on a variety of
-factors, as discussed on the KOKKOS accelerator page. 
-
-<LI>Styles with an "omp" suffix are part of the USER-OMP package and allow
-a pair-style to be run in multi-threaded mode using OpenMP.  This can
-be useful on nodes with high-core counts when using less MPI processes
-than cores is advantageous, e.g. when running with PPPM so that FFTs
-are run on fewer MPI processors or when the many MPI tasks would
-overload the available bandwidth for communication. 
-
-<LI>Styles with an "opt" suffix are part of the OPT package and typically
-speed-up the pairwise calculations of your simulation by 5-25% on a
-CPU. 
-</UL>
-<P>The individual accelerator package doc pages explain:
-</P>
-<UL><LI>what hardware and software the accelerated package requires
-<LI>how to build LAMMPS with the accelerated package
-<LI>how to run with the accelerated package either via command-line switches or modifying the input script
-<LI>speed-ups to expect
-<LI>guidelines for best performance
-<LI>restrictions 
-</UL>
-<HR>
-
-<H4><A NAME = "acc_4"></A>5.4 Comparison of various accelerator packages 
-</H4>
-<P>NOTE: this section still needs to be re-worked with additional KOKKOS
-and USER-INTEL information.
-</P>
-<P>The next section compares and contrasts the various accelerator
-options, since there are multiple ways to perform OpenMP threading,
-run on GPUs, and run on Intel Xeon Phi coprocessors.
-</P>
-<P>All 3 of these packages accelerate a LAMMPS calculation using NVIDIA
-hardware, but they do it in different ways.
-</P>
-<P>As a consequence, for a particular simulation on specific hardware,
-one package may be faster than the other.  We give guidelines below,
-but the best way to determine which package is faster for your input
-script is to try both of them on your machine.  See the benchmarking
-section below for examples where this has been done.
-</P>
-<P><B>Guidelines for using each package optimally:</B>
-</P>
-<UL><LI>The GPU package allows you to assign multiple CPUs (cores) to a single
-GPU (a common configuration for "hybrid" nodes that contain multicore
-CPU(s) and GPU(s)) and works effectively in this mode.  The USER-CUDA
-package does not allow this; you can only use one CPU per GPU. 
-
-<LI>The GPU package moves per-atom data (coordinates, forces)
-back-and-forth between the CPU and GPU every timestep.  The USER-CUDA
-package only does this on timesteps when a CPU calculation is required
-(e.g. to invoke a fix or compute that is non-GPU-ized).  Hence, if you
-can formulate your input script to only use GPU-ized fixes and
-computes, and avoid doing I/O too often (thermo output, dump file
-snapshots, restart files), then the data transfer cost of the
-USER-CUDA package can be very low, causing it to run faster than the
-GPU package. 
-
-<LI>The GPU package is often faster than the USER-CUDA package, if the
-number of atoms per GPU is "small".  The crossover point, in terms of
-atoms/GPU at which the USER-CUDA package becomes faster depends
-strongly on the pair style.  For example, for a simple Lennard Jones
-system the crossover (in single precision) is often about 50K-100K
-atoms per GPU.  When performing double precision calculations the
-crossover point can be significantly smaller. 
-
-<LI>Both packages compute bonded interactions (bonds, angles, etc) on the
-CPU.  This means a model with bonds will force the USER-CUDA package
-to transfer per-atom data back-and-forth between the CPU and GPU every
-timestep.  If the GPU package is running with several MPI processes
-assigned to one GPU, the cost of computing the bonded interactions is
-spread across more CPUs and hence the GPU package can run faster. 
-
-<LI>When using the GPU package with multiple CPUs assigned to one GPU, its
-performance depends to some extent on high bandwidth between the CPUs
-and the GPU.  Hence its performance is affected if full 16 PCIe lanes
-are not available for each GPU.  In HPC environments this can be the
-case if S2050/70 servers are used, where two devices generally share
-one PCIe 2.0 16x slot.  Also many multi-GPU mainboards do not provide
-full 16 lanes to each of the PCIe 2.0 16x slots. 
-</UL>
-<P><B>Differences between the two packages:</B>
-</P>
-<UL><LI>The GPU package accelerates only pair force, neighbor list, and PPPM
-calculations.  The USER-CUDA package currently supports a wider range
-of pair styles and can also accelerate many fix styles and some
-compute styles, as well as neighbor list and PPPM calculations. 
-
-<LI>The USER-CUDA package does not support acceleration for minimization. 
-
-<LI>The USER-CUDA package does not support hybrid pair styles. 
-
-<LI>The USER-CUDA package can order atoms in the neighbor list differently
-from run to run resulting in a different order for force accumulation. 
-
-<LI>The USER-CUDA package has a limit on the number of atom types that can be
-used in a simulation. 
-
-<LI>The GPU package requires neighbor lists to be built on the CPU when using
-exclusion lists or a triclinic simulation box. 
-
-<LI>The GPU package uses more GPU memory than the USER-CUDA package.  This
-is generally not a problem since typical runs are computation-limited
-rather than memory-limited. 
-</UL>
-<P><B>Examples:</B>
-</P>
-<P>The LAMMPS distribution has two directories with sample input scripts
-for the GPU and USER-CUDA packages.
-</P>
-<UL><LI>lammps/examples/gpu = GPU package files
-<LI>lammps/examples/USER/cuda = USER-CUDA package files 
-</UL>
-<P>These contain input scripts for identical systems, so they can be used
-to benchmark the performance of both packages on your system.
-</P>
-</HTML>

doc/Section_accelerate.txt

@@ -1,397 +0,0 @@
-"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
-Section"_Section_howto.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-5. Accelerating LAMMPS performance :h3
-
-This section describes various methods for improving LAMMPS
-performance for different classes of problems running on different
-kinds of machines.
-
-There are two thrusts to the discussion that follows.  The
-first is using code options that implement alternate algorithms
-that can speed-up a simulation.  The second is to use one
-of the several accelerator packages provided with LAMMPS that
-contain code optimized for certain kinds of hardware, including
-multi-core CPUs, GPUs, and Intel Xeon Phi coprocessors.
-
-5.1 "Measuring performance"_#acc_1 :ulb,l
-5.2 "Algorithms and code options to boost performace"_#acc_2 :l
-5.3 "Accelerator packages with optimized styles"_#acc_3 :l
-    5.3.1 "USER-CUDA package"_accelerate_cuda.html :ulb,l
-    5.3.2 "GPU package"_accelerate_gpu.html :l
-    5.3.3 "USER-INTEL package"_accelerate_intel.html :l
-    5.3.4 "KOKKOS package"_accelerate_kokkos.html :l
-    5.3.5 "USER-OMP package"_accelerate_omp.html :l
-    5.3.6 "OPT package"_accelerate_opt.html :l,ule
-5.4 "Comparison of various accelerator packages"_#acc_4 :l,ule
-
-The "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS
-web site gives performance results for the various accelerator
-packages discussed in Section 5.2, for several of the standard LAMMPS
-benchmark problems, as a function of problem size and number of
-compute nodes, on different hardware platforms.
-
-:line
-:line
-
-5.1 Measuring performance :h4,link(acc_1)
-
-Before trying to make your simulation run faster, you should
-understand how it currently performs and where the bottlenecks are.
-
-The best way to do this is run the your system (actual number of
-atoms) for a modest number of timesteps (say 100 steps) on several
-different processor counts, including a single processor if possible.
-Do this for an equilibrium version of your system, so that the
-100-step timings are representative of a much longer run.  There is
-typically no need to run for 1000s of timesteps to get accurate
-timings; you can simply extrapolate from short runs.
-
-For the set of runs, look at the timing data printed to the screen and
-log file at the end of each LAMMPS run.  "This
-section"_Section_start.html#start_8 of the manual has an overview.
-
-Running on one (or a few processors) should give a good estimate of
-the serial performance and what portions of the timestep are taking
-the most time.  Running the same problem on a few different processor
-counts should give an estimate of parallel scalability.  I.e. if the
-simulation runs 16x faster on 16 processors, its 100% parallel
-efficient; if it runs 8x faster on 16 processors, it's 50% efficient.
-
-The most important data to look at in the timing info is the timing
-breakdown and relative percentages.  For example, trying different
-options for speeding up the long-range solvers will have little impact
-if they only consume 10% of the run time.  If the pairwise time is
-dominating, you may want to look at GPU or OMP versions of the pair
-style, as discussed below.  Comparing how the percentages change as
-you increase the processor count gives you a sense of how different
-operations within the timestep are scaling.  Note that if you are
-running with a Kspace solver, there is additional output on the
-breakdown of the Kspace time.  For PPPM, this includes the fraction
-spent on FFTs, which can be communication intensive.
-
-Another important detail in the timing info are the histograms of
-atoms counts and neighbor counts.  If these vary widely across
-processors, you have a load-imbalance issue.  This often results in
-inaccurate relative timing data, because processors have to wait when
-communication occurs for other processors to catch up.  Thus the
-reported times for "Communication" or "Other" may be higher than they
-really are, due to load-imbalance.  If this is an issue, you can
-uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile
-LAMMPS, to obtain synchronized timings.
-
-:line
-
-5.2 General strategies :h4,link(acc_2)
-
-NOTE: this section 5.2 is still a work in progress
-
-Here is a list of general ideas for improving simulation performance.
-Most of them are only applicable to certain models and certain
-bottlenecks in the current performance, so let the timing data you
-generate be your guide.  It is hard, if not impossible, to predict how
-much difference these options will make, since it is a function of
-problem size, number of processors used, and your machine.  There is
-no substitute for identifying performance bottlenecks, and trying out
-various options.
-
-rRESPA
-2-FFT PPPM
-Staggered PPPM
-single vs double PPPM
-partial charge PPPM
-verlet/split run style
-processor command for proc layout and numa layout
-load-balancing: balance and fix balance :ul
-
-2-FFT PPPM, also called {analytic differentiation} or {ad} PPPM, uses
-2 FFTs instead of the 4 FFTs used by the default {ik differentiation}
-PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to
-achieve the same accuracy as 4-FFT PPPM. For problems where the FFT
-cost is the performance bottleneck (typically large problems running
-on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM.
-  
-Staggered PPPM performs calculations using two different meshes, one
-shifted slightly with respect to the other.  This can reduce force
-aliasing errors and increase the accuracy of the method, but also
-doubles the amount of work required. For high relative accuracy, using
-staggered PPPM allows one to half the mesh size in each dimension as
-compared to regular PPPM, which can give around a 4x speedup in the
-kspace time. However, for low relative accuracy, using staggered PPPM
-gives little benefit and can be up to 2x slower in the kspace
-time. For example, the rhodopsin benchmark was run on a single
-processor, and results for kspace time vs. relative accuracy for the
-different methods are shown in the figure below.  For this system,
-staggered PPPM (using ik differentiation) becomes useful when using a
-relative accuracy of slightly greater than 1e-5 and above.
-
-:c,image(JPG/rhodo_staggered.jpg)
-
-IMPORTANT NOTE: Using staggered PPPM may not give the same increase in
-accuracy of energy and pressure as it does in forces, so some caution
-must be used if energy and/or pressure are quantities of interest,
-such as when using a barostat.
-
-:line
-
-5.3 Packages with optimized styles :h4,link(acc_3)
-
-Accelerated versions of various "pair_style"_pair_style.html,
-"fixes"_fix.html, "computes"_compute.html, and other commands have
-been added to LAMMPS, which will typically run faster than the
-standard non-accelerated versions.  Some require appropriate hardware
-to be present on your system, e.g. GPUs or Intel Xeon Phi
-coprocessors.
-
-All of these commands are in packages provided with LAMMPS.  An
-overview of packages is give in "Section
-packages"_Section_packages.html.  These are the accelerator packages
-currently in LAMMPS, either as standard or user packages:
-
-"USER-CUDA"_accelerate_cuda.html : for NVIDIA GPUs
-"GPU"_accelerate_gpu.html : for NVIDIA GPUs as well as OpenCL support
-"USER-INTEL"_accelerate_intel.html : for Intel CPUs and Intel Xeon Phi
-"KOKKOS"_accelerate_kokkos.html : for GPUs, Intel Xeon Phi, and OpenMP threading
-"USER-OMP"_accelerate_omp.html : for OpenMP threading
-"OPT"_accelerate_opt.html : generic CPU optimizations :tb(s=:)
-
-Any accelerated style has the same name as the corresponding standard
-style, except that a suffix is appended.  Otherwise, the syntax for
-the command that uses the style is identical, their functionality is
-the same, and the numerical results it produces should also be the
-same, except for precision and round-off effects.
-
-For example, all of these styles are accelerated variants of the
-Lennard-Jones "pair_style lj/cut"_pair_lj.html:
-
-"pair_style lj/cut/cuda"_pair_lj.html
-"pair_style lj/cut/gpu"_pair_lj.html
-"pair_style lj/cut/intel"_pair_lj.html
-"pair_style lj/cut/kk"_pair_lj.html
-"pair_style lj/cut/omp"_pair_lj.html
-"pair_style lj/cut/opt"_pair_lj.html :ul
-
-To see what accelerate styles are currently available, see
-"Section_commands 5"_Section_commands.html#cmd_5 of the manual.  The
-doc pages for individual commands (e.g. "pair lj/cut"_pair_lj.html or
-"fix nve"_fix_nve.html) also list any accelerated variants available
-for that style.
-
-To use an accelerator package in LAMMPS, and one or more of the styles
-it provides, follow these general steps.  Details vary from package to
-package and are explained in the individual accelerator doc pages,
-listed above:
-
-build the accelerator library |
-  only for USER-CUDA and GPU packages |
-install the accelerator package |
-  make yes-opt, make yes-user-intel, etc |
-add compile/link flags to Makefile.machine |
-  in src/MAKE, <br>
-  only for USER-INTEL, KOKKOS, USER-OMP packages |
-re-build LAMMPS |
-  make machine |
-run a LAMMPS simulation |
-  lmp_machine < in.script |
-enable the accelerator package |
-  via "-c on" and "-k on" "command-line switches"_Section_start.html#start_7, <br>
-  only for USER-CUDA and KOKKOS packages |
-set any needed options for the package |
-  via "-pk" "command-line switch"_Section_start.html#start_7 or
-  "package"_package.html command, <br>
-  only if defaults need to be changed |
-use accelerated styles in your input script |
-  via "-sf" "command-line switch"_Section_start.html#start_7 or
-  "suffix"_suffix.html command :tb(c=2,s=|)
-
-The first 4 steps can be done as a single command, using the
-src/Make.py tool.  The Make.py tool is discussed in "Section
-2.4"_Section_start.html#start_4 of the manual, and its use is
-illustrated in the individual accelerator sections.  Typically these
-steps only need to be done once, to create an executable that uses one
-or more accelerator packages.
-
-The last 4 steps can all be done from the command-line when LAMMPS is
-launched, without changing your input script, as illustrated in the
-individual accelerator sections.  Or you can add
-"package"_package.html and "suffix"_suffix.html commands to your input
-script.
-
-IMPORTANT NOTE: With a few exceptions, you can build a single LAMMPS
-executable with all its accelerator packages installed.  Note that the
-USER-INTEL and KOKKOS packages require you to choose one of their
-options when building.  I.e. CPU or Phi for USER-INTEL.  OpenMP, Cuda,
-or Phi for KOKKOS.  Here are the exceptions; you cannot build a single
-executable with:
-
-both the USER-INTEL Phi and KOKKOS Phi options
-the USER-INTEL Phi or Kokkos Phi option, and either the USER-CUDA or GPU packages :ul
-
-See the examples/accelerate/README and make.list files for sample
-Make.py commands that build LAMMPS with any or all of the accelerator
-packages.  As an example, here is a command that builds with all the
-GPU related packages installed (USER-CUDA, GPU, KOKKOS with Cuda),
-including settings to build the needed auxiliary USER-CUDA and GPU
-libraries for Kepler GPUs:
-
-Make.py -j 16 -p omp gpu cuda kokkos -cc nvcc wrap=mpi \
-  -cuda mode=double arch=35 -gpu mode=double arch=35 \\
-  -kokkos cuda arch=35 lib-all file mpi :pre
-
-The examples/accelerate directory also has input scripts that can be
-used with all of the accelerator packages.  See its README file for
-details.
-
-Likewise, the bench directory has FERMI and KEPLER and PHI
-sub-directories with Make.py commands and input scripts for using all
-the accelerator packages on various machines.  See the README files in
-those dirs.
-
-As mentioned above, the "Benchmark
-page"_http://lammps.sandia.gov/bench.html of the LAMMPS web site gives
-performance results for the various accelerator packages for several
-of the standard LAMMPS benchmark problems, as a function of problem
-size and number of compute nodes, on different hardware platforms.
-
-Here is a brief summary of what the various packages provide.  Details
-are in the individual accelerator sections.
-
-Styles with a "cuda" or "gpu" suffix are part of the USER-CUDA or GPU
-packages, and can be run on NVIDIA GPUs.  The speed-up on a GPU
-depends on a variety of factors, discussed in the accelerator
-sections. :ulb,l
-
-Styles with an "intel" suffix are part of the USER-INTEL
-package. These styles support vectorized single and mixed precision
-calculations, in addition to full double precision.  In extreme cases,
-this can provide speedups over 3.5x on CPUs.  The package also
-supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM)
-coprocessors.  This can result in additional speedup over 2x depending
-on the hardware configuration. :l
-
-Styles with a "kk" suffix are part of the KOKKOS package, and can be
-run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel
-Xeon Phi in "native" mode.  The speed-up depends on a variety of
-factors, as discussed on the KOKKOS accelerator page. :l
-
-Styles with an "omp" suffix are part of the USER-OMP package and allow
-a pair-style to be run in multi-threaded mode using OpenMP.  This can
-be useful on nodes with high-core counts when using less MPI processes
-than cores is advantageous, e.g. when running with PPPM so that FFTs
-are run on fewer MPI processors or when the many MPI tasks would
-overload the available bandwidth for communication. :l
-
-Styles with an "opt" suffix are part of the OPT package and typically
-speed-up the pairwise calculations of your simulation by 5-25% on a
-CPU. :l,ule
-
-The individual accelerator package doc pages explain:
-
-what hardware and software the accelerated package requires
-how to build LAMMPS with the accelerated package
-how to run with the accelerated package either via command-line switches or modifying the input script
-speed-ups to expect
-guidelines for best performance
-restrictions :ul
-
-:line
-
-5.4 Comparison of various accelerator packages :h4,link(acc_4)
-
-NOTE: this section still needs to be re-worked with additional KOKKOS
-and USER-INTEL information.
-
-The next section compares and contrasts the various accelerator
-options, since there are multiple ways to perform OpenMP threading,
-run on GPUs, and run on Intel Xeon Phi coprocessors.
-
-All 3 of these packages accelerate a LAMMPS calculation using NVIDIA
-hardware, but they do it in different ways.
-
-As a consequence, for a particular simulation on specific hardware,
-one package may be faster than the other.  We give guidelines below,
-but the best way to determine which package is faster for your input
-script is to try both of them on your machine.  See the benchmarking
-section below for examples where this has been done.
-
-[Guidelines for using each package optimally:]
-
-The GPU package allows you to assign multiple CPUs (cores) to a single
-GPU (a common configuration for "hybrid" nodes that contain multicore
-CPU(s) and GPU(s)) and works effectively in this mode.  The USER-CUDA
-package does not allow this; you can only use one CPU per GPU. :ulb,l
-
-The GPU package moves per-atom data (coordinates, forces)
-back-and-forth between the CPU and GPU every timestep.  The USER-CUDA
-package only does this on timesteps when a CPU calculation is required
-(e.g. to invoke a fix or compute that is non-GPU-ized).  Hence, if you
-can formulate your input script to only use GPU-ized fixes and
-computes, and avoid doing I/O too often (thermo output, dump file
-snapshots, restart files), then the data transfer cost of the
-USER-CUDA package can be very low, causing it to run faster than the
-GPU package. :l
-
-The GPU package is often faster than the USER-CUDA package, if the
-number of atoms per GPU is "small".  The crossover point, in terms of
-atoms/GPU at which the USER-CUDA package becomes faster depends
-strongly on the pair style.  For example, for a simple Lennard Jones
-system the crossover (in single precision) is often about 50K-100K
-atoms per GPU.  When performing double precision calculations the
-crossover point can be significantly smaller. :l
-
-Both packages compute bonded interactions (bonds, angles, etc) on the
-CPU.  This means a model with bonds will force the USER-CUDA package
-to transfer per-atom data back-and-forth between the CPU and GPU every
-timestep.  If the GPU package is running with several MPI processes
-assigned to one GPU, the cost of computing the bonded interactions is
-spread across more CPUs and hence the GPU package can run faster. :l
-
-When using the GPU package with multiple CPUs assigned to one GPU, its
-performance depends to some extent on high bandwidth between the CPUs
-and the GPU.  Hence its performance is affected if full 16 PCIe lanes
-are not available for each GPU.  In HPC environments this can be the
-case if S2050/70 servers are used, where two devices generally share
-one PCIe 2.0 16x slot.  Also many multi-GPU mainboards do not provide
-full 16 lanes to each of the PCIe 2.0 16x slots. :l,ule
-
-[Differences between the two packages:]
-
-The GPU package accelerates only pair force, neighbor list, and PPPM
-calculations.  The USER-CUDA package currently supports a wider range
-of pair styles and can also accelerate many fix styles and some
-compute styles, as well as neighbor list and PPPM calculations. :ulb,l
-
-The USER-CUDA package does not support acceleration for minimization. :l
-
-The USER-CUDA package does not support hybrid pair styles. :l
-
-The USER-CUDA package can order atoms in the neighbor list differently
-from run to run resulting in a different order for force accumulation. :l
-
-The USER-CUDA package has a limit on the number of atom types that can be
-used in a simulation. :l
-
-The GPU package requires neighbor lists to be built on the CPU when using
-exclusion lists or a triclinic simulation box. :l
-
-The GPU package uses more GPU memory than the USER-CUDA package.  This
-is generally not a problem since typical runs are computation-limited
-rather than memory-limited. :l,ule
-
-[Examples:]
-
-The LAMMPS distribution has two directories with sample input scripts
-for the GPU and USER-CUDA packages.
-
-lammps/examples/gpu = GPU package files
-lammps/examples/USER/cuda = USER-CUDA package files :ul
-
-These contain input scripts for identical systems, so they can be used
-to benchmark the performance of both packages on your system.

doc/Section_commands.html

@@ -1,643 +0,0 @@
-<HTML>
-<CENTER><A HREF = "Section_start.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_packages.html">Next Section</A> 
-</CENTER>
-
-
-
-
-
-
-<HR>
-
-<H3>3. Commands 
-</H3>
-<P>This section describes how a LAMMPS input script is formatted and the
-input script commands used to define a LAMMPS simulation.
-</P>
-3.1 <A HREF = "#cmd_1">LAMMPS input script</A><BR>
-3.2 <A HREF = "#cmd_2">Parsing rules</A><BR>
-3.3 <A HREF = "#cmd_3">Input script structure</A><BR>
-3.4 <A HREF = "#cmd_4">Commands listed by category</A><BR>
-3.5 <A HREF = "#cmd_5">Commands listed alphabetically</A> <BR>
-
-<HR>
-
-<HR>
-
-<A NAME = "cmd_1"></A><H4>3.1 LAMMPS input script 
-</H4>
-<P>LAMMPS executes by reading commands from a input script (text file),
-one line at a time.  When the input script ends, LAMMPS exits.  Each
-command causes LAMMPS to take some action.  It may set an internal
-variable, read in a file, or run a simulation.  Most commands have
-default settings, which means you only need to use the command if you
-wish to change the default.
-</P>
-<P>In many cases, the ordering of commands in an input script is not
-important.  However the following rules apply:
-</P>
-<P>(1) LAMMPS does not read your entire input script and then perform a
-simulation with all the settings.  Rather, the input script is read
-one line at a time and each command takes effect when it is read.
-Thus this sequence of commands:
-</P>
-<PRE>timestep 0.5 
-run      100 
-run      100 
-</PRE>
-<P>does something different than this sequence:
-</P>
-<PRE>run      100 
-timestep 0.5 
-run      100 
-</PRE>
-<P>In the first case, the specified timestep (0.5 fmsec) is used for two
-simulations of 100 timesteps each.  In the 2nd case, the default
-timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5
-fmsec timestep is used for the 2nd one.
-</P>
-<P>(2) Some commands are only valid when they follow other commands.  For
-example you cannot set the temperature of a group of atoms until atoms
-have been defined and a group command is used to define which atoms
-belong to the group.
-</P>
-<P>(3) Sometimes command B will use values that can be set by command A.
-This means command A must precede command B in the input script if it
-is to have the desired effect.  For example, the
-<A HREF = "read_data.html">read_data</A> command initializes the system by setting
-up the simulation box and assigning atoms to processors.  If default
-values are not desired, the <A HREF = "processors.html">processors</A> and
-<A HREF = "boundary.html">boundary</A> commands need to be used before read_data to
-tell LAMMPS how to map processors to the simulation box.
-</P>
-<P>Many input script errors are detected by LAMMPS and an ERROR or
-WARNING message is printed.  <A HREF = "Section_errors.html">This section</A> gives
-more information on what errors mean.  The documentation for each
-command lists restrictions on how the command can be used.
-</P>
-<HR>
-
-<A NAME = "cmd_2"></A><H4>3.2 Parsing rules 
-</H4>
-<P>Each non-blank line in the input script is treated as a command.
-LAMMPS commands are case sensitive.  Command names are lower-case, as
-are specified command arguments.  Upper case letters may be used in
-file names or user-chosen ID strings.
-</P>
-<P>Here is how each line in the input script is parsed by LAMMPS:
-</P>
-<P>(1) If the last printable character on the line is a "&" character
-(with no surrounding quotes), the command is assumed to continue on
-the next line.  The next line is concatenated to the previous line by
-removing the "&" character and newline.  This allows long commands to
-be continued across two or more lines.
-</P>
-<P>(2) All characters from the first "#" character onward are treated as
-comment and discarded.  See an exception in (6).  Note that a
-comment after a trailing "&" character will prevent the command from
-continuing on the next line.  Also note that for multi-line commands a
-single leading "#" will comment out the entire command.
-</P>
-<P>(3) The line is searched repeatedly for $ characters, which indicate
-variables that are replaced with a text string.  See an exception in
-(6).  
-</P>
-<P>If the $ is followed by curly brackets, then the variable name is the
-text inside the curly brackets.  If no curly brackets follow the $,
-then the variable name is the single character immediately following
-the $.  Thus ${myTemp} and $x refer to variable names "myTemp" and
-"x".
-</P>
-<P>How the variable is converted to a text string depends on what style
-of variable it is; see the <A HREF = "variable">variable</A> doc page for details.
-It can be a variable that stores multiple text strings, and return one
-of them.  The returned text string can be multiple "words" (space
-separated) which will then be interpreted as multiple arguments in the
-input command.  The variable can also store a numeric formula which
-will be evaluated and its numeric result returned as a string.
-</P>
-<P>As a special case, if the $ is followed by parenthesis, then the text
-inside the parenthesis is treated as an "immediate" variable and
-evaluated as an <A HREF = "variable.html">equal-style variable</A>.  This is a way
-to use numeric formulas in an input script without having to assign
-them to variable names.  For example, these 3 input script lines:
-</P>
-<PRE>variable X equal (xlo+xhi)/2+sqrt(v_area)
-region 1 block $X 2 INF INF EDGE EDGE
-variable X delete 
-</PRE>
-<P>can be replaced by 
-</P>
-<PRE>region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE 
-</PRE>
-<P>so that you do not have to define (or discard) a temporary variable X.
-</P>
-<P>Note that neither the curly-bracket or immediate form of variables can
-contain nested $ characters for other variables to substitute for.
-Thus you cannot do this:
-</P>
-<PRE>variable        a equal 2
-variable        b2 equal 4
-print           "B2 = ${b$a}" 
-</PRE>
-<P>Nor can you specify this $($x-1.0) for an immediate variable, but
-you could use $(v_x-1.0), since the latter is valid syntax for an
-<A HREF = "variable.html">equal-style variable</A>.
-</P>
-<P>See the <A HREF = "variable.html">variable</A> command for more details of how
-strings are assigned to variables and evaluated, and how they can be
-used in input script commands.
-</P>
-<P>(4) The line is broken into "words" separated by whitespace (tabs,
-spaces).  Note that words can thus contain letters, digits,
-underscores, or punctuation characters.
-</P>
-<P>(5) The first word is the command name.  All successive words in the
-line are arguments.
-</P>
-<P>(6) If you want text with spaces to be treated as a single argument,
-it can be enclosed in either double or single quotes.  A long single
-argument enclosed in quotes can even span multiple lines if the "&"
-character is used, as described above.  E.g.
-</P>
-<PRE>print "Volume = $v"
-print 'Volume = $v'
-variable a string "red green blue &
-                   purple orange cyan"
-if "$<I>steps</I> > 1000" then quit 
-</PRE>
-<P>The quotes are removed when the single argument is stored internally.
-</P>
-<P>See the <A HREF = "dump_modify.html">dump modify format</A> or <A HREF = "print.html">print</A> or
-<A HREF = "if.html">if</A> commands for examples.  A "#" or "$" character that is
-between quotes will not be treated as a comment indicator in (2) or
-substituted for as a variable in (3). 
-</P>
-<P>IMPORTANT NOTE: If the argument is itself a command that requires a
-quoted argument (e.g. using a <A HREF = "print.html">print</A> command as part of an
-<A HREF = "if.html">if</A> or <A HREF = "run.html">run every</A> command), then the double and
-single quotes can be nested in the usual manner.  See the doc pages
-for those commands for examples.  Only one of level of nesting is
-allowed, but that should be sufficient for most use cases.
-</P>
-<HR>
-
-<H4><A NAME = "cmd_3"></A>3.3 Input script structure 
-</H4>
-<P>This section describes the structure of a typical LAMMPS input script.
-The "examples" directory in the LAMMPS distribution contains many
-sample input scripts; the corresponding problems are discussed in
-<A HREF = "Section_example.html">Section_example</A>, and animated on the <A HREF = "http://lammps.sandia.gov">LAMMPS
-WWW Site</A>.
-</P>
-<P>A LAMMPS input script typically has 4 parts:
-</P>
-<OL><LI>Initialization
-<LI>Atom definition
-<LI>Settings
-<LI>Run a simulation 
-</OL>
-<P>The last 2 parts can be repeated as many times as desired.  I.e. run a
-simulation, change some settings, run some more, etc.  Each of the 4
-parts is now described in more detail.  Remember that almost all the
-commands need only be used if a non-default value is desired.
-</P>
-<P>(1) Initialization
-</P>
-<P>Set parameters that need to be defined before atoms are created or
-read-in from a file.
-</P>
-<P>The relevant commands are <A HREF = "units.html">units</A>,
-<A HREF = "dimension.html">dimension</A>, <A HREF = "newton.html">newton</A>,
-<A HREF = "processors.html">processors</A>, <A HREF = "boundary.html">boundary</A>,
-<A HREF = "atom_style.html">atom_style</A>, <A HREF = "atom_modify.html">atom_modify</A>.
-</P>
-<P>If force-field parameters appear in the files that will be read, these
-commands tell LAMMPS what kinds of force fields are being used:
-<A HREF = "pair_style.html">pair_style</A>, <A HREF = "bond_style.html">bond_style</A>,
-<A HREF = "angle_style.html">angle_style</A>, <A HREF = "dihedral_style.html">dihedral_style</A>,
-<A HREF = "improper_style.html">improper_style</A>.
-</P>
-<P>(2) Atom definition
-</P>
-<P>There are 3 ways to define atoms in LAMMPS.  Read them in from a data
-or restart file via the <A HREF = "read_data.html">read_data</A> or
-<A HREF = "read_restart.html">read_restart</A> commands.  These files can contain
-molecular topology information.  Or create atoms on a lattice (with no
-molecular topology), using these commands: <A HREF = "lattice.html">lattice</A>,
-<A HREF = "region.html">region</A>, <A HREF = "create_box.html">create_box</A>,
-<A HREF = "create_atoms.html">create_atoms</A>.  The entire set of atoms can be
-duplicated to make a larger simulation using the
-<A HREF = "replicate.html">replicate</A> command.
-</P>
-<P>(3) Settings
-</P>
-<P>Once atoms and molecular topology are defined, a variety of settings
-can be specified: force field coefficients, simulation parameters,
-output options, etc.
-</P>
-<P>Force field coefficients are set by these commands (they can also be
-set in the read-in files): <A HREF = "pair_coeff.html">pair_coeff</A>,
-<A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "angle_coeff.html">angle_coeff</A>,
-<A HREF = "dihedral_coeff.html">dihedral_coeff</A>,
-<A HREF = "improper_coeff.html">improper_coeff</A>,
-<A HREF = "kspace_style.html">kspace_style</A>, <A HREF = "dielectric.html">dielectric</A>,
-<A HREF = "special_bonds.html">special_bonds</A>.
-</P>
-<P>Various simulation parameters are set by these commands:
-<A HREF = "neighbor.html">neighbor</A>, <A HREF = "neigh_modify.html">neigh_modify</A>,
-<A HREF = "group.html">group</A>, <A HREF = "timestep.html">timestep</A>,
-<A HREF = "reset_timestep.html">reset_timestep</A>, <A HREF = "run_style.html">run_style</A>,
-<A HREF = "min_style.html">min_style</A>, <A HREF = "min_modify.html">min_modify</A>.
-</P>
-<P>Fixes impose a variety of boundary conditions, time integration, and
-diagnostic options.  The <A HREF = "fix.html">fix</A> command comes in many flavors.
-</P>
-<P>Various computations can be specified for execution during a
-simulation using the <A HREF = "compute.html">compute</A>,
-<A HREF = "compute_modify.html">compute_modify</A>, and <A HREF = "variable.html">variable</A>
-commands.
-</P>
-<P>Output options are set by the <A HREF = "thermo.html">thermo</A>, <A HREF = "dump.html">dump</A>,
-and <A HREF = "restart.html">restart</A> commands.
-</P>
-<P>(4) Run a simulation
-</P>
-<P>A molecular dynamics simulation is run using the <A HREF = "run.html">run</A>
-command.  Energy minimization (molecular statics) is performed using
-the <A HREF = "minimize.html">minimize</A> command.  A parallel tempering
-(replica-exchange) simulation can be run using the
-<A HREF = "temper.html">temper</A> command.
-</P>
-<HR>
-
-<A NAME = "cmd_4"></A><H4>3.4 Commands listed by category 
-</H4>
-<P>This section lists all LAMMPS commands, grouped by category.  The
-<A HREF = "#cmd_5">next section</A> lists the same commands alphabetically.  Note
-that some style options for some commands are part of specific LAMMPS
-packages, which means they cannot be used unless the package was
-included when LAMMPS was built.  Not all packages are included in a
-default LAMMPS build.  These dependencies are listed as Restrictions
-in the command's documentation.
-</P>
-<P>Initialization:
-</P>
-<P><A HREF = "atom_modify.html">atom_modify</A>, <A HREF = "atom_style.html">atom_style</A>,
-<A HREF = "boundary.html">boundary</A>, <A HREF = "dimension.html">dimension</A>,
-<A HREF = "newton.html">newton</A>, <A HREF = "processors.html">processors</A>, <A HREF = "units.html">units</A>
-</P>
-<P>Atom definition:
-</P>
-<P><A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "create_box.html">create_box</A>,
-<A HREF = "lattice.html">lattice</A>, <A HREF = "read_data.html">read_data</A>,
-<A HREF = "read_dump.html">read_dump</A>, <A HREF = "read_restart.html">read_restart</A>,
-<A HREF = "region.html">region</A>, <A HREF = "replicate.html">replicate</A>
-</P>
-<P>Force fields:
-</P>
-<P><A HREF = "angle_coeff.html">angle_coeff</A>, <A HREF = "angle_style.html">angle_style</A>,
-<A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "bond_style.html">bond_style</A>,
-<A HREF = "dielectric.html">dielectric</A>, <A HREF = "dihedral_coeff.html">dihedral_coeff</A>,
-<A HREF = "dihedral_style.html">dihedral_style</A>,
-<A HREF = "improper_coeff.html">improper_coeff</A>,
-<A HREF = "improper_style.html">improper_style</A>,
-<A HREF = "kspace_modify.html">kspace_modify</A>, <A HREF = "kspace_style.html">kspace_style</A>,
-<A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_modify.html">pair_modify</A>,
-<A HREF = "pair_style.html">pair_style</A>, <A HREF = "pair_write.html">pair_write</A>,
-<A HREF = "special_bonds.html">special_bonds</A>
-</P>
-<P>Settings:
-</P>
-<P><A HREF = "comm_style.html">comm_style</A>, <A HREF = "group.html">group</A>, <A HREF = "mass.html">mass</A>,
-<A HREF = "min_modify.html">min_modify</A>, <A HREF = "min_style.html">min_style</A>,
-<A HREF = "neigh_modify.html">neigh_modify</A>, <A HREF = "neighbor.html">neighbor</A>,
-<A HREF = "reset_timestep.html">reset_timestep</A>, <A HREF = "run_style.html">run_style</A>,
-<A HREF = "set.html">set</A>, <A HREF = "timestep.html">timestep</A>, <A HREF = "velocity.html">velocity</A>
-</P>
-<P>Fixes:
-</P>
-<P><A HREF = "fix.html">fix</A>, <A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "unfix.html">unfix</A>
-</P>
-<P>Computes:
-</P>
-<P><A HREF = "compute.html">compute</A>, <A HREF = "compute_modify.html">compute_modify</A>,
-<A HREF = "uncompute.html">uncompute</A>
-</P>
-<P>Output:
-</P>
-<P><A HREF = "dump.html">dump</A>, <A HREF = "dump_image.html">dump image</A>,
-<A HREF = "dump_modify.html">dump_modify</A>, <A HREF = "dump_image.html">dump movie</A>,
-<A HREF = "restart.html">restart</A>, <A HREF = "thermo.html">thermo</A>,
-<A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "thermo_style.html">thermo_style</A>,
-<A HREF = "undump.html">undump</A>, <A HREF = "write_data.html">write_data</A>,
-<A HREF = "write_dump.html">write_dump</A>, <A HREF = "write_restart.html">write_restart</A>
-</P>
-<P>Actions:
-</P>
-<P><A HREF = "delete_atoms.html">delete_atoms</A>, <A HREF = "delete_bonds.html">delete_bonds</A>,
-<A HREF = "displace_atoms.html">displace_atoms</A>, <A HREF = "change_box.html">change_box</A>,
-<A HREF = "minimize.html">minimize</A>, <A HREF = "neb.html">neb</A> <A HREF = "prd.html">prd</A>,
-<A HREF = "rerun.html">rerun</A>, <A HREF = "run.html">run</A>, <A HREF = "temper.html">temper</A>
-</P>
-<P>Miscellaneous:
-</P>
-<P><A HREF = "clear.html">clear</A>, <A HREF = "echo.html">echo</A>, <A HREF = "if.html">if</A>,
-<A HREF = "include.html">include</A>, <A HREF = "jump.html">jump</A>, <A HREF = "label.html">label</A>,
-<A HREF = "log.html">log</A>, <A HREF = "next.html">next</A>, <A HREF = "print.html">print</A>,
-<A HREF = "shell.html">shell</A>, <A HREF = "variable.html">variable</A>
-</P>
-<HR>
-
-<H4><A NAME = "cmd_5"></A><A NAME = "comm"></A>3.5 Individual commands 
-</H4>
-<P>This section lists all LAMMPS commands alphabetically, with a separate
-listing below of styles within certain commands.  The <A HREF = "#cmd_4">previous
-section</A> lists the same commands, grouped by category.  Note
-that some style options for some commands are part of specific LAMMPS
-packages, which means they cannot be used unless the package was
-included when LAMMPS was built.  Not all packages are included in a
-default LAMMPS build.  These dependencies are listed as Restrictions
-in the command's documentation.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "angle_coeff.html">angle_coeff</A></TD><TD ><A HREF = "angle_style.html">angle_style</A></TD><TD ><A HREF = "atom_modify.html">atom_modify</A></TD><TD ><A HREF = "atom_style.html">atom_style</A></TD><TD ><A HREF = "balance.html">balance</A></TD><TD ><A HREF = "bond_coeff.html">bond_coeff</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "bond_style.html">bond_style</A></TD><TD ><A HREF = "boundary.html">boundary</A></TD><TD ><A HREF = "box.html">box</A></TD><TD ><A HREF = "change_box.html">change_box</A></TD><TD ><A HREF = "clear.html">clear</A></TD><TD ><A HREF = "comm_modify.html">comm_modify</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "comm_style.html">comm_style</A></TD><TD ><A HREF = "compute.html">compute</A></TD><TD ><A HREF = "compute_modify.html">compute_modify</A></TD><TD ><A HREF = "create_atoms.html">create_atoms</A></TD><TD ><A HREF = "create_box.html">create_box</A></TD><TD ><A HREF = "delete_atoms.html">delete_atoms</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "delete_bonds.html">delete_bonds</A></TD><TD ><A HREF = "dielectric.html">dielectric</A></TD><TD ><A HREF = "dihedral_coeff.html">dihedral_coeff</A></TD><TD ><A HREF = "dihedral_style.html">dihedral_style</A></TD><TD ><A HREF = "dimension.html">dimension</A></TD><TD ><A HREF = "displace_atoms.html">displace_atoms</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "dump.html">dump</A></TD><TD ><A HREF = "dump_image.html">dump image</A></TD><TD ><A HREF = "dump_modify.html">dump_modify</A></TD><TD ><A HREF = "dump_image.html">dump movie</A></TD><TD ><A HREF = "echo.html">echo</A></TD><TD ><A HREF = "fix.html">fix</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_modify.html">fix_modify</A></TD><TD ><A HREF = "group.html">group</A></TD><TD ><A HREF = "if.html">if</A></TD><TD ><A HREF = "improper_coeff.html">improper_coeff</A></TD><TD ><A HREF = "improper_style.html">improper_style</A></TD><TD ><A HREF = "include.html">include</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "jump.html">jump</A></TD><TD ><A HREF = "kspace_modify.html">kspace_modify</A></TD><TD ><A HREF = "kspace_style.html">kspace_style</A></TD><TD ><A HREF = "label.html">label</A></TD><TD ><A HREF = "lattice.html">lattice</A></TD><TD ><A HREF = "log.html">log</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "mass.html">mass</A></TD><TD ><A HREF = "minimize.html">minimize</A></TD><TD ><A HREF = "min_modify.html">min_modify</A></TD><TD ><A HREF = "min_style.html">min_style</A></TD><TD ><A HREF = "molecule.html">molecule</A></TD><TD ><A HREF = "neb.html">neb</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "neigh_modify.html">neigh_modify</A></TD><TD ><A HREF = "neighbor.html">neighbor</A></TD><TD ><A HREF = "newton.html">newton</A></TD><TD ><A HREF = "next.html">next</A></TD><TD ><A HREF = "package.html">package</A></TD><TD ><A HREF = "pair_coeff.html">pair_coeff</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_modify.html">pair_modify</A></TD><TD ><A HREF = "pair_style.html">pair_style</A></TD><TD ><A HREF = "pair_write.html">pair_write</A></TD><TD ><A HREF = "partition.html">partition</A></TD><TD ><A HREF = "prd.html">prd</A></TD><TD ><A HREF = "print.html">print</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "processors.html">processors</A></TD><TD ><A HREF = "quit.html">quit</A></TD><TD ><A HREF = "read_data.html">read_data</A></TD><TD ><A HREF = "read_dump.html">read_dump</A></TD><TD ><A HREF = "read_restart.html">read_restart</A></TD><TD ><A HREF = "region.html">region</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "replicate.html">replicate</A></TD><TD ><A HREF = "rerun.html">rerun</A></TD><TD ><A HREF = "reset_timestep.html">reset_timestep</A></TD><TD ><A HREF = "restart.html">restart</A></TD><TD ><A HREF = "run.html">run</A></TD><TD ><A HREF = "run_style.html">run_style</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "set.html">set</A></TD><TD ><A HREF = "shell.html">shell</A></TD><TD ><A HREF = "special_bonds.html">special_bonds</A></TD><TD ><A HREF = "suffix.html">suffix</A></TD><TD ><A HREF = "tad.html">tad</A></TD><TD ><A HREF = "temper.html">temper</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "thermo.html">thermo</A></TD><TD ><A HREF = "thermo_modify.html">thermo_modify</A></TD><TD ><A HREF = "thermo_style.html">thermo_style</A></TD><TD ><A HREF = "timestep.html">timestep</A></TD><TD ><A HREF = "uncompute.html">uncompute</A></TD><TD ><A HREF = "undump.html">undump</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "unfix.html">unfix</A></TD><TD ><A HREF = "units.html">units</A></TD><TD ><A HREF = "variable.html">variable</A></TD><TD ><A HREF = "velocity.html">velocity</A></TD><TD ><A HREF = "write_data.html">write_data</A></TD><TD ><A HREF = "write_dump.html">write_dump</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "write_restart.html">write_restart</A> 
-</TD></TR></TABLE></DIV>
-
-<P>These are additional commands in USER packages, which can be used if
-<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
-package</A>.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "group2ndx.html">group2ndx</A> 
-</TD></TR></TABLE></DIV>
-
-<HR>
-
-<H4>Fix styles 
-</H4>
-<P>See the <A HREF = "fix.html">fix</A> command for one-line descriptions of each style
-or click on the style itself for a full description.  Some of the
-styles have accelerated versions, which can be used if LAMMPS is built
-with the <A HREF = "Section_accelerate.html">appropriate accelerated package</A>.
-This is indicated by additional letters in parenthesis: c = USER-CUDA,
-g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "fix_adapt.html">adapt</A></TD><TD ><A HREF = "fix_addforce.html">addforce (c)</A></TD><TD ><A HREF = "fix_append_atoms.html">append/atoms</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce (c)</A></TD><TD ><A HREF = "fix_ave_atom.html">ave/atom</A></TD><TD ><A HREF = "fix_ave_correlate.html">ave/correlate</A></TD><TD ><A HREF = "fix_ave_histo.html">ave/histo</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD><TD ><A HREF = "fix_balance.html">balance</A></TD><TD ><A HREF = "fix_bond_break.html">bond/break</A></TD><TD ><A HREF = "fix_bond_create.html">bond/create</A></TD><TD ><A HREF = "fix_bond_swap.html">bond/swap</A></TD><TD ><A HREF = "fix_box_relax.html">box/relax</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d (c)</A></TD><TD ><A HREF = "fix_evaporate.html">evaporate</A></TD><TD ><A HREF = "fix_external.html">external</A></TD><TD ><A HREF = "fix_freeze.html">freeze (c)</A></TD><TD ><A HREF = "fix_gcmc.html">gcmc</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_gld.html">gld</A></TD><TD ><A HREF = "fix_gravity.html">gravity (co)</A></TD><TD ><A HREF = "fix_heat.html">heat</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin (k)</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_move.html">move</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_msst.html">msst</A></TD><TD ><A HREF = "fix_neb.html">neb</A></TD><TD ><A HREF = "fix_nh.html">nph (o)</A></TD><TD ><A HREF = "fix_nphug.html">nphug (o)</A></TD><TD ><A HREF = "fix_nph_asphere.html">nph/asphere (o)</A></TD><TD ><A HREF = "fix_nph_sphere.html">nph/sphere (o)</A></TD><TD ><A HREF = "fix_nh.html">npt (co)</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_npt_sphere.html">npt/sphere (o)</A></TD><TD ><A HREF = "fix_nve.html">nve (cko)</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_asphere_noforce.html">nve/asphere/noforce</A></TD><TD ><A HREF = "fix_nve_body.html">nve/body</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_line.html">nve/line</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_nve_sphere.html">nve/sphere (o)</A></TD><TD ><A HREF = "fix_nve_tri.html">nve/tri</A></TD><TD ><A HREF = "fix_nh.html">nvt (co)</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere (o)</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod (o)</A></TD><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere (o)</A></TD><TD ><A HREF = "fix_oneway.html">oneway</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_property_atom.html">property/atom</A></TD><TD ><A HREF = "fix_qeq_comb.html">qeq/comb (o)</A></TD><TD ><A HREF = "fix_qeq.html">qeq/dynamic</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_qeq.html">qeq/point</A></TD><TD ><A HREF = "fix_qeq.html">qeq/shielded</A></TD><TD ><A HREF = "fix_qeq.html">qeq/slater</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_restrain.html">restrain</A></TD><TD ><A HREF = "fix_rigid.html">rigid (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nph (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_rigid.html">rigid/npt (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nve (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nvt (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/nph</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/npt</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/nve</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/nvt</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_setforce.html">setforce (c)</A></TD><TD ><A HREF = "fix_shake.html">shake (c)</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_srd.html">srd</A></TD><TD ><A HREF = "fix_store_force.html">store/force</A></TD><TD ><A HREF = "fix_store_state.html">store/state</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen (c)</A></TD><TD ><A HREF = "fix_temp_csvr.html">temp/csvr</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale (c)</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_tune_kspace.html">tune/kspace</A></TD><TD ><A HREF = "fix_vector.html">vector</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous (c)</A></TD><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall.html">wall/harmonic</A></TD><TD ><A HREF = "fix_wall.html">wall/lj1043</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_wall_piston.html">wall/piston</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wall_region.html">wall/region</A></TD><TD ><A HREF = "fix_wall_srd.html">wall/srd</A> 
-</TD></TR></TABLE></DIV>
-
-<P>These are additional fix styles in USER packages, which can be used if
-<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
-package</A>.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "fix_adapt_fep.html">adapt/fep</A></TD><TD ><A HREF = "fix_addtorque.html">addtorque</A></TD><TD ><A HREF = "fix_atc.html">atc</A></TD><TD ><A HREF = "fix_colvars.html">colvars</A></TD><TD ><A HREF = "fix_imd.html">imd</A></TD><TD ><A HREF = "fix_langevin_eff.html">langevin/eff</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_lb_fluid.html">lb/fluid</A></TD><TD ><A HREF = "fix_lb_momentum.html">lb/momentum</A></TD><TD ><A HREF = "fix_lb_pc.html">lb/pc</A></TD><TD ><A HREF = "fix_lb_rigid_pc_sphere.html">lb/rigid/pc/sphere</A></TD><TD ><A HREF = "fix_lb_viscous.html">lb/viscous</A></TD><TD ><A HREF = "fix_meso.html">meso</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_meso_stationary.html">meso/stationary</A></TD><TD ><A HREF = "fix_nh_eff.html">nph/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">npt/eff</A></TD><TD ><A HREF = "fix_nve_eff.html">nve/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD><TD ><A HREF = "fix_nvt_sllod_eff.html">nvt/sllod/eff</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_phonon.html">phonon</A></TD><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD><TD ><A HREF = "fix_qmmm.html">qmmm</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/c/bonds</A></TD><TD ><A HREF = "fix_reaxc_species.html">reax/c/species</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A></TD><TD ><A HREF = "fix_ti_rs.html">ti/rs</A></TD><TD ><A HREF = "fix_ti_spring.html">ti/spring</A> 
-</TD></TR></TABLE></DIV>
-
-<HR>
-
-<H4>Compute styles 
-</H4>
-<P>See the <A HREF = "compute.html">compute</A> command for one-line descriptions of
-each style or click on the style itself for a full description.  Some
-of the styles have accelerated versions, which can be used if LAMMPS
-is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
-package</A>.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "compute_angle_local.html">angle/local</A></TD><TD ><A HREF = "compute_atom_molecule.html">atom/molecule</A></TD><TD ><A HREF = "compute_body_local.html">body/local</A></TD><TD ><A HREF = "compute_bond_local.html">bond/local</A></TD><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_cluster_atom.html">cluster/atom</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_com.html">com</A></TD><TD ><A HREF = "compute_com_molecule.html">com/molecule</A></TD><TD ><A HREF = "compute_contact_atom.html">contact/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_dihedral_local.html">dihedral/local</A></TD><TD ><A HREF = "compute_dilatation_atom.html">dilatation/atom</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD><TD ><A HREF = "compute_erotate_rigid.html">erotate/rigid</A></TD><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_erotate_sphere_atom.html">erotate/sphere/atom</A></TD><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_gyration.html">gyration</A></TD><TD ><A HREF = "compute_gyration_molecule.html">gyration/molecule</A></TD><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_improper_local.html">improper/local</A></TD><TD ><A HREF = "compute_inertia_molecule.html">inertia/molecule</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_ke_rigid.html">ke/rigid</A></TD><TD ><A HREF = "compute_msd.html">msd</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_msd_molecule.html">msd/molecule</A></TD><TD ><A HREF = "compute_msd_nongauss.html">msd/nongauss</A></TD><TD ><A HREF = "compute_pair.html">pair</A></TD><TD ><A HREF = "compute_pair_local.html">pair/local</A></TD><TD ><A HREF = "compute_pe.html">pe (c)</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_plasticity_atom.html">plasticity/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure (c)</A></TD><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_property_local.html">property/local</A></TD><TD ><A HREF = "compute_property_molecule.html">property/molecule</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_slice.html">slice</A></TD><TD ><A HREF = "compute_sna.html">sna/atom</A></TD><TD ><A HREF = "compute_sna.html">snad/atom</A></TD><TD ><A HREF = "compute_sna.html">snav/atom</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp (c)</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial (c)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A></TD><TD ><A HREF = "compute_ti.html">ti</A></TD><TD ><A HREF = "compute_vacf.html">vacf</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_voronoi_atom.html">voronoi/atom</A> 
-</TD></TR></TABLE></DIV>
-
-<P>These are additional compute styles in USER packages, which can be
-used if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
-package</A>.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "compute_ackland_atom.html">ackland/atom</A></TD><TD ><A HREF = "compute_basal_atom.html">basal/atom</A></TD><TD ><A HREF = "compute_fep.html">fep</A></TD><TD ><A HREF = "compute_ke_eff.html">ke/eff</A></TD><TD ><A HREF = "compute_ke_atom_eff.html">ke/atom/eff</A></TD><TD ><A HREF = "compute_meso_e_atom.html">meso_e/atom</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_meso_rho_atom.html">meso_rho/atom</A></TD><TD ><A HREF = "compute_meso_t_atom.html">meso_t/atom</A></TD><TD ><A HREF = "compute_temp_eff.html">temp/eff</A></TD><TD ><A HREF = "compute_temp_deform_eff.html">temp/deform/eff</A></TD><TD ><A HREF = "compute_temp_region_eff.html">temp/region/eff</A></TD><TD ><A HREF = "compute_temp_rotate.html">temp/rotate</A> 
-</TD></TR></TABLE></DIV>
-
-<HR>
-
-<H4>Pair_style potentials 
-</H4>
-<P>See the <A HREF = "pair_style.html">pair_style</A> command for an overview of pair
-potentials.  Click on the style itself for a full description.  Many
-of the styles have accelerated versions, which can be used if LAMMPS
-is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
-package</A>.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "pair_none.html">none</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid/overlay</A></TD><TD ><A HREF = "pair_adp.html">adp (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_airebo.html">airebo (o)</A></TD><TD ><A HREF = "pair_beck.html">beck (go)</A></TD><TD ><A HREF = "pair_body.html">body</A></TD><TD ><A HREF = "pair_bop.html">bop</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born (go)</A></TD><TD ><A HREF = "pair_born.html">born/coul/long (cgo)</A></TD><TD ><A HREF = "pair_born.html">born/coul/msm (o)</A></TD><TD ><A HREF = "pair_born.html">born/coul/wolf (go)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_brownian.html">brownian (o)</A></TD><TD ><A HREF = "pair_brownian.html">brownian/poly (o)</A></TD><TD ><A HREF = "pair_buck.html">buck (cgo)</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/cut (cgo)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/long (cgo)</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/msm (o)</A></TD><TD ><A HREF = "pair_buck_long.html">buck/long/coul/long (o)</A></TD><TD ><A HREF = "pair_colloid.html">colloid (go)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_comb.html">comb (o)</A></TD><TD ><A HREF = "pair_comb.html">comb3</A></TD><TD ><A HREF = "pair_coul.html">coul/cut (gko)</A></TD><TD ><A HREF = "pair_coul.html">coul/debye (go)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/dsf (go)</A></TD><TD ><A HREF = "pair_coul.html">coul/long (go)</A></TD><TD ><A HREF = "pair_coul.html">coul/msm</A></TD><TD ><A HREF = "pair_coul.html">coul/wolf (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_dpd.html">dpd (o)</A></TD><TD ><A HREF = "pair_dpd.html">dpd/tstat (o)</A></TD><TD ><A HREF = "pair_dsmc.html">dsmc</A></TD><TD ><A HREF = "pair_eam.html">eam (cgot)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/alloy (cgot)</A></TD><TD ><A HREF = "pair_eam.html">eam/fs (cgot)</A></TD><TD ><A HREF = "pair_eim.html">eim (o)</A></TD><TD ><A HREF = "pair_gauss.html">gauss (go)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_gayberne.html">gayberne (gio)</A></TD><TD ><A HREF = "pair_gran.html">gran/hertz/history (o)</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke (co)</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/lj (o)</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse (o)</A></TD><TD ><A HREF = "pair_kim.html">kim</A></TD><TD ><A HREF = "pair_lcbop.html">lcbop</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_line_lj.html">line/lj (o)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm (co)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit (co)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long (cgio)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/msm</A></TD><TD ><A HREF = "pair_class2.html">lj/class2 (cgo)</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut (co)</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long (cgo)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut (cgikot)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut (cgko)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye (cgo)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/dsf (go)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long (cgikot)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/msm (go)</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/cut (go)</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/long</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/cut (o)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long (ot)</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand (cgo)</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs (cgo)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs (co)</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/coul/long (o)</A></TD><TD ><A HREF = "pair_dipole.html">lj/long/dipole/long</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/tip4p/long</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_lj_smooth.html">lj/smooth (co)</A></TD><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear (o)</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut (cgo)</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_lubricate.html">lubricate/poly (o)</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU/poly</A></TD><TD ><A HREF = "pair_meam.html">meam (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_mie.html">mie/cut (o)</A></TD><TD ><A HREF = "pair_morse.html">morse (cgot)</A></TD><TD ><A HREF = "pair_nb3b_harmonic.html">nb3b/harmonic (o)</A></TD><TD ><A HREF = "pair_nm.html">nm/cut (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_nm.html">nm/cut/coul/cut (o)</A></TD><TD ><A HREF = "pair_nm.html">nm/cut/coul/long (o)</A></TD><TD ><A HREF = "pair_peri.html">peri/eps</A></TD><TD ><A HREF = "pair_peri.html">peri/lps (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/pmb (o)</A></TD><TD ><A HREF = "pair_peri.html">peri/ves</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_airebo.html">rebo (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_resquared.html">resquared (go)</A></TD><TD ><A HREF = "pair_snap.html">snap</A></TD><TD ><A HREF = "pair_soft.html">soft (go)</A></TD><TD ><A HREF = "pair_sw.html">sw (cgo)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_table.html">table (gko)</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff (co)</A></TD><TD ><A HREF = "pair_tersoff_mod.html">tersoff/mod (o)</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">tip4p/cut (o)</A></TD><TD ><A HREF = "pair_coul.html">tip4p/long (o)</A></TD><TD ><A HREF = "pair_tri_lj.html">tri/lj (o)</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa (go)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid (go)</A></TD><TD ><A HREF = "pair_zbl.html">zbl (o)</A> 
-</TD></TR></TABLE></DIV>
-
-<P>These are additional pair styles in USER packages, which can be used
-if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
-package</A>.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "pair_awpmd.html">awpmd/cut</A></TD><TD ><A HREF = "pair_lj_soft.html">coul/cut/soft (o)</A></TD><TD ><A HREF = "pair_coul_diel.html">coul/diel (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">coul/long/soft (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/cd (o)</A></TD><TD ><A HREF = "pair_edip.html">edip (o)</A></TD><TD ><A HREF = "pair_eff.html">eff/cut</A></TD><TD ><A HREF = "pair_gauss.html">gauss/cut</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_list.html">list</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/soft (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/coul/cut/soft (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/coul/long/soft (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/sf (go)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/soft (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/tip4p/long/soft (o)</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk (go)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long (go)</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/msm (o)</A></TD><TD ><A HREF = "pair_lj_sf.html">lj/sf (o)</A></TD><TD ><A HREF = "pair_meam_spline.html">meam/spline</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_meam_sw_spline.html">meam/sw/spline</A></TD><TD ><A HREF = "pair_reax_c.html">reax/c</A></TD><TD ><A HREF = "pair_sph_heatconduction.html">sph/heatconduction</A></TD><TD ><A HREF = "pair_sph_idealgas.html">sph/idealgas</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_sph_lj.html">sph/lj</A></TD><TD ><A HREF = "pair_sph_rhosum.html">sph/rhosum</A></TD><TD ><A HREF = "pair_sph_taitwater.html">sph/taitwater</A></TD><TD ><A HREF = "pair_sph_taitwater_morris.html">sph/taitwater/morris</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_tersoff.html">tersoff/table (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">tip4p/long/soft (o)</A> 
-</TD></TR></TABLE></DIV>
-
-<HR>
-
-<H4>Bond_style potentials 
-</H4>
-<P>See the <A HREF = "bond_style.html">bond_style</A> command for an overview of bond
-potentials.  Click on the style itself for a full description.  Some
-of the styles have accelerated versions, which can be used if LAMMPS
-is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
-package</A>.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "bond_none.html">none</A></TD><TD ><A HREF = "bond_hybrid.html">hybrid</A></TD><TD ><A HREF = "bond_class2.html">class2 (o)</A></TD><TD ><A HREF = "bond_fene.html">fene (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "bond_fene_expand.html">fene/expand (o)</A></TD><TD ><A HREF = "bond_harmonic.html">harmonic (o)</A></TD><TD ><A HREF = "bond_morse.html">morse (o)</A></TD><TD ><A HREF = "bond_nonlinear.html">nonlinear (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "bond_quartic.html">quartic (o)</A></TD><TD ><A HREF = "bond_table.html">table (o)</A> 
-</TD></TR></TABLE></DIV>
-
-<P>These are additional bond styles in USER packages, which can be used
-if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
-package</A>.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "bond_harmonic_shift.html">harmonic/shift (o)</A></TD><TD ><A HREF = "bond_harmonic_shift_cut.html">harmonic/shift/cut (o)</A> 
-</TD></TR></TABLE></DIV>
-
-<HR>
-
-<H4>Angle_style potentials 
-</H4>
-<P>See the <A HREF = "angle_style.html">angle_style</A> command for an overview of
-angle potentials.  Click on the style itself for a full description.
-Some of the styles have accelerated versions, which can be used if
-LAMMPS is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
-package</A>.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "angle_none.html">none</A></TD><TD ><A HREF = "angle_hybrid.html">hybrid</A></TD><TD ><A HREF = "angle_charmm.html">charmm (o)</A></TD><TD ><A HREF = "angle_class2.html">class2 (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "angle_cosine.html">cosine (o)</A></TD><TD ><A HREF = "angle_cosine_delta.html">cosine/delta (o)</A></TD><TD ><A HREF = "angle_cosine_periodic.html">cosine/periodic (o)</A></TD><TD ><A HREF = "angle_cosine_squared.html">cosine/squared (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "angle_harmonic.html">harmonic (o)</A></TD><TD ><A HREF = "angle_table.html">table (o)</A> 
-</TD></TR></TABLE></DIV>
-
-<P>These are additional angle styles in USER packages, which can be used
-if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
-package</A>.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "angle_cosine_shift.html">cosine/shift (o)</A></TD><TD ><A HREF = "angle_cosine_shift_exp.html">cosine/shift/exp (o)</A></TD><TD ><A HREF = "angle_dipole.html">dipole (o)</A></TD><TD ><A HREF = "angle_fourier.html">fourier (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "angle_fourier_simple.html">fourier/simple (o)</A></TD><TD ><A HREF = "angle_quartic.html">quartic (o)</A></TD><TD ><A HREF = "angle_sdk.html">sdk</A> 
-</TD></TR></TABLE></DIV>
-
-<HR>
-
-<H4>Dihedral_style potentials 
-</H4>
-<P>See the <A HREF = "dihedral_style.html">dihedral_style</A> command for an overview
-of dihedral potentials.  Click on the style itself for a full
-description.  Some of the styles have accelerated versions, which can
-be used if LAMMPS is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
-package</A>.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "dihedral_none.html">none</A></TD><TD ><A HREF = "dihedral_hybrid.html">hybrid</A></TD><TD ><A HREF = "dihedral_charmm.html">charmm (o)</A></TD><TD ><A HREF = "dihedral_class2.html">class2 (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "dihedral_harmonic.html">harmonic (o)</A></TD><TD ><A HREF = "dihedral_helix.html">helix (o)</A></TD><TD ><A HREF = "dihedral_multi_harmonic.html">multi/harmonic (o)</A></TD><TD ><A HREF = "dihedral_opls.html">opls (o)</A> 
-</TD></TR></TABLE></DIV>
-
-<P>These are additional dihedral styles in USER packages, which can be
-used if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
-package</A>.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "dihedral_cosine_shift_exp.html">cosine/shift/exp (o)</A></TD><TD ><A HREF = "dihedral_fourier.html">fourier (o)</A></TD><TD ><A HREF = "dihedral_nharmonic.html">nharmonic (o)</A></TD><TD ><A HREF = "dihedral_quadratic.html">quadratic (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "dihedral_table.html">table (o)</A> 
-</TD></TR></TABLE></DIV>
-
-<HR>
-
-<H4>Improper_style potentials 
-</H4>
-<P>See the <A HREF = "improper_style.html">improper_style</A> command for an overview
-of improper potentials.  Click on the style itself for a full
-description.  Some of the styles have accelerated versions, which can
-be used if LAMMPS is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
-package</A>.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "improper_none.html">none</A></TD><TD ><A HREF = "improper_hybrid.html">hybrid</A></TD><TD ><A HREF = "improper_class2.html">class2 (o)</A></TD><TD ><A HREF = "improper_cvff.html">cvff (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "improper_harmonic.html">harmonic (o)</A></TD><TD ><A HREF = "improper_umbrella.html">umbrella (o)</A> 
-</TD></TR></TABLE></DIV>
-
-<P>These are additional improper styles in USER packages, which can be
-used if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
-package</A>.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "improper_cossq.html">cossq (o)</A></TD><TD ><A HREF = "improper_fourier.html">fourier (o)</A></TD><TD ><A HREF = "improper_ring.html">ring (o)</A> 
-</TD></TR></TABLE></DIV>
-
-<HR>
-
-<H4>Kspace solvers 
-</H4>
-<P>See the <A HREF = "kspace_style.html">kspace_style</A> command for an overview of
-Kspace solvers.  Click on the style itself for a full description.
-Some of the styles have accelerated versions, which can be used if
-LAMMPS is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
-package</A>.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "kspace_style.html">ewald (o)</A></TD><TD ><A HREF = "kspace_style.html">ewald/disp</A></TD><TD ><A HREF = "kspace_style.html">msm (o)</A></TD><TD ><A HREF = "kspace_style.html">msm/cg (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "kspace_style.html">pppm (cgo)</A></TD><TD ><A HREF = "kspace_style.html">pppm/cg (o)</A></TD><TD ><A HREF = "kspace_style.html">pppm/disp</A></TD><TD ><A HREF = "kspace_style.html">pppm/disp/tip4p</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "kspace_style.html">pppm/tip4p (o)</A> 
-</TD></TR></TABLE></DIV>
-
-</HTML>

doc/Section_commands.txt

@@ -1,993 +0,0 @@
-"Previous Section"_Section_start.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_packages.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-3. Commands :h3
-
-This section describes how a LAMMPS input script is formatted and the
-input script commands used to define a LAMMPS simulation.
-
-3.1 "LAMMPS input script"_#cmd_1
-3.2 "Parsing rules"_#cmd_2
-3.3 "Input script structure"_#cmd_3
-3.4 "Commands listed by category"_#cmd_4
-3.5 "Commands listed alphabetically"_#cmd_5 :all(b)
-
-:line
-:line
-
-3.1 LAMMPS input script :link(cmd_1),h4
-
-LAMMPS executes by reading commands from a input script (text file),
-one line at a time.  When the input script ends, LAMMPS exits.  Each
-command causes LAMMPS to take some action.  It may set an internal
-variable, read in a file, or run a simulation.  Most commands have
-default settings, which means you only need to use the command if you
-wish to change the default.
-
-In many cases, the ordering of commands in an input script is not
-important.  However the following rules apply:
-
-(1) LAMMPS does not read your entire input script and then perform a
-simulation with all the settings.  Rather, the input script is read
-one line at a time and each command takes effect when it is read.
-Thus this sequence of commands:
-
-timestep 0.5 
-run      100 
-run      100 :pre
-
-does something different than this sequence:
-
-run      100 
-timestep 0.5 
-run      100 :pre
-
-In the first case, the specified timestep (0.5 fmsec) is used for two
-simulations of 100 timesteps each.  In the 2nd case, the default
-timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5
-fmsec timestep is used for the 2nd one.
-
-(2) Some commands are only valid when they follow other commands.  For
-example you cannot set the temperature of a group of atoms until atoms
-have been defined and a group command is used to define which atoms
-belong to the group.
-
-(3) Sometimes command B will use values that can be set by command A.
-This means command A must precede command B in the input script if it
-is to have the desired effect.  For example, the
-"read_data"_read_data.html command initializes the system by setting
-up the simulation box and assigning atoms to processors.  If default
-values are not desired, the "processors"_processors.html and
-"boundary"_boundary.html commands need to be used before read_data to
-tell LAMMPS how to map processors to the simulation box.
-
-Many input script errors are detected by LAMMPS and an ERROR or
-WARNING message is printed.  "This section"_Section_errors.html gives
-more information on what errors mean.  The documentation for each
-command lists restrictions on how the command can be used.
-
-:line
-
-3.2 Parsing rules :link(cmd_2),h4
-
-Each non-blank line in the input script is treated as a command.
-LAMMPS commands are case sensitive.  Command names are lower-case, as
-are specified command arguments.  Upper case letters may be used in
-file names or user-chosen ID strings.
-
-Here is how each line in the input script is parsed by LAMMPS:
-
-(1) If the last printable character on the line is a "&" character
-(with no surrounding quotes), the command is assumed to continue on
-the next line.  The next line is concatenated to the previous line by
-removing the "&" character and newline.  This allows long commands to
-be continued across two or more lines.
-
-(2) All characters from the first "#" character onward are treated as
-comment and discarded.  See an exception in (6).  Note that a
-comment after a trailing "&" character will prevent the command from
-continuing on the next line.  Also note that for multi-line commands a
-single leading "#" will comment out the entire command.
-
-(3) The line is searched repeatedly for $ characters, which indicate
-variables that are replaced with a text string.  See an exception in
-(6).  
-
-If the $ is followed by curly brackets, then the variable name is the
-text inside the curly brackets.  If no curly brackets follow the $,
-then the variable name is the single character immediately following
-the $.  Thus $\{myTemp\} and $x refer to variable names "myTemp" and
-"x".
-
-How the variable is converted to a text string depends on what style
-of variable it is; see the "variable"_variable doc page for details.
-It can be a variable that stores multiple text strings, and return one
-of them.  The returned text string can be multiple "words" (space
-separated) which will then be interpreted as multiple arguments in the
-input command.  The variable can also store a numeric formula which
-will be evaluated and its numeric result returned as a string.
-
-As a special case, if the $ is followed by parenthesis, then the text
-inside the parenthesis is treated as an "immediate" variable and
-evaluated as an "equal-style variable"_variable.html.  This is a way
-to use numeric formulas in an input script without having to assign
-them to variable names.  For example, these 3 input script lines:
-
-variable X equal (xlo+xhi)/2+sqrt(v_area)
-region 1 block $X 2 INF INF EDGE EDGE
-variable X delete :pre
-
-can be replaced by 
-
-region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre
-
-so that you do not have to define (or discard) a temporary variable X.
-
-Note that neither the curly-bracket or immediate form of variables can
-contain nested $ characters for other variables to substitute for.
-Thus you cannot do this:
-
-variable        a equal 2
-variable        b2 equal 4
-print           "B2 = $\{b$a\}" :pre
-
-Nor can you specify this $($x-1.0) for an immediate variable, but
-you could use $(v_x-1.0), since the latter is valid syntax for an
-"equal-style variable"_variable.html.
-
-See the "variable"_variable.html command for more details of how
-strings are assigned to variables and evaluated, and how they can be
-used in input script commands.
-
-(4) The line is broken into "words" separated by whitespace (tabs,
-spaces).  Note that words can thus contain letters, digits,
-underscores, or punctuation characters.
-
-(5) The first word is the command name.  All successive words in the
-line are arguments.
-
-(6) If you want text with spaces to be treated as a single argument,
-it can be enclosed in either double or single quotes.  A long single
-argument enclosed in quotes can even span multiple lines if the "&"
-character is used, as described above.  E.g.
-
-print "Volume = $v"
-print 'Volume = $v'
-variable a string "red green blue &
-                   purple orange cyan"
-if "${steps} > 1000" then quit :pre
-
-The quotes are removed when the single argument is stored internally.
-
-See the "dump modify format"_dump_modify.html or "print"_print.html or
-"if"_if.html commands for examples.  A "#" or "$" character that is
-between quotes will not be treated as a comment indicator in (2) or
-substituted for as a variable in (3). 
-
-IMPORTANT NOTE: If the argument is itself a command that requires a
-quoted argument (e.g. using a "print"_print.html command as part of an
-"if"_if.html or "run every"_run.html command), then the double and
-single quotes can be nested in the usual manner.  See the doc pages
-for those commands for examples.  Only one of level of nesting is
-allowed, but that should be sufficient for most use cases.
-
-:line
-
-3.3 Input script structure :h4,link(cmd_3)
-
-This section describes the structure of a typical LAMMPS input script.
-The "examples" directory in the LAMMPS distribution contains many
-sample input scripts; the corresponding problems are discussed in
-"Section_example"_Section_example.html, and animated on the "LAMMPS
-WWW Site"_lws.
-
-A LAMMPS input script typically has 4 parts:
-
-Initialization
-Atom definition
-Settings
-Run a simulation :ol
-
-The last 2 parts can be repeated as many times as desired.  I.e. run a
-simulation, change some settings, run some more, etc.  Each of the 4
-parts is now described in more detail.  Remember that almost all the
-commands need only be used if a non-default value is desired.
-
-(1) Initialization
-
-Set parameters that need to be defined before atoms are created or
-read-in from a file.
-
-The relevant commands are "units"_units.html,
-"dimension"_dimension.html, "newton"_newton.html,
-"processors"_processors.html, "boundary"_boundary.html,
-"atom_style"_atom_style.html, "atom_modify"_atom_modify.html.
-
-If force-field parameters appear in the files that will be read, these
-commands tell LAMMPS what kinds of force fields are being used:
-"pair_style"_pair_style.html, "bond_style"_bond_style.html,
-"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html,
-"improper_style"_improper_style.html.
-
-(2) Atom definition
-
-There are 3 ways to define atoms in LAMMPS.  Read them in from a data
-or restart file via the "read_data"_read_data.html or
-"read_restart"_read_restart.html commands.  These files can contain
-molecular topology information.  Or create atoms on a lattice (with no
-molecular topology), using these commands: "lattice"_lattice.html,
-"region"_region.html, "create_box"_create_box.html,
-"create_atoms"_create_atoms.html.  The entire set of atoms can be
-duplicated to make a larger simulation using the
-"replicate"_replicate.html command.
-
-(3) Settings
-
-Once atoms and molecular topology are defined, a variety of settings
-can be specified: force field coefficients, simulation parameters,
-output options, etc.
-
-Force field coefficients are set by these commands (they can also be
-set in the read-in files): "pair_coeff"_pair_coeff.html,
-"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html,
-"dihedral_coeff"_dihedral_coeff.html,
-"improper_coeff"_improper_coeff.html,
-"kspace_style"_kspace_style.html, "dielectric"_dielectric.html,
-"special_bonds"_special_bonds.html.
-
-Various simulation parameters are set by these commands:
-"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html,
-"group"_group.html, "timestep"_timestep.html,
-"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
-"min_style"_min_style.html, "min_modify"_min_modify.html.
-
-Fixes impose a variety of boundary conditions, time integration, and
-diagnostic options.  The "fix"_fix.html command comes in many flavors.
-
-Various computations can be specified for execution during a
-simulation using the "compute"_compute.html,
-"compute_modify"_compute_modify.html, and "variable"_variable.html
-commands.
-
-Output options are set by the "thermo"_thermo.html, "dump"_dump.html,
-and "restart"_restart.html commands.
-
-(4) Run a simulation
-
-A molecular dynamics simulation is run using the "run"_run.html
-command.  Energy minimization (molecular statics) is performed using
-the "minimize"_minimize.html command.  A parallel tempering
-(replica-exchange) simulation can be run using the
-"temper"_temper.html command.
-
-:line
-
-3.4 Commands listed by category :link(cmd_4),h4
-
-This section lists all LAMMPS commands, grouped by category.  The
-"next section"_#cmd_5 lists the same commands alphabetically.  Note
-that some style options for some commands are part of specific LAMMPS
-packages, which means they cannot be used unless the package was
-included when LAMMPS was built.  Not all packages are included in a
-default LAMMPS build.  These dependencies are listed as Restrictions
-in the command's documentation.
-
-Initialization:
-
-"atom_modify"_atom_modify.html, "atom_style"_atom_style.html,
-"boundary"_boundary.html, "dimension"_dimension.html,
-"newton"_newton.html, "processors"_processors.html, "units"_units.html
-
-Atom definition:
-
-"create_atoms"_create_atoms.html, "create_box"_create_box.html,
-"lattice"_lattice.html, "read_data"_read_data.html,
-"read_dump"_read_dump.html, "read_restart"_read_restart.html,
-"region"_region.html, "replicate"_replicate.html
-
-Force fields:
-
-"angle_coeff"_angle_coeff.html, "angle_style"_angle_style.html,
-"bond_coeff"_bond_coeff.html, "bond_style"_bond_style.html,
-"dielectric"_dielectric.html, "dihedral_coeff"_dihedral_coeff.html,
-"dihedral_style"_dihedral_style.html,
-"improper_coeff"_improper_coeff.html,
-"improper_style"_improper_style.html,
-"kspace_modify"_kspace_modify.html, "kspace_style"_kspace_style.html,
-"pair_coeff"_pair_coeff.html, "pair_modify"_pair_modify.html,
-"pair_style"_pair_style.html, "pair_write"_pair_write.html,
-"special_bonds"_special_bonds.html
-
-Settings:
-
-"comm_style"_comm_style.html, "group"_group.html, "mass"_mass.html,
-"min_modify"_min_modify.html, "min_style"_min_style.html,
-"neigh_modify"_neigh_modify.html, "neighbor"_neighbor.html,
-"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
-"set"_set.html, "timestep"_timestep.html, "velocity"_velocity.html
-
-Fixes:
-
-"fix"_fix.html, "fix_modify"_fix_modify.html, "unfix"_unfix.html
-
-Computes:
-
-"compute"_compute.html, "compute_modify"_compute_modify.html,
-"uncompute"_uncompute.html
-
-Output:
-
-"dump"_dump.html, "dump image"_dump_image.html,
-"dump_modify"_dump_modify.html, "dump movie"_dump_image.html,
-"restart"_restart.html, "thermo"_thermo.html,
-"thermo_modify"_thermo_modify.html, "thermo_style"_thermo_style.html,
-"undump"_undump.html, "write_data"_write_data.html,
-"write_dump"_write_dump.html, "write_restart"_write_restart.html
-
-Actions:
-
-"delete_atoms"_delete_atoms.html, "delete_bonds"_delete_bonds.html,
-"displace_atoms"_displace_atoms.html, "change_box"_change_box.html,
-"minimize"_minimize.html, "neb"_neb.html "prd"_prd.html,
-"rerun"_rerun.html, "run"_run.html, "temper"_temper.html
-
-Miscellaneous:
-
-"clear"_clear.html, "echo"_echo.html, "if"_if.html,
-"include"_include.html, "jump"_jump.html, "label"_label.html,
-"log"_log.html, "next"_next.html, "print"_print.html,
-"shell"_shell.html, "variable"_variable.html
-
-:line
-
-3.5 Individual commands :h4,link(cmd_5),link(comm)
-
-This section lists all LAMMPS commands alphabetically, with a separate
-listing below of styles within certain commands.  The "previous
-section"_#cmd_4 lists the same commands, grouped by category.  Note
-that some style options for some commands are part of specific LAMMPS
-packages, which means they cannot be used unless the package was
-included when LAMMPS was built.  Not all packages are included in a
-default LAMMPS build.  These dependencies are listed as Restrictions
-in the command's documentation.
-
-"angle_coeff"_angle_coeff.html,
-"angle_style"_angle_style.html,
-"atom_modify"_atom_modify.html,
-"atom_style"_atom_style.html,
-"balance"_balance.html,
-"bond_coeff"_bond_coeff.html,
-"bond_style"_bond_style.html,
-"boundary"_boundary.html,
-"box"_box.html,
-"change_box"_change_box.html,
-"clear"_clear.html,
-"comm_modify"_comm_modify.html,
-"comm_style"_comm_style.html,
-"compute"_compute.html,
-"compute_modify"_compute_modify.html,
-"create_atoms"_create_atoms.html,
-"create_box"_create_box.html,
-"delete_atoms"_delete_atoms.html,
-"delete_bonds"_delete_bonds.html,
-"dielectric"_dielectric.html,
-"dihedral_coeff"_dihedral_coeff.html,
-"dihedral_style"_dihedral_style.html,
-"dimension"_dimension.html,
-"displace_atoms"_displace_atoms.html,
-"dump"_dump.html,
-"dump image"_dump_image.html,
-"dump_modify"_dump_modify.html,
-"dump movie"_dump_image.html,
-"echo"_echo.html,
-"fix"_fix.html,
-"fix_modify"_fix_modify.html,
-"group"_group.html,
-"if"_if.html,
-"improper_coeff"_improper_coeff.html,
-"improper_style"_improper_style.html,
-"include"_include.html,
-"jump"_jump.html,
-"kspace_modify"_kspace_modify.html,
-"kspace_style"_kspace_style.html,
-"label"_label.html,
-"lattice"_lattice.html,
-"log"_log.html,
-"mass"_mass.html,
-"minimize"_minimize.html,
-"min_modify"_min_modify.html,
-"min_style"_min_style.html,
-"molecule"_molecule.html,
-"neb"_neb.html,
-"neigh_modify"_neigh_modify.html,
-"neighbor"_neighbor.html,
-"newton"_newton.html,
-"next"_next.html,
-"package"_package.html,
-"pair_coeff"_pair_coeff.html,
-"pair_modify"_pair_modify.html,
-"pair_style"_pair_style.html,
-"pair_write"_pair_write.html,
-"partition"_partition.html,
-"prd"_prd.html,
-"print"_print.html,
-"processors"_processors.html,
-"quit"_quit.html,
-"read_data"_read_data.html,
-"read_dump"_read_dump.html,
-"read_restart"_read_restart.html,
-"region"_region.html,
-"replicate"_replicate.html,
-"rerun"_rerun.html,
-"reset_timestep"_reset_timestep.html,
-"restart"_restart.html,
-"run"_run.html,
-"run_style"_run_style.html,
-"set"_set.html,
-"shell"_shell.html,
-"special_bonds"_special_bonds.html,
-"suffix"_suffix.html,
-"tad"_tad.html,
-"temper"_temper.html,
-"thermo"_thermo.html,
-"thermo_modify"_thermo_modify.html,
-"thermo_style"_thermo_style.html,
-"timestep"_timestep.html,
-"uncompute"_uncompute.html,
-"undump"_undump.html,
-"unfix"_unfix.html,
-"units"_units.html,
-"variable"_variable.html,
-"velocity"_velocity.html,
-"write_data"_write_data.html,
-"write_dump"_write_dump.html,
-"write_restart"_write_restart.html :tb(c=6,ea=c)
-
-These are additional commands in USER packages, which can be used if
-"LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"group2ndx"_group2ndx.html :tb(c=1,ea=c)
-
-:line
-
-Fix styles :h4
-
-See the "fix"_fix.html command for one-line descriptions of each style
-or click on the style itself for a full description.  Some of the
-styles have accelerated versions, which can be used if LAMMPS is built
-with the "appropriate accelerated package"_Section_accelerate.html.
-This is indicated by additional letters in parenthesis: c = USER-CUDA,
-g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
-
-"adapt"_fix_adapt.html,
-"addforce (c)"_fix_addforce.html,
-"append/atoms"_fix_append_atoms.html,
-"aveforce (c)"_fix_aveforce.html,
-"ave/atom"_fix_ave_atom.html,
-"ave/correlate"_fix_ave_correlate.html,
-"ave/histo"_fix_ave_histo.html,
-"ave/spatial"_fix_ave_spatial.html,
-"ave/time"_fix_ave_time.html,
-"balance"_fix_balance.html,
-"bond/break"_fix_bond_break.html,
-"bond/create"_fix_bond_create.html,
-"bond/swap"_fix_bond_swap.html,
-"box/relax"_fix_box_relax.html,
-"deform"_fix_deform.html,
-"deposit"_fix_deposit.html,
-"drag"_fix_drag.html,
-"dt/reset"_fix_dt_reset.html,
-"efield"_fix_efield.html,
-"enforce2d (c)"_fix_enforce2d.html,
-"evaporate"_fix_evaporate.html,
-"external"_fix_external.html,
-"freeze (c)"_fix_freeze.html,
-"gcmc"_fix_gcmc.html,
-"gld"_fix_gld.html,
-"gravity (co)"_fix_gravity.html,
-"heat"_fix_heat.html,
-"indent"_fix_indent.html,
-"langevin (k)"_fix_langevin.html,
-"lineforce"_fix_lineforce.html,
-"momentum"_fix_momentum.html,
-"move"_fix_move.html,
-"msst"_fix_msst.html,
-"neb"_fix_neb.html,
-"nph (o)"_fix_nh.html,
-"nphug (o)"_fix_nphug.html,
-"nph/asphere (o)"_fix_nph_asphere.html,
-"nph/sphere (o)"_fix_nph_sphere.html,
-"npt (co)"_fix_nh.html,
-"npt/asphere (o)"_fix_npt_asphere.html,
-"npt/sphere (o)"_fix_npt_sphere.html,
-"nve (cko)"_fix_nve.html,
-"nve/asphere"_fix_nve_asphere.html,
-"nve/asphere/noforce"_fix_nve_asphere_noforce.html,
-"nve/body"_fix_nve_body.html,
-"nve/limit"_fix_nve_limit.html,
-"nve/line"_fix_nve_line.html,
-"nve/noforce"_fix_nve_noforce.html,
-"nve/sphere (o)"_fix_nve_sphere.html,
-"nve/tri"_fix_nve_tri.html,
-"nvt (co)"_fix_nh.html,
-"nvt/asphere (o)"_fix_nvt_asphere.html,
-"nvt/sllod (o)"_fix_nvt_sllod.html,
-"nvt/sphere (o)"_fix_nvt_sphere.html,
-"oneway"_fix_oneway.html,
-"orient/fcc"_fix_orient_fcc.html,
-"planeforce"_fix_planeforce.html,
-"poems"_fix_poems.html,
-"pour"_fix_pour.html,
-"press/berendsen"_fix_press_berendsen.html,
-"print"_fix_print.html,
-"property/atom"_fix_property_atom.html,
-"qeq/comb (o)"_fix_qeq_comb.html,
-"qeq/dynamic"_fix_qeq.html,
-"qeq/point"_fix_qeq.html,
-"qeq/shielded"_fix_qeq.html,
-"qeq/slater"_fix_qeq.html,
-"reax/bonds"_fix_reax_bonds.html,
-"recenter"_fix_recenter.html,
-"restrain"_fix_restrain.html,
-"rigid (o)"_fix_rigid.html,
-"rigid/nph (o)"_fix_rigid.html,
-"rigid/npt (o)"_fix_rigid.html,
-"rigid/nve (o)"_fix_rigid.html,
-"rigid/nvt (o)"_fix_rigid.html,
-"rigid/small (o)"_fix_rigid.html,
-"rigid/small/nph"_fix_rigid.html,
-"rigid/small/npt"_fix_rigid.html,
-"rigid/small/nve"_fix_rigid.html,
-"rigid/small/nvt"_fix_rigid.html,
-"setforce (c)"_fix_setforce.html,
-"shake (c)"_fix_shake.html,
-"spring"_fix_spring.html,
-"spring/rg"_fix_spring_rg.html,
-"spring/self"_fix_spring_self.html,
-"srd"_fix_srd.html,
-"store/force"_fix_store_force.html,
-"store/state"_fix_store_state.html,
-"temp/berendsen (c)"_fix_temp_berendsen.html,
-"temp/csvr"_fix_temp_csvr.html,
-"temp/rescale (c)"_fix_temp_rescale.html,
-"thermal/conductivity"_fix_thermal_conductivity.html,
-"tmd"_fix_tmd.html,
-"ttm"_fix_ttm.html,
-"tune/kspace"_fix_tune_kspace.html,
-"vector"_fix_vector.html,
-"viscosity"_fix_viscosity.html,
-"viscous (c)"_fix_viscous.html,
-"wall/colloid"_fix_wall.html,
-"wall/gran"_fix_wall_gran.html,
-"wall/harmonic"_fix_wall.html,
-"wall/lj1043"_fix_wall.html,
-"wall/lj126"_fix_wall.html,
-"wall/lj93"_fix_wall.html,
-"wall/piston"_fix_wall_piston.html,
-"wall/reflect"_fix_wall_reflect.html,
-"wall/region"_fix_wall_region.html,
-"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c)
-
-These are additional fix styles in USER packages, which can be used if
-"LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"adapt/fep"_fix_adapt_fep.html,
-"addtorque"_fix_addtorque.html,
-"atc"_fix_atc.html,
-"colvars"_fix_colvars.html,
-"imd"_fix_imd.html,
-"langevin/eff"_fix_langevin_eff.html,
-"lb/fluid"_fix_lb_fluid.html,
-"lb/momentum"_fix_lb_momentum.html,
-"lb/pc"_fix_lb_pc.html,
-"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html,
-"lb/viscous"_fix_lb_viscous.html,
-"meso"_fix_meso.html,
-"meso/stationary"_fix_meso_stationary.html,
-"nph/eff"_fix_nh_eff.html,
-"npt/eff"_fix_nh_eff.html,
-"nve/eff"_fix_nve_eff.html,
-"nvt/eff"_fix_nh_eff.html,
-"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
-"phonon"_fix_phonon.html,
-"qeq/reax"_fix_qeq_reax.html,
-"qmmm"_fix_qmmm.html,
-"reax/c/bonds"_fix_reax_bonds.html,
-"reax/c/species"_fix_reaxc_species.html,
-"smd"_fix_smd.html,
-"temp/rescale/eff"_fix_temp_rescale_eff.html,
-"ti/rs"_fix_ti_rs.html,
-"ti/spring"_fix_ti_spring.html :tb(c=6,ea=c)
-
-:line
-
-Compute styles :h4
-
-See the "compute"_compute.html command for one-line descriptions of
-each style or click on the style itself for a full description.  Some
-of the styles have accelerated versions, which can be used if LAMMPS
-is built with the "appropriate accelerated
-package"_Section_accelerate.html.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-
-"angle/local"_compute_angle_local.html,
-"atom/molecule"_compute_atom_molecule.html,
-"body/local"_compute_body_local.html,
-"bond/local"_compute_bond_local.html,
-"centro/atom"_compute_centro_atom.html,
-"cluster/atom"_compute_cluster_atom.html,
-"cna/atom"_compute_cna_atom.html,
-"com"_compute_com.html,
-"com/molecule"_compute_com_molecule.html,
-"contact/atom"_compute_contact_atom.html,
-"coord/atom"_compute_coord_atom.html,
-"damage/atom"_compute_damage_atom.html,
-"dihedral/local"_compute_dihedral_local.html,
-"dilatation/atom"_compute_dilatation_atom.html,
-"displace/atom"_compute_displace_atom.html,
-"erotate/asphere"_compute_erotate_asphere.html,
-"erotate/rigid"_compute_erotate_rigid.html,
-"erotate/sphere"_compute_erotate_sphere.html,
-"erotate/sphere/atom"_compute_erotate_sphere_atom.html,
-"event/displace"_compute_event_displace.html,
-"group/group"_compute_group_group.html,
-"gyration"_compute_gyration.html,
-"gyration/molecule"_compute_gyration_molecule.html,
-"heat/flux"_compute_heat_flux.html,
-"improper/local"_compute_improper_local.html,
-"inertia/molecule"_compute_inertia_molecule.html,
-"ke"_compute_ke.html,
-"ke/atom"_compute_ke_atom.html,
-"ke/rigid"_compute_ke_rigid.html,
-"msd"_compute_msd.html,
-"msd/molecule"_compute_msd_molecule.html,
-"msd/nongauss"_compute_msd_nongauss.html,
-"pair"_compute_pair.html,
-"pair/local"_compute_pair_local.html,
-"pe (c)"_compute_pe.html,
-"pe/atom"_compute_pe_atom.html,
-"plasticity/atom"_compute_plasticity_atom.html,
-"pressure (c)"_compute_pressure.html,
-"property/atom"_compute_property_atom.html,
-"property/local"_compute_property_local.html,
-"property/molecule"_compute_property_molecule.html,
-"rdf"_compute_rdf.html,
-"reduce"_compute_reduce.html,
-"reduce/region"_compute_reduce.html,
-"slice"_compute_slice.html,
-"sna/atom"_compute_sna.html,
-"snad/atom"_compute_sna.html,
-"snav/atom"_compute_sna.html,
-"stress/atom"_compute_stress_atom.html,
-"temp (c)"_compute_temp.html,
-"temp/asphere"_compute_temp_asphere.html,
-"temp/com"_compute_temp_com.html,
-"temp/deform"_compute_temp_deform.html,
-"temp/partial (c)"_compute_temp_partial.html,
-"temp/profile"_compute_temp_profile.html,
-"temp/ramp"_compute_temp_ramp.html,
-"temp/region"_compute_temp_region.html,
-"temp/sphere"_compute_temp_sphere.html,
-"ti"_compute_ti.html,
-"vacf"_compute_vacf.html,
-"voronoi/atom"_compute_voronoi_atom.html :tb(c=6,ea=c)
-
-These are additional compute styles in USER packages, which can be
-used if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"ackland/atom"_compute_ackland_atom.html,
-"basal/atom"_compute_basal_atom.html,
-"fep"_compute_fep.html,
-"ke/eff"_compute_ke_eff.html,
-"ke/atom/eff"_compute_ke_atom_eff.html,
-"meso_e/atom"_compute_meso_e_atom.html,
-"meso_rho/atom"_compute_meso_rho_atom.html,
-"meso_t/atom"_compute_meso_t_atom.html,
-"temp/eff"_compute_temp_eff.html,
-"temp/deform/eff"_compute_temp_deform_eff.html,
-"temp/region/eff"_compute_temp_region_eff.html,
-"temp/rotate"_compute_temp_rotate.html :tb(c=6,ea=c)
-
-:line
-
-Pair_style potentials :h4
-
-See the "pair_style"_pair_style.html command for an overview of pair
-potentials.  Click on the style itself for a full description.  Many
-of the styles have accelerated versions, which can be used if LAMMPS
-is built with the "appropriate accelerated
-package"_Section_accelerate.html.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-
-"none"_pair_none.html,
-"hybrid"_pair_hybrid.html,
-"hybrid/overlay"_pair_hybrid.html,
-"adp (o)"_pair_adp.html,
-"airebo (o)"_pair_airebo.html,
-"beck (go)"_pair_beck.html,
-"body"_pair_body.html,
-"bop"_pair_bop.html,
-"born (go)"_pair_born.html,
-"born/coul/long (cgo)"_pair_born.html,
-"born/coul/msm (o)"_pair_born.html,
-"born/coul/wolf (go)"_pair_born.html,
-"brownian (o)"_pair_brownian.html,
-"brownian/poly (o)"_pair_brownian.html,
-"buck (cgo)"_pair_buck.html,
-"buck/coul/cut (cgo)"_pair_buck.html,
-"buck/coul/long (cgo)"_pair_buck.html,
-"buck/coul/msm (o)"_pair_buck.html,
-"buck/long/coul/long (o)"_pair_buck_long.html,
-"colloid (go)"_pair_colloid.html,
-"comb (o)"_pair_comb.html,
-"comb3"_pair_comb.html,
-"coul/cut (gko)"_pair_coul.html,
-"coul/debye (go)"_pair_coul.html,
-"coul/dsf (go)"_pair_coul.html,
-"coul/long (go)"_pair_coul.html,
-"coul/msm"_pair_coul.html,
-"coul/wolf (o)"_pair_coul.html,
-"dpd (o)"_pair_dpd.html,
-"dpd/tstat (o)"_pair_dpd.html,
-"dsmc"_pair_dsmc.html,
-"eam (cgot)"_pair_eam.html,
-"eam/alloy (cgot)"_pair_eam.html,
-"eam/fs (cgot)"_pair_eam.html,
-"eim (o)"_pair_eim.html,
-"gauss (go)"_pair_gauss.html,
-"gayberne (gio)"_pair_gayberne.html,
-"gran/hertz/history (o)"_pair_gran.html,
-"gran/hooke (co)"_pair_gran.html,
-"gran/hooke/history (o)"_pair_gran.html,
-"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,
-"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html,
-"kim"_pair_kim.html,
-"lcbop"_pair_lcbop.html,
-"line/lj (o)"_pair_line_lj.html,
-"lj/charmm/coul/charmm (co)"_pair_charmm.html,
-"lj/charmm/coul/charmm/implicit (co)"_pair_charmm.html,
-"lj/charmm/coul/long (cgio)"_pair_charmm.html,
-"lj/charmm/coul/msm"_pair_charmm.html,
-"lj/class2 (cgo)"_pair_class2.html,
-"lj/class2/coul/cut (co)"_pair_class2.html,
-"lj/class2/coul/long (cgo)"_pair_class2.html,
-"lj/cut (cgikot)"_pair_lj.html,
-"lj/cut/coul/cut (cgko)"_pair_lj.html,
-"lj/cut/coul/debye (cgo)"_pair_lj.html,
-"lj/cut/coul/dsf (go)"_pair_lj.html,
-"lj/cut/coul/long (cgikot)"_pair_lj.html,
-"lj/cut/coul/msm (go)"_pair_lj.html,
-"lj/cut/dipole/cut (go)"_pair_dipole.html,
-"lj/cut/dipole/long"_pair_dipole.html,
-"lj/cut/tip4p/cut (o)"_pair_lj.html,
-"lj/cut/tip4p/long (ot)"_pair_lj.html,
-"lj/expand (cgo)"_pair_lj_expand.html,
-"lj/gromacs (cgo)"_pair_gromacs.html,
-"lj/gromacs/coul/gromacs (co)"_pair_gromacs.html,
-"lj/long/coul/long (o)"_pair_lj_long.html,
-"lj/long/dipole/long"_pair_dipole.html,
-"lj/long/tip4p/long"_pair_lj_long.html,
-"lj/smooth (co)"_pair_lj_smooth.html,
-"lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
-"lj96/cut (cgo)"_pair_lj96.html,
-"lubricate (o)"_pair_lubricate.html,
-"lubricate/poly (o)"_pair_lubricate.html,
-"lubricateU"_pair_lubricateU.html,
-"lubricateU/poly"_pair_lubricateU.html,
-"meam (o)"_pair_meam.html,
-"mie/cut (o)"_pair_mie.html,
-"morse (cgot)"_pair_morse.html,
-"nb3b/harmonic (o)"_pair_nb3b_harmonic.html,
-"nm/cut (o)"_pair_nm.html,
-"nm/cut/coul/cut (o)"_pair_nm.html,
-"nm/cut/coul/long (o)"_pair_nm.html,
-"peri/eps"_pair_peri.html,
-"peri/lps (o)"_pair_peri.html,
-"peri/pmb (o)"_pair_peri.html,
-"peri/ves"_pair_peri.html,
-"reax"_pair_reax.html,
-"rebo (o)"_pair_airebo.html,
-"resquared (go)"_pair_resquared.html,
-"snap"_pair_snap.html,
-"soft (go)"_pair_soft.html,
-"sw (cgo)"_pair_sw.html,
-"table (gko)"_pair_table.html,
-"tersoff (co)"_pair_tersoff.html,
-"tersoff/mod (o)"_pair_tersoff_mod.html,
-"tersoff/zbl (o)"_pair_tersoff_zbl.html,
-"tip4p/cut (o)"_pair_coul.html,
-"tip4p/long (o)"_pair_coul.html,
-"tri/lj (o)"_pair_tri_lj.html,
-"yukawa (go)"_pair_yukawa.html,
-"yukawa/colloid (go)"_pair_yukawa_colloid.html,
-"zbl (o)"_pair_zbl.html :tb(c=4,ea=c)
-
-These are additional pair styles in USER packages, which can be used
-if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"awpmd/cut"_pair_awpmd.html,
-"coul/cut/soft (o)"_pair_lj_soft.html,
-"coul/diel (o)"_pair_coul_diel.html,
-"coul/long/soft (o)"_pair_lj_soft.html,
-"eam/cd (o)"_pair_eam.html,
-"edip (o)"_pair_edip.html,
-"eff/cut"_pair_eff.html,
-"gauss/cut"_pair_gauss.html,
-"list"_pair_list.html,
-"lj/charmm/coul/long/soft (o)"_pair_charmm.html,
-"lj/cut/coul/cut/soft (o)"_pair_lj_soft.html,
-"lj/cut/coul/long/soft (o)"_pair_lj_soft.html,
-"lj/cut/dipole/sf (go)"_pair_dipole.html,
-"lj/cut/soft (o)"_pair_lj_soft.html,
-"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html,
-"lj/sdk (go)"_pair_sdk.html,
-"lj/sdk/coul/long (go)"_pair_sdk.html,
-"lj/sdk/coul/msm (o)"_pair_sdk.html,
-"lj/sf (o)"_pair_lj_sf.html,
-"meam/spline"_pair_meam_spline.html,
-"meam/sw/spline"_pair_meam_sw_spline.html,
-"reax/c"_pair_reax_c.html,
-"sph/heatconduction"_pair_sph_heatconduction.html,
-"sph/idealgas"_pair_sph_idealgas.html,
-"sph/lj"_pair_sph_lj.html,
-"sph/rhosum"_pair_sph_rhosum.html,
-"sph/taitwater"_pair_sph_taitwater.html,
-"sph/taitwater/morris"_pair_sph_taitwater_morris.html,
-"tersoff/table (o)"_pair_tersoff.html,
-"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)
-
-:line
-
-Bond_style potentials :h4
-
-See the "bond_style"_bond_style.html command for an overview of bond
-potentials.  Click on the style itself for a full description.  Some
-of the styles have accelerated versions, which can be used if LAMMPS
-is built with the "appropriate accelerated
-package"_Section_accelerate.html.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-
-"none"_bond_none.html,
-"hybrid"_bond_hybrid.html,
-"class2 (o)"_bond_class2.html,
-"fene (o)"_bond_fene.html,
-"fene/expand (o)"_bond_fene_expand.html,
-"harmonic (o)"_bond_harmonic.html,
-"morse (o)"_bond_morse.html,
-"nonlinear (o)"_bond_nonlinear.html,
-"quartic (o)"_bond_quartic.html,
-"table (o)"_bond_table.html :tb(c=4,ea=c)
-
-These are additional bond styles in USER packages, which can be used
-if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"harmonic/shift (o)"_bond_harmonic_shift.html,
-"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html :tb(c=4,ea=c)
-
-:line
-
-Angle_style potentials :h4
-
-See the "angle_style"_angle_style.html command for an overview of
-angle potentials.  Click on the style itself for a full description.
-Some of the styles have accelerated versions, which can be used if
-LAMMPS is built with the "appropriate accelerated
-package"_Section_accelerate.html.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-
-"none"_angle_none.html,
-"hybrid"_angle_hybrid.html,
-"charmm (o)"_angle_charmm.html,
-"class2 (o)"_angle_class2.html,
-"cosine (o)"_angle_cosine.html,
-"cosine/delta (o)"_angle_cosine_delta.html,
-"cosine/periodic (o)"_angle_cosine_periodic.html,
-"cosine/squared (o)"_angle_cosine_squared.html,
-"harmonic (o)"_angle_harmonic.html,
-"table (o)"_angle_table.html :tb(c=4,ea=c)
-
-These are additional angle styles in USER packages, which can be used
-if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"cosine/shift (o)"_angle_cosine_shift.html,
-"cosine/shift/exp (o)"_angle_cosine_shift_exp.html,
-"dipole (o)"_angle_dipole.html,
-"fourier (o)"_angle_fourier.html,
-"fourier/simple (o)"_angle_fourier_simple.html,
-"quartic (o)"_angle_quartic.html,
-"sdk"_angle_sdk.html :tb(c=4,ea=c)
-
-:line
-
-Dihedral_style potentials :h4
-
-See the "dihedral_style"_dihedral_style.html command for an overview
-of dihedral potentials.  Click on the style itself for a full
-description.  Some of the styles have accelerated versions, which can
-be used if LAMMPS is built with the "appropriate accelerated
-package"_Section_accelerate.html.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-
-"none"_dihedral_none.html,
-"hybrid"_dihedral_hybrid.html,
-"charmm (o)"_dihedral_charmm.html,
-"class2 (o)"_dihedral_class2.html,
-"harmonic (o)"_dihedral_harmonic.html,
-"helix (o)"_dihedral_helix.html,
-"multi/harmonic (o)"_dihedral_multi_harmonic.html,
-"opls (o)"_dihedral_opls.html :tb(c=4,ea=c)
-
-These are additional dihedral styles in USER packages, which can be
-used if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
-"fourier (o)"_dihedral_fourier.html,
-"nharmonic (o)"_dihedral_nharmonic.html,
-"quadratic (o)"_dihedral_quadratic.html,
-"table (o)"_dihedral_table.html :tb(c=4,ea=c)
-
-:line
-
-Improper_style potentials :h4
-
-See the "improper_style"_improper_style.html command for an overview
-of improper potentials.  Click on the style itself for a full
-description.  Some of the styles have accelerated versions, which can
-be used if LAMMPS is built with the "appropriate accelerated
-package"_Section_accelerate.html.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-
-"none"_improper_none.html,
-"hybrid"_improper_hybrid.html,
-"class2 (o)"_improper_class2.html,
-"cvff (o)"_improper_cvff.html,
-"harmonic (o)"_improper_harmonic.html,
-"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)
-
-These are additional improper styles in USER packages, which can be
-used if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"cossq (o)"_improper_cossq.html,
-"fourier (o)"_improper_fourier.html,
-"ring (o)"_improper_ring.html :tb(c=4,ea=c)
-
-:line
-
-Kspace solvers :h4
-
-See the "kspace_style"_kspace_style.html command for an overview of
-Kspace solvers.  Click on the style itself for a full description.
-Some of the styles have accelerated versions, which can be used if
-LAMMPS is built with the "appropriate accelerated
-package"_Section_accelerate.html.  This is indicated by additional
-letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-
-"ewald (o)"_kspace_style.html,
-"ewald/disp"_kspace_style.html,
-"msm (o)"_kspace_style.html,
-"msm/cg (o)"_kspace_style.html,
-"pppm (cgo)"_kspace_style.html,
-"pppm/cg (o)"_kspace_style.html,
-"pppm/disp"_kspace_style.html,
-"pppm/disp/tip4p"_kspace_style.html,
-"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c)

doc/Section_example.html

@@ -1,126 +0,0 @@
-<HTML>
-<CENTER><A HREF = "Section_howto.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_perf.html">Next Section</A> 
-</CENTER>
-
-
-
-
-
-
-<HR>
-
-<H3>7. Example problems 
-</H3>
-<P>The LAMMPS distribution includes an examples sub-directory with
-several sample problems.  Each problem is in a sub-directory of its
-own.  Most are 2d models so that they run quickly, requiring at most a
-couple of minutes to run on a desktop machine.  Each problem has an
-input script (in.*) and produces a log file (log.*) and dump file
-(dump.*) when it runs.  Some use a data file (data.*) of initial
-coordinates as additional input.  A few sample log file outputs on
-different machines and different numbers of processors are included in
-the directories to compare your answers to.  E.g. a log file like
-log.crack.foo.P means it ran on P processors of machine "foo".
-</P>
-<P>For examples that use input data files, many of them were produced by
-<A HREF = "http://pizza.sandia.gov">Pizza.py</A> or setup tools described in the
-<A HREF = "Section_tools.html">Additional Tools</A> section of the LAMMPS
-documentation and provided with the LAMMPS distribution.
-</P>
-<P>If you uncomment the <A HREF = "dump.html">dump</A> command in the input script, a
-text dump file will be produced, which can be animated by various
-<A HREF = "http://lammps.sandia.gov/viz.html">visualization programs</A>.  It can
-also be animated using the xmovie tool described in the <A HREF = "Section_tools.html">Additional
-Tools</A> section of the LAMMPS documentation.
-</P>
-<P>If you uncomment the <A HREF = "dump.html">dump image</A> command in the input
-script, and assuming you have built LAMMPS with a JPG library, JPG
-snapshot images will be produced when the simulation runs.  They can
-be quickly post-processed into a movie using commands described on the
-<A HREF = "dump_image.html">dump image</A> doc page.
-</P>
-<P>Animations of many of these examples can be viewed on the Movies
-section of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>.
-</P>
-<P>These are the sample problems in the examples sub-directories:
-</P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR><TD >balance</TD><TD >  dynamic load balancing, 2d system</TD></TR>
-<TR><TD >body</TD><TD >     body particles, 2d system</TD></TR>
-<TR><TD >colloid</TD><TD >  big colloid particles in a small particle solvent, 2d system</TD></TR>
-<TR><TD >comb</TD><TD >	  models using the COMB potential</TD></TR>
-<TR><TD >crack</TD><TD >	  crack propagation in a 2d solid</TD></TR>
-<TR><TD >cuda</TD><TD >     use of the USER-CUDA package for GPU acceleration</TD></TR>
-<TR><TD >dipole</TD><TD >   point dipolar particles, 2d system</TD></TR>
-<TR><TD >dreiding</TD><TD > methanol via Dreiding FF</TD></TR>
-<TR><TD >eim</TD><TD >      NaCl using the EIM potential</TD></TR>
-<TR><TD >ellipse</TD><TD >  ellipsoidal particles in spherical solvent, 2d system</TD></TR>
-<TR><TD >flow</TD><TD >	  Couette and Poiseuille flow in a 2d channel</TD></TR>
-<TR><TD >friction</TD><TD > frictional contact of spherical asperities between 2d surfaces</TD></TR>
-<TR><TD >gpu</TD><TD >      use of the GPU package for GPU acceleration</TD></TR>
-<TR><TD >hugoniostat</TD><TD > Hugoniostat shock dynamics</TD></TR>
-<TR><TD >indent</TD><TD >	  spherical indenter into a 2d solid</TD></TR>
-<TR><TD >intel</TD><TD >    use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor</TD></TR>
-<TR><TD >kim</TD><TD >      use of potentials in Knowledge Base for Interatomic Models (KIM)</TD></TR>
-<TR><TD >line</TD><TD >     line segment particles in 2d rigid bodies</TD></TR>
-<TR><TD >meam</TD><TD >	  MEAM test for SiC and shear (same as shear examples)</TD></TR>
-<TR><TD >melt</TD><TD >	  rapid melt of 3d LJ system</TD></TR>
-<TR><TD >micelle</TD><TD >  self-assembly of small lipid-like molecules into 2d bilayers</TD></TR>
-<TR><TD >min</TD><TD >	  energy minimization of 2d LJ melt</TD></TR>
-<TR><TD >msst</TD><TD >	  MSST shock dynamics</TD></TR>
-<TR><TD >nb3b</TD><TD >     use of nonbonded 3-body harmonic pair style</TD></TR>
-<TR><TD >neb</TD><TD >	  nudged elastic band (NEB) calculation for barrier finding</TD></TR>
-<TR><TD >nemd</TD><TD >	  non-equilibrium MD of 2d sheared system</TD></TR>
-<TR><TD >obstacle</TD><TD > flow around two voids in a 2d channel</TD></TR>
-<TR><TD >peptide</TD><TD >  dynamics of a small solvated peptide chain (5-mer)</TD></TR>
-<TR><TD >peri</TD><TD >	  Peridynamic model of cylinder impacted by indenter</TD></TR>
-<TR><TD >pour</TD><TD >     pouring of granular particles into a 3d box, then chute flow</TD></TR>
-<TR><TD >prd</TD><TD >      parallel replica dynamics of vacancy diffusion in bulk Si</TD></TR>
-<TR><TD >qeq</TD><TD >      use of the QEQ pacakge for charge equilibration</TD></TR>
-<TR><TD >reax</TD><TD >     RDX and TATB models using the ReaxFF</TD></TR>
-<TR><TD >rigid</TD><TD >    rigid bodies modeled as independent or coupled</TD></TR>
-<TR><TD >shear</TD><TD >    sideways shear applied to 2d solid, with and without a void</TD></TR>
-<TR><TD >snap</TD><TD >     NVE dynamics for BCC tantalum crystal using SNAP potential</TD></TR>
-<TR><TD >srd</TD><TD >      stochastic rotation dynamics (SRD) particles as solvent</TD></TR>
-<TR><TD >tad</TD><TD >      temperature-accelerated dynamics of vacancy diffusion in bulk Si</TD></TR>
-<TR><TD >tri</TD><TD >      triangular particles in rigid bodies 
-</TD></TR></TABLE></DIV>
-
-<P>Here is how you might run and visualize one of the sample problems:
-</P>
-<PRE>cd indent
-cp ../../src/lmp_linux .           # copy LAMMPS executable to this dir
-lmp_linux < in.indent              # run the problem 
-</PRE>
-<P>Running the simulation produces the files <I>dump.indent</I> and
-<I>log.lammps</I>.  You can visualize the dump file as follows:
-</P>
-<PRE>../../tools/xmovie/xmovie -scale dump.indent 
-</PRE>
-<P>If you uncomment the <A HREF = "dump_image.html">dump image</A> line(s) in the input
-script a series of JPG images will be produced by the run.  These can
-be viewed individually or turned into a movie or animated by tools
-like ImageMagick or QuickTime or various Windows-based tools.  See the
-<A HREF = "dump_image.html">dump image</A> doc page for more details.  E.g. this
-Imagemagick command would create a GIF file suitable for viewing in a
-browser.
-</P>
-<PRE>% convert -loop 1 *.jpg foo.gif 
-</PRE>
-<HR>
-
-<P>There is also a COUPLE directory with examples of how to use LAMMPS as
-a library, either by itself or in tandem with another code or library.
-See the COUPLE/README file to get started.
-</P>
-<P>There is also an ELASTIC directory with an example script for
-computing elastic constants, using a zero temperature Si example.  See
-the in.elastic file for more info.
-</P>
-<P>There is also a USER directory which contains subdirectories of
-user-provided examples for user packages.  See the README files in
-those directories for more info.  See the
-<A HREF = "Section_start.html">Section_start.html</A> file for more info about user
-packages.
-</P>
-</HTML>

doc/Section_example.txt

@@ -1,119 +0,0 @@
-"Previous Section"_Section_howto.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_perf.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-7. Example problems :h3
-
-The LAMMPS distribution includes an examples sub-directory with
-several sample problems.  Each problem is in a sub-directory of its
-own.  Most are 2d models so that they run quickly, requiring at most a
-couple of minutes to run on a desktop machine.  Each problem has an
-input script (in.*) and produces a log file (log.*) and dump file
-(dump.*) when it runs.  Some use a data file (data.*) of initial
-coordinates as additional input.  A few sample log file outputs on
-different machines and different numbers of processors are included in
-the directories to compare your answers to.  E.g. a log file like
-log.crack.foo.P means it ran on P processors of machine "foo".
-
-For examples that use input data files, many of them were produced by
-"Pizza.py"_http://pizza.sandia.gov or setup tools described in the
-"Additional Tools"_Section_tools.html section of the LAMMPS
-documentation and provided with the LAMMPS distribution.
-
-If you uncomment the "dump"_dump.html command in the input script, a
-text dump file will be produced, which can be animated by various
-"visualization programs"_http://lammps.sandia.gov/viz.html.  It can
-also be animated using the xmovie tool described in the "Additional
-Tools"_Section_tools.html section of the LAMMPS documentation.
-
-If you uncomment the "dump image"_dump.html command in the input
-script, and assuming you have built LAMMPS with a JPG library, JPG
-snapshot images will be produced when the simulation runs.  They can
-be quickly post-processed into a movie using commands described on the
-"dump image"_dump_image.html doc page.
-
-Animations of many of these examples can be viewed on the Movies
-section of the "LAMMPS WWW Site"_lws.
-
-These are the sample problems in the examples sub-directories:
-
-balance:  dynamic load balancing, 2d system
-body:     body particles, 2d system
-colloid:  big colloid particles in a small particle solvent, 2d system
-comb:	  models using the COMB potential
-crack:	  crack propagation in a 2d solid
-cuda:     use of the USER-CUDA package for GPU acceleration
-dipole:   point dipolar particles, 2d system
-dreiding: methanol via Dreiding FF
-eim:      NaCl using the EIM potential
-ellipse:  ellipsoidal particles in spherical solvent, 2d system
-flow:	  Couette and Poiseuille flow in a 2d channel
-friction: frictional contact of spherical asperities between 2d surfaces
-gpu:      use of the GPU package for GPU acceleration
-hugoniostat: Hugoniostat shock dynamics
-indent:	  spherical indenter into a 2d solid
-intel:    use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor
-kim:      use of potentials in Knowledge Base for Interatomic Models (KIM)
-line:     line segment particles in 2d rigid bodies
-meam:	  MEAM test for SiC and shear (same as shear examples)
-melt:	  rapid melt of 3d LJ system
-micelle:  self-assembly of small lipid-like molecules into 2d bilayers
-min:	  energy minimization of 2d LJ melt
-msst:	  MSST shock dynamics
-nb3b:     use of nonbonded 3-body harmonic pair style
-neb:	  nudged elastic band (NEB) calculation for barrier finding
-nemd:	  non-equilibrium MD of 2d sheared system
-obstacle: flow around two voids in a 2d channel
-peptide:  dynamics of a small solvated peptide chain (5-mer)
-peri:	  Peridynamic model of cylinder impacted by indenter
-pour:     pouring of granular particles into a 3d box, then chute flow
-prd:      parallel replica dynamics of vacancy diffusion in bulk Si
-qeq:      use of the QEQ pacakge for charge equilibration
-reax:     RDX and TATB models using the ReaxFF
-rigid:    rigid bodies modeled as independent or coupled
-shear:    sideways shear applied to 2d solid, with and without a void
-snap:     NVE dynamics for BCC tantalum crystal using SNAP potential
-srd:      stochastic rotation dynamics (SRD) particles as solvent
-tad:      temperature-accelerated dynamics of vacancy diffusion in bulk Si
-tri:      triangular particles in rigid bodies :tb(s=:)
-
-Here is how you might run and visualize one of the sample problems:
-
-cd indent
-cp ../../src/lmp_linux .           # copy LAMMPS executable to this dir
-lmp_linux < in.indent              # run the problem :pre
-
-Running the simulation produces the files {dump.indent} and
-{log.lammps}.  You can visualize the dump file as follows:
-
-../../tools/xmovie/xmovie -scale dump.indent :pre
-
-If you uncomment the "dump image"_dump_image.html line(s) in the input
-script a series of JPG images will be produced by the run.  These can
-be viewed individually or turned into a movie or animated by tools
-like ImageMagick or QuickTime or various Windows-based tools.  See the
-"dump image"_dump_image.html doc page for more details.  E.g. this
-Imagemagick command would create a GIF file suitable for viewing in a
-browser.
-
-% convert -loop 1 *.jpg foo.gif :pre
-
-:line
-
-There is also a COUPLE directory with examples of how to use LAMMPS as
-a library, either by itself or in tandem with another code or library.
-See the COUPLE/README file to get started.
-
-There is also an ELASTIC directory with an example script for
-computing elastic constants, using a zero temperature Si example.  See
-the in.elastic file for more info.
-
-There is also a USER directory which contains subdirectories of
-user-provided examples for user packages.  See the README files in
-those directories for more info.  See the
-"Section_start.html"_Section_start.html file for more info about user
-packages.

doc/Section_history.html

@@ -1,129 +0,0 @@
-<HTML>
-<CENTER><A HREF = "Section_errors.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
-<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Manual.html">Next
-Section</A> 
-</CENTER>
-
-
-
-
-
-
-<HR>
-
-<H3>13. Future and history 
-</H3>
-<P>This section lists features we plan to add to LAMMPS, features of
-previous versions of LAMMPS, and features of other parallel molecular
-dynamics codes our group has distributed.
-</P>
-13.1 <A HREF = "#hist_1">Coming attractions</A><BR>
-13.2 <A HREF = "#hist_2">Past versions</A> <BR>
-
-<HR>
-
-<HR>
-
-<H4><A NAME = "hist_1"></A>13.1 Coming attractions 
-</H4>
-<P>The <A HREF = "http://lammps.sandia.gov/future.html">Wish list link</A> on the
-LAMMPS WWW page gives a list of features we are hoping to add to
-LAMMPS in the future, including contact names of individuals you can
-email if you are interested in contributing to the developement or
-would be a future user of that feature.
-</P>
-<P>You can also send <A HREF = "http://lammps.sandia.gov/authors.html">email to the
-developers</A> if you want to add
-your wish to the list.
-</P>
-<HR>
-
-<H4><A NAME = "hist_2"></A>13.2 Past versions 
-</H4>
-<P>LAMMPS development began in the mid 1990s under a cooperative research
-& development agreement (CRADA) between two DOE labs (Sandia and LLNL)
-and 3 companies (Cray, Bristol Myers Squibb, and Dupont). The goal was
-to develop a large-scale parallel classical MD code; the coding effort
-was led by Steve Plimpton at Sandia.
-</P>
-<P>After the CRADA ended, a final F77 version, LAMMPS 99, was
-released. As development of LAMMPS continued at Sandia, its memory
-management was converted to F90; a final F90 version was released as
-LAMMPS 2001.
-</P>
-<P>The current LAMMPS is a rewrite in C++ and was first publicly released
-as an open source code in 2004. It includes many new features beyond
-those in LAMMPS 99 or 2001. It also includes features from older
-parallel MD codes written at Sandia, namely ParaDyn, Warp, and
-GranFlow (see below).
-</P>
-<P>In late 2006 we began merging new capabilities into LAMMPS that were
-developed by Aidan Thompson at Sandia for his MD code GRASP, which has
-a parallel framework similar to LAMMPS. Most notably, these have
-included many-body potentials - Stillinger-Weber, Tersoff, ReaxFF -
-and the associated charge-equilibration routines needed for ReaxFF.
-</P>
-<P>The <A HREF = "http://lammps.sandia.gov/history.html">History link</A> on the 
-LAMMPS WWW page gives a timeline of features added to the
-C++ open-source version of LAMMPS over the last several years.
-</P>
-<P>These older codes are available for download from the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW
-site</A>, except for Warp & GranFlow which were primarily used
-internally.  A brief listing of their features is given here.
-</P>
-<P>LAMMPS 2001
-</P>
-<UL><LI>    F90 + MPI
-<LI>    dynamic memory
-<LI>    spatial-decomposition parallelism
-<LI>    NVE, NVT, NPT, NPH, rRESPA integrators
-<LI>    LJ and Coulombic pairwise force fields
-<LI>    all-atom, united-atom, bead-spring polymer force fields
-<LI>    CHARMM-compatible force fields
-<LI>    class 2 force fields
-<LI>    3d/2d Ewald & PPPM
-<LI>    various force and temperature constraints
-<LI>    SHAKE
-<LI>    Hessian-free truncated-Newton minimizer
-<LI>    user-defined diagnostics 
-</UL>
-<P>LAMMPS 99
-</P>
-<UL><LI>    F77 + MPI
-<LI>    static memory allocation
-<LI>    spatial-decomposition parallelism
-<LI>    most of the LAMMPS 2001 features with a few exceptions
-<LI>    no 2d Ewald & PPPM
-<LI>    molecular force fields are missing a few CHARMM terms
-<LI>    no SHAKE 
-</UL>
-<P>Warp
-</P>
-<UL><LI>    F90 + MPI
-<LI>    spatial-decomposition parallelism
-<LI>    embedded atom method (EAM) metal potentials + LJ
-<LI>    lattice and grain-boundary atom creation
-<LI>    NVE, NVT integrators
-<LI>    boundary conditions for applying shear stresses
-<LI>    temperature controls for actively sheared systems
-<LI>    per-atom energy and centro-symmetry computation and output 
-</UL>
-<P>ParaDyn
-</P>
-<UL><LI>    F77 + MPI
-<LI>    atom- and force-decomposition parallelism
-<LI>    embedded atom method (EAM) metal potentials
-<LI>    lattice atom creation
-<LI>    NVE, NVT, NPT integrators
-<LI>    all serial DYNAMO features for controls and constraints 
-</UL>
-<P>GranFlow
-</P>
-<UL><LI>    F90 + MPI
-<LI>    spatial-decomposition parallelism
-<LI>    frictional granular potentials
-<LI>    NVE integrator
-<LI>    boundary conditions for granular flow and packing and walls
-<LI>    particle insertion 
-</UL>
-</HTML>