Merge branch 'master' of github.com:lammps/lammps

tweak an eq in USER-MESO, also allow neigh to be built w/out styles

.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

@@ -32,3 +32,11 @@ log.cite
 .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/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
-package precision.  See the README files in the lib/gpu and lib/cuda
-directories for instructions on how to build the packages with
-different precisions.  The GPU and USER-CUDA sub-sections of the
-doc/Section_accelerate.html file also describes this process.
-
-Make.py -d ~/lammps -j 16 -p #all orig -m linux -o cpu -a exe
-Make.py -d ~/lammps -j 16 -p #all opt orig -m linux -o opt -a exe
-Make.py -d ~/lammps -j 16 -p #all omp orig -m linux -o omp -a exe
-Make.py -d ~/lammps -j 16 -p #all gpu orig -m linux \
-        -gpu mode=double arch=20 -o gpu_double -a libs exe
-Make.py -d ~/lammps -j 16 -p #all gpu orig -m linux \
-        -gpu mode=mixed arch=20 -o gpu_mixed -a libs exe
-Make.py -d ~/lammps -j 16 -p #all gpu orig -m linux \
-        -gpu mode=single arch=20 -o gpu_single -a libs exe
-Make.py -d ~/lammps -j 16 -p #all cuda orig -m linux \
-        -cuda mode=double arch=20 -o cuda_double -a libs exe
-Make.py -d ~/lammps -j 16 -p #all cuda orig -m linux \
-        -cuda mode=mixed arch=20 -o cuda_mixed -a libs exe
-Make.py -d ~/lammps -j 16 -p #all cuda orig -m linux \
-        -cuda mode=single arch=20 -o cuda_single -a libs exe
-Make.py -d ~/lammps -j 16 -p #all intel orig -m linux -o intel_cpu -a exe
-Make.py -d ~/lammps -j 16 -p #all kokkos orig -m linux -o kokkos_omp -a exe
-Make.py -d ~/lammps -j 16 -p #all kokkos orig -kokkos cuda arch=20 \
-        -m cuda -o kokkos_cuda -a exe
-
-Make.py -d ~/lammps -j 16 -p #all opt omp gpu cuda intel kokkos orig \
-        -gpu mode=double arch=20 -cuda mode=double arch=20 -m linux \
-        -o all -a libs exe
-
-Make.py -d ~/lammps -j 16 -p #all opt omp gpu cuda intel kokkos orig \
-        -kokkos cuda arch=20 -gpu mode=double arch=20 \
-        -cuda mode=double arch=20 -m cuda -o all_cuda -a libs exe
-
 ------------------------------------------------------------------------
 
-To run on just CPUs (without using the GPU or USER-CUDA styles),
+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/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 rigid 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

cmake/CMakeLists.txt

@@ -0,0 +1,547 @@
+########################################
+# 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_SOURCE_DIR}/../src)
+set(LAMMPS_LIB_SOURCE_DIR ${CMAKE_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_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)
+
+foreach(STYLE_FILE style_angle.h style_atom.h style_body.h style_bond.h style_command.h style_compute.h style_dihedral.h style_dump.h
+             style_fix.h style_improper.h style_integrate.h style_kspace.h style_minimize.h style_nbin.h style_npair.h style_nstencil.h
+             style_ntopo.h style_pair.h style_reader.h style_region.h)
+  if(EXISTS ${LAMMPS_SOURCE_DIR}/${STYLE_FILE})
+    message(FATAL_ERROR "There is a ${STYLE_FILE} in ${LAMMPS_SOURCE_DIR}, please clean up the source directory first")
+  endif()
+endforeach()
+
+enable_language(CXX)
+
+######################################################################
+# compiler tests
+# these need ot be done early (before further tests).
+#####################################################################
+include(CheckCCompilerFlag)
+
+########################################################################
+# User input options                                                   #
+########################################################################
+option(BUILD_SHARED_LIBS "Build shared libs" OFF)
+option(INSTALL_LIB "Install lammps library and header" ON)
+include(GNUInstallDirs)
+
+set(LAMMPS_LINK_LIBS)
+option(ENABLE_MPI "Build MPI version" OFF)
+if(ENABLE_MPI)
+  find_package(MPI REQUIRED)
+  include_directories(${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)
+  list(APPEND LIB_SOURCES ${MPI_SOURCES})
+  include_directories(${LAMMPS_SOURCE_DIR}/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${LAMMPS_SIZE_LIMIT})
+
+set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS")
+add_definitions(-DLAMMPS_MEMALIGN=${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)
+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
+   USER-ATC USER-AWPMD USER-CGDNA
+  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-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD 
+  USER-SMTBQ USER-SPH USER-TALLY 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 ${PKG2}")
+  endif()
+endmacro()
+
+pkg_depends(MPIIO MPI)
+pkg_depends(QEQ MANYBODY)
+pkg_depends(USER-ATC MANYBODY)
+pkg_depends(USER-H5MD MPI)
+pkg_depends(USER-LB MPI)
+pkg_depends(USER-MISC MANYBODY)
+pkg_depends(USER-PHONON KSPACE)
+
+if(ENABLE_BODY AND ENABLE_POEMS)
+  message(FATAL_ERROR "BODY and POEMS cannot be enabled at the same time")
+endif()
+
+######################################################
+# packages with special compiler needs or external libs
+######################################################
+if(ENABLE_REAX OR ENABLE_MEAM OR ENABLE_USER-QUIP OR ENABLE_USER-QMMM)
+  enable_language(Fortran)
+endif()
+
+if(ENABLE_KOKKOS OR ENABLE_MSCG)
+  # starting with CMake 3.1 this is all you have to do to enforce C++11
+  set(CMAKE_CXX_STANDARD 11) # C++11...
+  set(CMAKE_CXX_STANDARD_REQUIRED ON) #...is required...
+  set(CMAKE_CXX_EXTENSIONS OFF) #...without compiler extensions like gnu++11
+endif()
+
+if(ENABLE_USER-OMP OR ENABLE_KOKKOS OR ENABLE_USER-INTEL)
+  find_package(OpenMP REQUIRED)
+  set (CMAKE_C_FLAGS "${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_MISC)
+  option(LAMMPS_XDR "include XDR compatibility files for doing particle dumps in XTC format" OFF)
+  if(LAMMPS_XDR)
+    add_definitions(-DLAMMPS_XDR)
+  endif()
+endif()
+
+if(ENABLE_MSCG OR ENABLE_USER-ATC OR ENABLE_USER-AWPMD OR ENABLE_USER-QUIP)
+  find_package(LAPACK)
+  if(LAPACK_FOUND)
+    list(APPEND LAMMPS_LINK_LIBS ${LAPACK_LIBRARIES})
+  else()
+    enable_language(Fortran)
+    file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.f)
+    list(APPEND LIB_SOURCES ${LAPACK_SOURCES})
+  endif()
+endif()
+
+if(ENABLE_PYTHON)
+  find_package(PythonInterp REQUIRED)
+  find_package(PythonLibs REQUIRED)
+  add_definitions(-DLMP_PYTHON)
+  include_directories(${PYTHON_INCLUDE_DIR})
+  list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY})
+  if(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_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})
+  if(NOT BUILD_SHARED_LIBS)
+    message(FATAL_ERROR "Python package need lammps to be build shared, use -DBUILD_SHARED_LIBS=ON")
+  endif()
+endif()
+
+find_package(JPEG)
+if(JPEG_FOUND)
+  add_definitions(-DLAMMPS_JPEG)
+  include_directories(${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_USER-MOLFILE)
+  list(APPEND LAMMPS_LINK_LIBS ${CMAKE_DL_LIBS})
+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} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+endif()
+
+if(ENABLE_USER-QMMM)
+  find_package(QE REQUIRED)
+  include_directories(${QE_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+endif()
+
+if(ENABLE_USER-AWPMD)
+  include_directories(${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact
+    ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include)
+endif()
+
+if(ENABLE_USER-H5MD)
+  find_package(HDF5 REQUIRED)
+  list(APPEND LAMMPS_LINK_LIBS ${HDF5_LIBRARIES})
+  include_directories(${HDF5_INCLUDE_DIRS} ${LAMMPS_LIB_SOURCE_DIR}/h5md/include)
+endif()
+
+if(ENABLE_USER-VTK)
+  find_package(VTK REQUIRED NO_MODULE)
+  include(${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)
+  list(APPEND LIB_SOURCES ${MSCG_SOURCES})
+  foreach(MSCG_SOURCE ${MSCG_SOURCES})
+    set_property(SOURCE ${MSCG_SOURCE} APPEND PROPERTY COMPILE_DEFINITIONS
+      DIMENSION=3 _exclude_gromacs=1)
+  endforeach()
+  include_directories(${LAMMPS_LIB_MSCG_BIN_DIR} ${GSL_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS ${GSL_LIBRARIES})
+endif()
+
+########################################################################
+# Basic system tests (standard libraries, headers, functions, types)   #
+########################################################################
+include(CheckIncludeFile)
+foreach(HEADER math.h)
+  check_include_file(${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} ${OTHER_PACKAGES})
+  if(ENABLE_${PKG})
+    set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
+
+    # detects styles in package and adds them to global list
+    RegisterStyles(${${PKG}_SOURCES_DIR})
+
+    file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp)
+    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-MOLFILE USER-QMMM)
+  if(ENABLE_${SIMPLE_LIB})
+    string(REGEX REPLACE "^USER-" "" SIMPLE_LIB "${SIMPLE_LIB}")
+    string(TOLOWER "${SIMPLE_LIB}" INC_DIR)
+    file(GLOB_RECURSE ${SIMPLE_LIB}_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/${INC_DIR}/*.F
+      ${LAMMPS_LIB_SOURCE_DIR}/${INC_DIR}/*.c ${LAMMPS_LIB_SOURCE_DIR}/${INC_DIR}/*.cpp)
+    list(APPEND LIB_SOURCES ${${SIMPLE_LIB}_SOURCES})
+    include_directories(${LAMMPS_LIB_SOURCE_DIR}/${INC_DIR})
+  endif()
+endforeach()
+
+######################################################################
+# 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}/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)
+
+  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)
+    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()
+    include_directories(${CUDA_INCLUDE_DIRS})
+    list(APPEND LAMMPS_LINK_LIBS ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
+    set(GPU_PREC "SINGLE_DOUBLE" CACHE STRING "Lammps gpu precision size")
+    set_property(CACHE GPU_PREC PROPERTY STRINGS SINGLE_DOUBLE SINGLE_SINGLE DOUBLE_DOUBLE)
+    add_definitions(-D_${GPU_PREC})
+    add_definitions(-DNV_KERNEL -DUCL_CUDADR)
+    option(CUDPP_OPT "Enable CUDPP_OPT" ON)
+
+    set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
+    set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h)
+
+    set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
+
+    # detects styles which have GPU version
+    RegisterStylesExt(${GPU_SOURCES_DIR} opt GPU_SOURCES)
+
+    get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
+    
+    file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cpp)
+    file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu ${CMAKE_SOURCE_DIR}/gpu/*.cu)
+    file(GLOB_RECURSE GPU_NOT_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
+    list(REMOVE_ITEM GPU_LIB_CU ${GPU_NOT_LIB_CU})
+    include_directories(${GPU_SOURCES_DIR} ${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
+    if(CUDPP_OPT)
+      include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
+      add_definitions(-DCUDPP_OPT)
+      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(GPU_OBJS ${GPU_LIB_CU} ${GPU_LIB_CUDPP_CU} OPTIONS $<$<BOOL:${BUILD_SHARED_LIBS}>:-Xcompiler=-fPIC>)    
+    file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
+    foreach(CU_OBJ ${GPU_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 LIB_SOURCES ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h)
+      if(${CU_NAME} STREQUAL "pppm_d") #pppm_d doesn't get linked into the lib
+        set(CU_FORBIDDEN_OBJ "${CU_OBJ}") 
+      endif()
+    endforeach()
+    list(REMOVE_ITEM GPU_OBJS "${CU_FORBIDDEN_OBJ}")
+    list(APPEND LIB_SOURCES ${GPU_SOURCES} ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
+    set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "${LAMMPS_LIB_BINARY_DIR}/gpu/*_cubin.h")
+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})
+set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
+if(INSTALL_LIB)
+  install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+  install(FILES ${LAMMPS_SOURCE_DIR}/lammps.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+elseif(BUILD_SHARED_LIBS)
+  message(FATAL_ERROR "Shared library has to be installed, use -DINSTALL_LIB=ON to install lammps with a library")
+endif()
+
+add_executable(lmp ${LMP_SOURCES})
+target_link_libraries(lmp lammps)
+install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
+if(ENABLE_TESTING)
+  add_test(ShowHelp ${CMAKE_CURRENT_BINARY_DIR}/lmp -help)
+endif()
+
+##################################
+# Print package summary
+##################################
+foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES} ${ACCEL_PACKAGES})
+  if(ENABLE_${PKG})
+    message(STATUS "Building package: ${PKG}")
+  endif()
+endforeach()

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/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/StyleHeaderUtils.cmake

@@ -0,0 +1,132 @@
+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(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" ${files})
+endfunction(GenerateStyleHeader)
+
+function(RegisterStyles search_path)
+    FindStyleHeaders(${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(${search_path} REGION_CLASS    region_    REGION    ) # region    ) # domain
+endfunction(RegisterStyles)
+
+function(RegisterStylesExt search_path extension sources)
+    FindStyleHeadersExt(${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

@@ -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"

doc/Makefile

@@ -100,6 +100,7 @@ epub: $(OBJECTS)
 
 pdf: utils/txt2html/txt2html.exe
 	@(\
+		set -e; \
 		cd src; \
 		../utils/txt2html/txt2html.exe -b *.txt; \
 		htmldoc --batch lammps.book;          \

doc/src/Eqs/cnp_cutoff.tex

@@ -0,0 +1,14 @@
+\documentclass[12pt,article]{article}
+
+\usepackage{indentfirst}
+\usepackage{amsmath}
+
+\begin{document}
+
+\begin{eqnarray*}
+  r_{c}^{fcc} & = & \frac{1}{2} \left(\frac{\sqrt{2}}{2} + 1\right) \mathrm{a} \simeq 0.8536 \:\mathrm{a} \\
+  r_{c}^{bcc} & = & \frac{1}{2}(\sqrt{2} + 1) \mathrm{a} \simeq 1.207 \:\mathrm{a} \\
+  r_{c}^{hcp} & = & \frac{1}{2}\left(1+\sqrt{\frac{4+2x^{2}}{3}}\right) \mathrm{a}
+\end{eqnarray*}
+
+\end{document}

doc/src/Eqs/cnp_cutoff2.tex

@@ -0,0 +1,12 @@
+\documentclass[12pt,article]{article}
+
+\usepackage{indentfirst}
+\usepackage{amsmath}
+
+\begin{document}
+
+$$
+  Rc + Rs > 2*{\rm cutoff}
+$$
+
+\end{document}

doc/src/Eqs/cnp_eq.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+   Q_{i} = \frac{1}{n_i}\sum_{j = 1}^{n_i} | \sum_{k = 1}^{n_{ij}}  \vec{R}_{ik} + \vec{R}_{jk} |^2
+$$
+
+\end{document}

doc/src/Eqs/fix_mvv_dpd.tex

@@ -0,0 +1,21 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  v(t+\frac{\Delta t}{2}) = v(t) + \frac{\Delta t}{2}\cdot a(t),
+$$
+
+$$
+  r(t+\Delta t) = r(t) + \Delta t\cdot v(t+\frac{\Delta t}{2}),
+$$
+
+$$
+  a(t+\Delta t) = \frac{1}{m}\cdot F\left[ r(t+\Delta t), v(t) +\lambda \cdot \Delta t\cdot a(t)\right],
+$$
+
+$$
+  v(t+\Delta t) = v(t+\frac{\Delta t}{2}) + \frac{\Delta t}{2}\cdot a(t+\Delta t)
+$$
+
+\end{document}

doc/src/Eqs/fix_wall_ees.tex

@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$ 
+E = \epsilon \left[ \frac{2  \sigma_{LJ}^{12} \left(7 r^5+14 r^3 \sigma_{n}^2+3 r \sigma_{n}^4\right) }{945 \left(r^2-\sigma_{n}^2\right)^7} -\frac{ \sigma_{LJ}^6 \left(2 r \sigma_{n}^3+\sigma_{n}^2 \left(r^2-\sigma_{n}^2\right)\log{ \left[\frac{r-\sigma_{n}}{r+\sigma_{n}}\right]}\right) }{12 \sigma_{n}^5 \left(r^2-\sigma_{n}^2\right)} \right]\qquad \sigma_n < r < r_c
+$$
+
+
+\end{document}

doc/src/Eqs/pair_edpd_force.tex

@@ -0,0 +1,33 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  \mathbf{F}_{ij}^{C} = \alpha_{ij}{\omega_{C}}(r_{ij})\mathbf{e}_{ij},
+$$
+
+$$
+  \mathbf{F}_{ij}^{D} = -\gamma {\omega_{D}}(r_{ij})(\mathbf{e}_{ij} \cdot \mathbf{v}_{ij})\mathbf{e}_{ij},
+$$
+
+$$
+  \mathbf{F}_{ij}^{R} = \sigma {\omega_{R}}(r_{ij}){\xi_{ij}}\Delta t^{-1/2} \mathbf{e}_{ij},
+$$
+
+$$
+  \omega_{C}(r) = 1 - r/r_c,
+$$
+
+$$
+  \alpha_{ij} = A\cdot k_B(T_i + T_j)/2,
+$$
+
+$$  
+  \omega_{D}(r) = \omega^2_{R}(r) = (1-r/r_c)^s,
+$$
+
+$$  
+  \sigma_{ij}^2 = 4\gamma k_B T_i T_j/(T_i + T_j),
+$$
+
+\end{document}

doc/src/Eqs/pair_edpd_gov.tex

@@ -0,0 +1,15 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  \frac{\mathrm{d}^2 \mathbf{r}_i}{\mathrm{d} t^2}=
+  \frac{\mathrm{d} \mathbf{v}_i}{\mathrm{d} t}
+  =\mathbf{F}_{i}=\sum_{i\neq j}(\mathbf{F}_{ij}^{C}+\mathbf{F}_{ij}^{D}+\mathbf{F}_{ij}^{R}),
+$$
+
+$$
+  C_v\frac{\mathrm{d} T_i}{\mathrm{d} t}= q_{i} = \sum_{i\neq j}(q_{ij}^{C}+q_{ij}^{V}+q_{ij}^{R}),
+$$
+
+\end{document}

doc/src/Eqs/pair_edpd_heat.tex

@@ -0,0 +1,29 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  q_i^C = \sum_{j \ne i} k_{ij} \omega_{CT}(r_{ij}) \left( \frac{1}{T_i} - \frac{1}{T_j} \right),
+$$  
+  
+$$
+  q_i^V = \frac{1}{2 C_v}\sum_{j \ne i}{ \left\{ \omega_D(r_{ij})\left[\gamma_{ij} \left( \mathbf{e}_{ij} \cdot \mathbf{v}_{ij} \right)^2 - \frac{\left( \sigma _{ij} \right)^2}{m}\right] - \sigma _{ij} \omega_R(r_{ij})\left( \mathbf{e}_{ij} \cdot \mathbf{v}_{ij} \right){\xi_{ij}} \right\} },
+$$  
+
+$$
+  q_i^R = \sum_{j \ne i} \beta _{ij} \omega_{RT}(r_{ij}) d {t^{ - 1/2}} \xi_{ij}^e,
+$$
+
+$$
+  \omega_{CT}(r)=\omega_{RT}^2(r)=\left(1-r/r_{ct}\right)^{s_T},
+$$
+
+$$
+  k_{ij}=C_v^2\kappa(T_i + T_j)^2/4k_B,
+$$
+
+$$
+  \beta_{ij}^2=2k_Bk_{ij},
+$$
+
+\end{document}

doc/src/Eqs/pair_edpd_kappa.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  \kappa  = \frac{315k_B\upsilon }{2\pi \rho C_v r_{ct}^5}\frac{1}{Pr},
+$$
+
+\end{document}

doc/src/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/src/Eqs/pair_mdpd_force.tex

@@ -0,0 +1,17 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  \mathbf{F}_{ij}^C = Aw_c(r_{ij})\mathbf{e}_{ij} + B(\rho_i+\rho_j)w_d(r_{ij})\mathbf{e}_{ij},
+$$
+
+$$
+  \mathbf{F}_{ij}^{D} = -\gamma {\omega_{D}}(r_{ij})(\mathbf{e}_{ij} \cdot \mathbf{v}_{ij})\mathbf{e}_{ij},
+$$
+
+$$
+  \mathbf{F}_{ij}^{R} = \sigma {\omega_{R}}(r_{ij}){\xi_{ij}}\Delta t^{-1/2} \mathbf{e}_{ij},
+$$
+
+\end{document}

doc/src/Eqs/pair_tdpd_flux.tex

@@ -0,0 +1,21 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  Q_{ij}^D = -\kappa_{ij} w_{DC}(r_{ij}) \left( C_i - C_j \right),
+$$  
+  
+$$  
+  Q_{ij}^R = \epsilon_{ij}\left( C_i + C_j \right) w_{RC}(r_{ij}) \xi_{ij},
+$$
+
+$$
+  w_{DC}(r_{ij})=w^2_{RC}(r_{ij}) = (1 - r/r_{cc})^{\rm power\_{cc}},
+$$
+
+$$
+  \epsilon_{ij}^2 = m_s^2\kappa_{ij}\rho,
+$$
+
+\end{document}

doc/src/Eqs/pair_tdpd_force.tex

@@ -0,0 +1,29 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  \mathbf{F}_{ij}^{C} = A{\omega_{C}}(r_{ij})\mathbf{e}_{ij},
+$$
+
+$$
+  \mathbf{F}_{ij}^{D} = -\gamma {\omega_{D}}(r_{ij})(\mathbf{e}_{ij} \cdot \mathbf{v}_{ij})\mathbf{e}_{ij},
+$$
+
+$$
+  \mathbf{F}_{ij}^{R} = \sigma {\omega_{R}}(r_{ij}){\xi_{ij}}\Delta t^{-1/2} \mathbf{e}_{ij},
+$$
+
+$$
+  \omega_{C}(r) = 1 - r/r_c,
+$$
+
+$$
+  \omega_{D}(r) = \omega^2_{R}(r) = (1-r/r_c)^{\rm power\_f},
+$$
+
+$$
+  \sigma^2 = 2\gamma k_B T,
+$$
+
+\end{document}

doc/src/Eqs/pair_tdpd_gov.tex

@@ -0,0 +1,13 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  \frac{\mathrm{d}^2 \mathbf{r}_i}{\mathrm{d} t^2} = \frac{\mathrm{d} \mathbf{v}_i}{\mathrm{d} t}=\mathbf{F}_{i}=\sum_{i\neq j}(\mathbf{F}_{ij}^{C}+\mathbf{F}_{ij}^{D}+\mathbf{F}_{ij}^{R}),
+$$
+
+$$
+  \frac{\mathrm{d} C_{i}}{\mathrm{d} t}= Q_{i} = \sum_{i\neq j}(Q_{ij}^{D}+Q_{ij}^{R}) + Q_{i}^{S}, 
+$$
+
+\end{document}

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="19 May 2017 version">
+<META NAME="docnumber" CONTENT="1 Sep 2017 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>
@@ -21,7 +21,7 @@
 <H1></H1>
 
 LAMMPS Documentation :c,h3
-19 May 2017 version :c,h4
+1 Sep 2017 version :c,h4
 
 Version info: :h4
 
@@ -79,7 +79,7 @@ bug reports and feature requests are mainly coordinated through the
 "LAMMPS project on GitHub."_https://github.com/lammps/lammps
 The lammps.org domain, currently hosting "public continuous integration
 testing"_https://ci.lammps.org/job/lammps/ and "precompiled Linux
-RPM and Windows installer packages"_http://rpm.lammps.org is located
+RPM and Windows installer packages"_http://packages.lammps.org is located
 at Temple University and managed by Richard Berger,
 richard.berger at temple.edu.
 
@@ -261,7 +261,6 @@ END_RST -->
 :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)

doc/src/Section_accelerate.txt

@@ -56,7 +56,7 @@ 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.
+section"_Section_start.html#start_7 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
@@ -226,16 +226,16 @@ re-build LAMMPS |
   make machine |
 prepare and test a regular LAMMPS simulation |
   lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script |
-enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_7, |
+enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_6, |
   only needed for KOKKOS package |
-set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_7 or "package"_package.html command, |
+set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_6 or "package"_package.html command, |
   only if defaults need to be changed |
-use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_7 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu
+use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_6 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu
 :tb(c=2,s=|)
 
-Note that the first 4 steps can be done as a single command, using the
-src/Make.py tool.  This tool is discussed in "Section
-2.4"_Section_start.html#start_4 of the manual, and its use is
+Note that the first 4 steps can be done as a single command with
+suitable make command invocations. This is discussed in "Section
+4"_Section_packages.html 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.

doc/src/Section_commands.txt

@@ -685,6 +685,7 @@ package"_Section_start.html#start_3.
 "drude"_fix_drude.html,
 "drude/transform/direct"_fix_drude_transform.html,
 "drude/transform/reverse"_fix_drude_transform.html,
+"edpd/source"_fix_dpd_source.html,
 "eos/cv"_fix_eos_cv.html,
 "eos/table"_fix_eos_table.html,
 "eos/table/rx"_fix_eos_table_rx.html,
@@ -704,6 +705,9 @@ package"_Section_start.html#start_3.
 "meso"_fix_meso.html,
 "manifoldforce"_fix_manifoldforce.html,
 "meso/stationary"_fix_meso_stationary.html,
+"mvv/dpd"_fix_mvv_dpd.html,
+"mvv/edpd"_fix_mvv_dpd.html,
+"mvv/tdpd"_fix_mvv_dpd.html,
 "nve/dot"_fix_nve_dot.html,
 "nve/dotc/langevin"_fix_nve_dotc_langevin.html,
 "nve/manifold/rattle"_fix_nve_manifold_rattle.html,
@@ -717,7 +721,7 @@ package"_Section_start.html#start_3.
 "phonon"_fix_phonon.html,
 "pimd"_fix_pimd.html,
 "qbmsst"_fix_qbmsst.html,
-"qeq/reax"_fix_qeq_reax.html,
+"qeq/reax (ko)"_fix_qeq_reax.html,
 "qmmm"_fix_qmmm.html,
 "qtb"_fix_qtb.html,
 "reax/c/bonds"_fix_reax_bonds.html,
@@ -732,9 +736,12 @@ package"_Section_start.html#start_3.
 "smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html,
 "smd/setvel"_fix_smd_setvel.html,
 "smd/wall/surface"_fix_smd_wall_surface.html,
+"tdpd/source"_fix_dpd_source.html,
 "temp/rescale/eff"_fix_temp_rescale_eff.html,
 "ti/spring"_fix_ti_spring.html,
-"ttm/mod"_fix_ttm.html :tb(c=6,ea=c)
+"ttm/mod"_fix_ttm.html,
+"wall/ees"_fix_wall_ees.html,
+"wall/region/ees"_fix_wall_ees.html :tb(c=6,ea=c)
 
 :line
 
@@ -773,6 +780,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "erotate/sphere"_compute_erotate_sphere.html,
 "erotate/sphere/atom"_compute_erotate_sphere_atom.html,
 "event/displace"_compute_event_displace.html,
+"fragment/atom"_compute_cluster_atom.html,
 "global/atom"_compute_global_atom.html,
 "group/group"_compute_group_group.html,
 "gyration"_compute_gyration.html,
@@ -831,8 +839,10 @@ package"_Section_start.html#start_3.
 
 "ackland/atom"_compute_ackland_atom.html,
 "basal/atom"_compute_basal_atom.html,
+"cnp/atom"_compute_cnp_atom.html,
 "dpd"_compute_dpd.html,
 "dpd/atom"_compute_dpd_atom.html,
+"edpd/temp/atom"_compute_edpd_temp_atom.html,
 "fep"_compute_fep.html,
 "force/tally"_compute_tally.html,
 "heat/flux/tally"_compute_tally.html,
@@ -865,6 +875,7 @@ package"_Section_start.html#start_3.
 "smd/ulsph/stress"_compute_smd_ulsph_stress.html,
 "smd/vol"_compute_smd_vol.html,
 "stress/tally"_compute_tally.html,
+"tdpd/cc/atom"_compute_tdpd_cc_atom.html,
 "temp/drude"_compute_temp_drude.html,
 "temp/eff"_compute_temp_eff.html,
 "temp/deform/eff"_compute_temp_deform_eff.html,
@@ -889,8 +900,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 "hybrid"_pair_hybrid.html,
 "hybrid/overlay"_pair_hybrid.html,
 "adp (o)"_pair_adp.html,
-"airebo (o)"_pair_airebo.html,
-"airebo/morse (o)"_pair_airebo.html,
+"airebo (oi)"_pair_airebo.html,
+"airebo/morse (oi)"_pair_airebo.html,
 "beck (go)"_pair_beck.html,
 "body"_pair_body.html,
 "bop"_pair_bop.html,
@@ -924,8 +935,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 "dpd/tstat (go)"_pair_dpd.html,
 "dsmc"_pair_dsmc.html,
 "eam (gkiot)"_pair_eam.html,
-"eam/alloy (gkot)"_pair_eam.html,
-"eam/fs (gkot)"_pair_eam.html,
+"eam/alloy (gkiot)"_pair_eam.html,
+"eam/fs (gkiot)"_pair_eam.html,
 "eim (o)"_pair_eim.html,
 "gauss (go)"_pair_gauss.html,
 "gayberne (gio)"_pair_gayberne.html,
@@ -939,9 +950,9 @@ KOKKOS, o = USER-OMP, t = OPT.
 "kim"_pair_kim.html,
 "lcbop"_pair_lcbop.html,
 "line/lj"_pair_line_lj.html,
-"lj/charmm/coul/charmm (ko)"_pair_charmm.html,
+"lj/charmm/coul/charmm (kio)"_pair_charmm.html,
 "lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
-"lj/charmm/coul/long (giko)"_pair_charmm.html,
+"lj/charmm/coul/long (gkio)"_pair_charmm.html,
 "lj/charmm/coul/msm"_pair_charmm.html,
 "lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
 "lj/charmmfsw/coul/long"_pair_charmm.html,
@@ -963,7 +974,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "lj/expand (gko)"_pair_lj_expand.html,
 "lj/gromacs (gko)"_pair_gromacs.html,
 "lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html,
-"lj/long/coul/long (o)"_pair_lj_long.html,
+"lj/long/coul/long (io)"_pair_lj_long.html,
 "lj/long/dipole/long"_pair_dipole.html,
 "lj/long/tip4p/long"_pair_lj_long.html,
 "lj/smooth (o)"_pair_lj_smooth.html,
@@ -987,7 +998,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "polymorphic"_pair_polymorphic.html,
 "python"_pair_python.html,
 "reax"_pair_reax.html,
-"rebo (o)"_pair_airebo.html,
+"rebo (oi)"_pair_airebo.html,
 "resquared (go)"_pair_resquared.html,
 "snap"_pair_snap.html,
 "soft (go)"_pair_soft.html,
@@ -1021,6 +1032,7 @@ package"_Section_start.html#start_3.
 "eam/cd (o)"_pair_eam.html,
 "edip (o)"_pair_edip.html,
 "edip/multi"_pair_edip.html,
+"edpd"_pair_meso.html,
 "eff/cut"_pair_eff.html,
 "exp6/rx"_pair_exp6_rx.html,
 "gauss/cut"_pair_gauss.html,
@@ -1038,7 +1050,9 @@ package"_Section_start.html#start_3.
 "lj/sdk (gko)"_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,
+"mdpd"_pair_meso.html,
+"mdpd/rhosum"_pair_meso.html,
+"meam/c"_pair_meam.html,
 "meam/spline (o)"_pair_meam_spline.html,
 "meam/sw/spline"_pair_meam_sw_spline.html,
 "mgpt"_pair_mgpt.html,
@@ -1057,7 +1071,7 @@ package"_Section_start.html#start_3.
 "oxdna2/excv"_pair_oxdna2.html,
 "oxdna2/stk"_pair_oxdna2.html,
 "quip"_pair_quip.html,
-"reax/c (k)"_pair_reaxc.html,
+"reax/c (ko)"_pair_reaxc.html,
 "smd/hertz"_pair_smd_hertz.html,
 "smd/tlsph"_pair_smd_tlsph.html,
 "smd/triangulated/surface"_pair_smd_triangulated_surface.html,
@@ -1071,9 +1085,10 @@ package"_Section_start.html#start_3.
 "sph/taitwater/morris"_pair_sph_taitwater_morris.html,
 "srp"_pair_srp.html,
 "table/rx"_pair_table_rx.html,
+"tdpd"_pair_meso.html,
 "tersoff/table (o)"_pair_tersoff.html,
 "thole"_pair_thole.html,
-"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c) 
+"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)
 
 :line
 
@@ -1225,7 +1240,7 @@ USER-OMP, t = OPT.
 "msm/cg (o)"_kspace_style.html,
 "pppm (go)"_kspace_style.html,
 "pppm/cg (o)"_kspace_style.html,
-"pppm/disp"_kspace_style.html,
+"pppm/disp (i)"_kspace_style.html,
 "pppm/disp/tip4p"_kspace_style.html,
 "pppm/stagger"_kspace_style.html,
 "pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c)

doc/src/Section_errors.txt

@@ -71,7 +71,7 @@ style", with ... being fix, compute, pair, etc, it means that you
 mistyped the style name or that the command is part of an optional
 package which was not compiled into your executable.  The list of
 available styles in your executable can be listed by using "the -h
-command-line argument"_Section_start.html#start_7.  The installation
+command-line argument"_Section_start.html#start_6.  The installation
 and compilation of optional packages is explained in the "installation
 instructions"_Section_start.html#start_3.
 
@@ -4696,9 +4696,9 @@ Self-explanatory. :dd
 
 {Fix bond/create induced too many angles/dihedrals/impropers per atom} :dt
 
-See the read_data command for info on setting the "extra angle per
-atom", etc header values to allow for additional angles, etc to be
-formed. :dd
+See the read_data command for info on using the "extra/angle/per/atom",
+(or dihedral, improper) keywords to allow for additional
+angles, dihedrals, and impropers to be formed. :dd
 
 {Fix bond/create needs ghost atoms from further away} :dt
 
@@ -7876,18 +7876,20 @@ See the setting for tagint in the src/lmptype.h file. :dd
 
 {New bond exceeded bonds per atom in create_bonds} :dt
 
-See the read_data command for info on setting the "extra bond per
-atom" header value to allow for additional bonds to be formed. :dd
+See the read_data command for info on using the "extra/bond/per/atom"
+keyword to allow for additional bonds to be formed
 
 {New bond exceeded bonds per atom in fix bond/create} :dt
 
-See the read_data command for info on setting the "extra bond per
-atom" header value to allow for additional bonds to be formed. :dd
+See the read_data command for info on using the "extra/bond/per/atom"
+keyword to allow for additional bonds to be formed :dd
 
 {New bond exceeded special list size in fix bond/create} :dt
 
-See the special_bonds extra command for info on how to leave space in
-the special bonds list to allow for additional bonds to be formed. :dd
+See the "read_data extra/special/per/atom" command
+(or the "create_box extra/special/per/atom" command)
+for info on how to leave space in the special bonds
+list to allow for additional bonds to be formed. :dd
 
 {Newton bond change after simulation box is defined} :dt
 
@@ -8890,6 +8892,14 @@ This is a requirement to use this potential. :dd
 
 See the newton command.  This is a restriction to use this potential. :dd
 
+{Pair style vashishta/gpu requires atom IDs} :dt
+
+This is a requirement to use this potential. :dd
+
+{Pair style vashishta/gpu requires newton pair off} :dt
+
+See the newton command.  This is a restriction to use this potential. :dd
+
 {Pair style tersoff/gpu requires atom IDs} :dt
 
 This is a requirement to use the tersoff/gpu potential. :dd
@@ -9656,9 +9666,10 @@ you are running. :dd
 
 {Special list size exceeded in fix bond/create} :dt
 
-See the read_data command for info on setting the "extra special per
-atom" header value to allow for additional special values to be
-stored. :dd
+See the "read_data extra/special/per/atom" command
+(or the "create_box extra/special/per/atom" command)
+for info on how to leave space in the special bonds
+list to allow for additional bonds to be formed. :dd
 
 {Specified processors != physical processors} :dt
 
@@ -9675,23 +9686,23 @@ Self-explanatory. :dd
 
 {Subsequent read data induced too many angles per atom} :dt
 
-See the create_box extra/angle/per/atom or read_data "extra angle per
-atom" header value to set this limit larger. :dd
+See the extra/angle/per/atom keyword for the create_box
+or the read_data command to set this limit larger :dd
 
 {Subsequent read data induced too many bonds per atom} :dt
 
-See the create_box extra/bond/per/atom or read_data "extra bond per
-atom" header value to set this limit larger. :dd
+See the extra/bond/per/atom keyword for the create_box
+or the read_data command to set this limit larger :dd
 
 {Subsequent read data induced too many dihedrals per atom} :dt
 
-See the create_box extra/dihedral/per/atom or read_data "extra
-dihedral per atom" header value to set this limit larger. :dd
+See the extra/dihedral/per/atom keyword for the create_box
+or the read_data command to set this limit larger :dd
 
 {Subsequent read data induced too many impropers per atom} :dt
 
-See the create_box extra/improper/per/atom or read_data "extra
-improper per atom" header value to set this limit larger. :dd
+See the extra/improper/per/atom keyword for the create_box
+or the read_data command to set this limit larger :dd
 
 {Substitution for illegal variable} :dt
 

doc/src/Section_example.txt

@@ -49,6 +49,7 @@ Lists of both kinds of directories are given below.
 Lowercase directories :h4
 
 accelerate: run with various acceleration options (OpenMP, GPU, Phi)
+airebo:   polyethylene with AIREBO potential
 balance:  dynamic load balancing, 2d system
 body:     body particles, 2d system
 cmap:     CMAP 5-body contributions to CHARMM force field

doc/src/Section_howto.txt

@@ -54,7 +54,7 @@ restart files can be saved to disk using the "restart"_restart.html
 command.  At a later time, these binary files can be read via a
 "read_restart"_read_restart.html command in a new script.  Or they can
 be converted to text data files using the "-r command-line
-switch"_Section_start.html#start_7 and read by a
+switch"_Section_start.html#start_6 and read by a
 "read_data"_read_data.html command in a new script.
 
 Here we give examples of 2 scripts that read either a binary restart
@@ -337,7 +337,7 @@ All of the above examples work whether you are running on 1 or
 multiple processors, but assumed you are running LAMMPS on a single
 partition of processors.  LAMMPS can be run on multiple partitions via
 the "-partition" command-line switch as described in "this
-section"_Section_start.html#start_7 of the manual.
+section"_Section_start.html#start_6 of the manual.
 
 In the last 2 examples, if LAMMPS were run on 3 partitions, the same
 scripts could be used if the "index" and "loop" variables were
@@ -387,7 +387,7 @@ for more info on packages.
 In all these cases, you must run with one or more processors per
 replica.  The processors assigned to each replica are determined at
 run-time by using the "-partition command-line
-switch"_Section_start.html#start_7 to launch LAMMPS on multiple
+switch"_Section_start.html#start_6 to launch LAMMPS on multiple
 partitions, which in this context are the same as replicas.  E.g.
 these commands:
 
@@ -395,7 +395,7 @@ mpirun -np 16 lmp_linux -partition 8x2 -in in.temper
 mpirun -np 8 lmp_linux -partition 8x1 -in in.neb :pre
 
 would each run 8 replicas, on either 16 or 8 processors.  Note the use
-of the "-in command-line switch"_Section_start.html#start_7 to specify
+of the "-in command-line switch"_Section_start.html#start_6 to specify
 the input script which is required when running in multi-replica mode.
 
 Also note that with MPI installed on a machine (e.g. your desktop),
@@ -1872,7 +1872,7 @@ void lammps_free(void *) :pre
 
 The lammps_open() function is used to initialize LAMMPS, passing in a
 list of strings as if they were "command-line
-arguments"_Section_start.html#start_7 when LAMMPS is run in
+arguments"_Section_start.html#start_6 when LAMMPS is run in
 stand-alone mode from the command line, and a MPI communicator for
 LAMMPS to run under.  It returns a ptr to the LAMMPS object that is
 created, and which is used in subsequent library calls.  The
@@ -1938,7 +1938,7 @@ documentation in the src/library.cpp file for details, including
 which quantities can be queried by name:
 
 void *lammps_extract_global(void *, char *)
-void lammps_extract_box(void *, double *, double *, 
+void lammps_extract_box(void *, double *, double *,
                         double *, double *, double *, int *, int *)
 void *lammps_extract_atom(void *, char *)
 void *lammps_extract_compute(void *, char *, int, int)
@@ -2682,14 +2682,14 @@ bond_coeff      2 25.724 0.0 :pre
 
 When running dynamics with the adiabatic core/shell model, the
 following issues should be considered.  The relative motion of
-the core and shell particles corresponds to the polarization, 
-hereby an instantaneous relaxation of the shells is approximated 
+the core and shell particles corresponds to the polarization,
+hereby an instantaneous relaxation of the shells is approximated
 and a fast core/shell spring frequency ensures a nearly constant
-internal kinetic energy during the simulation. 
+internal kinetic energy during the simulation.
 Thermostats can alter this polarization behaviour, by scaling the
-internal kinetic energy, meaning the shell will not react freely to 
-its electrostatic environment. 
-Therefore it is typically desirable to decouple the relative motion of 
+internal kinetic energy, meaning the shell will not react freely to
+its electrostatic environment.
+Therefore it is typically desirable to decouple the relative motion of
 the core/shell pair, which is an imaginary degree of freedom, from the
 real physical system.  To do that, the "compute
 temp/cs"_compute_temp_cs.html command can be used, in conjunction with
@@ -2721,13 +2721,13 @@ fix thermostatequ all nve                               # integrator as needed f
 fix_modify thermoberendsen temp CSequ
 thermo_modify temp CSequ                                # output of center-of-mass derived temperature :pre
 
-The pressure for the core/shell system is computed via the regular 
-LAMMPS convention by "treating the cores and shells as individual 
-particles"_#MitchellFincham2. For the thermo output of the pressure 
-as well as for the application of a barostat, it is necessary to 
-use an additional "pressure"_compute_pressure compute based on the 
-default "temperature"_compute_temp and specifying it as a second 
-argument in "fix modify"_fix_modify.html and 
+The pressure for the core/shell system is computed via the regular
+LAMMPS convention by "treating the cores and shells as individual
+particles"_#MitchellFincham2. For the thermo output of the pressure
+as well as for the application of a barostat, it is necessary to
+use an additional "pressure"_compute_pressure compute based on the
+default "temperature"_compute_temp and specifying it as a second
+argument in "fix modify"_fix_modify.html and
 "thermo_modify"_thermo_modify.html resulting in:
 
 (...)
@@ -2757,18 +2757,18 @@ temp/cs"_compute_temp_cs.html command to the {temp} keyword of the
 velocity all create 1427 134 bias yes temp CSequ
 velocity all scale 1427 temp CSequ :pre
 
-To maintain the correct polarizability of the core/shell pairs, the 
-kinetic energy of the internal motion shall remain nearly constant. 
-Therefore the choice of spring force and mass ratio need to ensure 
-much faster relative motion of the 2 atoms within the core/shell pair 
-than their center-of-mass velocity. This allows the shells to 
-effectively react instantaneously to the electrostatic environment and 
+To maintain the correct polarizability of the core/shell pairs, the
+kinetic energy of the internal motion shall remain nearly constant.
+Therefore the choice of spring force and mass ratio need to ensure
+much faster relative motion of the 2 atoms within the core/shell pair
+than their center-of-mass velocity. This allows the shells to
+effectively react instantaneously to the electrostatic environment and
 limits energy transfer to or from the core/shell oscillators.
 This fast movement also dictates the timestep that can be used.
 
 The primary literature of the adiabatic core/shell model suggests that
 the fast relative motion of the core/shell pairs only allows negligible
-energy transfer to the environment. 
+energy transfer to the environment.
 The mentioned energy transfer will typically lead to a small drift
 in total energy over time.  This internal energy can be monitored
 using the "compute chunk/atom"_compute_chunk_atom.html and "compute
@@ -2790,7 +2790,7 @@ pairs as chunks.
 
 For example if core/shell pairs are the only molecules:
 
-read_data NaCl_CS_x0.1_prop.data 
+read_data NaCl_CS_x0.1_prop.data
 compute prop all property/atom molecule
 compute cs_chunk all chunk/atom c_prop
 compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0     # note the chosen degrees of freedom for the core/shell pairs

doc/src/Section_python.txt

@@ -198,7 +198,7 @@ file and the shared library.
 11.3 Building LAMMPS as a shared library :link(py_3),h4
 
 Instructions on how to build LAMMPS as a shared library are given in
-"Section 2.5"_Section_start.html#start_5.  A shared library is one
+"Section 2.4"_Section_start.html#start_4.  A shared library is one
 that is dynamically loadable, which is what Python requires to wrap
 LAMMPS.  On Linux this is a library file that ends in ".so", not ".a".
 
@@ -217,7 +217,7 @@ NOTE: If you are building LAMMPS with an MPI or FFT library or other
 auxiliary libraries (used by various packages), then all of these
 extra libraries must also be shared libraries.  If the LAMMPS
 shared-library build fails with an error complaining about this, see
-"Section 2.5"_Section_start.html#start_5 for more details.
+"Section 2.4"_Section_start.html#start_4 for more details.
 
 :line
 
@@ -439,7 +439,7 @@ first importing from the lammps.py file:
 >>> CDLL("liblammps.so") :pre
 
 If an error occurs, carefully go thru the steps in "Section
-2.5"_Section_start.html#start_5 and above about building a shared
+2.4"_Section_start.html#start_4 and above about building a shared
 library and about insuring Python can find the necessary two files
 it needs.
 
@@ -714,7 +714,7 @@ stored in the "image" property. All three image flags are stored in
 a packed format in a single integer, so count would be 1 to retrieve
 that integer, however also a count value of 3 can be used and then
 the image flags will be unpacked into 3 individual integers, ordered
-in a similar fashion as coordinates. 
+in a similar fashion as coordinates.
 
 Note that the data structure gather_atoms("x") returns is different
 from the data structure returned by extract_atom("x") in four ways.

doc/src/Section_start.txt

@@ -14,11 +14,11 @@ experienced users.
 2.1 "What's in the LAMMPS distribution"_#start_1
 2.2 "Making LAMMPS"_#start_2
 2.3 "Making LAMMPS with optional packages"_#start_3
-2.5 "Building LAMMPS as a library"_#start_4
-2.6 "Running LAMMPS"_#start_5
-2.7 "Command-line options"_#start_6
-2.8 "Screen output"_#start_7
-2.9 "Tips for users of previous versions"_#start_8 :all(b)
+2.4 "Building LAMMPS as a library"_#start_4
+2.5 "Running LAMMPS"_#start_5
+2.6 "Command-line options"_#start_6
+2.7 "Screen output"_#start_7
+2.8 "Tips for users of previous versions"_#start_8 :all(b)
 
 :line
 
@@ -434,20 +434,39 @@ files.  Note that on some large parallel machines which use "modules"
 for their compile/link environements, you may simply need to include
 the correct module in your build environment.  Or the parallel machine
 may have a vendor-provided FFT library which the compiler has no
-trouble finding.
+trouble finding.  See the src/MAKE/OPTIONS/Makefile.fftw file for an
+example of how to specify these variables to use the FFTW3 library.
 
-FFTW is a fast, portable library that should also work on any
-platform.  You can download it from
+FFTW is fast, portable library that should also work on any platform
+and typically be faster than KISS FFT.  You can download it from
 "www.fftw.org"_http://www.fftw.org.  Both the legacy version 2.1.X and
 the newer 3.X versions are supported as -DFFT_FFTW2 or -DFFT_FFTW3.
-Building FFTW for your box should be as simple as ./configure; make.
-Note that on some platforms FFTW2 has been pre-installed, and uses
-renamed files indicating the precision it was compiled with,
-e.g. sfftw.h, or dfftw.h instead of fftw.h.  In this case, you can
-specify an additional define variable for FFT_INC called -DFFTW_SIZE,
-which will select the correct include file.  In this case, for FFT_LIB
-you must also manually specify the correct library, namely -lsfftw or
--ldfftw.
+Building FFTW for your box should be as simple as ./configure; make;
+make install.  The install command typically requires root privileges
+(e.g. invoke it via sudo), unless you specify a local directory with
+the "--prefix" option of configure.  Type "./configure --help" to see
+various options.
+
+If you wish to have FFTW support for single-precision FFTs (see below
+about -DFFT_SINGLE) in addition to the default double-precision FFTs,
+you will need to build FFTW a second time for single-precision.  For
+FFTW3, do this via:
+
+make clean
+./configure --enable-single; make; make install :pre
+
+which should produce the additional library libfftw3f.a.
+
+For FFTW2, do this:
+
+make clean
+./configure --enable-float --enable-type-prefix; make; make install :pre
+
+which should produce the additional library libsfftw.a and additional
+include file sfttw.a.  Note that on some platforms FFTW2 has been
+pre-installed for both single- and double-precision, and may already
+have these files as well as libdfftw.a and dfftw.h for double
+precision.
 
 The FFT_INC variable also allows for a -DFFT_SINGLE setting that will
 use single-precision FFTs with PPPM, which can speed-up long-range
@@ -459,6 +478,16 @@ accuracy for reduced memory use and parallel communication costs for
 transposing 3d FFT data.  Note that single precision FFTs have only
 been tested with the FFTW3, FFTW2, MKL, and KISS FFT options.
 
+When using -DFFT_SINGLE with FFTW3 or FFTW2, you need to build FFTW
+with support for single-precision, as explained above.  For FFTW3 you
+also need to include -lfftw3f with the FFT_LIB setting, in addition to
+-lfftw3.  For FFTW2, you also need to specify -DFFT_SIZE with the
+FFT_INC setting and -lsfftw with the FFT_LIB setting (in place of
+-lfftw).  Similarly, if FFTW2 has been preinstalled with an explicit
+double-precision library (libdfftw.a and not the default libfftw.a),
+then you can specify -DFFT_SIZE (and not -DFFT_SINGLE), and specify
+-ldfftw to use double-precision FFTs.
+
 Step 7 :h6
 
 The 3 JPG variables allow you to specify a JPEG and/or PNG library
@@ -507,7 +536,7 @@ You should get the executable lmp_foo when the build is complete.
 
 :line
 
-Errors that can occur when making LAMMPS: h5 :link(start_2_3)
+Errors that can occur when making LAMMPS :h5 :link(start_2_3)
 
 If an error occurs when building LAMMPS, the compiler or linker will
 state very explicitly what the problem is.  The error message should
@@ -558,8 +587,7 @@ Typing "make clean-all" or "make clean-machine" will delete *.o object
 files created when LAMMPS is built, for either all builds or for a
 particular machine.
 
-Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or
--DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
+Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
 
 As explained above, any of these 3 settings can be specified on the
 LMP_INC line in your low-level src/MAKE/Makefile.foo.
@@ -630,22 +658,29 @@ utilities.
 For Cygwin and the MinGW cross-compilers, suitable makefiles are
 provided in src/MAKE/MACHINES. When using other compilers, like
 Visual C++ or Intel compilers for Windows, you may have to implement
-your own build system. Since none of the current LAMMPS core developers
-has significant experience building executables on Windows, we are
-happy to distribute contributed instructions and modifications, but
-we cannot provide support for those.
+your own build system. Due to differences between the Windows OS
+and Windows system libraries to Unix-like environments like Linux
+or MacOS, when compiling for Windows a few adjustments may be needed:
+
+Do [not] set the -DLAMMPS_MEMALIGN define (see LMP_INC makefile variable)
+Add -lwsock32 -lpsapi to the linker flags (see LIB makefile variable)
+Try adding -static-libgcc or -static or both to the linker flags when your LAMMPS executable complains about missing .dll files  :ul
+
+Since none of the current LAMMPS core developers has significant
+experience building executables on Windows, we are happy to distribute
+contributed instructions and modifications to improve the situation,
+but we cannot provide support for those.
 
 With the so-called "Anniversary Update" to Windows 10, there is a
 Ubuntu Linux subsystem available for Windows, that can be installed
 and then used to compile/install LAMMPS as if you are running on a
 Ubuntu Linux system instead of Windows.
 
-As an alternative, you can download "daily builds" (and some older
-versions) of the installer packages from
-"rpm.lammps.org/windows.html"_http://rpm.lammps.org/windows.html.
-These executables are built with most optional packages and the
-download includes documentation, potential files, some tools and
-many examples, but no source code.
+As an alternative, you can download pre-compiled installer packages from
+"packages.lammps.org/windows.html"_http://packages.lammps.org/windows.html.
+These executables are built with most optional packages included and the
+download includes documentation, potential files, some tools and many
+examples, but no source code.
 
 :line
 
@@ -685,7 +720,7 @@ type
 lmp_machine -h :pre
 
 to run your executable with the optional "-h command-line
-switch"_#start_7 for "help", which will list the styles and commands
+switch"_#start_6 for "help", which will list the styles and commands
 known to your executable, and immediately exit.
 
 :line
@@ -880,7 +915,7 @@ src/MAKE/OPTIONS, which include the settings.  Note that the
 USER-INTEL and KOKKOS packages can use settings that build LAMMPS for
 different hardware.  The USER-INTEL package can be compiled for Intel
 CPUs and KNLs; the KOKKOS package builds for CPUs (OpenMP), GPUs
-(Cuda), and Intel KNLs.
+(CUDA), and Intel KNLs.
 
 Makefile.intel_cpu
 Makefile.intel_phi
@@ -1058,7 +1093,7 @@ LAMMPS to be built with one or more of its optional packages.
 :line
 
 On a Windows box, you can skip making LAMMPS and simply download an
-installer package from "here"_http://rpm.lammps.org/windows.html
+installer package from "here"_http://packages.lammps.org/windows.html
 
 For running the non-MPI executable, follow these steps:
 
@@ -1070,18 +1105,27 @@ the [in.lj] input from the bench folder. (e.g. by typing: cd "Documents"). :l
 
 At the command prompt, type "lmp_serial -in in.lj", replacing [in.lj]
 with the name of your LAMMPS input script. :l
+
+The serial executable includes support for multi-threading
+parallelization from the styles in the USER-OMP packages.
+
+To run with, e.g. 4 threads, type "lmp_serial -in in.lj -pk omp 4 -sf omp"
 :ule
 
-For the MPI version, which allows you to run LAMMPS under Windows on
-multiple processors, follow these steps:
+For the MPI version, which allows you to run LAMMPS under Windows with
+the more general message passing parallel library (LAMMPS has been
+designed from ground up to use MPI efficiently), follow these steps:
 
-Download and install
-"MPICH2"_http://www.mcs.anl.gov/research/projects/mpich2/downloads/index.php?s=downloads
-for Windows. :ulb,l
+Download and install a compatible MPI library binary package:
+for 32-bit Windows
+"mpich2-1.4.1p1-win-ia32.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi
+and for 64-bit Windows
+"mpich2-1.4.1p1-win-x86-64.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi
+:ulb,l
 
 The LAMMPS Windows installer packages will automatically adjust your
 path for the default location of this MPI package. After the installation
-of the MPICH software, it needs to be integrated into the system.
+of the MPICH2 software, it needs to be integrated into the system.
 For this you need to start a Command Prompt in {Administrator Mode}
 (right click on the icon and select it). Change into the MPICH2
 installation directory, then into the subdirectory [bin] and execute
@@ -1100,7 +1144,7 @@ or
 
 mpiexec -np 4 lmp_mpi -in in.lj :pre
 
-replacing in.lj with the name of your LAMMPS input script. For the latter
+replacing [in.lj] with the name of your LAMMPS input script. For the latter
 case, you may be prompted to enter your password. :l
 
 In this mode, output may not immediately show up on the screen, so if
@@ -1112,6 +1156,11 @@ something like:
 
 lmp_mpi -in in.lj :pre
 
+And the parallel executable also includes OpenMP multi-threading, which
+can be combined with MPI using something like:
+
+mpiexec -localonly 2 lmp_mpi -in in.lj -pk omp 2 -sf omp :pre
+
 :ule
 
 :line

doc/src/accelerate_gpu.txt

@@ -54,7 +54,7 @@ specify the # of GPUs per node
 use GPU styles in your input script :ul
 
 The latter two steps can be done using the "-pk gpu" and "-sf gpu"
-"command-line switches"_Section_start.html#start_7 respectively.  Or
+"command-line switches"_Section_start.html#start_6 respectively.  Or
 the effect of the "-pk" or "-sf" switches can be duplicated by adding
 the "package gpu"_package.html or "suffix gpu"_suffix.html commands
 respectively to your input script.
@@ -62,7 +62,7 @@ respectively to your input script.
 [Required hardware/software:]
 
 To use this package, you currently need to have an NVIDIA GPU and
-install the NVIDIA Cuda software on your system:
+install the NVIDIA CUDA software on your system:
 
 Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/0/information
 Go to http://www.nvidia.com/object/cuda_get.html
@@ -74,13 +74,8 @@ Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) t
 This requires two steps (a,b): build the GPU library, then build
 LAMMPS with the GPU package.
 
-You can do both these steps in one line, using the src/Make.py script,
-described in "Section 2.4"_Section_start.html#start_4 of the manual.
-Type "Make.py -h" for help.  If run from the src directory, this
-command will create src/lmp_gpu using src/MAKE/Makefile.mpi as the
-starting Makefile.machine:
-
-Make.py -p gpu -gpu mode=single arch=31 -o gpu -a lib-gpu file mpi :pre
+You can do both these steps in one line as described in
+"Section 4"_Section_packages.html of the manual.
 
 Or you can follow these two (a,b) steps:
 
@@ -90,7 +85,7 @@ The GPU library is in lammps/lib/gpu.  Select a Makefile.machine (in
 lib/gpu) appropriate for your system.  You should pay special
 attention to 3 settings in this makefile.
 
-CUDA_HOME = needs to be where NVIDIA Cuda software is installed on your system
+CUDA_HOME = needs to be where NVIDIA CUDA software is installed on your system
 CUDA_ARCH = needs to be appropriate to your GPUs
 CUDA_PREC = precision (double, mixed, single) you desire :ul
 
@@ -151,9 +146,9 @@ automatically if you create more MPI tasks/node than there are
 GPUs/mode.  E.g. with 8 MPI tasks/node and 2 GPUs, each GPU will be
 shared by 4 MPI tasks.
 
-Use the "-sf gpu" "command-line switch"_Section_start.html#start_7,
+Use the "-sf gpu" "command-line switch"_Section_start.html#start_6,
 which will automatically append "gpu" to styles that support it.  Use
-the "-pk gpu Ng" "command-line switch"_Section_start.html#start_7 to
+the "-pk gpu Ng" "command-line switch"_Section_start.html#start_6 to
 set Ng = # of GPUs/node to use.
 
 lmp_machine -sf gpu -pk gpu 1 -in in.script                         # 1 MPI task uses 1 GPU
@@ -188,7 +183,7 @@ pair_style lj/cut/gpu 2.5 :pre
 
 You must also use the "package gpu"_package.html command to enable the
 GPU package, unless the "-sf gpu" or "-pk gpu" "command-line
-switches"_Section_start.html#start_7 were used.  It specifies the
+switches"_Section_start.html#start_6 were used.  It specifies the
 number of GPUs/node to use, as well as other options.
 
 [Speed-ups to expect:]

doc/src/accelerate_intel.txt

@@ -29,9 +29,11 @@ Bond Styles: fene, harmonic :l
 Dihedral Styles: charmm, harmonic, opls :l
 Fixes: nve, npt, nvt, nvt/sllod :l
 Improper Styles: cvff, harmonic :l
-Pair Styles: buck/coul/cut, buck/coul/long, buck, eam, gayberne,
-charmm/coul/long, lj/cut, lj/cut/coul/long, sw, tersoff :l
-K-Space Styles: pppm :l
+Pair Styles: airebo, airebo/morse, buck/coul/cut, buck/coul/long, 
+buck, eam, eam/alloy, eam/fs, gayberne, lj/charmm/coul/charmm, 
+lj/charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long, rebo,
+sw, tersoff :l
+K-Space Styles: pppm, pppm/disp :l
 :ule
 
 [Speed-ups to expect:]
@@ -42,62 +44,90 @@ precision mode. Performance improvements are shown compared to
 LAMMPS {without using other acceleration packages} as these are
 under active development (and subject to performance changes). The
 measurements were performed using the input files available in
-the src/USER-INTEL/TEST directory. These are scalable in size; the
-results given are with 512K particles (524K for Liquid Crystal).
-Most of the simulations are standard LAMMPS benchmarks (indicated
-by the filename extension in parenthesis) with modifications to the
-run length and to add a warmup run (for use with offload
-benchmarks).
+the src/USER-INTEL/TEST directory with the provided run script.
+These are scalable in size; the results given are with 512K
+particles (524K for Liquid Crystal). Most of the simulations are
+standard LAMMPS benchmarks (indicated by the filename extension in
+parenthesis) with modifications to the run length and to add a
+warmup run (for use with offload benchmarks).
 
 :c,image(JPG/user_intel.png)
 
 Results are speedups obtained on Intel Xeon E5-2697v4 processors
 (code-named Broadwell) and Intel Xeon Phi 7250 processors
-(code-named Knights Landing) with "18 Jun 2016" LAMMPS built with
-Intel Parallel Studio 2016 update 3. Results are with 1 MPI task
+(code-named Knights Landing) with "June 2017" LAMMPS built with
+Intel Parallel Studio 2017 update 2. Results are with 1 MPI task
 per physical core. See {src/USER-INTEL/TEST/README} for the raw
 simulation rates and instructions to reproduce.
 
 :line
 
+[Accuracy and order of operations:]
+
+In most molecular dynamics software, parallelization parameters
+(# of MPI, OpenMP, and vectorization) can change the results due
+to changing the order of operations with finite-precision
+calculations. The USER-INTEL package is deterministic. This means
+that the results should be reproducible from run to run with the
+{same} parallel configurations and when using determinstic
+libraries or library settings (MPI, OpenMP, FFT). However, there
+are differences in the USER-INTEL package that can change the
+order of operations compared to LAMMPS without acceleration:
+
+Neighbor lists can be created in a different order :ulb,l
+Bins used for sorting atoms can be oriented differently :l
+The default stencil order for PPPM is 7. By default, LAMMPS will
+calculate other PPPM parameters to fit the desired acuracy with
+this order :l
+The {newton} setting applies to all atoms, not just atoms shared
+between MPI tasks :l
+Vectorization can change the order for adding pairwise forces :l
+:ule
+
+The precision mode (described below) used with the USER-INTEL
+package can change the {accuracy} of the calculations. For the
+default {mixed} precision option, calculations between pairs or
+triplets of atoms are performed in single precision, intended to
+be within the inherent error of MD simulations. All accumulation
+is performed in double precision to prevent the error from growing
+with the number of atoms in the simulation. {Single} precision
+mode should not be used without appropriate validation.
+
+:line
+
 [Quick Start for Experienced Users:]
 
 LAMMPS should be built with the USER-INTEL package installed.
 Simulations should be run with 1 MPI task per physical {core},
 not {hardware thread}.
 
-For Intel Xeon CPUs:
-
 Edit src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi as necessary. :ulb,l
-If using {kspace_style pppm} in the input script, add "neigh_modify binsize cutoff" and "kspace_modify diff ad" to the input script for better
-performance.  Cutoff should be roughly the neighbor list cutoff.  By
-default the binsize is half the neighbor list cutoff.  :l
-"-pk intel 0 omp 2 -sf intel" added to LAMMPS command-line :l
+Set the environment variable KMP_BLOCKTIME=0 :l
+"-pk intel 0 omp $t -sf intel" added to LAMMPS command-line :l
+$t should be 2 for Intel Xeon CPUs and 2 or 4 for Intel Xeon Phi :l
+For some of the simple 2-body potentials without long-range
+electrostatics, performance and scalability can be better with
+the "newton off" setting added to the input script :l
+For simulations on higher node counts, add "processors * * * grid 
+numa" to the beginning of the input script for better scalability :l
+If using {kspace_style pppm} in the input script, add
+"kspace_modify diff ad" for better performance :l
 :ule
 
-For Intel Xeon Phi CPUs for simulations without {kspace_style
-pppm} in the input script :
+For Intel Xeon Phi CPUs:
 
-Edit src/MAKE/OPTIONS/Makefile.knl as necessary. :ulb,l
-Runs should be performed using MCDRAM. :l
-"-pk intel 0 omp 2 -sf intel" {or} "-pk intel 0 omp 4 -sf intel"
-should be added to the LAMMPS command-line. Choice for best
-performance will depend on the simulation. :l
+Runs should be performed using MCDRAM. :ulb,l
 :ule
 
-For Intel Xeon Phi CPUs for simulations with {kspace_style
-pppm} in the input script:
+For simulations using {kspace_style pppm} on Intel CPUs
+supporting AVX-512:
 
-Edit src/MAKE/OPTIONS/Makefile.knl as necessary. :ulb,l
-Runs should be performed using MCDRAM. :l
-Add "neigh_modify binsize 3" to the input script for better
-performance. :l
-Add "kspace_modify diff ad" to the input script for better
-performance. :l
-export KMP_AFFINITY=none :l
-"-pk intel 0 omp 3 lrt yes -sf intel" or "-pk intel 0 omp 1 lrt yes
--sf intel" added to LAMMPS command-line. Choice for best performance
-will depend on the simulation. :l
+Add "kspace_modify diff ad" to the input script :ulb,l
+The command-line option should be changed to
+"-pk intel 0 omp $r lrt yes -sf intel" where $r is the number of
+threads minus 1. :l
+Do not use thread affinity (set KMP_AFFINITY=none) :l
+The "newton off" setting may provide better scalability :l
 :ule
 
 For Intel Xeon Phi coprocessors (Offload):
@@ -169,6 +199,10 @@ cat /proc/cpuinfo :pre
 
 [Building LAMMPS with the USER-INTEL package:]
 
+NOTE: See the src/USER-INTEL/README file for additional flags that
+might be needed for best performance on Intel server processors
+code-named "Skylake".
+
 The USER-INTEL package must be installed into the source directory:
 
 make yes-user-intel :pre
@@ -193,11 +227,9 @@ source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
 # or psxevars.csh for C-shell
 make intel_cpu_intelmpi :pre
 
-Alternatively, the build can be accomplished with the src/Make.py
-script, described in "Section 2.4"_Section_start.html#start_4 of the
-manual. Type "Make.py -h" for help. For an example:
-
-Make.py -v -p intel omp -intel cpu -a file intel_cpu_intelmpi :pre
+Alternatively this can be done as a single command with
+suitable make command invocations. This is discussed in "Section
+4"_Section_packages.html of the manual.
 
 Note that if you build with support for a Phi coprocessor, the same
 binary can be used on nodes with or without coprocessors installed.
@@ -212,8 +244,7 @@ highly recommended for CCFLAGS and LINKFLAGS. LIB should include
 is required for CCFLAGS and "-qoffload" is required for LINKFLAGS.
 Other recommended CCFLAG options for best performance are
 "-O2 -fno-alias -ansi-alias -qoverride-limits fp-model fast=2
--no-prec-div". The Make.py command will add all of these
-automatically.
+-no-prec-div".
 
 NOTE: The vectorization and math capabilities can differ depending on
 the CPU. For Intel compilers, the "-x" flag specifies the type of
@@ -269,7 +300,7 @@ Hyper-Threading technology disabled.
 
 To enable USER-INTEL optimizations for all available styles used in
 the input script, the "-sf intel"
-"command-line switch"_Section_start.html#start_7 can be used without
+"command-line switch"_Section_start.html#start_6 can be used without
 any requirement for editing the input script. This switch will
 automatically append "intel" to styles that support it. It also
 invokes a default command: "package intel 1"_package.html. This
@@ -282,7 +313,7 @@ support, that 1 coprocessor per node will be used with automatic
 balancing of work between the CPU and the coprocessor.
 
 You can specify different options for the USER-INTEL package by using
-the "-pk intel Nphi" "command-line switch"_Section_start.html#start_7
+the "-pk intel Nphi" "command-line switch"_Section_start.html#start_6
 with keyword/value pairs as specified in the documentation. Here,
 Nphi = # of Xeon Phi coprocessors/node (ignored without offload
 support). Common options to the USER-INTEL package include {omp} to
@@ -322,8 +353,8 @@ follow in the input script.
 
 NOTE: The USER-INTEL package will perform better with modifications
 to the input script when "PPPM"_kspace_style.html is used:
-"kspace_modify diff ad"_kspace_modify.html and "neigh_modify binsize
-3"_neigh_modify.html should be added to the input script.
+"kspace_modify diff ad"_kspace_modify.html should be added to the
+input script.
 
 Long-Range Thread (LRT) mode is an option to the "package
 intel"_package.html command that can improve performance when using
@@ -342,6 +373,10 @@ would normally perform best with "-pk intel 0 omp 4", instead use
 environment variable "KMP_AFFINITY=none". LRT mode is not supported
 when using offload.
 
+NOTE: Changing the "newton"_newton.html setting to off can improve
+performance and/or scalability for simple 2-body potentials such as
+lj/cut or when using LRT mode on processors supporting AVX-512.
+
 Not all styles are supported in the USER-INTEL package. You can mix
 the USER-INTEL package with styles from the "OPT"_accelerate_opt.html
 package or the "USER-OMP package"_accelerate_omp.html. Of course,
@@ -351,13 +386,17 @@ can performed automatically by using "-sf hybrid intel opt" or
 and "omp" suffixes can be appended manually in the input script. For
 the latter, the "package omp"_package.html command must be in the
 input script or the "-pk omp Nt" "command-line
-switch"_Section_start.html#start_7 must be used where Nt is the
+switch"_Section_start.html#start_6 must be used where Nt is the
 number of OpenMP threads. The number of OpenMP threads should not be
 set differently for the different packages. Note that the "suffix
 hybrid intel omp"_suffix.html command can also be used within the
 input script to automatically append the "omp" suffix to styles when
 USER-INTEL styles are not available.
 
+NOTE: For simulations on higher node counts, add "processors * * * 
+grid numa"_processors.html" to the beginning of the input script for
+better scalability.
+
 When running on many nodes, performance might be better when using
 fewer OpenMP threads and more MPI tasks. This will depend on the
 simulation and the machine. Using the "verlet/split"_run_style.html
@@ -446,7 +485,7 @@ sorting"_atom_modify.html is changed to 1 so that the per-atom data is
 effectively sorted at every rebuild of the neighbor lists. All the
 available coprocessor threads on each Phi will be divided among MPI
 tasks, unless the {tptask} option of the "-pk intel" "command-line
-switch"_Section_start.html#start_7 is used to limit the coprocessor
+switch"_Section_start.html#start_6 is used to limit the coprocessor
 threads per MPI task.
 
 [Restrictions:]
@@ -467,7 +506,7 @@ supported.
 
 Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakker, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. :ulb,l
 
-Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. 2016 International Conference for High Performance Computing. In press. :l
+Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. "Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency."_http://dl.acm.org/citation.cfm?id=3014915 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95). :l
 
 Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101. :l
 :ule

doc/src/accelerate_kokkos.txt

@@ -60,8 +60,7 @@ More details follow.
 use a C++11 compatible compiler
 make yes-kokkos
 make mpi KOKKOS_DEVICES=OpenMP                 # build with the KOKKOS package
-make kokkos_omp                                # or Makefile.kokkos_omp already has variable set
-Make.py -v -p kokkos -kokkos omp -o mpi -a file mpi   # or one-line build via Make.py :pre
+make kokkos_omp                                # or Makefile.kokkos_omp already has variable set :pre
 
 mpirun -np 16 lmp_mpi -k on -sf kk -in in.lj              # 1 node, 16 MPI tasks/node, no threads
 mpirun -np 2 -ppn 1 lmp_mpi -k on t 16 -sf kk -in in.lj   # 2 nodes, 1 MPI task/node, 16 threads/task
@@ -82,8 +81,7 @@ use a C++11 compatible compiler
 KOKKOS_DEVICES = Cuda, OpenMP
 KOKKOS_ARCH = Kepler35
 make yes-kokkos
-make machine
-Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda :pre
+make machine :pre
 
 mpirun -np 1 lmp_cuda -k on t 6 -sf kk -in in.lj          # one MPI task, 6 threads on CPU
 mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj   # ditto on 4 nodes :pre
@@ -98,8 +96,7 @@ use a C++11 compatible compiler
 KOKKOS_DEVICES = OpenMP
 KOKKOS_ARCH = KNC
 make yes-kokkos
-make machine
-Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi :pre
+make machine :pre
 
 host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading):
 mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj           # 1 MPI task on 1 Phi, 1*240 = 240
@@ -116,7 +113,7 @@ To build with Kokkos support for CPUs, your compiler must support the
 OpenMP interface.  You should have one or more multi-core CPUs so that
 multiple threads can be launched by each MPI task running on a CPU.
 
-To build with Kokkos support for NVIDIA GPUs, NVIDIA Cuda software
+To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA software
 version 7.5 or later must be installed on your system.  See the
 discussion for the "GPU"_accelerate_gpu.html package for details of
 how to check and do this.
@@ -135,16 +132,16 @@ mode like the USER-INTEL package supports.
 You must choose at build time whether to build for CPUs (OpenMP),
 GPUs, or Phi.
 
-You can do any of these in one line, using the src/Make.py script,
-described in "Section 2.4"_Section_start.html#start_4 of the manual.
-Type "Make.py -h" for help.  If run from the src directory, these
+You can do any of these in one line, using the suitable make command
+line flags as described in "Section 4"_Section_packages.html of the
+manual. If run from the src directory, these
 commands will create src/lmp_kokkos_omp, lmp_kokkos_cuda, and
 lmp_kokkos_phi.  Note that the OMP and PHI options use
 src/MAKE/Makefile.mpi as the starting Makefile.machine.  The CUDA
 option uses src/MAKE/OPTIONS/Makefile.kokkos_cuda.
 
 The latter two steps can be done using the "-k on", "-pk kokkos" and
-"-sf kk" "command-line switches"_Section_start.html#start_7
+"-sf kk" "command-line switches"_Section_start.html#start_6
 respectively.  Or the effect of the "-pk" or "-sf" switches can be
 duplicated by adding the "package kokkos"_package.html or "suffix
 kk"_suffix.html commands respectively to your input script.
@@ -280,10 +277,10 @@ specify how many Phi coprocessors there are per node; each
 coprocessors is simply treated as running some number of MPI tasks.
 
 You must use the "-k on" "command-line
-switch"_Section_start.html#start_7 to enable the KOKKOS package.  It
+switch"_Section_start.html#start_6 to enable the KOKKOS package.  It
 takes additional arguments for hardware settings appropriate to your
 system.  Those arguments are "documented
-here"_Section_start.html#start_7.  The two most commonly used
+here"_Section_start.html#start_6.  The two most commonly used
 options are:
 
 -k on t Nt g Ng :pre
@@ -304,12 +301,12 @@ The "-k on" switch also issues a "package kokkos" command (with no
 additional arguments) which sets various KOKKOS options to default
 values, as discussed on the "package"_package.html command doc page.
 
-Use the "-sf kk" "command-line switch"_Section_start.html#start_7,
+Use the "-sf kk" "command-line switch"_Section_start.html#start_6,
 which will automatically append "kk" to styles that support it.  Use
-the "-pk kokkos" "command-line switch"_Section_start.html#start_7 if
+the "-pk kokkos" "command-line switch"_Section_start.html#start_6 if
 you wish to change any of the default "package kokkos"_package.html
 optionns set by the "-k on" "command-line
-switch"_Section_start.html#start_7.
+switch"_Section_start.html#start_6.
 
 
 
@@ -323,7 +320,7 @@ However, when running in MPI-only mode with 1 thread per MPI task, it
 will typically be faster to use "half" neighbor lists and set the
 Newton flag to "on", just as is the case for non-accelerated pair
 styles.  You can do this with the "-pk" "command-line
-switch"_Section_start.html#start_7.
+switch"_Section_start.html#start_6.
 
 [Or run with the KOKKOS package by editing an input script:]
 
@@ -332,7 +329,7 @@ appropriate thread and GPU values for host=OMP or host=MIC or
 device=CUDA are the same.
 
 You must still use the "-k on" "command-line
-switch"_Section_start.html#start_7 to enable the KOKKOS package, and
+switch"_Section_start.html#start_6 to enable the KOKKOS package, and
 specify its additional arguments for hardware options appropriate to
 your system, as documented above.
 
@@ -343,7 +340,7 @@ pair_style lj/cut/kk 2.5 :pre
 
 You only need to use the "package kokkos"_package.html command if you
 wish to change any of its option defaults, as set by the "-k on"
-"command-line switch"_Section_start.html#start_7.
+"command-line switch"_Section_start.html#start_6.
 
 [Speed-ups to expect:]
 
@@ -389,7 +386,7 @@ If N is the number of physical cores/node, then the number of MPI
 tasks/node * number of threads/task should not exceed N, and should
 typically equal N.  Note that the default threads/task is 1, as set by
 the "t" keyword of the "-k" "command-line
-switch"_Section_start.html#start_7.  If you do not change this, no
+switch"_Section_start.html#start_6.  If you do not change this, no
 additional parallelism (beyond MPI) will be invoked on the host
 CPU(s).
 
@@ -429,7 +426,7 @@ details).
 The -np setting of the mpirun command should set the number of MPI
 tasks/node to be equal to the # of physical GPUs on the node.
 
-Use the "-k" "command-line switch"_Section_commands.html#start_7 to
+Use the "-k" "command-line switch"_Section_commands.html#start_6 to
 specify the number of GPUs per node, and the number of threads per MPI
 task.  As above for multi-core CPUs (and no GPU), if N is the number
 of physical cores/node, then the number of MPI tasks/node * number of

doc/src/accelerate_omp.txt

@@ -23,8 +23,7 @@ one or more 16-core nodes.  More details follow.
 use -fopenmp with CCFLAGS and LINKFLAGS in Makefile.machine
 make yes-user-omp
 make mpi                                   # build with USER-OMP package, if settings added to Makefile.mpi
-make omp                                   # or Makefile.omp already has settings
-Make.py -v -p omp -o mpi -a file mpi       # or one-line build via Make.py :pre
+make omp                                   # or Makefile.omp already has settings :pre
 
 lmp_mpi -sf omp -pk omp 16 < in.script                         # 1 MPI task, 16 threads
 mpirun -np 4 lmp_mpi -sf omp -pk omp 4 -in in.script           # 4 MPI tasks, 4 threads/task
@@ -40,14 +39,11 @@ each MPI task running on a CPU.
 
 The lines above illustrate how to include/build with the USER-OMP
 package in two steps, using the "make" command.  Or how to do it with
-one command via the src/Make.py script, described in "Section
-2.4"_Section_start.html#start_4 of the manual.  Type "Make.py -h" for
-help.
+one command as described in "Section 4"_Section_packages.html of the manual.
 
 Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must
 include "-fopenmp".  Likewise, if you use an Intel compiler, the
-CCFLAGS setting must include "-restrict".  The Make.py command will
-add these automatically.
+CCFLAGS setting must include "-restrict".
 
 [Run with the USER-OMP package from the command line:]
 
@@ -62,14 +58,14 @@ threads/task should not exceed the physical number of cores (on a
 node), otherwise performance will suffer.
 
 As in the lines above, use the "-sf omp" "command-line
-switch"_Section_start.html#start_7, which will automatically append
+switch"_Section_start.html#start_6, which will automatically append
 "omp" to styles that support it.  The "-sf omp" switch also issues a
 default "package omp 0"_package.html command, which will set the
 number of threads per MPI task via the OMP_NUM_THREADS environment
 variable.
 
 You can also use the "-pk omp Nt" "command-line
-switch"_Section_start.html#start_7, to explicitly set Nt = # of OpenMP
+switch"_Section_start.html#start_6, to explicitly set Nt = # of OpenMP
 threads per MPI task to use, as well as additional options.  Its
 syntax is the same as the "package omp"_package.html command whose doc
 page gives details, including the default values used if it is not

doc/src/accelerate_opt.txt

@@ -21,8 +21,7 @@ Here is a quick overview of how to use the OPT package.  More details
 follow.
 
 make yes-opt
-make mpi                               # build with the OPT package
-Make.py -v -p opt -o mpi -a file mpi   # or one-line build via Make.py :pre
+make mpi                               # build with the OPT package :pre
 
 lmp_mpi -sf opt -in in.script                # run in serial
 mpirun -np 4 lmp_mpi -sf opt -in in.script   # run in parallel :pre
@@ -35,18 +34,15 @@ None.
 
 The lines above illustrate how to build LAMMPS with the OPT package in
 two steps, using the "make" command.  Or how to do it with one command
-via the src/Make.py script, described in "Section
-2.4"_Section_start.html#start_4 of the manual.  Type "Make.py -h" for
-help.
+as described in "Section 4"_Section_packages.html of the manual.
 
 Note that if you use an Intel compiler to build with the OPT package,
 the CCFLAGS setting in your Makefile.machine must include "-restrict".
-The Make.py command will add this automatically.
 
 [Run with the OPT package from the command line:]
 
 As in the lines above, use the "-sf opt" "command-line
-switch"_Section_start.html#start_7, which will automatically append
+switch"_Section_start.html#start_6, which will automatically append
 "opt" to styles that support it.
 
 [Or run with the OPT package by editing an input script:]

doc/src/angle_charmm.txt

@@ -63,7 +63,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/angle_class2.txt

@@ -94,7 +94,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/angle_cosine.txt

@@ -50,7 +50,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/angle_cosine_delta.txt

@@ -55,7 +55,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/angle_cosine_periodic.txt

@@ -63,7 +63,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/angle_cosine_shift.txt

@@ -53,7 +53,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/angle_cosine_shift_exp.txt

@@ -65,7 +65,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/angle_cosine_squared.txt

@@ -55,7 +55,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/angle_fourier.txt

@@ -51,7 +51,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/angle_fourier_simple.txt

@@ -50,7 +50,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/angle_harmonic.txt

@@ -57,7 +57,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/angle_quartic.txt

@@ -57,7 +57,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/angle_table.txt

@@ -136,7 +136,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/atom_style.txt

@@ -13,17 +13,19 @@ atom_style command :h3
 atom_style style args :pre
 
 style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \
-        {dpd} or {electron} or {ellipsoid} or {full} or {line} or {meso} or \
-        {molecular} or {peri} or {smd} or {sphere} or {tri} or \
-        {template} or {hybrid} :ulb,l
+        {dpd} or {edpd} or {mdpd} or {tdpd} or {electron} or {ellipsoid} or \
+        {full} or {line} or {meso} or {molecular} or {peri} or {smd} or \
+        {sphere} or {tri} or {template} or {hybrid} :ulb,l
   args = none for any style except the following
-  {body} args = bstyle bstyle-args
-    bstyle = style of body particles
-    bstyle-args = additional arguments specific to the bstyle
-                  see the "body"_body.html doc page for details
-  {template} args = template-ID
-    template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
-  {hybrid} args = list of one or more sub-styles, each with their args :pre
+    {body} args = bstyle bstyle-args
+      bstyle = style of body particles
+      bstyle-args = additional arguments specific to the bstyle
+                    see the "body"_body.html doc page for details
+    {tdpd} arg = Nspecies
+      Nspecies = # of chemical species
+    {template} arg = template-ID
+      template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
+    {hybrid} args = list of one or more sub-styles, each with their args :pre
 
 accelerated styles (with same args) = {angle/kk} or {atomic/kk} or {bond/kk} or {charge/kk} or {full/kk} or {molecular/kk} :l
 :ule
@@ -36,7 +38,8 @@ atom_style full
 atom_style body nparticle 2 10
 atom_style hybrid charge bond
 atom_style hybrid charge body nparticle 2 5
-atom_style template myMols :pre
+atom_style template myMols 
+atom_style tdpd 2 :pre
 
 [Description:]
 
@@ -74,6 +77,9 @@ quantities.
 {charge} | charge | atomic system with charges |
 {dipole} | charge and dipole moment | system with dipolar particles |
 {dpd} | internal temperature and internal energies | DPD particles |
+{edpd} | temperature and heat capacity | eDPD particles |
+{mdpd} | density | mDPD particles |
+{tdpd} | chemical concentration | tDPD particles |
 {electron} | charge and spin and eradius | electronic force field |
 {ellipsoid} | shape, quaternion, angular momentum | aspherical particles |
 {full} | molecular + charge | bio-molecules |
@@ -145,6 +151,19 @@ properties with internal temperature (dpdTheta), internal conductive
 energy (uCond), internal mechanical energy (uMech), and internal
 chemical energy (uChem).
 
+The {edpd} style is for energy-conserving dissipative particle
+dynamics (eDPD) particles which store a temperature (edpd_temp), and
+heat capacity(edpd_cv).
+
+The {mdpd} style is for many-body dissipative particle dynamics (mDPD)
+particles which store a density (rho) for considering
+density-dependent many-body interactions.
+
+The {tdpd} style is for transport dissipative particle dynamics (tDPD)
+particles which store a set of chemical concentration. An integer
+"cc_species" is required to specify the number of chemical species
+involved in a tDPD system.
+
 The {meso} style is for smoothed particle hydrodynamics (SPH)
 particles which store a density (rho), energy (e), and heat capacity
 (cv).
@@ -284,6 +303,11 @@ force fields"_pair_eff.html.
 The {dpd} style is part of the USER-DPD package for dissipative
 particle dynamics (DPD).
 
+The {edpd}, {mdpd}, and {tdpd} styles are part of the USER-MESO package 
+for energy-conserving dissipative particle dynamics (eDPD), many-body 
+dissipative particle dynamics (mDPD), and transport dissipative particle 
+dynamics (tDPD), respectively.
+
 The {meso} style is part of the USER-SPH package for smoothed particle
 hydrodynamics (SPH).  See "this PDF
 guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS.