patch 24Jul17

LICENSE: update address of Free Software Foundation

.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)_
+
+

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

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;          \
@@ -158,7 +159,7 @@ $(VENV):
 	@( \
 		virtualenv -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
-		pip install Sphinx; \
+		pip install Sphinx==1.5.6; \
 		pip install sphinxcontrib-images; \
 		deactivate;\
 	)

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_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_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_meam_spline.tex

@@ -1,13 +1,14 @@
 \documentclass[12pt]{article}
+\usepackage{amsmath}
 
 \begin{document}
 
 $$
-   E=\sum_{ij}\phi(r_{ij})+\sum_{i}U(\rho_{i}),
+   E=\sum_{i<j}\phi(r_{ij})+\sum_{i}U(n_{i}),
 $$
 
 $$
-   \rho_{i}=\sum_{j}\rho(r_{ij})+\sum_{jk}f(r_{ij})f(r_{ik})g[\cos(\theta_{jik})]
+   n_{i}=\sum_{j}\rho(r_{ij})+\sum_{\substack{j<k,\\j,k\neq i}}f(r_{ij})f(r_{ik})g[\cos(\theta_{jik})]
 $$
 
 \end{document}

doc/src/Eqs/pair_meam_spline_multicomponent.tex

@@ -0,0 +1,14 @@
+\documentclass[12pt]{article}
+\usepackage{amsmath}
+
+\begin{document}
+
+$$
+   E=\sum_{i<j}\phi_{ij}(r_{ij})+\sum_{i}U_i(n_{i}),
+$$
+
+$$
+   n_{i}=\sum_{j\ne i}\rho_j(r_{ij})+\sum_{\substack{j<k,\\j,k\neq i}}f_{j}(r_{ij})f_{k}(r_{ik})g_{jk}[\cos(\theta_{jik})]
+$$
+
+\end{document}

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="4 May 2017 version">
+<META NAME="docnumber" CONTENT="24 Jul 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
-4 May 2017 version :c,h4
+24 Jul 2017 version :c,h4
 
 Version info: :h4
 
@@ -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
+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

@@ -527,9 +527,9 @@ These are additional commands in USER packages, which can be used if
 "LAMMPS is built with the appropriate
 package"_Section_start.html#start_3.
 
-"dump custom/vtk"_dump_custom_vtk.html,
-"dump nc"_dump_nc.html,
-"dump nc/mpiio"_dump_nc.html,
+"dump netcdf"_dump_netcdf.html,
+"dump netcdf/mpiio"_dump_netcdf.html,
+"dump vtk"_dump_vtk.html,
 "group2ndx"_group2ndx.html,
 "ndx2group"_group2ndx.html,
 "temper/grem"_temper_grem.html :tb(c=3,ea=c)
@@ -618,6 +618,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "press/berendsen"_fix_press_berendsen.html,
 "print"_fix_print.html,
 "property/atom"_fix_property_atom.html,
+"python"_fix_python.html,
 "qeq/comb (o)"_fix_qeq_comb.html,
 "qeq/dynamic"_fix_qeq.html,
 "qeq/fire"_fix_qeq.html,
@@ -716,7 +717,7 @@ 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,
@@ -733,7 +734,9 @@ package"_Section_start.html#start_3.
 "smd/wall/surface"_fix_smd_wall_surface.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
 
@@ -830,6 +833,7 @@ 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,
 "fep"_compute_fep.html,
@@ -931,6 +935,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 "gran/hertz/history (o)"_pair_gran.html,
 "gran/hooke (o)"_pair_gran.html,
 "gran/hooke/history (o)"_pair_gran.html,
+"gw"_pair_gw.html,
+"gw/zbl"_pair_gw.html,
 "hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,
 "hbond/dreiding/morse (o)"_pair_hbond_dreiding.html,
 "kim"_pair_kim.html,
@@ -960,7 +966,7 @@ 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,
@@ -982,6 +988,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "peri/pmb (o)"_pair_peri.html,
 "peri/ves"_pair_peri.html,
 "polymorphic"_pair_polymorphic.html,
+"python"_pair_python.html,
 "reax"_pair_reax.html,
 "rebo (o)"_pair_airebo.html,
 "resquared (go)"_pair_resquared.html,
@@ -1016,6 +1023,7 @@ package"_Section_start.html#start_3.
 "dpd/fdt/energy"_pair_dpd_fdt.html,
 "eam/cd (o)"_pair_eam.html,
 "edip (o)"_pair_edip.html,
+"edip/multi"_pair_edip.html,
 "eff/cut"_pair_eff.html,
 "exp6/rx"_pair_exp6_rx.html,
 "gauss/cut"_pair_gauss.html,
@@ -1033,7 +1041,7 @@ 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,
+"meam/c"_pair_meam.html,
 "meam/spline (o)"_pair_meam_spline.html,
 "meam/sw/spline"_pair_meam_sw_spline.html,
 "mgpt"_pair_mgpt.html,
@@ -1052,7 +1060,7 @@ 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,
@@ -1068,7 +1076,7 @@ package"_Section_start.html#start_3.
 "table/rx"_pair_table_rx.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
 
@@ -1220,7 +1228,7 @@ 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 "special_bonds extra" command
+(or the "read_data 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 special_bonds extra command
+(or the read_data 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_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_packages.txt

@@ -121,9 +121,10 @@ Package, Description, Doc page, Example, Library
 "USER-INTEL"_#USER-INTEL, optimized Intel CPU and KNL styles,"Section 5.3.2"_accelerate_intel.html, WWW bench, -
 "USER-LB"_#USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, -
 "USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, -
+"USER-MEAMC"_#USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, -
 "USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -
 "USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, -
-"USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
+"USER-MOLFILE"_#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
 "USER-NETCDF"_#USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext
 "USER-OMP"_#USER-OMP, OpenMP-enabled styles,"Section 5.3.4"_accelerate_omp.html, WWW bench, -
 "USER-PHONON"_#USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, -
@@ -135,7 +136,7 @@ Package, Description, Doc page, Example, Library
 "USER-SMTBQ"_#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
 "USER-SPH"_#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
 "USER-TALLY"_#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
-"USER-VTK"_#USER-VTK, dump output via VTK, "compute custom/vtk"_dump_custom_vtk.html, -, ext
+"USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext
 :tb(ea=c,ca1=l)
 
 :line
@@ -368,7 +369,7 @@ suffix in their style name.  "Section 5.3.1"_accelerate_gpu.html gives
 details of what hardware and Cuda software is required on your system,
 and details on how to build and use this package.  Its styles can be
 invoked at run time via the "-sf gpu" or "-suffix gpu" "command-line
-switches"_Section_start.html#start_7.  See also the "KOKKOS"_#KOKKOS
+switches"_Section_start.html#start_6.  See also the "KOKKOS"_#KOKKOS
 package, which has GPU-enabled styles.
 
 [Authors:] Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen
@@ -426,8 +427,8 @@ src/GPU/README
 lib/gpu/README
 "Section 5.3"_Section_accelerate.html#acc_3
 "Section 5.3.1"_accelerate_gpu.html
-"Section 2.7 -sf gpu"_Section_start.html#start_7
-"Section 2.7 -pk gpu"_Section_start.html#start_7
+"Section 2.6 -sf gpu"_Section_start.html#start_6
+"Section 2.6 -pk gpu"_Section_start.html#start_6
 "package gpu"_package.html
 Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (g)
 "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
@@ -528,8 +529,8 @@ style name.  "Section 5.3.3"_accelerate_kokkos.html gives details of
 what hardware and software is required on your system, and how to
 build and use this package.  Its styles can be invoked at run time via
 the "-sf kk" or "-suffix kk" "command-line
-switches"_Section_start.html#start_7.  Also see the "GPU"_#GPU,
-"OPT"_#OPT, "USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER_OMP
+switches"_Section_start.html#start_6.  Also see the "GPU"_#GPU,
+"OPT"_#OPT, "USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP
 packages, which have styles optimized for CPUs, KNLs, and GPUs.
 
 You must have a C++11 compatible compiler to use this package.
@@ -585,7 +586,7 @@ do not recommend building with other acceleration packages installed
 
 make yes-kokkos
 make machine :pre
- 
+
 make no-kokkos
 make machine :pre
 
@@ -596,9 +597,9 @@ src/KOKKOS/README
 lib/kokkos/README
 "Section 5.3"_Section_accelerate.html#acc_3
 "Section 5.3.3"_accelerate_kokkos.html
-"Section 2.7 -k on ..."_Section_start.html#start_7
-"Section 2.7 -sf kk"_Section_start.html#start_7
-"Section 2.7 -pk kokkos"_Section_start.html#start_7
+"Section 2.6 -k on ..."_Section_start.html#start_6
+"Section 2.6 -sf kk"_Section_start.html#start_6
+"Section 2.6 -pk kokkos"_Section_start.html#start_6
 "package kokkos"_package.html
 Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (k)
 "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
@@ -839,13 +840,13 @@ written and read in parallel.
 Note that MPIIO is part of the standard message-passing interface
 (MPI) library, so you should not need any additional compiler or link
 settings, beyond what LAMMPS normally uses for MPI on your system.
- 
+
 make yes-mpiio
 make machine :pre
- 
+
 make no-mpiio
 make machine :pre
- 
+
 [Supporting info:]
 
 src/MPIIO: filenames -> commands
@@ -855,16 +856,16 @@ src/MPIIO: filenames -> commands
 "read_restart"_read_restart.html :ul
 
 :line
- 
-MSCG package :link(MSCG),h4
+
+MSCG package :link(mscg),h4
 
 [Contents:]
 
 A "fix mscg"_fix_mscg.html command which can parameterize a
 Mulit-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG
-library"_mscg.
+library"_mscg_home.
 
-:link(mscg,https://github.com/uchicago-voth/MSCG-release)
+:link(mscg_home,https://github.com/uchicago-voth/MSCG-release)
 
 To use this package you must have the MS-CG library available on your
 system.
@@ -914,7 +915,7 @@ lib/mscg/README
 examples/mscg :ul
 
 :line
- 
+
 OPT package :link(OPT),h4
 
 [Contents:]
@@ -925,7 +926,7 @@ CHARMM, and Morse potentials.  The styles have an "opt" suffix in
 their style name.  "Section 5.3.5"_accelerate_opt.html gives details
 of how to build and use this package.  Its styles can be invoked at
 run time via the "-sf opt" or "-suffix opt" "command-line
-switches"_Section_start.html#start_7.  See also the "KOKKOS"_#KOKKOS,
+switches"_Section_start.html#start_6.  See also the "KOKKOS"_#KOKKOS,
 "USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP packages, which
 have styles optimized for CPU performance.
 
@@ -952,7 +953,7 @@ CCFLAGS: add -restrict :ul
 src/OPT: filenames -> commands
 "Section 5.3"_Section_accelerate.html#acc_3
 "Section 5.3.5"_accelerate_opt.html
-"Section 2.7 -sf opt"_Section_start.html#start_7
+"Section 2.6 -sf opt"_Section_start.html#start_6
 Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (t)
 "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
 
@@ -1323,11 +1324,11 @@ VORONOI package :link(VORONOI),h4
 [Contents:]
 
 A compute command which calculates the Voronoi tesselation of a
-collection of atoms by wrapping the "Voro++ library"_voronoi.  This
+collection of atoms by wrapping the "Voro++ library"_voro_home.  This
 can be used to calculate the local volume or each atoms or its near
 neighbors.
 
-:link(voronoi,http://math.lbl.gov/voro++)
+:link(voro_home,http://math.lbl.gov/voro++)
 
 To use this package you must have the Voro++ library available on your
 system.
@@ -1387,7 +1388,7 @@ atomic information to continuum fields.
 [Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).
 
 [Install or un-install:]
-  
+
 Before building LAMMPS with this package, you must first build the ATC
 library in lib/atc.  You can do this manually if you prefer; follow
 the instructions in lib/atc/README.  You can also do it in one step
@@ -1420,10 +1421,10 @@ usual manner:
 
 make yes-user-atc
 make machine :pre
- 
+
 make no-user-atc
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-ATC: filenames -> commands
@@ -1446,7 +1447,7 @@ model.
 [Author:] Ilya Valuev (JIHT, Russia).
 
 [Install or un-install:]
-  
+
 Before building LAMMPS with this package, you must first build the
 AWPMD library in lib/awpmd.  You can do this manually if you prefer;
 follow the instructions in lib/awpmd/README.  You can also do it in
@@ -1479,16 +1480,15 @@ usual manner:
 
 make yes-user-awpmd
 make machine :pre
- 
+
 make no-user-awpmd
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-AWPMD: filenames -> commands
 src/USER-AWPMD/README
 "pair awpmd/cut"_pair_awpmd.html
-"fix nve/awpmd"_fix_nve_awpmd.html
 examples/USER/awpmd :ul
 
 :line
@@ -1503,16 +1503,16 @@ oxDNA model of Doye, Louis and Ouldridge at the University of Oxford.
 This includes Langevin-type rigid-body integrators with improved
 stability.
 
-[Author:] Oliver Henrich (University of Edinburgh).
+[Author:] Oliver Henrich (University of Strathclyde, Glasgow).
 
 [Install or un-install:]
-  
+
 make yes-user-cgdna
 make machine :pre
- 
+
 make no-user-cgdna
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-CGDNA: filenames -> commands
@@ -1520,7 +1520,7 @@ src/USER-CGDNA: filenames -> commands
 "pair_style oxdna/*"_pair_oxdna.html
 "pair_style oxdna2/*"_pair_oxdna2.html
 "bond_style oxdna/*"_bond_oxdna.html
-"bond_style oxdna2/*"_bond_oxdna2.html
+"bond_style oxdna2/*"_bond_oxdna.html
 "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul
 
 :line
@@ -1537,13 +1537,13 @@ acids.
 [Author:] Axel Kohlmeyer (Temple U).
 
 [Install or un-install:]
-  
+
 make yes-user-cgsdk
 make machine :pre
- 
+
 make no-user-cgsdk
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-CGSDK: filenames -> commands
@@ -1571,7 +1571,7 @@ by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and
 Jerome Henin (LISM, CNRS, Marseille, France).
 
 [Install or un-install:]
-  
+
 Before building LAMMPS with this package, you must first build the
 COLVARS library in lib/colvars.  You can do this manually if you
 prefer; follow the instructions in lib/colvars/README.  You can also
@@ -1595,10 +1595,10 @@ usual manner:
 
 make yes-user-colvars
 make machine :pre
- 
+
 make no-user-colvars
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-COLVARS: filenames -> commands
@@ -1620,13 +1620,13 @@ intensities based on kinematic diffraction theory.
 [Author:] Shawn Coleman while at the U Arkansas.
 
 [Install or un-install:]
-  
+
 make yes-user-diffraction
 make machine :pre
- 
+
 make no-user-diffraction
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-DIFFRACTION: filenames -> commands
@@ -1655,13 +1655,13 @@ algorithm.
 Brennan (ARL).
 
 [Install or un-install:]
-  
+
 make yes-user-dpd
 make machine :pre
- 
+
 make no-user-dpd
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-DPD: filenames -> commands
@@ -1697,13 +1697,13 @@ tools/drude.
 Devemy (CNRS), and Agilio Padua (U Blaise Pascal).
 
 [Install or un-install:]
-  
+
 make yes-user-drude
 make machine :pre
- 
+
 make no-user-drude
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-DRUDE: filenames -> commands
@@ -1735,21 +1735,21 @@ tools/eff; see its README file.
 [Author:] Andres Jaramillo-Botero (CalTech).
 
 [Install or un-install:]
-  
+
 make yes-user-eff
 make machine :pre
- 
+
 make no-user-eff
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-EFF: filenames -> commands
 src/USER-EFF/README
 "atom_style electron"_atom_style.html
 "fix nve/eff"_fix_nve_eff.html
-"fix nvt/eff"_fix_nvt_eff.html
-"fix npt/eff"_fix_npt_eff.html
+"fix nvt/eff"_fix_nh_eff.html
+"fix npt/eff"_fix_nh_eff.html
 "fix langevin/eff"_fix_langevin_eff.html
 "compute temp/eff"_compute_temp_eff.html
 "pair eff/cut"_pair_eff.html
@@ -1774,13 +1774,13 @@ for using this package in tools/fep; see its README file.
 [Author:] Agilio Padua (Universite Blaise Pascal Clermont-Ferrand)
 
 [Install or un-install:]
-  
+
 make yes-user-fep
 make machine :pre
- 
+
 make no-user-fep
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-FEP: filenames -> commands
@@ -1837,13 +1837,13 @@ file.
 
 You can then install/un-install the package and build LAMMPS in the
 usual manner:
-  
+
 make yes-user-h5md
 make machine :pre
- 
+
 make no-user-h5md
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-H5MD: filenames -> commands
@@ -1863,7 +1863,7 @@ All of them have an "intel" in their style name.  "Section
 5.3.2"_accelerate_intel.html gives details of what hardware and
 compilers are required on your system, and how to build and use this
 package.  Its styles can be invoked at run time via the "-sf intel" or
-"-suffix intel" "command-line switches"_Section_start.html#start_7.
+"-suffix intel" "command-line switches"_Section_start.html#start_6.
 Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and "USER-OMP"_#USER-OMP
 packages, which have styles optimized for CPUs and KNLs.
 
@@ -1909,7 +1909,7 @@ explained in "Section 5.3.2"_accelerate_intel.html.
 
 make yes-user-intel yes-user-omp
 make machine :pre
- 
+
 make no-user-intel no-user-omp
 make machine :pre
 
@@ -1919,8 +1919,8 @@ src/USER-INTEL: filenames -> commands
 src/USER-INTEL/README
 "Section 5.3"_Section_accelerate.html#acc_3
 "Section 5.3.2"_accelerate_gpu.html
-"Section 2.7 -sf intel"_Section_start.html#start_7
-"Section 2.7 -pk intel"_Section_start.html#start_7
+"Section 2.6 -sf intel"_Section_start.html#start_6
+"Section 2.6 -pk intel"_Section_start.html#start_6
 "package intel"_package.html
 Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (i)
 src/USER-INTEL/TEST
@@ -1939,13 +1939,13 @@ can be used to model MD particles influenced by hydrodynamic forces.
 Ontario).
 
 [Install or un-install:]
-  
+
 make yes-user-lb
 make machine :pre
- 
+
 make no-user-lb
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-LB: filenames -> commands
@@ -1973,13 +1973,13 @@ matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL.
 [Authors:] Tomas Oppelstrup and John Moriarty (LLNL).
 
 [Install or un-install:]
-  
+
 make yes-user-mgpt
 make machine :pre
- 
+
 make no-user-mgpt
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-MGPT: filenames -> commands
@@ -2001,13 +2001,13 @@ dihedral, improper, or command style.
 src/USER-MISC/README file.
 
 [Install or un-install:]
-  
+
 make yes-user-misc
 make machine :pre
- 
+
 make no-user-misc
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-MISC: filenames -> commands
@@ -2028,40 +2028,73 @@ algorithm to formulate single-particle constraint functions
 g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold)
 n = grad(g).
 
-[Author:] Stefan Paquay (Eindhoven University of Technology (TU/e), The
-Netherlands)
+[Author:] Stefan Paquay (until 2017: Eindhoven University of Technology (TU/e), The
+Netherlands; since 2017: Brandeis University, Waltham, MA, USA)
 
 [Install or un-install:]
-  
+
 make yes-user-manifold
 make machine :pre
- 
+
 make no-user-manifold
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-MANIFOLD: filenames -> commands
 src/USER-MANIFOLD/README
 "doc/manifolds"_manifolds.html
 "fix manifoldforce"_fix_manifoldforce.html
-"fix nve/manifold/rattle"_fix_nve_manifold/rattle.html
-"fix nvt/manifold/rattle"_fix_nvt_manifold/rattle.html
+"fix nve/manifold/rattle"_fix_nve_manifold_rattle.html
+"fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html
 examples/USER/manifold
 http://lammps.sandia.gov/movies.html#manifold :ul
 
 :line
 
+USER-MEAMC package :link(USER-MEAMC),h4
+
+[Contents:]
+
+A pair style for the modified embedded atom (MEAM) potential
+translated from the Fortran version in the "MEAM"_MEAM package
+to plain C++. In contrast to the MEAM package, no library
+needs to be compiled and the pair style can be instantiated
+multiple times.
+
+[Author:] Sebastian Huetter, (Otto-von-Guericke University Magdeburg)
+based on the Fortran version of Greg Wagner (Northwestern U) while at
+Sandia.
+
+[Install or un-install:]
+  
+make yes-user-meamc
+make machine :pre
+ 
+make no-user-meamc
+make machine :pre
+ 
+[Supporting info:]
+
+src/USER-MEAMC: filenames -> commands
+src/USER-MEAMC/README
+"pair meam/c"_pair_meam.html
+examples/meam :ul
+
+:line
+
 USER-MOLFILE package :link(USER-MOLFILE),h4
 
 [Contents:]
 
 A "dump molfile"_dump_molfile.html command which uses molfile plugins
-that are bundled with the "VMD"_http://www.ks.uiuc.edu/Research/vmd
+that are bundled with the "VMD"_vmd_home
 molecular visualization and analysis program, to enable LAMMPS to dump
 snapshots in formats compatible with various molecular simulation
 tools.
 
+:link(vmd_home,http://www.ks.uiuc.edu/Research/vmd)
+
 To use this package you must have the desired VMD plugins available on
 your system.
 
@@ -2079,7 +2112,7 @@ at
 [Author:] Axel Kohlmeyer (Temple U).
 
 [Install or un-install:]
-  
+
 Note that the lib/molfile/Makefile.lammps file has a setting for a
 dynamic loading library libdl.a that should is typically present on
 all systems, which is required for LAMMPS to link with this package.
@@ -2089,10 +2122,10 @@ lib/molfile/Makefile.lammps for details.
 
 make yes-user-molfile
 make machine :pre
- 
+
 make no-user-molfile
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-MOLFILE: filenames -> commands
@@ -2118,7 +2151,7 @@ Note that NetCDF files can be directly visualized with the following
 tools:
 
 "Ovito"_ovito (Ovito supports the AMBER convention and the extensions mentioned above)
-"VMD"_vmd
+"VMD"_vmd_home
 "AtomEye"_atomeye (the libAtoms version of AtomEye contains a NetCDF reader not present in the standard distribution) :ul
 
 :link(ovito,http://www.ovito.org)
@@ -2127,7 +2160,7 @@ tools:
 [Author:] Lars Pastewka (Karlsruhe Institute of Technology).
 
 [Install or un-install:]
-   
+
 Note that to follow these steps, you need the standard NetCDF software
 package installed on your system.  The lib/netcdf/Makefile.lammps file
 has settings for NetCDF include and library files that LAMMPS needs to
@@ -2137,7 +2170,7 @@ lib/netcdf/README for details.
 
 make yes-user-netcdf
 make machine :pre
-  
+
 make no-user-netcdf
 make machine :pre
 
@@ -2160,7 +2193,7 @@ via OpenMP directives.  All of them have an "omp" in their style name.
 "Section 5.3.4"_accelerate_omp.html gives details of what hardware and
 compilers are required on your system, and how to build and use this
 package.  Its styles can be invoked at run time via the "-sf omp" or
-"-suffix omp" "command-line switches"_Section_start.html#start_7.
+"-suffix omp" "command-line switches"_Section_start.html#start_6.
 Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and
 "USER-INTEL"_#USER-INTEL packages, which have styles optimized for
 CPUs.
@@ -2177,10 +2210,10 @@ Once you have an appropriate Makefile.machine, you can
 install/un-install the package and build LAMMPS in the usual manner:
 
 [Install or un-install:]
-  
+
 make yes-user-omp
 make machine :pre
- 
+
 make no-user-omp
 make machine :pre
 
@@ -2193,8 +2226,8 @@ src/USER-OMP: filenames -> commands
 src/USER-OMP/README
 "Section 5.3"_Section_accelerate.html#acc_3
 "Section 5.3.4"_accelerate_omp.html
-"Section 2.7 -sf omp"_Section_start.html#start_7
-"Section 2.7 -pk omp"_Section_start.html#start_7
+"Section 2.6 -sf omp"_Section_start.html#start_6
+"Section 2.6 -pk omp"_Section_start.html#start_6
 "package omp"_package.html
 Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (o)
 "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
@@ -2212,13 +2245,13 @@ relations, directly from molecular dynamics simulations.
 [Author:] Ling-Ti Kong (Shanghai Jiao Tong University).
 
 [Install or un-install:]
-   
+
 make yes-user-phonon
 make machine :pre
-  
+
 make no-user-phonon
 make machine :pre
-  
+
 [Supporting info:]
 
 src/USER-PHONON: filenames -> commands
@@ -2234,7 +2267,7 @@ USER-QMMM package :link(USER-QMMM),h4
 
 A "fix qmmm"_fix_qmmm.html command which allows LAMMPS to be used in a
 QM/MM simulation, currently only in combination with the "Quantum
-ESPRESSO"_espresso package.  
+ESPRESSO"_espresso package.
 
 :link(espresso,http://www.quantum-espresso.org)
 
@@ -2274,7 +2307,7 @@ usual manner:
 
 make yes-user-qmmm
 make machine :pre
-  
+
 make no-user-qmmm
 make machine :pre
 
@@ -2283,7 +2316,7 @@ for a QM/MM simulation.  You must also build Quantum ESPRESSO and
 create a new executable which links LAMMPS and Quanutm ESPRESSO
 together.  These are steps 3 and 4 described in the lib/qmmm/README
 file.
-  
+
 [Supporting info:]
 
 src/USER-QMMM: filenames -> commands
@@ -2311,13 +2344,13 @@ simulation.
 [Author:] Yuan Shen (Stanford U).
 
 [Install or un-install:]
-   
+
 make yes-user-qtb
 make machine :pre
-  
+
 make no-user-qtb
 make machine :pre
-  
+
 [Supporting info:]
 
 src/USER-QTB: filenames -> commands
@@ -2361,10 +2394,10 @@ usual manner:
 
 make yes-user-quip
 make machine :pre
-  
+
 make no-user-quip
 make machine :pre
-  
+
 [Supporting info:]
 
 src/USER-QUIP: filenames -> commands
@@ -2387,13 +2420,13 @@ for monitoring molecules as bonds are created and destroyed.
 [Author:] Hasan Metin Aktulga (MSU) while at Purdue University.
 
 [Install or un-install:]
-   
+
 make yes-user-reaxc
 make machine :pre
-  
+
 make no-user-reaxc
 make machine :pre
-  
+
 [Supporting info:]
 
 src/USER-REAXC: filenames -> commands
@@ -2450,10 +2483,10 @@ usual manner:
 
 make yes-user-smd
 make machine :pre
-  
+
 make no-user-smd
 make machine :pre
-  
+
 [Supporting info:]
 
 src/USER-SMD: filenames -> commands
@@ -2476,13 +2509,13 @@ ionocovalent bonds in oxides.
 Tetot (LAAS-CNRS, France).
 
 [Install or un-install:]
-   
+
 make yes-user-smtbq
 make machine :pre
-  
+
 make no-user-smtbq
 make machine :pre
-  
+
 [Supporting info:]
 
 src/USER-SMTBQ: filenames -> commands
@@ -2515,13 +2548,13 @@ property/atom"_compute_property_atom.html command.
 Dynamics, Ernst Mach Institute, Germany).
 
 [Install or un-install:]
-   
+
 make yes-user-sph
 make machine :pre
-  
+
 make no-user-sph
 make machine :pre
-  
+
 [Supporting info:]
 
 src/USER-SPH: filenames -> commands
@@ -2543,13 +2576,13 @@ stress, etc) about individual interactions.
 [Author:] Axel Kohlmeyer (Temple U).
 
 [Install or un-install:]
-   
+
 make yes-user-tally
 make machine :pre
-  
+
 make no-user-tally
 make machine :pre
-  
+
 [Supporting info:]
 
 src/USER-TALLY: filenames -> commands
@@ -2563,7 +2596,7 @@ USER-VTK package :link(USER-VTK),h4
 
 [Contents:]
 
-A "dump custom/vtk"_dump_custom_vtk.html command which outputs
+A "dump vtk"_dump_vtk.html command which outputs
 snapshot info in the "VTK format"_vtk, enabling visualization by
 "Paraview"_paraview or other visuzlization packages.
 
@@ -2576,7 +2609,7 @@ system.
 [Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing).
 
 [Install or un-install:]
-   
+
 The lib/vtk/Makefile.lammps file has settings for accessing VTK files
 and its library, which are required for LAMMPS to build and link with
 this package.  If the settings are not valid for your system, check if
@@ -2589,13 +2622,13 @@ usual manner:
 
 make yes-user-vtk
 make machine :pre
-  
+
 make no-user-vtk
 make machine :pre
-  
+
 [Supporting info:]
 
 src/USER-VTK: filenames -> commands
 src/USER-VTK/README
 lib/vtk/README
-"dump custom/vtk"_dump_custom_vtk.html :ul
+"dump vtk"_dump_vtk.html :ul

doc/src/Section_python.txt

@@ -118,18 +118,21 @@ check which version of Python you have installed, by simply typing
 
 11.2 Overview of using Python from a LAMMPS script :link(py_2),h4
 
-NOTE: It is not currently possible to use the "python"_python.html
-command described in this section with Python 3, only with Python 2.
-The C API changed from Python 2 to 3 and the LAMMPS code is not
-compatible with both.
+LAMMPS has several commands which can be used to invoke Python
+code directly from an input script:
 
-LAMMPS has a "python"_python.html command which can be used in an
-input script to define and execute a Python function that you write
-the code for.  The Python function can also be assigned to a LAMMPS
-python-style variable via the "variable"_variable.html command.  Each
-time the variable is evaluated, either in the LAMMPS input script
-itself, or by another LAMMPS command that uses the variable, this will
-trigger the Python function to be invoked.
+"python"_python.html
+"variable python"_variable.html
+"fix python"_fix_python.html
+"pair_style python"_pair_python.html :ul
+
+The "python"_python.html command which can be used to define and
+execute a Python function that you write the code for.  The Python
+function can also be assigned to a LAMMPS python-style variable via
+the "variable"_variable.html command.  Each time the variable is
+evaluated, either in the LAMMPS input script itself, or by another
+LAMMPS command that uses the variable, this will trigger the Python
+function to be invoked.
 
 The Python code for the function can be included directly in the input
 script or in an auxiliary file.  The function can have arguments which
@@ -162,8 +165,16 @@ doc page for its python-style variables for more info, including
 examples of Python code you can write for both pure Python operations
 and callbacks to LAMMPS.
 
-To run pure Python code from LAMMPS, you only need to build LAMMPS
-with the PYTHON package installed:
+The "fix python"_fix_python.html command can execute
+Python code at selected timesteps during a simulation run.
+
+The "pair_style python"_pair_python command allows you to define
+pairwise potentials as python code which encodes a single pairwise
+interaction.  This is useful for rapid-developement and debugging of a
+new potential.
+
+To use any of these commands, you only need to build LAMMPS with the
+PYTHON package installed:
 
 make yes-python
 make machine :pre
@@ -187,7 +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".
 
@@ -206,7 +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
 
@@ -428,7 +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.
 
@@ -703,7 +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
@@ -655,8 +684,7 @@ This section has the following sub-sections:
 
 2.3.1 "Package basics"_#start_3_1
 2.3.2 "Including/excluding packages"_#start_3_2
-2.3.3 "Packages that require extra libraries"_#start_3_3
-2.3.4 "Packages that require Makefile.machine settings"_#start_3_4 :all(b)
+2.3.3 "Packages that require extra libraries"_#start_3_3 :all(b)
 
 :line
 
@@ -686,7 +714,7 @@ 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
@@ -828,13 +856,13 @@ Packages in the tables "Section 4"_Section_packages.html with an "ext"
 in the last column link to exernal libraries whose source code is not
 included with LAMMPS.  You must first download and install the library
 before building LAMMPS with that package installed.  E.g. the voronoi
-package links to the freely available "Voro++ library"_voronoi.  You
+package links to the freely available "Voro++ library"_voro_home2.  You
 can often do the download/build in one step by typing "make lib-name
 args=..." from the src dir, with appropriate arguments.  You can leave
 off the args to see a help message.  See "Section
 4"_Section_packages.html for details for each package.
 
-:link(voronoi,http://math.lbl.gov/voro++)
+:link(voro_home2,http://math.lbl.gov/voro++)
 
 [Possible errors:]
 

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.
@@ -75,7 +75,7 @@ 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.
+described in "Section 4"_Section_packages.html 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:
@@ -151,9 +151,9 @@ 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 +188,7 @@ 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

@@ -30,8 +30,8 @@ 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
+charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long, sw, tersoff :l
+K-Space Styles: pppm, pppm/disp :l
 :ule
 
 [Speed-ups to expect:]
@@ -42,61 +42,90 @@ 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 3" and "kspace_modify diff ad" to the input script for better
-performance. :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):
@@ -168,6 +197,10 @@ 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
@@ -193,7 +226,7 @@ source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
 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
+script, described in "Section 4"_Section_packages.html 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
@@ -268,7 +301,7 @@ 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
@@ -281,7 +314,7 @@ 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
@@ -321,8 +354,8 @@ 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
@@ -341,6 +374,10 @@ 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,
@@ -350,13 +387,17 @@ 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
@@ -445,7 +486,7 @@ 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:]
@@ -466,7 +507,7 @@ 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

@@ -136,7 +136,7 @@ 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.
+described in "Section 4"_Section_packages.html of the manual.
 Type "Make.py -h" for help.  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
@@ -144,7 +144,7 @@ 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 +280,10 @@ 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 +304,12 @@ 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 +323,7 @@ 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 +332,7 @@ 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 +343,7 @@ 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 +389,7 @@ 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).
 
@@ -415,21 +415,21 @@ For binding threads with the KOKKOS OMP option, use thread affinity
 environment variables to force binding.  With OpenMP 3.1 (gcc 4.7 or
 later, intel 12 or later) setting the environment variable
 OMP_PROC_BIND=true should be sufficient.  For binding threads with the
-KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option, as
-discussed in "Section 2.3.4"_Sections_start.html#start_3_4 of the
-manual.
+KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option
+(see "this section"_Section_packages.html#KOKKOS of the manual for
+details).
 
 [Running on GPUs:]
 
 Insure the -arch setting in the machine makefile you are using,
-e.g. src/MAKE/Makefile.cuda, is correct for your GPU hardware/software
-(see "this section"_Section_start.html#start_3_4 of the manual for
+e.g. src/MAKE/Makefile.cuda, is correct for your GPU hardware/software.
+(see "this section"_Section_packages.html#KOKKOS of the manual for
 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

@@ -41,7 +41,7 @@ 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
+4"_Section_packages.html of the manual.  Type "Make.py -h" for
 help.
 
 Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must
@@ -62,14 +62,14 @@ 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

@@ -36,7 +36,7 @@ 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
+4"_Section_packages.html of the manual.  Type "Make.py -h" for
 help.
 
 Note that if you use an Intel compiler to build with the OPT package,
@@ -46,7 +46,7 @@ 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/balance.txt

@@ -394,7 +394,7 @@ weights.  It assigns the same weight to each particle owned by a
 processor based on the total computational time spent by that
 processor.  See details below on what time window is used.  It uses
 the same timing information as is used for the "MPI task timing
-breakdown"_Section_start.html#start_8, namely, for sections {Pair},
+breakdown"_Section_start.html#start_7, namely, for sections {Pair},
 {Bond}, {Kspace}, and {Neigh}.  The time spent in those portions of
 the timestep are measured for each MPI rank, summed, then divided by
 the number of particles owned by that processor.  I.e. the weight is

doc/src/bond_class2.txt

@@ -56,7 +56,7 @@ 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/bond_fene.txt

@@ -59,7 +59,7 @@ 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/bond_fene_expand.txt

@@ -62,7 +62,7 @@ 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/bond_harmonic.txt

@@ -54,7 +54,7 @@ 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/bond_harmonic_shift.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/bond_harmonic_shift_cut.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/bond_morse.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/bond_nonlinear.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/bond_oxdna.txt

@@ -30,7 +30,7 @@ The {oxdna/fene} and {oxdna2/fene} bond styles use the potential
 
 to define a modified finite extensible nonlinear elastic (FENE) potential
 "(Ouldridge)"_#oxdna_fene to model the connectivity of the phosphate backbone
-in the oxDNA force field for coarse-grained modelling of DNA. 
+in the oxDNA force field for coarse-grained modelling of DNA.
 
 The following coefficients must be defined for the bond type via the
 "bond_coeff"_bond_coeff.html command as given in the above example, or in
@@ -43,8 +43,8 @@ r0 (distance) :ul
 
 NOTE: The oxDNA bond style has to be used together with the corresponding oxDNA pair styles
 for excluded volume interaction {oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
-and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of 
-"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair 
+and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of
+"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair
 style {oxdna2/dh} have to be defined.
 The coefficients in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
 
@@ -66,7 +66,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]
 
-"pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html 
+"pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html
 
 [Default:] none
 

doc/src/bond_quartic.txt

@@ -88,7 +88,7 @@ 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/bond_table.txt

@@ -133,7 +133,7 @@ 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/commands.txt

@@ -32,12 +32,12 @@ Commands :h1
    dimension
    displace_atoms
    dump
-   dump_custom_vtk
    dump_h5md
    dump_image
    dump_modify
    dump_molfile
-   dump_nc
+   dump_netcdf
+   dump_vtk
    echo
    fix
    fix_modify

doc/src/compute_cna_atom.txt

@@ -26,7 +26,7 @@ Define a computation that calculates the CNA (Common Neighbor
 Analysis) pattern for each atom in the group.  In solid-state systems
 the CNA pattern is a useful measure of the local crystal structure
 around an atom.  The CNA methodology is described in "(Faken)"_#Faken
-and "(Tsuzuki)"_#Tsuzuki.
+and "(Tsuzuki)"_#Tsuzuki1.
 
 Currently, there are five kinds of CNA patterns LAMMPS recognizes:
 
@@ -93,5 +93,5 @@ above.
 :link(Faken)
 [(Faken)] Faken, Jonsson, Comput Mater Sci, 2, 279 (1994).
 
-:link(Tsuzuki)
+:link(Tsuzuki1)
 [(Tsuzuki)] Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007).

doc/src/compute_cnp_atom.txt

@@ -0,0 +1,111 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute cnp/atom command :h3
+
+[Syntax:]
+
+compute ID group-ID cnp/atom cutoff :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+cnp/atom = style name of this compute command
+cutoff = cutoff distance for nearest neighbors (distance units) :ul
+
+[Examples:]
+
+compute 1 all cnp/atom 3.08 :pre
+
+[Description:]
+
+Define a computation that calculates the Common Neighborhood
+Parameter (CNP) for each atom in the group.  In solid-state systems
+the CNP is a useful measure of the local crystal structure
+around an atom and can be used to characterize whether the
+atom is part of a perfect lattice, a local defect (e.g. a dislocation
+or stacking fault), or at a surface.
+
+The value of the CNP parameter will be 0.0 for atoms not in the
+specified compute group.  Note that normally a CNP calculation should
+only be performed on single component systems.
+
+This parameter is computed using the following formula from
+"(Tsuzuki)"_#Tsuzuki2
+
+:c,image(Eqs/cnp_eq.jpg)
+
+where the index {j} goes over the {n}i nearest neighbors of atom
+{i}, and the index {k} goes over the {n}ij common nearest neighbors
+between atom {i} and atom {j}. Rik and Rjk are the vectors connecting atom
+{k} to atoms {i} and {j}.  The quantity in the double sum is computed
+for each atom.
+
+The CNP calculation is sensitive to the specified cutoff value.
+You should ensure that the appropriate nearest neighbors of an atom are
+found within the cutoff distance for the presumed crystal structure.
+E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest
+neighbors for perfect BCC crystals.  These formulas can be used to
+obtain a good cutoff distance:
+
+:c,image(Eqs/cnp_cutoff.jpg)
+
+where a is the lattice constant for the crystal structure concerned
+and in the HCP case, x = (c/a) / 1.633, where 1.633 is the ideal c/a
+for HCP crystals.
+
+Also note that since the CNP calculation in LAMMPS uses the neighbors
+of an owned atom to find the nearest neighbors of a ghost atom, the
+following relation should also be satisfied:
+
+:c,image(Eqs/cnp_cutoff2.jpg)
+
+where Rc is the cutoff distance of the potential, Rs is the skin
+distance as specified by the "neighbor"_neighbor.html command, and
+cutoff is the argument used with the compute cnp/atom command.  LAMMPS
+will issue a warning if this is not the case.
+
+The neighbor list needed to compute this quantity is constructed each
+time the calculation is performed (e.g. each time a snapshot of atoms
+is dumped).  Thus it can be inefficient to compute/dump this quantity
+too frequently or to have multiple compute/dump commands, each with a
+{cnp/atom} style.
+
+[Output info:]
+
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input.  See
+"Section 6.15"_Section_howto.html#howto_15 for an overview of
+LAMMPS output options.
+
+The per-atom vector values will be real positive numbers. Some typical CNP
+values:
+
+FCC lattice = 0.0
+BCC lattice = 0.0
+HCP lattice = 4.4 :pre
+
+FCC (111) surface ~ 13.0
+FCC (100) surface ~ 26.5
+FCC dislocation core ~ 11 :pre
+
+[Restrictions:]
+
+This compute is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"compute cna/atom"_compute_cna_atom.html
+"compute centro/atom"_compute_centro_atom.html
+
+[Default:] none
+
+:line
+
+:link(Tsuzuki2)
+[(Tsuzuki)] Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007).

doc/src/compute_pair_local.txt

@@ -76,7 +76,9 @@ command for the types of the two atoms is used.  For the {radius}
 setting, the sum of the radii of the two particles is used as a
 cutoff.  For example, this is appropriate for granular particles which
 only interact when they are overlapping, as computed by "granular pair
-styles"_pair_gran.txt.
+styles"_pair_gran.txt.  Note that if a granular model defines atom
+types such that all particles of a specific type are monodisperse
+(same diameter), then the two settings are effectively identical.
 
 Note that as atoms migrate from processor to processor, there will be
 no consistent ordering of the entries within the local vector or array

doc/src/compute_pressure.txt

@@ -117,7 +117,7 @@ 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/compute_property_local.txt

@@ -79,6 +79,9 @@ the two atoms is used.  For the {radius} setting, the sum of the radii
 of the two particles is used as a cutoff.  For example, this is
 appropriate for granular particles which only interact when they are
 overlapping, as computed by "granular pair styles"_pair_gran.html.
+Note that if a granular model defines atom types such that all
+particles of a specific type are monodisperse (same diameter), then
+the two settings are effectively identical.
 
 If the inputs are bond, angle, etc attributes, the local data is
 generated by looping over all the atoms owned on a processor and

doc/src/compute_rdf.txt

@@ -180,9 +180,18 @@ will register an arbitrarily large spike at whatever distance they
 happen to be at, and zero everywhere else.  Coord(r) will show a step
 change from zero to one at the location of the spike in g(r).
 
+NOTE: compute rdf can handle dynamic groups and systems where atoms
+are added or removed, but this causes that certain normalization
+parameters need to be recomputed in every step and include collective
+communication operations. This will reduce performance and limit
+parallel efficiency and scaling. For systems, where only the type
+of atoms changes (e.g. when using "fix atom/swap"_fix_atom_swap.html),
+you need to explicitly request the dynamic normalization updates
+via "compute_modify dynamic yes"_compute_modify.html
+
 [Related commands:]
 
-"fix ave/time"_fix_ave_time.html
+"fix ave/time"_fix_ave_time.html, "compute_modify"_compute_modify.html
 
 [Default:]
 

doc/src/compute_saed.txt

@@ -111,26 +111,26 @@ Coefficients parameterized by "(Fox)"_#Fox are assigned for each
 atom type designating the chemical symbol and charge of each atom
 type. Valid chemical symbols for compute saed are:
 
-         H:      He:      Li:      Be:       B:
-         C:       N:       O:       F:      Ne:
-        Na:      Mg:      Al:      Si:       P:
-         S:      Cl:      Ar:       K:      Ca:
-        Sc:      Ti:       V:      Cr:      Mn:
-        Fe:      Co:      Ni:      Cu:      Zn:
-        Ga:      Ge:      As:      Se:      Br:
-        Kr:      Rb:      Sr:       Y:      Zr:
-        Nb:      Mo:      Tc:      Ru:      Rh:
-        Pd:      Ag:      Cd:      In:      Sn:
-        Sb:      Te:       I:      Xe:      Cs:
-        Ba:      La:      Ce:      Pr:      Nd:
-        Pm:      Sm:      Eu:      Gd:      Tb:
-        Dy:      Ho:      Er:      Tm:      Yb:
-        Lu:      Hf:      Ta:       W:      Re:
-        Os:      Ir:      Pt:      Au:      Hg:
-        Tl:      Pb:      Bi:      Po:      At:
-        Rn:      Fr:      Ra:      Ac:      Th:
-        Pa:       U:      Np:      Pu:      Am:
-        Cm:      Bk:      Cf:tb(c=5,s=:)
+H:       He:      Li:      Be:       B:
+C:        N:       O:       F:      Ne:
+Na:      Mg:      Al:      Si:       P:
+S:       Cl:      Ar:       K:      Ca:
+Sc:      Ti:       V:      Cr:      Mn:
+Fe:      Co:      Ni:      Cu:      Zn:
+Ga:      Ge:      As:      Se:      Br:
+Kr:      Rb:      Sr:       Y:      Zr:
+Nb:      Mo:      Tc:      Ru:      Rh:
+Pd:      Ag:      Cd:      In:      Sn:
+Sb:      Te:       I:      Xe:      Cs:
+Ba:      La:      Ce:      Pr:      Nd:
+Pm:      Sm:      Eu:      Gd:      Tb:
+Dy:      Ho:      Er:      Tm:      Yb:
+Lu:      Hf:      Ta:       W:      Re:
+Os:      Ir:      Pt:      Au:      Hg:
+Tl:      Pb:      Bi:      Po:      At:
+Rn:      Fr:      Ra:      Ac:      Th:
+Pa:       U:      Np:      Pu:      Am:
+Cm:      Bk:      Cf:tb(c=5,s=:)
 
 
 If the {echo} keyword is specified, compute saed will provide extra

doc/src/compute_sna_atom.txt

@@ -231,11 +231,12 @@ the numbers of columns are 930, 2790, and 5580, respectively.
 
 If the {quadratic} keyword value is set to 1, then additional
 columns are appended to each per-atom array, corresponding to
-a matrix of quantities that are products of two bispectrum components. If the
-number of bispectrum components is {K}, then the number of matrix elements
-is {K}^2. These are output in subblocks of {K}^2 columns, using the same
-ordering of columns and sub-blocks as was used for the bispectrum
-components.
+the products of all distinct pairs of  bispectrum components. If the
+number of bispectrum components is {K}, then the number of distinct pairs
+is  {K}({K}+1)/2. These are output in subblocks of  {K}({K}+1)/2 columns, using the same
+ordering of sub-blocks as was used for the bispectrum
+components. Within each sub-block, the ordering is upper-triangular,
+(1,1),(1,2)...(1,{K}),(2,1)...({K}-1,{K}-1),({K}-1,{K}),({K},{K})
 
 These values can be accessed by any command that uses per-atom values
 from a compute as input.  See "Section

doc/src/compute_temp.txt

@@ -79,7 +79,7 @@ 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/compute_temp_partial.txt

@@ -86,7 +86,7 @@ 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/computes.txt

@@ -17,6 +17,7 @@ Computes :h1
    compute_chunk_atom
    compute_cluster_atom
    compute_cna_atom
+   compute_cnp_atom
    compute_com
    compute_com_chunk
    compute_contact_atom

doc/src/create_bonds.txt

@@ -10,53 +10,93 @@ create_bonds command :h3
 
 [Syntax:]
 
-create_bonds group-ID group2-ID btype rmin rmax :pre
+create_bonds style args ... keyword value ... :pre
 
-group-ID = ID of first group
-group2-ID = ID of second group, bonds will be between atoms in the 2 groups
-btype = bond type of created bonds
-rmin = minimum distance between pair of atoms to bond together
-rmax = minimum distance between pair of atoms to bond together :ul
+style = {many} or {single/bond} or {single/angle} or {single/dihedral} :ule,l
+  {many} args = group-ID group2-ID btype rmin rmax
+    group-ID = ID of first group
+    group2-ID = ID of second group, bonds will be between atoms in the 2 groups
+    btype = bond type of created bonds
+    rmin = minimum distance between pair of atoms to bond together
+    rmax = minimum distance between pair of atoms to bond together
+  {single/bond} args = btype batom1 batom2
+    btype = bond type of new bond
+    batom1,batom2 = atom IDs for two atoms in bond
+  {single/angle} args = atype aatom1 aatom2 aatom3
+    atype = bond type of new angle
+    aatom1,aatom2,aatom3 = atom IDs for three atoms in angle
+  {single/dihedral} args = dtype datom1 datom2 datom3 datom4
+    dtype = bond type of new dihedral
+    datom1,datom2,datom3,datom4 = atom IDs for four atoms in dihedral :pre
+zero or more keyword/value pairs may be appended :l
+keyword = {special} :l
+  {special} value = {yes} or {no} :pre
+:ule
 
 [Examples:]
 
-create_bonds all all 1 1.0 1.2
-create_bonds surf solvent 3 2.0 2.4 :pre
+create_bonds many all all 1 1.0 1.2
+create_bonds many surf solvent 3 2.0 2.4
+create_bond single/bond 1 1 2
+create_bond single/angle 5 52 98 107 special no :pre
 
 [Description:]
 
-Create bonds between pairs of atoms that meet specified distance
-criteria.  The bond interactions can then be computed during a
-simulation by the bond potential defined by the
-"bond_style"_bond_style.html and "bond_coeff"_bond_coeff.html
-commands.  This command is useful for adding bonds to a system,
-e.g. between nearest neighbors in a lattice of atoms, without having
-to enumerate all the bonds in the data file read by the
-"read_data"_read_data.html command.
+Create bonds between pairs of atoms that meet a specified distance
+criteria.  Or create a single bond, angle, or dihedral between 2, 3,
+or 4 specified atoms.
 
-Note that the flexibility of this command is limited.  It can be used
-several times to create different types of bond at different
-distances.  But it cannot typically create all the bonds that would
-normally be defined in a complex system of molecules.  Also note that
-this command does not add any 3-body or 4-body interactions which,
-depending on your model, may be induced by added bonds,
-e.g. "angle"_angle_style.html, "dihedral"_dihedral_style.html, or
-"improper"_improper_style.html interactions.
+The new bond (angle, dihedral) interactions will then be computed
+during a simulation by the bond (angle, dihedral) potential defined by
+the "bond_style"_bond_style.html, "bond_coeff"_bond_coeff.html,
+"angle_style"_angle_style.html, "angle_coeff"_angle_coeff.html,
+"dihedral_style"_dihedral_style.html,
+"dihedral_coeff"_dihedral_coeff.html commands.
 
-All created bonds will be between pairs of atoms I,J where I is in one
-of the two specified groups, and J is in the other.  The two groups
-can be the same, e.g. group "all".  The created bonds will be of bond
-type {btype}, where {btype} must be a value between 1 and the number
-of bond types defined.  This maximum value is set by the "bond types"
-field in the header of the data file read by the
-"read_data"_read_data.html command, or via the optional "bond/types"
-argument of the "create_box"_create_box.html command.
+The {many} style is useful for adding bonds to a system, e.g. between
+nearest neighbors in a lattice of atoms, without having to enumerate
+all the bonds in the data file read by the "read_data"_read_data.html
+command.
+
+The {single} styles are useful for adding bonds, angles, dihedrals
+to a system incrementally, then continuing a simulation.
+
+Note that this command does not auto-create any angle or dihedral
+interactions when a bond is added.  Nor does it auto-create any bonds
+when an angle or dihedral is added.  Or auto-create any angles when a
+dihedral is added.  Thus the flexibility of this command is limited.
+It can be used several times to create different types of bond at
+different distances.  But it cannot typically auto-create all the
+bonds or angles or dihedral that would normally be defined in a data
+file for a complex system of molecules.
+
+NOTE: If the system has no bonds (angles, dihedrals) to begin with, or
+if more bonds per atom are being added than currently exist, then you
+must insure that the number of bond types and the maximum number of
+bonds per atom are set to large enough values.  And similarly for
+angles and dihedrals.  Otherwise an error may occur when too many
+bonds (angles, dihedrals) are added to an atom.  If the
+"read_data"_read_data.html command is used to define the system, these
+parameters can be set via the "bond types" and "extra bond per atom"
+fields in the header section of the data file.  If the
+"create_box"_create_box.html command is used to define the system,
+these 2 parameters can be set via its optional "bond/types" and
+"extra/bond/per/atom" arguments.  And similarly for angles and
+dihedrals.  See the doc pages for these 2 commands for details.
+
+:line
+
+The {many} style will create bonds between pairs of atoms I,J where I
+is in one of the two specified groups, and J is in the other.  The two
+groups can be the same, e.g. group "all".  The created bonds will be
+of bond type {btype}, where {btype} must be a value between 1 and the
+number of bond types defined. 
 
 For a bond to be created, an I,J pair of atoms must be a distance D
 apart such that {rmin} <= D <= {rmax}.
 
-The following settings must have been made in an input
-script before this command is used:
+The following settings must have been made in an input script before
+this style is used:
 
 special_bonds weight for 1-2 interactions must be 0.0
 a "pair_style"_pair_style.html must be defined
@@ -69,8 +109,8 @@ cannot appear in the neighbor list, to avoid creation of duplicate
 bonds.  The neighbor list for all atom type pairs must also extend to
 a distance that encompasses the {rmax} for new bonds to create.
 
-An additional requirement is that your system must be ready to perform
-a simulation.  This means, for example, that all
+An additional requirement for this style is that your system must be
+ready to perform a simulation.  This means, for example, that all
 "pair_style"_pair_style.html coefficients be set via the
 "pair_coeff"_pair_coeff.html command.  A "bond_style"_bond_style.html
 command and all bond coefficients must also be set, even if no bonds
@@ -83,17 +123,58 @@ executes, e.g. if you wish to use long-range Coulombic interactions
 via the "kspace_style"_kspace_style.html command for your subsequent
 simulation.
 
-NOTE: If the system has no bonds to begin with, or if more bonds per
-atom are being added than currently exist, then you must insure that
-the number of bond types and the maximum number of bonds per atom are
-set to large enough values.  Otherwise an error may occur when too
-many bonds are added to an atom.  If the "read_data"_read_data.html
-command is used to define the system, these 2 parameters can be set
-via the "bond types" and "extra bond per atom" fields in the header
-section of the data file.  If the "create_box"_create_box.html command
-is used to define the system, these 2 parameters can be set via its
-optional "bond/types" and "extra/bond/per/atom" arguments.  See the
-doc pages for the 2 commands for details.
+:line
+
+The {single/bond} style creates a single bond of type {btype} between
+two atoms with IDs {batom1} and {batom2}.  {Btype} must be a value
+between 1 and the number of bond types defined.
+
+The {single/angle} style creates a single angle of type {atype}
+between three atoms with IDs {aatom1}, {aatom2}, and {aatom3}.  The
+ordering of the atoms is the same as in the {Angles} section of a data
+file read by the "read_data"_read_data command.  I.e. the 3 atoms are
+ordered linearly within the angle; the central atom is {aatom2}.
+{Atype} must be a value between 1 and the number of angle types
+defined.
+
+The {single/dihedral} style creates a single dihedral of type {btype}
+between two atoms with IDs {batom1} and {batom2}.  The ordering of the
+atoms is the same as in the {Dihedrals} section of a data file read by
+the "read_data"_read_data command.  I.e. the 4 atoms are ordered
+linearly within the dihedral.  {Dtype} must be a value between 1 and
+the number of dihedral types defined.
+
+:line
+
+The keyword {special} controls whether an internal list of special
+bonds is created after one or more bonds, or a single angle or
+dihedral is added to the system.
+
+The default value is {yes}.  A value of {no} cannot be used
+with the {many} style.
+
+This is an expensive operation since the bond topology for the system
+must be walked to find all 1-2, 1-3, 1-4 interactions to store in an
+internal list, which is used when pairwise interactions are weighted;
+see the "special_bonds"_special_bonds.html command for details.
+
+Thus if you are adding a few bonds or a large list of angles all at
+the same time, by using this command repeatedly, it is more efficient
+to only trigger the internal list to be created once, after the last
+bond (or angle, or dihedral) is added:
+
+create_bonds single/bond 5 52 98 special no
+create_bonds single/bond  5 73 74 special no
+...
+create_bonds single/bond 5 17 386 special no
+create_bonds single/bond 4 112 183 special yes :pre
+
+Note that you MUST insure the internal list is re-built after the last
+bond (angle, dihedral) is added, before performing a simulation.
+Otherwise pairwise interactions will not be properly excluded or
+weighted.  LAMMPS does NOT check that you have done this correctly.
+
+:line
 
 [Restrictions:]
 
@@ -105,4 +186,6 @@ molecule template files via the "molecule"_molecule.html and
 
 "create_atoms"_create_atoms.html, "delete_bonds"_delete_bonds.html
 
-[Default:] none
+[Default:]
+
+The keyword default is special = yes.

doc/src/dihedral_charmm.txt

@@ -128,7 +128,7 @@ 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
@@ -138,7 +138,15 @@ more instructions on how to use the accelerated styles effectively.
 
 [Restrictions:]
 
-This dihedral style can only be used if LAMMPS was built with the
+When using run_style "respa"_run_style.html, these dihedral styles
+must be assigned to the same r-RESPA level as {pair} or {outer}.
+
+When used in combination with CHARMM pair styles, the 1-4
+"special_bonds"_special_bonds.html scaling factors must be set to 0.0.
+Otherwise non-bonded contributions for these 1-4 pairs will be
+computed multiple times.
+
+These dihedral styles can only be used if LAMMPS was built with the
 MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 

doc/src/dihedral_class2.txt

@@ -153,7 +153,7 @@ 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/dihedral_cosine_shift_exp.txt

@@ -64,7 +64,7 @@ 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/dihedral_fourier.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/dihedral_harmonic.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/dihedral_helix.txt

@@ -58,7 +58,7 @@ 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/dihedral_multi_harmonic.txt

@@ -52,7 +52,7 @@ 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/dihedral_nharmonic.txt

@@ -52,7 +52,7 @@ 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/dihedral_opls.txt

@@ -60,7 +60,7 @@ 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/dihedral_quadratic.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/dihedral_spherical.txt

@@ -14,10 +14,11 @@ dihedral_style spherical :pre
 
 [Examples:]
 
-dihedral_coeff 1 1  286.1  1 124 1   1 90.0 0   1 90.0 0
-dihedral_coeff 1 3  286.1  1 114 1   1 90  0    1 90.0  0  &
-                    17.3   0 0.0 0   1 158 1    0 0.0   0  &
-                    15.1   0 0.0 0   0 0.0 0    1 167.3 1   :pre
+dihedral_coeff 1 1  286.1  1 124  1    1 90.0 0    1 90.0 0
+dihedral_coeff 1 3  69.3   1 93.9 1    1 90   0    1 90   0  &
+                    49.1   0 0.00 0    1 74.4 1    0 0.00 0  &
+                    25.2   0 0.00 0    0 0.00 0    1 48.1 1
+:pre
 
 [Description:]
 
@@ -35,13 +36,14 @@ the dihedral interaction even if it requires adding additional terms to
 the expansion (as was done in the second example).  A careful choice of
 parameters can prevent singularities that occur with traditional
 force-fields whenever theta1 or theta2 approach 0 or 180 degrees.
+
 The last example above corresponds to an interaction with a single energy
-minima located at phi=114, theta1=158, theta2=167.3 degrees, and it remains
+minima located near phi=93.9, theta1=74.4, theta2=48.1 degrees, and it remains
 numerically stable at all angles (phi, theta1, theta2). In this example,
-the coefficients 17.3, and 15.1 can be physically interpreted as the
+the coefficients 49.1, and 25.2 can be physically interpreted as the
 harmonic spring constants for theta1 and theta2 around their minima.
-The coefficient 286.1 is the harmonic spring constant for phi after
-division by sin(158)*sin(167.3) (the minima positions for theta1 and theta2).
+The coefficient 69.3 is the harmonic spring constant for phi after
+division by sin(74.4)*sin(48.1) (the minima positions for theta1 and theta2).
 
 The following coefficients must be defined for each dihedral type via the
 "dihedral_coeff"_dihedral_coeff.html command as in the example above, or in

doc/src/dump_modify.txt

@@ -16,7 +16,8 @@ dump-ID = ID of dump to modify :ulb,l
 one or more keyword/value pairs may be appended :l
 these keywords apply to various dump styles :l
 keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
-  {append} arg = {yes} or {no}
+  {append} arg = {yes} or {no} or {at} N
+    N = index of frame written upon first dump
   {buffer} arg = {yes} or {no}
   {element} args = E1 E2 ... EN, where N = # of atom types
     E1,...,EN = element name, e.g. C or Fe or Ga
@@ -41,6 +42,7 @@ keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} o
   {region} arg = region-ID or "none"
   {scale} arg = {yes} or {no}
   {sfactor} arg = coordinate scaling factor (> 0.0)
+  {thermo} arg = {yes} or {no}
   {tfactor} arg = time scaling factor (> 0.0)
   {sort} arg = {off} or {id} or N or -N
      off = no sorting of per-atom lines within a snapshot
@@ -139,12 +141,13 @@ and {dcd}.  It also applies only to text output files, not to binary
 or gzipped or image/movie files.  If specified as {yes}, then dump
 snapshots are appended to the end of an existing dump file.  If
 specified as {no}, then a new dump file will be created which will
-overwrite an existing file with the same name.  This keyword can only
-take effect if the dump_modify command is used after the
-"dump"_dump.html command, but before the first command that causes
-dump snapshots to be output, e.g. a "run"_run.html or
-"minimize"_minimize.html command.  Once the dump file has been opened,
-this keyword has no further effect.
+overwrite an existing file with the same name.  If the {at} option is present
+({netcdf} only), then the frame to append to can be specified.  Negative values
+are counted from the end of the file.  This keyword can only take effect if the
+dump_modify command is used after the "dump"_dump.html command, but before the
+first command that causes dump snapshots to be output, e.g. a "run"_run.html or
+"minimize"_minimize.html command.  Once the dump file has been opened, this
+keyword has no further effect.
 
 :line
 
@@ -413,6 +416,13 @@ most effective when the typical magnitude of position data is between
 
 :line
 
+The {thermo} keyword ({netcdf} only) triggers writing of "thermo"_thermo.html
+information to the dump file alongside per-atom data. The data included in the
+dump file is identical to the data specified by
+"thermo_style"_thermo_style.html.
+
+:line
+
 The {region} keyword only applies to the dump {custom}, {cfg},
 {image}, and {movie} styles.  If specified, only atoms in the region
 will be written to the dump file or included in the image/movie.  Only

doc/src/dump_netcdf.txt

@@ -24,7 +24,7 @@ args = list of atom attributes, same as for "dump_style custom"_dump.html :l,ule
 [Examples:]
 
 dump 1 all netcdf 100 traj.nc type x y z vx vy vz
-dump_modify 1 append yes at -1 global c_thermo_pe c_thermo_temp c_thermo_press
+dump_modify 1 append yes at -1 thermo yes
 dump 1 all netcdf/mpiio 1000 traj.nc id type x y z :pre
 
 [Description:]
@@ -44,7 +44,7 @@ rank.
 NetCDF files can be directly visualized via the following tools:
 
 Ovito (http://www.ovito.org/). Ovito supports the AMBER convention and
-all of the above extensions. :ule,b
+all extensions of this dump style. :ule,b
 
 VMD (http://www.ks.uiuc.edu/Research/vmd/). :l
 
@@ -52,15 +52,9 @@ AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye
 contains a NetCDF reader that is not present in the standard
 distribution of AtomEye. :l,ule
 
-In addition to per-atom data, global data can be included in the dump
-file, which are the kinds of values output by the
-"thermo_style"_thermo_style.html command .  See "Section howto
-6.15"_Section_howto.html#howto_15 for an explanation of per-atom
-versus global data.  The global output written into the dump file can
-be from computes, fixes, or variables, by prefixing the compute/fix ID
-or variable name with "c_" or "f_" or "v_" respectively, as in the
-example above.  These global values are specified via the "dump_modify
-global"_dump_modify.html command.
+In addition to per-atom data, "thermo"_thermo.html data can be included in the
+dump file. The data included in the dump file is identical to the data specified
+by "thermo_style"_thermo_style.html.
 
 :link(netcdf-home,http://www.unidata.ucar.edu/software/netcdf/)
 :link(pnetcdf-home,http://trac.mcs.anl.gov/projects/parallel-netcdf/)

doc/src/dump_vtk.txt

@@ -16,7 +16,7 @@ ID = user-assigned name for the dump
 group-ID = ID of the group of atoms to be dumped
 vtk = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page)
 N = dump every this many timesteps
-file = name of file to write dump info to 
+file = name of file to write dump info to
 args = same as arguments for "dump_style custom"_dump.html :ul
 
 [Examples:]
@@ -83,7 +83,7 @@ Triclinic simulation boxes (non-orthogonal) are saved as
 hexahedrons in either legacy .vtk or .vtu XML format.
 
 Style {vtk} allows you to specify a list of atom attributes to be
-written to the dump file for each atom.  The list of possible attributes 
+written to the dump file for each atom.  The list of possible attributes
 is the same as for the "dump_style custom"_dump.html command; see
 its doc page for a listing and an explanation of each attribute.
 

doc/src/echo.txt

@@ -26,7 +26,7 @@ command to the screen and/or log file as it is read and processed.  If
 an input script has errors, it can be useful to look at echoed output
 to see the last command processed.
 
-The "command-line switch"_Section_start.html#start_5 -echo can be used
+The "command-line switch"_Section_start.html#start_6 -echo can be used
 in place of this command.
 
 [Restrictions:] none

doc/src/fix_adapt.txt

@@ -47,7 +47,7 @@ keyword = {scale} or {reset} :l
 fix 1 all adapt 1 pair soft a 1 1 v_prefactor
 fix 1 all adapt 1 pair soft a 2* 3 v_prefactor
 fix 1 all adapt 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
-fix 1 all adapt 10 atom diameter v_size
+fix 1 all adapt 10 atom diameter v_size :pre
 
 variable ramp_up equal "ramp(0.01,0.5)"
 fix stretch all adapt 1 bond harmonic r0 1 v_ramp_up :pre

doc/src/fix_addforce.txt

@@ -117,7 +117,7 @@ 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/fix_aveforce.txt

@@ -77,7 +77,7 @@ 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/fix_box_relax.txt

@@ -245,8 +245,8 @@ appear the system is converging to your specified pressure.  The
 solution for this is to either (a) zero the velocities of all atoms
 before performing the minimization, or (b) make sure you are
 monitoring the pressure without its kinetic component.  The latter can
-be done by outputting the pressure from the fix this command creates
-(see below) or a pressure fix you define yourself.
+be done by outputting the pressure from the pressure compute this
+command creates (see below) or a pressure compute you define yourself.
 
 NOTE: Because pressure is often a very sensitive function of volume,
 it can be difficult for the minimizer to equilibrate the system the
@@ -308,7 +308,7 @@ thermo_modify command (or in two separate commands), then the order in
 which the keywords are specified is important.  Note that a "pressure
 compute"_compute_pressure.html defines its own temperature compute as
 an argument when it is specified.  The {temp} keyword will override
-this (for the pressure compute being used by fix npt), but only if the
+this (for the pressure compute being used by fix box/relax), but only if the
 {temp} keyword comes after the {press} keyword.  If the {temp} keyword
 comes before the {press} keyword, then the new pressure compute
 specified by the {press} keyword will be unaffected by the {temp}
@@ -316,18 +316,16 @@ setting.
 
 This fix computes a global scalar which can be accessed by various
 "output commands"_Section_howto.html#howto_15. The scalar is the
-pressure-volume energy, plus the strain energy, if it exists.
-
-This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is given
-by the energy expression shown above. The energy values reported
-at the end of a minimization run under "Minimization stats" include
-this energy, and so differ from what LAMMPS normally reports as
-potential energy. This fix does not support the
-"fix_modify"_fix_modify.html {energy} option,
-because that would result in double-counting of the fix energy in the
-minimization energy. Instead, the fix energy can be explicitly
-added to the potential energy using one of these two variants:
+pressure-volume energy, plus the strain energy, if it exists,
+as described above.
+The energy values reported at the
+end of a minimization run under "Minimization stats" include this
+energy, and so differ from what LAMMPS normally reports as potential
+energy. This fix does not support the "fix_modify"_fix_modify.html
+{energy} option, because that would result in double-counting of the
+fix energy in the minimization energy. Instead, the fix energy can be
+explicitly added to the potential energy using one of these two
+variants:
 
 variable emin equal pe+f_1  :pre
 

doc/src/fix_deform.txt

@@ -557,7 +557,7 @@ 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
@@ -565,8 +565,10 @@ more instructions on how to use the accelerated styles effectively.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
-No information about this fix is written to "binary restart
-files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+This fix will restore the initial box settings from "binary restart
+files"_restart.html, which allows the fix to be properly continue
+deformation, when using the start/stop options of the "run"_run.html
+command.  None of the "fix_modify"_fix_modify.html options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various "output
 commands"_Section_howto.html#howto_15.

doc/src/fix_enforce2d.txt

@@ -41,7 +41,7 @@ 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/fix_eos_table_rx.txt

@@ -45,14 +45,14 @@ species {j} in particle {i}, {u_j} is the internal energy of species j,
 {DeltaH_f,j} is the heat of formation of species {j}, N is the number of
 molecules represented by the coarse-grained particle, kb is the
 Boltzmann constant, and T is the temperature of the system.  Additionally,
-it is possible to modify the concentration-dependent particle internal 
-energy relation by adding an energy correction, temperature-dependent 
+it is possible to modify the concentration-dependent particle internal
+energy relation by adding an energy correction, temperature-dependent
 correction, and/or a molecule-dependent correction.  An energy correction can
-be specified as a constant (in energy units).  A temperature correction can be 
-specified by multiplying a temperature correction coefficient by the 
-internal temperature.  A molecular correction can be specified by 
-by multiplying a molecule correction coefficient by the average number of 
-product gas particles in the coarse-grain particle. 
+be specified as a constant (in energy units).  A temperature correction can be
+specified by multiplying a temperature correction coefficient by the
+internal temperature.  A molecular correction can be specified by
+by multiplying a molecule correction coefficient by the average number of
+product gas particles in the coarse-grain particle.
 
 Fix {eos/table/rx} creates interpolation tables of length {N} from {m}
 internal energy values of each species {u_j} listed in a file as a
@@ -72,12 +72,12 @@ The second filename specifies a file containing heat of formation
 {DeltaH_f,j} for each species.
 
 In cases where the coarse-grain particle represents a single molecular
-species (i.e., no reactions occur and fix {rx} is not present in the input file), 
-fix {eos/table/rx} can be applied in a similar manner to fix {eos/table} 
-within a non-reactive DPD simulation.  In this case, the heat of formation 
+species (i.e., no reactions occur and fix {rx} is not present in the input file),
+fix {eos/table/rx} can be applied in a similar manner to fix {eos/table}
+within a non-reactive DPD simulation.  In this case, the heat of formation
 filename is replaced with the heat of formation value for the single species.
-Additionally, the energy correction and temperature correction coefficients may 
-also be specified as fix arguments.  
+Additionally, the energy correction and temperature correction coefficients may
+also be specified as fix arguments.
 
 :line
 
@@ -138,8 +138,8 @@ used as the species name must correspond with the tags used to define
 the reactions with the "fix rx"_fix_rx.html command.
 
 Alternatively, corrections to the EOS can be included by specifying
-three additional columns that correspond to the energy correction, 
-the temperature correction coefficient and molecule correction 
+three additional columns that correspond to the energy correction,
+the temperature correction coefficient and molecule correction
 coefficient.  In this case, the format of the file is as follows:
 
 # HEAT OF FORMATION TABLE     (one or more comment or blank lines) :pre

doc/src/fix_filter_corotate.txt

@@ -70,8 +70,8 @@ minimization"_minimize.html.
 
 [Restrictions:]
 
-This fix is part of the USER-MISC package. It is only enabled if 
-LAMMPS was built with that package. See the "Making 
+This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 
 Currently, it does not support "molecule templates"_molecule.html.

doc/src/fix_freeze.txt

@@ -45,7 +45,7 @@ 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/fix_gcmc.txt

@@ -383,6 +383,9 @@ called.  Reneighboring is required.
 Can be run in parallel, but aspects of the GCMC part will not scale
 well in parallel. Only usable for 3D simulations.
 
+When using fix gcmc in combination with fix shake or fix rigid,
+only gcmc exchange moves are supported.
+
 Note that very lengthy simulations involving insertions/deletions of
 billions of gas molecules may run out of atom or molecule IDs and
 trigger an error, so it is better to run multiple shorter-duration
@@ -406,7 +409,7 @@ the user for each subsequent fix gcmc command.
 [Default:]
 
 The option defaults are mol = no, maxangle = 10, overlap_cutoff = 0.0,
-fugacity_coeff = 1, and full_energy = no, 
+fugacity_coeff = 1, and full_energy = no,
 except for the situations where full_energy is required, as
 listed above.