patch 6Jul17

bugfix for fix msst

.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)_
+
+

doc/Makefile

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

doc/src/Eqs/cnp_cutoff.tex

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

doc/src/Eqs/cnp_cutoff2.tex

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

doc/src/Eqs/cnp_eq.tex

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

doc/src/Eqs/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/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="19 May 2017 version">
+<META NAME="docnumber" CONTENT="6 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
-19 May 2017 version :c,h4
+6 Jul 2017 version :c,h4
 
 Version info: :h4
 

doc/src/Section_commands.txt

@@ -717,7 +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,
@@ -831,6 +831,7 @@ 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,
@@ -963,7 +964,7 @@ 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,
@@ -1038,7 +1039,7 @@ 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,
@@ -1057,7 +1058,7 @@ 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,
@@ -1073,7 +1074,7 @@ 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
 
@@ -1225,7 +1226,7 @@ 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

@@ -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

@@ -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

@@ -121,6 +121,7 @@ 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_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
@@ -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
 
@@ -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
@@ -855,7 +856,7 @@ src/MPIIO: filenames -> commands
 "read_restart"_read_restart.html :ul
 
 :line
- 
+
 MSCG package :link(mscg),h4
 
 [Contents:]
@@ -914,7 +915,7 @@ lib/mscg/README
 examples/mscg :ul
 
 :line
- 
+
 OPT package :link(OPT),h4
 
 [Contents:]
@@ -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
@@ -1479,10 +1480,10 @@ usual manner:
 
 make yes-user-awpmd
 make machine :pre
- 
+
 make no-user-awpmd
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-AWPMD: filenames -> commands
@@ -1502,16 +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
@@ -1536,13 +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
@@ -1570,7 +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
@@ -1594,10 +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
@@ -1619,13 +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
@@ -1654,13 +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
@@ -1696,13 +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
@@ -1734,13 +1735,13 @@ 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
@@ -1773,13 +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
@@ -1836,13 +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
@@ -1908,7 +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
 
@@ -1938,13 +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
@@ -1972,13 +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
@@ -2000,13 +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
@@ -2027,17 +2028,17 @@ 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
@@ -2051,6 +2052,37 @@ 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:]
@@ -2080,7 +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.
@@ -2090,10 +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
@@ -2128,7 +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
@@ -2138,7 +2170,7 @@ lib/netcdf/README for details.
 
 make yes-user-netcdf
 make machine :pre
-  
+
 make no-user-netcdf
 make machine :pre
 
@@ -2178,10 +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
 
@@ -2213,13 +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
@@ -2235,7 +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)
 
@@ -2275,7 +2307,7 @@ usual manner:
 
 make yes-user-qmmm
 make machine :pre
-  
+
 make no-user-qmmm
 make machine :pre
 
@@ -2284,7 +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
@@ -2312,13 +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
@@ -2362,10 +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
@@ -2388,13 +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
@@ -2451,10 +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
@@ -2477,13 +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
@@ -2516,13 +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
@@ -2544,13 +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
@@ -2577,7 +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
@@ -2590,10 +2622,10 @@ usual manner:
 
 make yes-user-vtk
 make machine :pre
-  
+
 make no-user-vtk
 make machine :pre
-  
+
 [Supporting info:]
 
 src/USER-VTK: filenames -> commands

doc/src/Section_python.txt

@@ -714,7 +714,7 @@ stored in the "image" property. All three image flags are stored in
 a packed format in a single integer, so count would be 1 to retrieve
 that integer, however also a count value of 3 can be used and then
 the image flags will be unpacked into 3 individual integers, ordered
-in a similar fashion as coordinates. 
+in a similar fashion as coordinates.
 
 Note that the data structure gather_atoms("x") returns is different
 from the data structure returned by extract_atom("x") in four ways.

doc/src/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:]
@@ -42,62 +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 cutoff" and "kspace_modify diff ad" to the input script for better
-performance.  Cutoff should be roughly the neighbor list cutoff.  By
-default the binsize is half the neighbor list cutoff.  :l
-"-pk intel 0 omp 2 -sf intel" added to LAMMPS command-line :l
+Set the environment variable KMP_BLOCKTIME=0 :l
+"-pk intel 0 omp $t -sf intel" added to LAMMPS command-line :l
+$t should be 2 for Intel Xeon CPUs and 2 or 4 for Intel Xeon Phi :l
+For some of the simple 2-body potentials without long-range
+electrostatics, performance and scalability can be better with
+the "newton off" setting added to the input script :l
+For simulations on higher node counts, add "processors * * * grid 
+numa" to the beginning of the input script for better scalability :l
+If using {kspace_style pppm} in the input script, add
+"kspace_modify diff ad" for better performance :l
 :ule
 
-For Intel Xeon Phi CPUs for simulations without {kspace_style
-pppm} in the input script :
+For Intel Xeon Phi CPUs:
 
-Edit src/MAKE/OPTIONS/Makefile.knl as necessary. :ulb,l
-Runs should be performed using MCDRAM. :l
-"-pk intel 0 omp 2 -sf intel" {or} "-pk intel 0 omp 4 -sf intel"
-should be added to the LAMMPS command-line. Choice for best
-performance will depend on the simulation. :l
+Runs should be performed using MCDRAM. :ulb,l
 :ule
 
-For Intel Xeon Phi CPUs for simulations with {kspace_style
-pppm} in the input script:
+For simulations using {kspace_style pppm} on Intel CPUs
+supporting AVX-512:
 
-Edit src/MAKE/OPTIONS/Makefile.knl as necessary. :ulb,l
-Runs should be performed using MCDRAM. :l
-Add "neigh_modify binsize 3" to the input script for better
-performance. :l
-Add "kspace_modify diff ad" to the input script for better
-performance. :l
-export KMP_AFFINITY=none :l
-"-pk intel 0 omp 3 lrt yes -sf intel" or "-pk intel 0 omp 1 lrt yes
--sf intel" added to LAMMPS command-line. Choice for best performance
-will depend on the simulation. :l
+Add "kspace_modify diff ad" to the input script :ulb,l
+The command-line option should be changed to
+"-pk intel 0 omp $r lrt yes -sf intel" where $r is the number of
+threads minus 1. :l
+Do not use thread affinity (set KMP_AFFINITY=none) :l
+The "newton off" setting may provide better scalability :l
 :ule
 
 For Intel Xeon Phi coprocessors (Offload):
@@ -169,6 +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
@@ -322,8 +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
@@ -342,6 +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,
@@ -358,6 +394,10 @@ 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
@@ -467,7 +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/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/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_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_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/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

@@ -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_spherical.txt

@@ -18,6 +18,7 @@ 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:]
 

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/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_box_relax.txt

@@ -245,7 +245,7 @@ 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 pressure compute this 
+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,

doc/src/fix_deform.txt

@@ -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_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_gcmc.txt

@@ -406,7 +406,7 @@ 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.
 

doc/src/fix_gle.txt

@@ -68,7 +68,7 @@ matrix that gives canonical sampling for a given A is computed automatically.
 However, the GLE framework also allow for non-equilibrium sampling, that
 can be used for instance to model inexpensively zero-point energy
 effects "(Ceriotti2)"_#Ceriotti2. This is achieved specifying the {noneq}
- keyword followed by the name of the file that contains the static covariance
+keyword followed by the name of the file that contains the static covariance
 matrix for the non-equilibrium dynamics.  Please note, that the covariance
 matrix is expected to be given in [temperature units].
 

doc/src/fix_grem.txt

@@ -85,13 +85,13 @@ No information about this fix is written to "binary restart
 files"_restart.html.
 
 The "thermo_modify"_thermo_modify.html {press} option is supported
-by this fix to add the rescaled kinetic pressure as part of 
+by this fix to add the rescaled kinetic pressure as part of
 "thermodynamic output"_thermo_style.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.
 
 [Related commands:]

doc/src/fix_ipi.txt

@@ -58,14 +58,14 @@ input are listed in the same order as in the data file of LAMMPS. The
 initial configuration is ignored, as it will be substituted with the
 coordinates received from i-PI before forces are ever evaluated.
 
-A note of caution when using potentials that contain long-range 
+A note of caution when using potentials that contain long-range
 electrostatics, or that contain parameters that depend on box size:
 all of these options will be initialized based on the cell size in the
-LAMMPS-side initial configuration and kept constant during the run. 
-This is required to e.g. obtain reproducible and conserved forces. 
-If the cell varies too wildly, it may be advisable to reinitialize 
-these interactions at each call. This behavior can be requested by 
-setting the {reset} switch. 
+LAMMPS-side initial configuration and kept constant during the run.
+This is required to e.g. obtain reproducible and conserved forces.
+If the cell varies too wildly, it may be advisable to reinitialize
+these interactions at each call. This behavior can be requested by
+setting the {reset} switch.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 

doc/src/fix_langevin_drude.txt

@@ -67,11 +67,11 @@ The Langevin forces are computed as
 \(F_r'\) is a random force proportional to
 \(\sqrt \{ \frac \{2\, k_B \mathtt\{Tcom\}\, m'\}
                  \{\mathrm dt\, \mathtt\{damp\_com\} \}
-        \} \). :b
+        \} \).
 \(f_r'\) is a random force proportional to
 \(\sqrt \{ \frac \{2\, k_B \mathtt\{Tdrude\}\, m'\}
                  \{\mathrm dt\, \mathtt\{damp\_drude\} \}
-        \} \). :b
+        \} \).
 Then the real forces acting on the particles are computed from the inverse
 transform:
 \begin\{equation\} F = \frac M \{M'\}\, F' - f' \end\{equation\}

doc/src/fix_mscg.txt

@@ -57,7 +57,7 @@ simulations is as follows:
 Perform all-atom simulations on the system to be coarse grained.
 Generate a trajectory mapped to the coarse-grained model.
 Create input files for the MS-CG library.
-Run the range finder functionality of the MS-CG library.  
+Run the range finder functionality of the MS-CG library.
 Run the force matching functionality of the MS-CG library.
 Check the results of the force matching.
 Run coarse-grained simulations using the new coarse-grained potentials. :ol
@@ -70,7 +70,7 @@ Step 2 can be performed using a Python script (what is the name?)
 provided with the MS-CG library which defines the coarse-grained model
 and converts a standard LAMMPS dump file for an all-atom simulation
 (step 1) into a LAMMPS dump file which has the positions of and forces
-on the coarse-grained beads.  
+on the coarse-grained beads.
 
 In step 3, an input file named "control.in" is needed by the MS-CG
 library which sets parameters for the range finding and force matching

doc/src/fix_msst.txt

@@ -17,19 +17,22 @@ msst = style name of this fix :l
 dir = {x} or {y} or {z} :l
 shockvel = shock velocity (strictly positive, distance/time units) :l
 zero or more keyword value pairs may be appended :l
-keyword = {q} or {mu} or {p0} or {v0} or {e0} or {tscale} :l
+keyword = {q} or {mu} or {p0} or {v0} or {e0} or {tscale} or {beta} or {dftb} :l
   {q} value = cell mass-like parameter (mass^2/distance^4 units)
   {mu} value = artificial viscosity (mass/length/time units)
   {p0} value = initial pressure in the shock equations (pressure units)
   {v0} value = initial simulation cell volume in the shock equations (distance^3 units)
   {e0} value = initial total energy (energy units)
-  {tscale} value = reduction in initial temperature (unitless fraction between 0.0 and 1.0) :pre
+  {tscale} value = reduction in initial temperature (unitless fraction between 0.0 and 1.0) 
+  {dftb} value = {yes} or {no} for whether using MSST in conjunction with DFTB+
+  {beta} value = scale factor on energy contribution of DFTB+ :pre
 :ule
 
 [Examples:]
 
 fix 1 all msst y 100.0 q 1.0e5 mu 1.0e5
-fix 2 all msst z 50.0 q 1.0e4 mu 1.0e4  v0 4.3419e+03 p0 3.7797e+03 e0 -9.72360e+02 tscale 0.01 :pre
+fix 2 all msst z 50.0 q 1.0e4 mu 1.0e4  v0 4.3419e+03 p0 3.7797e+03 e0 -9.72360e+02 tscale 0.01
+fix 1 all msst y 100.0 q 1.0e5 mu 1.0e5 dftb yes beta 0.5 :pre
 
 [Description:]
 
@@ -58,11 +61,11 @@ oscillations have physical significance in some cases.  The optional
 symmetry to equilibrate to the shock Hugoniot and Rayleigh line more
 rapidly in such cases.
 
-{tscale} is a factor between 0 and 1 that determines what fraction of
-thermal kinetic energy is converted to compressive strain kinetic
-energy at the start of the simulation.  Setting this parameter to a
-non-zero value may assist in compression at the start of simulations
-where it is slow to occur.
+The keyword {tscale} is a factor between 0 and 1 that determines what
+fraction of thermal kinetic energy is converted to compressive strain
+kinetic energy at the start of the simulation.  Setting this parameter
+to a non-zero value may assist in compression at the start of
+simulations where it is slow to occur.
 
 If keywords {e0}, {p0},or {v0} are not supplied, these quantities will
 be calculated on the first step, after the energy specified by
@@ -77,17 +80,40 @@ For all pressure styles, the simulation box stays orthogonal in shape.
 Parrinello-Rahman boundary conditions (tilted box) are supported by
 LAMMPS, but are not implemented for MSST.
 
-This fix computes a temperature and pressure each timestep. To do
-this, the fix creates its own computes of style "temp" and "pressure",
-as if these commands had been issued:
+This fix computes a temperature and pressure and potential energy each
+timestep. To do this, the fix creates its own computes of style "temp"
+"pressure", and "pe", as if these commands had been issued:
 
-compute fix-ID_temp group-ID temp
-compute fix-ID_press group-ID pressure fix-ID_temp :pre
+compute fix-ID_MSST_temp all temp
+compute fix-ID_MSST_press all pressure fix-ID_MSST_temp :pre
+compute fix-ID_MSST_pe all pe :pre
 
 See the "compute temp"_compute_temp.html and "compute
 pressure"_compute_pressure.html commands for details.  Note that the
-IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
-+ underscore + "press".  The group for the new computes is "all".
+IDs of the new computes are the fix-ID + "_MSST_temp" or "_MSST_press"
+or "_MSST_pe".  The group for the new computes is "all".
+
+:line
+
+The {dftb} and {beta} keywords are to allow this fix to be used when
+LAMMPS is being driven by DFTB+, a density-functional tight-binding
+code.
+
+If the keyword {dftb} is used with a value of {yes}, then the MSST
+equations are altered to account for an energy contribution compute by
+DFTB+.  In this case, you must define a "fix
+external"_fix_external.html command in your input script, which is
+used to callback to DFTB+ during the LAMMPS timestepping.  DFTB+ will
+communicate its info to LAMMPS via that fix.
+
+The keyword {beta} is a scale factor on the DFTB+ energy contribution.
+The value of {beta} must be between 0.0 and 1.0 inclusive.  A value of
+0.0 means no contribution, a value of 1.0 means a full contribution.
+
+(July 2017) More information about these keywords and the use of
+LAMMPS with DFTB+ will be added to the LAMMMPS documention soon.
+
+:line
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
@@ -149,8 +175,9 @@ all.
 
 [Default:]
 
-The keyword defaults are q = 10, mu = 0, tscale = 0.01. p0, v0, and e0
-are calculated on the first step.
+The keyword defaults are q = 10, mu = 0, tscale = 0.01, dftb = no,
+beta = 0.0.  Note that p0, v0, and e0 are calculated on the first
+timestep.
 
 :line
 

doc/src/fix_neb.txt

@@ -10,68 +10,183 @@ fix neb command :h3
 
 [Syntax:]
 
-fix ID group-ID neb Kspring :pre
+fix ID group-ID neb Kspring keyword value :pre
 
-ID, group-ID are documented in "fix"_fix.html command
-neb = style name of this fix command
-Kspring = inter-replica spring constant (force/distance units) :ul
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+neb = style name of this fix command :l
+Kspring = spring constant for parallel nudging force (force/distance units or force units, see parallel keyword) :l
+zero or more keyword/value pairs may be appended :l
+keyword = {parallel} or {perp} or {end} :l
+  {parallel} value = {neigh} or {ideal}
+    {neigh} = parallel nudging force based on distance to neighbor replicas (Kspring = force/distance units)
+    {ideal} = parallel nudging force based on interpolated ideal position (Kspring = force units)
+  {perp} value = {Kspring2}
+    {Kspring2} = spring constant for perpendicular nudging force (force/distance units)
+  {end} values = estyle Kspring3
+    {estyle} = {first} or {last} or {last/efirst} or {last/efirst/middle}
+      {first} = apply force to first replica
+      {last} = apply force to last replica
+      {last/efirst} = apply force to last replica and set its target energy to that of first replica
+      {last/efirst/middle} = same as {last/efirst} plus prevent middle replicas having lower energy than first replica
+    {Kspring3} = spring constant for target energy term (1/distance units) :pre,ule
 
 [Examples:]
 
-fix 1 active neb 10.0 :pre
+fix 1 active neb 10.0
+fix 2 all neb 1.0 perp 1.0 end last
+fix 2 all neb 1.0 perp 1.0 end first 1.0 end last 1.0
+fix 1 all neb 1.0 nudge ideal end last/efirst 1 :pre
 
 [Description:]
 
-Add inter-replica forces to atoms in the group for a multi-replica
+Add nudging forces to atoms in the group for a multi-replica
 simulation run via the "neb"_neb.html command to perform a nudged
-elastic band (NEB) calculation for transition state finding.  Hi-level
-explanations of NEB are given with the "neb"_neb.html command and in
-"Section 6.5"_Section_howto.html#howto_5 of the manual.  The fix
-neb command must be used with the "neb" command to define how
-inter-replica forces are computed.
+elastic band (NEB) calculation for finding the transition state.
+Hi-level explanations of NEB are given with the "neb"_neb.html command
+and in "Section_howto 5"_Section_howto.html#howto_5 of the manual.
+The fix neb command must be used with the "neb" command and defines
+how inter-replica nudging forces are computed.  A NEB calculation is
+divided in two stages. In the first stage n replicas are relaxed
+toward a MEP until convergence.  In the second stage, the climbing
+image scheme (see "(Henkelman2)"_#Henkelman2) is enabled, so that the
+replica having the highest energy relaxes toward the saddle point
+(i.e. the point of highest energy along the MEP), and a second
+relaxation is performed.
 
-Only the N atoms in the fix group experience inter-replica forces.
-Atoms in the two end-point replicas do not experience these forces,
-but those in intermediate replicas do.  During the initial stage of
-NEB, the 3N-length vector of interatomic forces Fi = -Grad(V) acting
-on the atoms of each intermediate replica I is altered, as described
-in the "(Henkelman1)"_#Henkelman1 paper, to become:
+A key purpose of the nudging forces is to keep the replicas equally
+spaced.  During the NEB calculation, the 3N-length vector of
+interatomic force Fi = -Grad(V) for each replica I is altered.  For
+all intermediate replicas (i.e. for 1 < I < N, except the climbing
+replica) the force vector becomes:
 
-Fi = -Grad(V) + (Grad(V) dot That) That + Kspring (| Ri+i - Ri | - | Ri - Ri-1 |) That :pre
+Fi = -Grad(V) + (Grad(V) dot T') T' + Fnudge_parallel + Fnudge_perp :pre
 
-Ri are the atomic coordinates of replica I; Ri-1 and Ri+1 are the
-coordinates of its neighbor replicas.  That (t with a hat over it) is
-the unit "tangent" vector for replica I which is a function of Ri,
+T' is the unit "tangent" vector for replica I and is a function of Ri,
 Ri-1, Ri+1, and the potential energy of the 3 replicas; it points
 roughly in the direction of (Ri+i - Ri-1); see the
-"(Henkelman1)"_#Henkelman1 paper for details.
+"(Henkelman1)"_#Henkelman1 paper for details.  Ri are the atomic
+coordinates of replica I; Ri-1 and Ri+1 are the coordinates of its
+neighbor replicas.  The term (Grad(V) dot T') is used to remove the
+component of the gradient parallel to the path which would tend to
+distribute the replica unevenly along the path.  Fnudge_parallel is an
+artificial nudging force which is applied only in the tangent
+direction and which maintains the equal spacing between replicas (see
+below for more information).  Fnudge_perp is an optional artificial
+spring which is applied in a direction perpendicular to the tangent
+direction and which prevent the paths from forming acute kinks (see
+below for more information).
 
-The first two terms in the above equation are the component of the
-interatomic forces perpendicular to the tangent vector.  The last term
-is a spring force between replica I and its neighbors, parallel to the
-tangent vector direction with the specified spring constant {Kspring}.
+In the second stage of the NEB calculation, the interatomic force Fi
+for the climbing replica (the replica of highest energy after the
+first stage) is changed to:
 
-The effect of the first two terms is to push the atoms of each replica
-toward the minimum energy path (MEP) of conformational states that
-transition over the energy barrier.  The MEP for an energy barrier is
-defined as a sequence of 3N-dimensional states which cross the barrier
-at its saddle point, each of which has a potential energy gradient
-parallel to the MEP itself.
+Fi = -Grad(V) + 2 (Grad(V) dot T') T' :pre
 
-The effect of the last term is to push each replica away from its two
-neighbors in a direction along the MEP, so that the final set of
-states are equidistant from each other.
+and the relaxation procedure is continued to a new converged MEP.
 
-During the second stage of NEB, the forces on the N atoms in the
-replica nearest the top of the energy barrier are altered so that it
-climbs to the top of the barrier and finds the saddle point.  The
-forces on atoms in this replica are described in the
-"(Henkelman2)"_#Henkelman2 paper, and become:
+:line
 
-Fi = -Grad(V) + 2 (Grad(V) dot That) That :pre
+The keyword {parallel} specifies how the parallel nudging force is
+computed.  With a value of {neigh}, the parallel nudging force is
+computed as in "(Henkelman1)"_#Henkelman1 by connecting each
+intermediate replica with the previous and the next image:
 
-The inter-replica forces for the other replicas are unchanged from the
-first equation.
+Fnudge_parallel = {Kspring} * (|Ri+1 - Ri| - |Ri - Ri-1|) :pre
+
+Note that in this case the specified {Kspring) is in force/distance
+units.
+
+With a value of {ideal}, the spring force is computed as suggested in
+"(WeinenE)"_#WeinenE :
+
+Fnudge_parallel = -{Kspring} * (RD-RDideal) / (2 * meanDist) :pre
+
+where RD is the "reaction coordinate" see "neb"_neb.html section, and
+RDideal is the ideal RD for which all the images are equally spaced.
+I.e. RDideal = (I-1)*meanDist when the climbing replica is off, where
+I is the replica number).  The meanDist is the average distance
+between replicas.  Note that in this case the specified {Kspring) is
+in force units.
+
+Note that the {ideal} form of nudging can often be more effective at
+keeping the replicas equally spaced.
+
+:line
+
+The keyword {perp} specifies if and how a perpendicual nudging force
+is computed.  It adds a spring force perpendicular to the path in
+order to prevent the path from becoming too kinky.  It can
+significantly improve the convergence of the NEB calculation when the
+resolution is poor.  I.e. when few replicas are used; see
+"(Maras)"_#Maras1 for details.
+
+The perpendicular spring force is given by
+
+Fnudge_perp = {Kspring2} * F(Ri-1,Ri,Ri+1) (Ri+1 + Ri-1 - 2 Ri) :pre
+
+where {Kspring2} is the specified value.  F(Ri-1 Ri R+1) is a smooth
+scalar function of the angle Ri-1 Ri Ri+1.  It is equal to 0.0 when
+the path is straight and is equal to 1 when the angle Ri-1 Ri Ri+1 is
+acute.  F(Ri-1 Ri R+1) is defined in "(Jonsson)"_#Jonsson.
+
+If {Kspring2} is set to 0.0 (the default) then no perpendicular spring
+force is added.
+
+:line
+
+By default, no additional forces act on the first and last replicas
+during the NEB relaxation, so these replicas simply relax toward their
+respective local minima.  By using the key word {end}, additional
+forces can be applied to the first and/or last replicas, to enable
+them to relax toward a MEP while constraining their energy.
+
+The interatomic force Fi for the specified replica becomes:
+
+Fi = -Grad(V) + (Grad(V) dot T' + (E-ETarget)*Kspring3) T',  {when} Grad(V) dot T' < 0
+Fi = -Grad(V) + (Grad(V) dot T' + (ETarget- E)*Kspring3) T', {when} Grad(V) dot T' > 0
+:pre
+
+where E is the current energy of the replica and ETarget is the target
+energy.  The "spring" constant on the difference in energies is the
+specified {Kspring3} value.
+
+When {estyle} is specified as {first}, the force is applied to the
+first replica.  When {estyle} is specified as {last}, the force is
+applied to the last replica.  Note that the {end} keyword can be used
+twice to add forces to both the first and last replicas.
+
+For both these {estyle} settings, the target energy {ETarget} is set
+to the initial energy of the replica (at the start of the NEB
+calculation).
+
+If the {estyle} is specified as {last/efirst} or {last/efirst/middle},
+force is applied to the last replica, but the target energy {ETarget}
+is continuously set to the energy of the first replica, as it evolves
+during the NEB relaxation.
+
+The difference between these two {estyle} options is as follows.  When
+{estyle} is specified as {last/efirst}, no change is made to the
+inter-replica force applied to the intermediate replicas (neither
+first or last).  If the initial path is too far from the MEP, an
+intermediate repilica may relax "faster" and reach a lower energy than
+the last replica.  In this case the intermediate replica will be
+relaxing toward its own local minima.  This behavior can be prevented
+by specifying {estyle} as {last/efirst/middle} which will alter the
+inter-replica force applied to intermediate replicas by removing the
+contribution of the gradient to the inter-replica force.  This will
+only be done if a particular intermediate replica has a lower energy
+than the first replica.  This should effectively prevent the
+intermediate replicas from over-relaxing.
+
+After converging a NEB calculation using an {estyle} of
+{last/efirst/middle}, you should check that all intermediate replicas
+have a larger energy than the first replica. If this is not the case,
+the path is probably not a MEP.
+
+Finally, note that if the last replica converges toward a local
+minimum which has a larger energy than the energy of the first
+replica, a NEB calculation using an {estyle} of {last/efirst} or
+{last/efirst/middle} cannot reach final convergence.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
@@ -96,7 +211,12 @@ for more info on packages.
 
 "neb"_neb.html
 
-[Default:] none
+[Default:]
+
+The option defaults are nudge = neigh, perp = 0.0, ends is not
+specified (no inter-replica force on the end replicas).
+
+:line
 
 :link(Henkelman1)
 [(Henkelman1)] Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).
@@ -104,3 +224,15 @@ for more info on packages.
 :link(Henkelman2)
 [(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
 9901-9904 (2000).
+
+:link(WeinenE)
+[(WeinenE)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002).
+
+:link(Jonsson)
+[(Jonsson)] Jonsson, Mills and Jacobsen, in Classical and Quantum
+Dynamics in Condensed Phase Simulations, edited by Berne, Ciccotti,
+and Coker World Scientific, Singapore, 1998, p 385.
+
+:link(Maras1)
+[(Maras)] Maras, Trushin, Stukowski, Ala-Nissila, Jonsson,
+Comp Phys Comm, 205, 13-21 (2016).

doc/src/fix_nve_dot.txt

@@ -23,13 +23,13 @@ fix 1 all nve/dot :pre
 [Description:]
 
 Apply a rigid-body integrator as described in "(Davidchack)"_#Davidchack1
-to a group of atoms, but without Langevin dynamics. 
+to a group of atoms, but without Langevin dynamics.
 This command performs Molecular dynamics (MD)
-via a velocity-Verlet algorithm and an evolution operator that rotates 
-the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller1. 
+via a velocity-Verlet algorithm and an evolution operator that rotates
+the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller1.
 
 This command is the equivalent of the "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
-without damping and noise and can be used to determine the stability range 
+without damping and noise and can be used to determine the stability range
 in a NVE ensemble prior to using the Langevin-type DOTC-integrator
 (see also "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html).
 The command is equivalent to the "fix nve"_fix_nve.html.

doc/src/fix_nve_dotc_langevin.txt

@@ -28,20 +28,20 @@ fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10 :pre
 
 [Description:]
 
-Apply a rigid-body Langevin-type integrator of the kind "Langevin C" 
+Apply a rigid-body Langevin-type integrator of the kind "Langevin C"
 as described in "(Davidchack)"_#Davidchack2
 to a group of atoms, which models an interaction with an implicit background
 solvent.  This command performs Brownian dynamics (BD)
-via a technique that splits the integration into a deterministic Hamiltonian 
-part and the Ornstein-Uhlenbeck process for noise and damping. 
+via a technique that splits the integration into a deterministic Hamiltonian
+part and the Ornstein-Uhlenbeck process for noise and damping.
 The quaternion degrees of freedom are updated though an evolution
 operator which performs a rotation in quaternion space, preserves
 the quaternion norm and is akin to "(Miller)"_#Miller2.
 
-In terms of syntax this command has been closely modelled on the 
-"fix langevin"_fix_langevin.html and its {angmom} option. But it combines 
-the "fix nve"_fix_nve.html and the "fix langevin"_fix_langevin.html in 
-one single command. The main feature is improved stability 
+In terms of syntax this command has been closely modelled on the
+"fix langevin"_fix_langevin.html and its {angmom} option. But it combines
+the "fix nve"_fix_nve.html and the "fix langevin"_fix_langevin.html in
+one single command. The main feature is improved stability
 over the standard integrator, permitting slightly larger timestep sizes.
 
 NOTE: Unlike the "fix langevin"_fix_langevin.html this command performs
@@ -57,7 +57,7 @@ Fc is the conservative force computed via the usual inter-particle
 interactions ("pair_style"_pair_style.html,
 "bond_style"_bond_style.html, etc).
 
-The Ff and Fr terms are implicitly taken into account by this fix 
+The Ff and Fr terms are implicitly taken into account by this fix
 on a per-particle basis.
 
 Ff is a frictional drag or viscous damping term proportional to the
@@ -77,7 +77,7 @@ a Gaussian random number) for speed.
 
 :line
 
-{Tstart} and {Tstop} have to be constant values, i.e. they cannot 
+{Tstart} and {Tstop} have to be constant values, i.e. they cannot
 be variables.
 
 The {damp} parameter is specified in time units and determines how
@@ -98,16 +98,16 @@ different numbers of processors.
 
 The keyword/value option has to be used in the following way:
 
-This fix has to be used together with the {angmom} keyword. The 
-particles are always considered to have a finite size. 
-The keyword {angmom} enables thermostatting of the rotational degrees of 
-freedom in addition to the usual translational degrees of freedom. 
+This fix has to be used together with the {angmom} keyword. The
+particles are always considered to have a finite size.
+The keyword {angmom} enables thermostatting of the rotational degrees of
+freedom in addition to the usual translational degrees of freedom.
 
-The scale factor after the {angmom} keyword gives the ratio of the rotational to 
+The scale factor after the {angmom} keyword gives the ratio of the rotational to
 the translational friction coefficient.
 
 An example input file can be found in /examples/USER/cgdna/examples/duplex2/.
-A technical report with more information on this integrator can be found 
+A technical report with more information on this integrator can be found
 "here"_PDF/USER-CGDNA-overview.pdf.
 
 :line
@@ -120,7 +120,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]
 
-"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html,  
+"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html,
 
 [Default:] none
 

doc/src/fix_nvk.txt

@@ -27,7 +27,7 @@ timestep.  V is volume; K is kinetic energy. This creates a system
 trajectory consistent with the isokinetic ensemble.
 
 The equations of motion used are those of Minary et al in
-"(Minary)"_#nvk-Minary, a variant of those initially given by Zhang in 
+"(Minary)"_#nvk-Minary, a variant of those initially given by Zhang in
 "(Zhang)"_#nvk-Zhang.
 
 The kinetic energy will be held constant at its value given when fix

doc/src/fix_qeq_reax.txt

@@ -8,17 +8,19 @@
 
 fix qeq/reax command :h3
 fix qeq/reax/kk command :h3
+fix qeq/reax/omp command :h3
 
 [Syntax:]
 
-fix ID group-ID qeq/reax Nevery cutlo cuthi tolerance params :pre
+fix ID group-ID qeq/reax Nevery cutlo cuthi tolerance params args :pre
 
 ID, group-ID are documented in "fix"_fix.html command
 qeq/reax = style name of this fix command
 Nevery = perform QEq every this many steps
 cutlo,cuthi = lo and hi cutoff for Taper radius
 tolerance = precision to which charges will be equilibrated
-params = reax/c or a filename :ul
+params = reax/c or a filename
+args   = {dual} (optional) :ul
 
 [Examples:]
 
@@ -59,6 +61,10 @@ potential file, except that eta is defined here as twice the eta value
 in the ReaxFF file. Note that unlike the rest of LAMMPS, the units
 of this fix are hard-coded to be A, eV, and electronic charge.
 
+The optional {dual} keyword allows to perform the optimization
+of the S and T matrices in parallel. This is only supported for
+the {qeq/reax/omp} style. Otherwise they are processed separately.
+
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
 No information about this fix is written to "binary restart

doc/src/fix_rigid.txt

@@ -31,11 +31,12 @@ bodystyle = {single} or {molecule} or {group} :l
     groupID1, groupID2, ... = list of N group IDs :pre
 
 zero or more keyword/value pairs may be appended :l
-keyword = {langevin} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {couple} or {tparam} or {pchain} or {dilate} or {force} or {torque} or {infile} :l
+keyword = {langevin} or {reinit} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {couple} or {tparam} or {pchain} or {dilate} or {force} or {torque} or {infile} :l
   {langevin} values = Tstart Tstop Tperiod seed
     Tstart,Tstop = desired temperature at start/stop of run (temperature units)
     Tdamp = temperature damping parameter (time units)
     seed = random number seed to use for white noise (positive integer)
+  {reinit} = {yes} or {no}
   {temp} values = Tstart Tstop Tdamp
     Tstart,Tstop = desired temperature at start/stop of run (temperature units)
     Tdamp = temperature damping parameter (time units)
@@ -68,10 +69,10 @@ keyword = {langevin} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {coup
 
 [Examples:]
 
-fix 1 clump rigid single
+fix 1 clump rigid single reinit yes
 fix 1 clump rigid/small molecule
 fix 1 clump rigid single force 1 off off on langevin 1.0 1.0 1.0 428984
-fix 1 polychains rigid/nvt molecule temp 1.0 1.0 5.0
+fix 1 polychains rigid/nvt molecule temp 1.0 1.0 5.0 reinit no
 fix 1 polychains rigid molecule force 1*5 off off off force 6*10 off off on
 fix 1 polychains rigid/small molecule langevin 1.0 1.0 1.0 428984
 fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off
@@ -87,7 +88,12 @@ means that each timestep the total force and torque on each rigid body
 is computed as the sum of the forces and torques on its constituent
 particles.  The coordinates, velocities, and orientations of the atoms
 in each body are then updated so that the body moves and rotates as a
-single entity.
+single entity.  This is implemented by creating internal data structures
+for each rigid body and performing time integration on these data
+structures.  Positions, velocities, and orientations of the constituent
+particles are regenerated from the rigid body data structures in every
+time step. This restricts which operations and fixes can be applied to
+rigid bodies. See below for a detailed discussion.
 
 Examples of large rigid bodies are a colloidal particle, or portions
 of a biomolecule such as a protein.
@@ -148,8 +154,9 @@ differences may accumulate to produce divergent trajectories.
 
 NOTE: You should not update the atoms in rigid bodies via other
 time-integration fixes (e.g. "fix nve"_fix_nve.html, "fix
-nvt"_fix_nh.html, "fix npt"_fix_nh.html), or you will be integrating
-their motion more than once each timestep.  When performing a hybrid
+nvt"_fix_nh.html, "fix npt"_fix_nh.html, "fix move"_fix_move.html),
+or you will have conflicting updates to positions and velocities
+resulting in unphysical behavior in most cases. When performing a hybrid
 simulation with some atoms in rigid bodies, and some not, a separate
 time integration fix like "fix nve"_fix_nve.html or "fix
 nvt"_fix_nh.html should be used for the non-rigid particles.
@@ -165,23 +172,29 @@ setting the force on them to 0.0 (via the "fix
 setforce"_fix_setforce.html command), and integrating them as usual
 (e.g. via the "fix nve"_fix_nve.html command).
 
-NOTE: The aggregate properties of each rigid body are calculated one
-time at the start of the first simulation run after these fixes are
-specified.  The properties include the position and velocity of the
-center-of-mass of the body, its moments of inertia, and its angular
-momentum.  This is done using the properties of the constituent atoms
-of the body at that point in time (or see the {infile} keyword
-option).  Thereafter, changing properties of individual atoms in the
-body will have no effect on a rigid body's dynamics, unless they
-affect the "pair_style"_pair_style.html interactions that individual
-particles are part of.  For example, you might think you could
-displace the atoms in a body or add a large velocity to each atom in a
-body to make it move in a desired direction before a 2nd run is
+IMPORTANT NOTE: The aggregate properties of each rigid body are
+calculated at the start of a simulation run and are maintained in
+internal data structures. The properties include the position and
+velocity of the center-of-mass of the body, its moments of inertia, and
+its angular momentum.  This is done using the properties of the
+constituent atoms of the body at that point in time (or see the {infile}
+keyword option).  Thereafter, changing these properties of individual
+atoms in the body will have no effect on a rigid body's dynamics, unless
+they effect any computation of per-atom forces or torques. If the
+keyword {reinit} is set to {yes} (the default), the rigid body data
+structures will be recreated at the beginning of each {run} command;
+if the keyword {reinit} is set to {no}, the rigid body data structures
+will be built only at the very first {run} command and maintained for
+as long as the rigid fix is defined. For example, you might think you
+could displace the atoms in a body or add a large velocity to each atom
+in a body to make it move in a desired direction before a 2nd run is
 performed, using the "set"_set.html or
 "displace_atoms"_displace_atoms.html or "velocity"_velocity.html
-command.  But these commands will not affect the internal attributes
-of the body, and the position and velocity of individual atoms in the
-body will be reset when time integration starts.
+commands.  But these commands will not affect the internal attributes
+of the body unless {reinit} is set to {yes}. With {reinit} set to {no}
+(or using the {infile} option, which implies {reinit} {no}) the position
+and velocity of individual atoms in the body will be reset when time
+integration starts again.
 
 :line
 
@@ -401,6 +414,14 @@ couple none :pre
 
 The keyword/value option pairs are used in the following ways.
 
+The {reinit} keyword determines, whether the rigid body properties
+are reinitialized between run commands. With the option {yes} (the
+default) this is done, with the option {no} this is not done. Turning
+off the reinitialization can be helpful to protect rigid bodies against
+unphysical manipulations between runs or when properties cannot be
+easily recomputed (e.g. when read from a file). When using the {infile}
+keyword, the {reinit} option is automatically set to {no}.
+
 The {langevin} and {temp} and {tparam} keywords perform thermostatting
 of the rigid bodies, altering both their translational and rotational
 degrees of freedom.  What is meant by "temperature" of a collection of
@@ -778,7 +799,7 @@ exclude, "fix shake"_fix_shake.html
 
 The option defaults are force * on on on and torque * on on on,
 meaning all rigid bodies are acted on by center-of-mass force and
-torque.  Also Tchain = Pchain = 10, Titer = 1, Torder = 3.
+torque.  Also Tchain = Pchain = 10, Titer = 1, Torder = 3, reinit = yes.
 
 :line
 

doc/src/fix_spring.txt

@@ -89,7 +89,7 @@ NOTE: The center of mass of a group of atoms is calculated in
 group can straddle a periodic boundary.  See the "dump"_dump.html doc
 page for a discussion of unwrapped coordinates.  It also means that a
 spring connecting two groups or a group and the tether point can cross
-a periodic boundary and its length be calculated correctly.  
+a periodic boundary and its length be calculated correctly.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 

doc/src/fix_ti_spring.txt

@@ -144,7 +144,11 @@ this fix.
 
 "fix spring"_fix_spring.html, "fix adapt"_fix_adapt.html
 
-[Restrictions:] none
+[Restrictions:]
+
+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.
 
 [Default:]
 

doc/src/kspace_modify.txt

@@ -219,10 +219,10 @@ instead of using the virial equation. This option cannot be used to access
 individual components of the pressure tensor, to compute per-atom virial,
 or with suffix kspace/pair styles of MSM, like OMP or GPU.
 
-The {fftbench} keyword applies only to PPPM. It is on by default. If
-this option is turned off, LAMMPS will not take the time at the end
-of a run to give FFT benchmark timings, and will finish a few seconds
-faster than it would if this option were on.
+The {fftbench} keyword applies only to PPPM. It is off by default. If
+this option is turned on, LAMMPS will perform a short FFT benchmark
+computation and report its timings, and will thus finish a some seconds
+later than it would if this option were off.
 
 The {collective} keyword applies only to PPPM.  It is set to {no} by
 default, except on IBM BlueGene machines.  If this option is set to
@@ -306,9 +306,10 @@ parameters, see the "How-To"_Section_howto.html#howto_24 discussion.
 The option defaults are mesh = mesh/disp = 0 0 0, order = order/disp =
 5 (PPPM), order = 10 (MSM), minorder = 2, overlap = yes, force = -1.0,
 gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust =
-yes (MSM), pressure/scalar = yes (MSM), fftbench = yes (PPPM), diff = ik
+yes (MSM), pressure/scalar = yes (MSM), fftbench = no (PPPM), diff = ik
 (PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace = -1.0,
-split = 0, tol = 1.0e-6, and disp/auto = no.
+split = 0, tol = 1.0e-6, and disp/auto = no. For pppm/intel, order =
+order/disp = 7.
 
 :line
 

doc/src/kspace_style.txt

@@ -33,12 +33,16 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg}
     accuracy = desired relative error in forces
   {pppm/gpu} value = accuracy
     accuracy = desired relative error in forces
+  {pppm/intel} value = accuracy
+    accuracy = desired relative error in forces
   {pppm/kk} value = accuracy
     accuracy = desired relative error in forces
   {pppm/omp} value = accuracy
     accuracy = desired relative error in forces
   {pppm/cg/omp} value = accuracy
     accuracy = desired relative error in forces
+  {pppm/disp/intel} value = accuracy
+    accuracy = desired relative error in forces
   {pppm/tip4p/omp} value = accuracy
     accuracy = desired relative error in forces
   {pppm/stagger} value = accuracy

doc/src/lammps.book

@@ -301,6 +301,7 @@ compute_centro_atom.html
 compute_chunk_atom.html
 compute_cluster_atom.html
 compute_cna_atom.html
+compute_cnp_atom.html
 compute_com.html
 compute_com_chunk.html
 compute_contact_atom.html
@@ -446,7 +447,6 @@ pair_lj96.html
 pair_lj_cubic.html
 pair_lj_expand.html
 pair_lj_long.html
-pair_lj_sf.html
 pair_lj_smooth.html
 pair_lj_smooth_linear.html
 pair_lj_soft.html

doc/src/manifolds.txt

@@ -24,14 +24,15 @@ to the relevant fixes.
 {manifold} @ {parameters} @ {equation} @ {description}
 cylinder @ R @ x^2 + y^2 - R^2 = 0 @ Cylinder along z-axis, axis going through (0,0,0)
 cylinder_dent @ R l a @ x^2 + y^2 - r(z)^2 = 0, r(x) = R if | z | > l, r(z) = R - a*(1 + cos(z/l))/2 otherwise @ A cylinder with a dent around z = 0
-dumbbell @ a A B c @ -( x^2 + y^2 ) * (a^2 - z^2/c^2) * ( 1 + (A*sin(B*z^2))^4) = 0 @ A dumbbell @
+dumbbell @ a A B c @ -( x^2 + y^2 ) + (a^2 - z^2/c^2) * ( 1 + (A*sin(B*z^2))^4) = 0 @ A dumbbell
 ellipsoid @ a  b c @ (x/a)^2 + (y/b)^2 + (z/c)^2 = 0 @ An ellipsoid
+gaussian_bump @ A l rc1 rc2 @ if( x < rc1) -z + A * exp( -x^2 / (2 l^2) ); else if( x < rc2 ) -z + a + b*x + c*x^2 + d*x^3; else z @ A Gaussian bump at x = y = 0, smoothly tapered to a flat plane z = 0.
 plane @ a b c x0 y0 z0 @ a*(x-x0) + b*(y-y0) + c*(z-z0) = 0 @ A plane with normal (a,b,c) going through point (x0,y0,z0)
 plane_wiggle @ a w @ z - a*sin(w*x) = 0 @ A plane with a sinusoidal modulation on z along x.
 sphere @ R @ x^2 + y^2 + z^2 - R^2 = 0 @ A sphere of radius R
 supersphere @ R q @ | x |^q + | y |^q + | z |^q - R^q = 0 @ A supersphere of hyperradius R
-spine @ a, A, B, B2, c @ -(x^2 + y^2)*(a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise  @ An approximation to a dendtritic spine
-spine_two @ a, A, B, B2, c @ -(x^2 + y^2)*(a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise  @ Another approximation to a dendtritic spine
+spine @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise  @ An approximation to a dendtritic spine
+spine_two @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise  @ Another approximation to a dendtritic spine
 thylakoid @ wB LB lB @ Various, see "(Paquay)"_#Paquay1 @ A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB
 torus @ R r  @  (R - sqrt( x^2 + y^2 ) )^2 + z^2 - r^2  @ A torus with large radius R and small radius r, centered on (0,0,0) :tb(s=@)
 

doc/src/neb.txt

@@ -10,28 +10,31 @@ neb command :h3
 
 [Syntax:]
 
-neb etol ftol N1 N2 Nevery file-style arg :pre
+neb etol ftol N1 N2 Nevery file-style arg keyword :pre
 
 etol = stopping tolerance for energy (energy units) :ulb,l
 ftol = stopping tolerance for force (force units) :l
 N1 = max # of iterations (timesteps) to run initial NEB :l
 N2 = max # of iterations (timesteps) to run barrier-climbing NEB :l
 Nevery = print replica energies and reaction coordinates every this many timesteps :l
-file-style= {final} or {each} or {none} :l
+file-style = {final} or {each} or {none} :l
   {final} arg = filename
     filename = file with initial coords for final replica
-      coords for intermediate replicas are linearly interpolated between first and last replica
+      coords for intermediate replicas are linearly interpolated
+      between first and last replica
   {each} arg = filename
-    filename = unique filename for each replica (except first) with its initial coords
-  {none} arg = no argument
-    all replicas assumed to already have their initial coords :pre
+    filename = unique filename for each replica (except first)
+      with its initial coords
+  {none} arg = no argument all replicas assumed to already have
+      their initial coords :pre
+keyword = {verbose}
 :ule
 
 [Examples:]
 
 neb 0.1 0.0 1000 500 50 final coords.final
 neb 0.0 0.001 1000 500 50 each coords.initial.$i
-neb 0.0 0.001 1000 500 50 none :pre
+neb 0.0 0.001 1000 500 50 none verbose :pre
 
 [Description:]
 
@@ -43,8 +46,8 @@ NEB is a method for finding both the atomic configurations and height
 of the energy barrier associated with a transition state, e.g. for an
 atom to perform a diffusive hop from one energy basin to another in a
 coordinated fashion with its neighbors.  The implementation in LAMMPS
-follows the discussion in these 3 papers: "(HenkelmanA)"_#HenkelmanA,
-"(HenkelmanB)"_#HenkelmanB, and "(Nakano)"_#Nakano3.
+follows the discussion in these 4 papers: "(HenkelmanA)"_#HenkelmanA,
+"(HenkelmanB)"_#HenkelmanB, "(Nakano)"_#Nakano3 and "(Maras)"_#Maras2.
 
 Each replica runs on a partition of one or more processors.  Processor
 partitions are defined at run-time using the -partition command-line
@@ -70,18 +73,17 @@ I.e. the simulation domain, the number of atoms, the interaction
 potentials, and the starting configuration when the neb command is
 issued should be the same for every replica.
 
-In a NEB calculation each atom in a replica is connected to the same
-atom in adjacent replicas by springs, which induce inter-replica
-forces.  These forces are imposed by the "fix neb"_fix_neb.html
-command, which must be used in conjunction with the neb command.  The
-group used to define the fix neb command defines the NEB atoms which
-are the only ones that inter-replica springs are applied to.  If the
-group does not include all atoms, then non-NEB atoms have no
-inter-replica springs and the forces they feel and their motion is
-computed in the usual way due only to other atoms within their
-replica.  Conceptually, the non-NEB atoms provide a background force
-field for the NEB atoms.  They can be allowed to move during the NEB
-minimization procedure (which will typically induce different
+In a NEB calculation each replica is connected to other replicas by
+inter-replica nudging forces.  These forces are imposed by the "fix
+neb"_fix_neb.html command, which must be used in conjunction with the
+neb command.  The group used to define the fix neb command defines the
+NEB atoms which are the only ones that inter-replica springs are
+applied to.  If the group does not include all atoms, then non-NEB
+atoms have no inter-replica springs and the forces they feel and their
+motion is computed in the usual way due only to other atoms within
+their replica.  Conceptually, the non-NEB atoms provide a background
+force field for the NEB atoms.  They can be allowed to move during the
+NEB minimization procedure (which will typically induce different
 coordinates for non-NEB atoms in different replicas), or held fixed
 using other LAMMPS commands such as "fix setforce"_fix_setforce.html.
 Note that the "partition"_partition.html command can be used to invoke
@@ -93,33 +95,18 @@ specified in different manners via the {file-style} setting, as
 discussed below.  Only atoms whose initial coordinates should differ
 from the current configuration need be specified.
 
-Conceptually, the initial configuration for the first replica should
-be a state with all the atoms (NEB and non-NEB) having coordinates on
-one side of the energy barrier.  A perfect energy minimum is not
-required, since atoms in the first replica experience no spring forces
-from the 2nd replica.  Thus the damped dynamics minimization will
-drive the first replica to an energy minimum if it is not already
-there.  However, you will typically get better convergence if the
-initial state is already at a minimum.  For example, for a system with
-a free surface, the surface should be fully relaxed before attempting
-a NEB calculation.
-
-Likewise, the initial configuration of the final replica should be a
-state with all the atoms (NEB and non-NEB) on the other side of the
-energy barrier.  Again, a perfect energy minimum is not required,
-since the atoms in the last replica also experience no spring forces
-from the next-to-last replica, and thus the damped dynamics
-minimization will drive it to an energy minimum.
+Conceptually, the initial and final configurations for the first
+replica should be states on either side of an energy barrier.
 
 As explained below, the initial configurations of intermediate
 replicas can be atomic coordinates interpolated in a linear fashion
-between the first and last replicas.  This is often adequate state for
+between the first and last replicas.  This is often adequate for
 simple transitions.  For more complex transitions, it may lead to slow
 convergence or even bad results if the minimum energy path (MEP, see
 below) of states over the barrier cannot be correctly converged to
-from such an initial configuration.  In this case, you will want to
-generate initial states for the intermediate replicas that are
-geometrically closer to the MEP and read them in.
+from such an initial path.  In this case, you will want to generate
+initial states for the intermediate replicas that are geometrically
+closer to the MEP and read them in.
 
 :line
 
@@ -135,10 +122,11 @@ is assigned to be a fraction of the distance.  E.g. if there are 10
 replicas, the 2nd replica will assign a position that is 10% of the
 distance along a line between the starting and final point, and the
 9th replica will assign a position that is 90% of the distance along
-the line.  Note that this procedure to produce consistent coordinates
-across all the replicas, the current coordinates need to be the same
-in all replicas.  LAMMPS does not check for this, but invalid initial
-configurations will likely result if it is not the case.
+the line.  Note that for this procedure to produce consistent
+coordinates across all the replicas, the current coordinates need to
+be the same in all replicas.  LAMMPS does not check for this, but
+invalid initial configurations will likely result if it is not the
+case.
 
 NOTE: The "distance" between the starting and final point is
 calculated in a minimum-image sense for a periodic simulation box.
@@ -150,8 +138,8 @@ interpolation is outside the periodic box, the atom will be wrapped
 back into the box when the NEB calculation begins.
 
 For a {file-style} setting of {each}, a filename is specified which is
-assumed to be unique to each replica.  This can be done by
-using a variable in the filename, e.g.
+assumed to be unique to each replica.  This can be done by using a
+variable in the filename, e.g.
 
 variable i equal part
 neb 0.0 0.001 1000 500 50 each coords.initial.$i :pre
@@ -198,11 +186,10 @@ The minimizer tolerances for energy and force are set by {etol} and
 A non-zero {etol} means that the NEB calculation will terminate if the
 energy criterion is met by every replica.  The energies being compared
 to {etol} do not include any contribution from the inter-replica
-forces, since these are non-conservative.  A non-zero {ftol} means
-that the NEB calculation will terminate if the force criterion is met
-by every replica.  The forces being compared to {ftol} include the
-inter-replica forces between an atom and its images in adjacent
-replicas.
+nudging forces, since these are non-conservative.  A non-zero {ftol}
+means that the NEB calculation will terminate if the force criterion
+is met by every replica.  The forces being compared to {ftol} include
+the inter-replica nudging forces.
 
 The maximum number of iterations in each stage is set by {N1} and
 {N2}.  These are effectively timestep counts since each iteration of
@@ -220,27 +207,27 @@ finding a good energy barrier.  {N1} and {N2} must both be multiples
 of {Nevery}.
 
 In the first stage of NEB, the set of replicas should converge toward
-the minimum energy path (MEP) of conformational states that transition
-over the barrier.  The MEP for a barrier is defined as a sequence of
-3N-dimensional states that cross the barrier at its saddle point, each
-of which has a potential energy gradient parallel to the MEP itself.
-The replica states will also be roughly equally spaced along the MEP
-due to the inter-replica spring force added by the "fix
-neb"_fix_neb.html command.
+a minimum energy path (MEP) of conformational states that transition
+over a barrier.  The MEP for a transition is defined as a sequence of
+3N-dimensional states, each of which has a potential energy gradient
+parallel to the MEP itself.  The configuration of highest energy along
+a MEP corresponds to a saddle point.  The replica states will also be
+roughly equally spaced along the MEP due to the inter-replica nugding
+force added by the "fix neb"_fix_neb.html command.
 
-In the second stage of NEB, the replica with the highest energy
-is selected and the inter-replica forces on it are converted to a
-force that drives its atom coordinates to the top or saddle point of
-the barrier, via the barrier-climbing calculation described in
+In the second stage of NEB, the replica with the highest energy is
+selected and the inter-replica forces on it are converted to a force
+that drives its atom coordinates to the top or saddle point of the
+barrier, via the barrier-climbing calculation described in
 "(HenkelmanB)"_#HenkelmanB.  As before, the other replicas rearrange
 themselves along the MEP so as to be roughly equally spaced.
 
 When both stages are complete, if the NEB calculation was successful,
-one of the replicas should be an atomic configuration at the top or
-saddle point of the barrier, the potential energies for the set of
-replicas should represent the energy profile of the barrier along the
-MEP, and the configurations of the replicas should be a sequence of
-configurations along the MEP.
+the configurations of the replicas should be along (close to) the MEP
+and the replica with the highest energy should be an atomic
+configuration at (close to) the saddle point of the transition. The
+potential energies for the set of replicas represents the energy
+profile of the transition along the MEP.
 
 :line
 
@@ -284,9 +271,9 @@ ID2 x2 y2 z2
 ...
 IDN xN yN zN :pre
 
-The fields are the atom ID, followed by the x,y,z coordinates.
-The lines can be listed in any order.  Additional trailing information
-on the line is OK, such as a comment.
+The fields are the atom ID, followed by the x,y,z coordinates.  The
+lines can be listed in any order.  Additional trailing information on
+the line is OK, such as a comment.
 
 Note that for a typical NEB calculation you do not need to specify
 initial coordinates for very many atoms to produce differing starting
@@ -310,38 +297,54 @@ this case), the print-out to the screen and master log.lammps file
 contains a line of output, printed once every {Nevery} timesteps.  It
 contains the timestep, the maximum force per replica, the maximum
 force per atom (in any replica), potential gradients in the initial,
-final, and climbing replicas, the forward and backward energy barriers,
-the total reaction coordinate (RDT), and the normalized reaction
-coordinate and potential energy of each replica.
+final, and climbing replicas, the forward and backward energy
+barriers, the total reaction coordinate (RDT), and the normalized
+reaction coordinate and potential energy of each replica.
 
-The "maximum force per replica" is
-the two-norm of the 3N-length force vector for the atoms in each
-replica, maximized across replicas, which is what the {ftol} setting
-is checking against.  In this case, N is all the atoms in each
-replica.  The "maximum force per atom" is the maximum force component
-of any atom in any replica.  The potential gradients are the two-norm
-of the 3N-length force vector solely due to the interaction potential i.e.
-without adding in inter-replica forces. Note that inter-replica forces
-are zero in the initial and final replicas, and only affect
-the direction in the climbing replica. For this reason, the "maximum
-force per replica" is often equal to the potential gradient in the
-climbing replica. In the first stage of NEB, there is no climbing
-replica, and so the potential gradient in the highest energy replica
-is reported, since this replica will become the climbing replica
-in the second stage of NEB.
+The "maximum force per replica" is the two-norm of the 3N-length force
+vector for the atoms in each replica, maximized across replicas, which
+is what the {ftol} setting is checking against.  In this case, N is
+all the atoms in each replica.  The "maximum force per atom" is the
+maximum force component of any atom in any replica.  The potential
+gradients are the two-norm of the 3N-length force vector solely due to
+the interaction potential i.e.  without adding in inter-replica
+forces.
 
-The "reaction coordinate" (RD) for each
-replica is the two-norm of the 3N-length vector of distances between
-its atoms and the preceding replica's atoms, added to the RD of the
-preceding replica. The RD of the first replica RD1 = 0.0;
-the RD of the final replica RDN = RDT, the total reaction coordinate.
-The normalized RDs are divided by RDT,
-so that they form a monotonically increasing sequence
-from zero to one. When computing RD, N only includes the atoms
-being operated on by the fix neb command.
+The "reaction coordinate" (RD) for each replica is the two-norm of the
+3N-length vector of distances between its atoms and the preceding
+replica's atoms, added to the RD of the preceding replica. The RD of
+the first replica RD1 = 0.0; the RD of the final replica RDN = RDT,
+the total reaction coordinate.  The normalized RDs are divided by RDT,
+so that they form a monotonically increasing sequence from zero to
+one. When computing RD, N only includes the atoms being operated on by
+the fix neb command.
+
+The forward (reverse) energy barrier is the potential energy of the
+highest replica minus the energy of the first (last) replica.
+
+Supplementary informations for all replicas can be printed out to the
+screen and master log.lammps file by adding the verbose keyword. These
+informations include the following.  The "path angle" (pathangle) for
+the replica i which is the angle between the 3N-length vectors (Ri-1 -
+Ri) and (Ri+1 - Ri) (where Ri is the atomic coordinates of replica
+i). A "path angle" of 180 indicates that replicas i-1, i and i+1 are
+aligned.  "angletangrad" is the angle between the 3N-length tangent
+vector and the 3N-length force vector at image i. The tangent vector
+is calculated as in "(HenkelmanA)"_#HenkelmanA for all intermediate
+replicas and at R2 - R1 and RM - RM-1 for the first and last replica,
+respectively.  "anglegrad" is the angle between the 3N-length energy
+gradient vector of replica i and that of replica i+1. It is not
+defined for the final replica and reads nan.  gradV is the norm of the
+energy gradient of image i.  ReplicaForce is the two-norm of the
+3N-length force vector (including nudging forces) for replica i.
+MaxAtomForce is the maximum force component of any atom in replica i.
+
+When a NEB calculation does not converge properly, these suplementary
+informations can help understanding what is going wrong. For instance
+when the path angle becomes accute the definition of tangent used in
+the NEB calculation is questionable and the NEB cannot may diverge
+"(Maras)"_#Maras2.
 
-The forward (reverse) energy barrier is the potential energy of the highest
-replica minus the energy of the first (last) replica.
 
 When running on multiple partitions, LAMMPS produces additional log
 files for each partition, e.g. log.lammps.0, log.lammps.1, etc.  For a
@@ -396,12 +399,16 @@ This command can only be used if LAMMPS was built with the REPLICA
 package.  See the "Making LAMMPS"_Section_start.html#start_3 section
 for more info on packages.
 
+:line
+
 [Related commands:]
 
-"prd"_prd.html, "temper"_temper.html, "fix
-langevin"_fix_langevin.html, "fix viscous"_fix_viscous.html
+"prd"_prd.html, "temper"_temper.html, "fix langevin"_fix_langevin.html,
+"fix viscous"_fix_viscous.html
 
-[Default:] none
+[Default:]
+
+none
 
 :line
 
@@ -414,3 +421,7 @@ langevin"_fix_langevin.html, "fix viscous"_fix_viscous.html
 
 :link(Nakano3)
 [(Nakano)] Nakano, Comp Phys Comm, 178, 280-289 (2008).
+
+:link(Maras2)
+[(Maras)] Maras, Trushin, Stukowski, Ala-Nissila, Jonsson,
+Comp Phys Comm, 205, 13-21 (2016)

doc/src/package.txt

@@ -574,9 +574,9 @@ is used.  If it is not used, you must invoke the package intel
 command in your input script or or via the "-pk intel" "command-line
 switch"_Section_start.html#start_7.
 
-For the KOKKOS package, the option defaults neigh = full, neigh/qeq
- = full, newton = off, binsize = 0.0, and comm = device.  These settings
- are made automatically by the required "-k on" "command-line
+For the KOKKOS package, the option defaults neigh = full,
+neigh/qeq = full, newton = off, binsize = 0.0, and comm = device.
+These settings are made automatically by the required "-k on" "command-line
 switch"_Section_start.html#start_7.  You can change them bu using the
 package kokkos command in your input script or via the "-pk kokkos"
 "command-line switch"_Section_start.html#start_7.

doc/src/pair_agni.txt

@@ -40,8 +40,8 @@ vectorial atomic forces.
 
 Only a single pair_coeff command is used with the {agni} style which
 specifies an AGNI potential file containing the parameters of the
-force field for the needed elements. These are mapped to LAMMPS atom 
-types by specifying N additional arguments after the filename in the 
+force field for the needed elements. These are mapped to LAMMPS atom
+types by specifying N additional arguments after the filename in the
 pair_coeff command, where N is the number of LAMMPS atom types:
 
 filename
@@ -52,13 +52,13 @@ to specify the path for the force field file.
 
 An AGNI force field is fully specified by the filename which contains the
 parameters of the force field, i.e., the reference training environments
-used to construct the machine learning force field. Example force field 
-and input files are provided in the examples/USER/misc/agni directory. 
+used to construct the machine learning force field. Example force field
+and input files are provided in the examples/USER/misc/agni directory.
 
 :line
 
-Styles with {omp} suffix is functionally the same as the corresponding 
-style without the suffix. They have been optimized to run faster, depending 
+Styles with {omp} suffix is functionally the same as the corresponding
+style without the suffix. They have been optimized to run faster, depending
 on your available hardware, as discussed in "Section 5"_Section_accelerate.html
 of the manual.  The accelerated style takes the same arguments and
 should produce the same results, except for round-off and precision

doc/src/pair_buck.txt

@@ -75,7 +75,7 @@ Lennard-Jones 12/6) given by
 :c,image(Eqs/pair_buck.jpg)
 
 where rho is an ionic-pair dependent length parameter, and Rc is the
-cutoff on both terms. 
+cutoff on both terms.
 
 The styles with {coul/cut} or {coul/long} or {coul/msm} add a
 Coulombic term as described for the "lj/cut"_pair_lj.html pair styles.

doc/src/pair_charmm.txt

@@ -104,7 +104,15 @@ charmmfsw"_dihedral_charmm.html command.  Eventually code from the new
 styles will propagate into the related pair styles (e.g. implicit,
 accelerator, free energy variants).
 
-The general CHARMM formulas are as follows
+NOTE: The newest CHARMM pair styles reset the Coulombic energy
+conversion factor used internally in the code, from the LAMMPS value
+to the CHARMM value, as if it were effectively a parameter of the
+force field.  This is because the CHARMM code uses a slightly
+different value for the this conversion factor in "real
+units"_units.html (Kcal/mole), namely CHARMM = 332.0716, LAMMPS =
+332.06371.  This is to enable more precise agreement by LAMMPS with
+the CHARMM force field energies and forces, when using one of these
+two CHARMM pair styles.
 
 :c,image(Eqs/pair_charmm.jpg)
 

doc/src/pair_dipole.txt

@@ -71,6 +71,14 @@ and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the
 torques do not act symmetrically.  These formulas are discussed in
 "(Allen)"_#Allen2 and in "(Toukmaji)"_#Toukmaji2.
 
+Also note, that in the code, all of these terms (except Elj) have a
+C/epsilon prefactor, the same as the Coulombic term in the LJ +
+Coulombic pair styles discussed "here"_pair_lj.html.  C is an
+energy-conversion constant and epsilon is the dielectric constant
+which can be set by the "dielectric"_dielectric.html command.  The
+same is true of the equations that follow for other dipole pair
+styles.
+
 Style {lj/sf/dipole/sf} computes "shifted-force" interactions between
 pairs of particles that each have a charge and/or a point dipole
 moment. In general, a shifted-force potential is a (sligthly) modified

doc/src/pair_exp6_rx.txt

@@ -55,33 +55,33 @@ defined in the reaction kinetics files specified with the "fix
 rx"_fix_rx.html command or they must correspond to the tag "1fluid",
 signifying interaction with a product species mixture determined
 through a one-fluid approximation.  The interaction potential is
-weighted by the geometric average of either the mole fraction concentrations 
-or the number of molecules associated with the interacting coarse-grained 
-particles (see the {fractional} or {molecular} weighting pair style options). 
+weighted by the geometric average of either the mole fraction concentrations
+or the number of molecules associated with the interacting coarse-grained
+particles (see the {fractional} or {molecular} weighting pair style options).
 The coarse-grained potential is stored before and after the
 reaction kinetics solver is applied, where the difference is defined
 to be the internal chemical energy (uChem).
 
-The fourth argument specifies the type of scaling that will be used 
+The fourth argument specifies the type of scaling that will be used
 to scale the EXP-6 parameters as reactions occur.  Currently, there
 are three scaling options:  {exponent}, {polynomial} and {none}.
 
-Exponent scaling requires two additional arguments for scaling 
+Exponent scaling requires two additional arguments for scaling
 the {Rm} and {epsilon} parameters, respectively.  The scaling factor
-is computed by phi^exponent, where phi is the number of molecules  
-represented by the coarse-grain particle and exponent is specified 
+is computed by phi^exponent, where phi is the number of molecules
+represented by the coarse-grain particle and exponent is specified
 as a pair coefficient argument for {Rm} and {epsilon}, respectively.
-The {Rm} and {epsilon} parameters are multiplied by the scaling 
+The {Rm} and {epsilon} parameters are multiplied by the scaling
 factor to give the scaled interaction parameters for the CG particle.
 
-Polynomial scaling requires a filename to be specified as a pair 
+Polynomial scaling requires a filename to be specified as a pair
 coeff argument.  The file contains the coefficients to a fifth order
-polynomial for the {alpha}, {epsilon} and {Rm} parameters that depend 
-upon phi (the number of molecules represented by the CG particle). 
+polynomial for the {alpha}, {epsilon} and {Rm} parameters that depend
+upon phi (the number of molecules represented by the CG particle).
 The format of a polynomial file is provided below.
 
 The {none} option to the scaling does not have any additional pair coeff
-arguments.  This is equivalent to specifying the {exponent} option with 
+arguments.  This is equivalent to specifying the {exponent} option with
 {Rm} and {epsilon} exponents of 0.0 and 0.0, respectively.
 
 The final argument specifies the interaction cutoff (optional).
@@ -102,7 +102,7 @@ parenthesized comments):
 
 # POLYNOMIAL FILE          (one or more comment or blank lines) :pre
 #  General Functional Form:
-#  A*phi^5 + B*phi^4 + C*phi^3 + D*phi^2 + E*phi + F 
+#  A*phi^5 + B*phi^4 + C*phi^3 + D*phi^2 + E*phi + F
 #
 #  Parameter  A        B         C        D         E        F
                            (blank)

doc/src/pair_kolmogorov_crespi_z.txt

@@ -24,25 +24,25 @@ pair_coeff 1 2 kolmogorov/crespi/z  CC.KC      C C :pre
 
 [Description:]
 
-The {kolmogorov/crespi/z} style computes the Kolmogorov-Crespi interaction 
-potential as described in "(KC05)"_#KC05. An important simplification is made, 
-which is to take all normals along the z-axis. 
+The {kolmogorov/crespi/z} style computes the Kolmogorov-Crespi interaction
+potential as described in "(KC05)"_#KC05. An important simplification is made,
+which is to take all normals along the z-axis.
 
 :c,image(Eqs/pair_kolmogorov_crespi_z.jpg)
 
-It is important to have a suffiently large cutoff to ensure smooth forces. 
-Energies are shifted so that they go continously to zero at the cutoff assuming 
+It is important to have a suffiently large cutoff to ensure smooth forces.
+Energies are shifted so that they go continously to zero at the cutoff assuming
 that the exponential part of {Vij} (first term) decays sufficiently fast.
 This shift is achieved by the last term in the equation for {Vij} above.
 
-This potential is intended for interactions between two layers of graphene. 
-Therefore, to avoid interaction between layers in multi-layered materials, 
-each layer should have a separate atom type and interactions should only 
+This potential is intended for interactions between two layers of graphene.
+Therefore, to avoid interaction between layers in multi-layered materials,
+each layer should have a separate atom type and interactions should only
 be computed between atom types of neighbouring layers.
 
-The parameter file (e.g. CC.KC), is intended for use with metal 
-"units"_units.html, with energies in meV. An additional parameter, {S}, 
-is available to facilitate scaling of energies in accordance with 
+The parameter file (e.g. CC.KC), is intended for use with metal
+"units"_units.html, with energies in meV. An additional parameter, {S},
+is available to facilitate scaling of energies in accordance with
 "(vanWijk)"_#vanWijk.
 
 This potential must be used in combination with hybrid/overlay.
@@ -64,7 +64,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 :line
 
-:link(KC05) 
+:link(KC05)
 [(KC05)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
 
 :link(vanWijk)

doc/src/pair_lj_long.txt

@@ -7,6 +7,7 @@
 :line
 
 pair_style lj/long/coul/long command :h3
+pair_style lj/long/coul/long/intel command :h3
 pair_style lj/long/coul/long/omp command :h3
 pair_style lj/long/coul/long/opt command :h3
 pair_style lj/long/tip4p/long command :h3

doc/src/pair_lj_sf.txt

@@ -1,114 +0,0 @@
-"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
-
-pair_style lj/sf command :h3
-pair_style lj/sf/omp command :h3
-
-[Syntax:]
-
-pair_style lj/sf cutoff :pre
-
-cutoff = global cutoff for Lennard-Jones interactions (distance units) :ul
-
-[Examples:]
-
-pair_style lj/sf 2.5
-pair_coeff * * 1.0 1.0
-pair_coeff 1 1 1.0 1.0 3.0 :pre
-
-[Description:]
-
-Style {lj/sf} computes a truncated and force-shifted LJ interaction
-(Shifted Force Lennard-Jones), so that both the potential and the
-force go continuously to zero at the cutoff "(Toxvaerd)"_#Toxvaerd:
-
-:c,image(Eqs/pair_lj_sf.jpg)
-
-The following coefficients must be defined for each pair of atoms
-types via the "pair_coeff"_pair_coeff.html command as in the examples
-above, or in the data file or restart files read by the
-"read_data"_read_data.html or "read_restart"_read_restart.html
-commands, or by mixing as described below:
-
-epsilon (energy units)
-sigma (distance units)
-cutoff (distance units) :ul
-
-The last coefficient is optional. If not specified, the global
-LJ cutoff specified in the pair_style command is used.
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual.  The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Making
-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
-use the "suffix"_suffix.html command in your input script.
-
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Mixing, shift, table, tail correction, restart, rRESPA info]:
-
-For atom type pairs I,J and I != J, the epsilon and sigma
-coefficients and cutoff distance for this pair style can be mixed.
-Rin is a cutoff value and is mixed like the cutoff. The
-default mix value is {geometric}.  See the "pair_modify" command for
-details.
-
-The "pair_modify"_pair_modify.html shift option is not relevant for
-this pair style, since the pair interaction goes to 0.0 at the cutoff.
-
-The "pair_modify"_pair_modify.html table option is not relevant
-for this pair style.
-
-This pair style does not support the "pair_modify"_pair_modify.html
-tail option for adding long-range tail corrections to energy and
-pressure, since the energy of the pair interaction is smoothed to 0.0
-at the cutoff.
-
-This pair style writes its information to "binary restart
-files"_restart.html, so pair_style and pair_coeff commands do not need
-to be specified in an input script that reads a restart file.
-
-This pair style can only be used via the {pair} keyword of the
-"run_style respa"_run_style.html command.  It does not support the
-{inner}, {middle}, {outer} keywords.
-
-:line
-
-[Restrictions:]
-
-This pair style 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:]
-
-"pair_coeff"_pair_coeff.html
-
-[Default:] none
-
-:line
-
-:link(Toxvaerd)
-[(Toxvaerd)] Toxvaerd, Dyre, J Chem Phys, 134, 081102 (2011).

doc/src/pair_lj_smooth_linear.txt

@@ -11,26 +11,26 @@ pair_style lj/smooth/linear/omp command :h3
 
 [Syntax:]
 
-pair_style lj/smooth/linear Rc :pre
+pair_style lj/smooth/linear cutoff :pre
 
-Rc = cutoff for lj/smooth/linear interactions (distance units) :ul
+cutoff = global cutoff for Lennard-Jones interactions (distance units) :ul
 
 [Examples:]
 
-pair_style lj/smooth/linear 5.456108274435118
-pair_coeff * * 0.7242785984051078 2.598146797350056
-pair_coeff 1 1 20.0 1.3 9.0 :pre
+pair_style lj/smooth/linear 2.5
+pair_coeff * * 1.0 1.0
+pair_coeff 1 1 0.3 3.0 9.0 :pre
 
 [Description:]
 
-Style {lj/smooth/linear} computes a LJ interaction that combines the
-standard 12/6 Lennard-Jones function and subtracts a linear term that
-includes the cutoff distance Rc, as in this formula:
+Style {lj/smooth/linear} computes a truncated and force-shifted LJ
+interaction (aka Shifted Force Lennard-Jones) that combines the
+standard 12/6 Lennard-Jones function and subtracts a linear term based
+on the cutoff distance, so that both, the potential and the force, go
+continuously to zero at the cutoff Rc "(Toxvaerd)"_#Toxvaerd:
 
 :c,image(Eqs/pair_lj_smooth_linear.jpg)
 
-At the cutoff Rc, the energy and force (its 1st derivative) will be 0.0.
-
 The following coefficients must be defined for each pair of atoms
 types via the "pair_coeff"_pair_coeff.html command as in the examples
 above, or in the data file or restart files read by the
@@ -41,8 +41,8 @@ epsilon (energy units)
 sigma (distance units)
 cutoff (distance units) :ul
 
-The last coefficient is optional.  If not specified, the global value
-for Rc is used.
+The last coefficient is optional. If not specified, the global
+LJ cutoff specified in the pair_style command is used.
 
 :line
 
@@ -76,10 +76,11 @@ and cutoff distance can be mixed. The default mix value is geometric.
 See the "pair_modify" command for details.
 
 This pair style does not support the "pair_modify"_pair_modify.html
-shift option for the energy of the pair interaction.
+shift option for the energy of the pair interaction, since it goes
+to 0.0 at the cutoff by construction.
 
-The "pair_modify"_pair_modify.html table option is not relevant for
-this pair style.
+The "pair_modify"_pair_modify.html table option is not relevant
+for this pair style.
 
 This pair style does not support the "pair_modify"_pair_modify.html
 tail option for adding long-range tail corrections to energy and
@@ -103,3 +104,8 @@ This pair style can only be used via the {pair} keyword of the
 "pair_coeff"_pair_coeff.html, "pair lj/smooth"_pair_lj_smooth.html
 
 [Default:] none
+
+:line
+
+:link(Toxvaerd)
+[(Toxvaerd)] Toxvaerd, Dyre, J Chem Phys, 134, 081102 (2011).

doc/src/pair_meam.txt

@@ -7,10 +7,13 @@
 :line
 
 pair_style meam command :h3
+pair_style meam/c command :h3
 
 [Syntax:]
 
-pair_style meam :pre
+pair_style style :pre
+
+style = {meam} or {meam/c}
 
 [Examples:]
 
@@ -30,7 +33,8 @@ using modified embedded-atom method (MEAM) potentials
 "EAM potentials"_pair_eam.html which adds angular forces.  It is
 thus suitable for modeling metals and alloys with fcc, bcc, hcp and
 diamond cubic structures, as well as covalently bonded materials like
-silicon and carbon.
+silicon and carbon. Style {meam/c} is a translation of the {meam} code
+from (mostly) Fortran to C++. It is functionally equivalent to {meam}.
 
 In the MEAM formulation, the total energy E of a system of atoms is
 given by:
@@ -331,10 +335,14 @@ This pair style can only be used via the {pair} keyword of the
 
 [Restrictions:]
 
-This style is part of the MEAM package.  It is only enabled if LAMMPS
+The {meam} style is part of the MEAM package.  It is only enabled if LAMMPS
 was built with that package, which also requires the MEAM library be
-built and linked with LAMMPS.  See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built and linked with LAMMPS.
+The {meam/c} style is provided in the USER-MEAMC package. It is only enabled
+if LAMMPS was built with that package. In contrast to the {meam} style,
+{meam/c} does not require a separate library to be compiled and it can be
+instantiated multiple times in a "hybrid"_pair_hybrid.html pair style.
+See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
 
 [Related commands:]
 

doc/src/pair_morse.txt

@@ -26,7 +26,7 @@ args = list of arguments for a particular style :ul
  {morse/smooth/linear} args = cutoff
    cutoff = global cutoff for Morse interactions (distance units)
  {morse/soft} args = n lf cutoff
-   n = soft-core parameter
+   n       = soft-core parameter
    lf      = transformation range is lf < lambda < 1
    cutoff  = global cutoff for Morse interactions (distance units)
 :pre
@@ -36,7 +36,7 @@ args = list of arguments for a particular style :ul
 pair_style morse 2.5
 pair_style morse/smooth/linear 2.5
 pair_coeff * * 100.0 2.0 1.5
-pair_coeff 1 1 100.0 2.0 1.5 3.0
+pair_coeff 1 1 100.0 2.0 1.5 3.0 :pre
 
 pair_style morse/soft 4 0.9 10.0
 pair_coeff * * 100.0 2.0 1.5 1.0

doc/src/pair_multi_lucy_rx.txt

@@ -97,9 +97,9 @@ tags must either correspond to the species defined in the reaction
 kinetics files specified with the "fix rx"_fix_rx.html command or they
 must correspond to the tag "1fluid", signifying interaction with a
 product species mixture determined through a one-fluid approximation.
-The interaction potential is weighted by the geometric average of 
-either the mole fraction concentrations or the number of molecules 
-associated with the interacting coarse-grained particles (see the 
+The interaction potential is weighted by the geometric average of
+either the mole fraction concentrations or the number of molecules
+associated with the interacting coarse-grained particles (see the
 {fractional} or {molecular} weighting pair style options). The coarse-grained potential is
 stored before and after the reaction kinetics solver is applied, where
 the difference is defined to be the internal chemical energy (uChem).

doc/src/pair_nb3b_harmonic.txt

@@ -80,10 +80,12 @@ For a given entry, if the first three arguments are all different,
 then the entry is for the {K} and {theta_0} parameters (the cutoff in
 this case is irrelevant).
 
-It is {not} required that the potential file contain entries for all
-of the elements listed in the pair_coeff command.  It can also contain
-entries for additional elements not being used in a particular
-simulation; LAMMPS ignores those entries.
+It is required that the potential file contains entries for {all}
+permutations of the elements listed in the pair_coeff command.
+If certain combinations are not parameterized the corresponding
+parameters should be set to zero. The potential file can also
+contain entries for additional elements which are not used in
+a particular simulation; LAMMPS ignores those entries.
 
 :line
 

doc/src/pair_oxdna.txt

@@ -39,17 +39,17 @@ pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1
 
 [Description:]
 
-The {oxdna} pair styles compute the pairwise-additive parts of the oxDNA force field 
-for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the 
+The {oxdna} pair styles compute the pairwise-additive parts of the oxDNA force field
+for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
 excluded volume interaction {oxdna/excv}, the stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
 and coaxial stacking interaction {oxdna/coaxstk} as well
 as the hydrogen-bonding interaction {oxdna/hbond} between complementary pairs of nucleotides on
 opposite strands.
 
-The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients 
-in the above example. The individual potentials consist of products of modulation factors, 
-which themselves are constructed from a number of more basic potentials 
-(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms. 
+The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients
+in the above example. The individual potentials consist of products of modulation factors,
+which themselves are constructed from a number of more basic potentials
+(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
 We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil1 and "(Ouldridge)"_#Ouldridge1
 for a detailed description of the oxDNA force field.
 
@@ -57,8 +57,8 @@ NOTE: These pair styles have to be used together with the related oxDNA bond sty
 {oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of
 "bond_style oxdna/fene"_bond_oxdna.html). With one exception the coefficients
 in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
-The exception is the first coefficient after {oxdna/stk} (T=0.1 in the above example).  
-When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html 
+The exception is the first coefficient after {oxdna/stk} (T=0.1 in the above example).
+When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html
 or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
 the temperature coefficients have to be matched to the one used in the fix.
 
@@ -79,7 +79,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]
 
-"bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html, 
+"bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html,
 "bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html
 
 [Default:] none

doc/src/pair_oxdna2.txt

@@ -45,17 +45,17 @@ pair_coeff * * oxdna2/dh      0.1 1.0 0.815 :pre
 
 [Description:]
 
-The {oxdna2} pair styles compute the pairwise-additive parts of the oxDNA force field 
-for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the 
+The {oxdna2} pair styles compute the pairwise-additive parts of the oxDNA force field
+for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
 excluded volume interaction {oxdna2/excv}, the stacking {oxdna2/stk}, cross-stacking {oxdna2/xstk}
 and coaxial stacking interaction {oxdna2/coaxstk}, electrostatic Debye-Hueckel interaction {oxdna2/dh}
 as well as the hydrogen-bonding interaction {oxdna2/hbond} between complementary pairs of nucleotides on
 opposite strands.
 
-The exact functional form of the pair styles is rather complex. 
-The individual potentials consist of products of modulation factors, 
-which themselves are constructed from a number of more basic potentials 
-(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms. 
+The exact functional form of the pair styles is rather complex.
+The individual potentials consist of products of modulation factors,
+which themselves are constructed from a number of more basic potentials
+(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
 We refer to "(Snodin)"_#Snodin and the original oxDNA publications "(Ouldridge-DPhil)"_#Ouldridge-DPhil2
 and  "(Ouldridge)"_#Ouldridge2 for a detailed description of the oxDNA2 force field.
 
@@ -63,7 +63,7 @@ NOTE: These pair styles have to be used together with the related oxDNA2 bond st
 {oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of
 "bond_style oxdna2/fene"_bond_oxdna.html). Almost all coefficients
 in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
-Exceptions are the first coefficient after {oxdna2/stk} (T=0.1 in the above example) and the coefficients 
+Exceptions are the first coefficient after {oxdna2/stk} (T=0.1 in the above example) and the coefficients
 after {oxdna2/dh} (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat
 e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
 the temperature coefficients have to be matched to the one used in the fix.
@@ -86,7 +86,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
 [Related commands:]
 
 "bond_style oxdna2/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html,
-"bond_style oxdna/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html 
+"bond_style oxdna/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html
 
 [Default:] none
 

doc/src/pair_python.txt

@@ -74,7 +74,7 @@ placeholders for atom types that will be used with other potentials.
 The python potential file has to start with the following code:
 
 from __future__ import print_function
-
+#
 class LAMMPSPairPotential(object):
     def __init__(self):
         self.pmap=dict()
@@ -163,9 +163,10 @@ pair_write  1 1 2000 rsq 0.01 2.5 lj1_lj2.table lj :pre
 
 Note that it is strongly recommended to try to [delete] the potential
 table file before generating it. Since the {pair_write} command will
-always append to a table file, which pair style table will use the
-first match. Thus when changing the potential function in the python
-class, the table pair style will still read the old variant.
+always [append] to a table file, while pair style table will use the
+[first match]. Thus when changing the potential function in the python
+class, the table pair style will still read the old variant unless the
+table file is first deleted.
 
 After switching the pair style to {table}, the potential tables need
 to be assigned to the LAMMPS atom types like this:

doc/src/pair_reaxc.txt

@@ -8,6 +8,7 @@
 
 pair_style reax/c command :h3
 pair_style reax/c/kk command :h3
+pair_style reax/c/omp command :h3
 
 [Syntax:]
 

doc/src/pair_snap.txt

@@ -10,7 +10,8 @@ pair_style snap command :h3
 
 [Syntax:]
 
-pair_style snap :pre
+pair_style snap
+:pre
 
 [Examples:]
 
@@ -19,11 +20,11 @@ pair_coeff * * InP.snapcoeff In P InP.snapparam In In P P :pre
 
 [Description:]
 
-Style {snap} computes interactions
+Pair style {snap} computes interactions
 using the spectral neighbor analysis potential (SNAP)
 "(Thompson)"_#Thompson20142. Like the GAP framework of Bartok et al.
 "(Bartok2010)"_#Bartok20102, "(Bartok2013)"_#Bartok2013
-it uses bispectrum components
+which uses bispectrum components
 to characterize the local neighborhood of each atom
 in a very general way. The mathematical definition of the
 bispectrum calculation used by SNAP is identical
@@ -139,10 +140,15 @@ The default values for these keywords are
 {rmin0} = 0.0
 {diagonalstyle} = 3
 {switchflag} = 0
-{bzeroflag} = 1 :ul
+{bzeroflag} = 1
+{quadraticflag} = 1 :ul
 
-Detailed definitions of these keywords are given on the "compute
+Detailed definitions for all the keywords are given on the "compute
 sna/atom"_compute_sna_atom.html doc page.
+If {quadraticflag} is set to 1, then the SNAP energy expression includes the quadratic term,
+0.5*B^t.alpha.B, where alpha is a symmetric {K} by {K} matrix.
+The SNAP element file should contain {K}({K}+1)/2 additional coefficients
+for each element, the upper-triangular elements of alpha.
 
 :line
 

doc/src/pair_table_rx.txt

@@ -85,9 +85,9 @@ tags must either correspond to the species defined in the reaction
 kinetics files specified with the "fix rx"_fix_rx.html command or they
 must correspond to the tag "1fluid", signifying interaction with a
 product species mixture determined through a one-fluid approximation.
-The interaction potential is weighted by the geometric average of 
-either the mole fraction concentrations or the number of molecules 
-associated with the interacting coarse-grained particles (see the 
+The interaction potential is weighted by the geometric average of
+either the mole fraction concentrations or the number of molecules
+associated with the interacting coarse-grained particles (see the
 {fractional} or {molecular} weighting pair style options). The coarse-grained potential is
 stored before and after the reaction kinetics solver is applied, where
 the difference is defined to be the internal chemical energy (uChem).

doc/src/pair_vashishta.txt

@@ -7,6 +7,7 @@
 :line
 
 pair_style vashishta command :h3
+pair_style vashishta/gpu command :h3
 pair_style vashishta/omp command :h3
 pair_style vashishta/kk command :h3
 pair_style vashishta/table command :h3

doc/src/pair_zero.txt

@@ -14,7 +14,7 @@ pair_style zero cutoff {nocoeff} :pre
 
 zero = style name of this pair style
 cutoff = global cutoff (distance units)
-nocoeff = ignore all pair_coeff parameters (optional) :l
+nocoeff = ignore all pair_coeff parameters (optional) :ul
 
 [Examples:]
 

doc/src/pairs.txt

@@ -49,7 +49,6 @@ Pair Styles :h1
    pair_lj_cubic
    pair_lj_expand
    pair_lj_long
-   pair_lj_sf
    pair_lj_smooth
    pair_lj_smooth_linear
    pair_lj_soft

doc/src/python.txt

@@ -489,7 +489,7 @@ python"_Section_python.html.  Note that it is important that the
 stand-alone LAMMPS executable and the LAMMPS shared library be
 consistent (built from the same source code files) in order for this
 to work.  If the two have been built at different times using
-different source files, problems may occur. 
+different source files, problems may occur.
 
 [Related commands:]
 

doc/src/read_data.txt

@@ -14,7 +14,7 @@ read_data file keyword args ... :pre
 
 file = name of data file to read in :ulb,l
 zero or more keyword/arg pairs may be appended :l
-keyword = {add} or {offset} or {shift} or {extra/atom/types} or {extra/bond/types} or {extra/angle/types} or {extra/dihedral/types} or {extra/improper/types} or {group} or {nocoeff} or {fix} :l
+keyword = {add} or {offset} or {shift} or {extra/atom/types} or {extra/bond/types} or {extra/angle/types} or {extra/dihedral/types} or {extra/improper/types} or {extra/bond/per/atom} or {extra/angle/per/atom} or {extra/dihedral/per/atom} or {extra/improper/per/atom} or {group} or {nocoeff} or {fix} :l
   {add} arg = {append} or {Nstart} or {merge}
     append = add new atoms with IDs appended to current IDs
     Nstart = add new atoms with IDs starting with Nstart
@@ -32,6 +32,11 @@ keyword = {add} or {offset} or {shift} or {extra/atom/types} or {extra/bond/type
   {extra/angle/types} arg = # of extra angle types
   {extra/dihedral/types} arg = # of extra dihedral types
   {extra/improper/types} arg = # of extra improper types
+  {extra/bond/per/atom} arg = leave space for this many new bonds per atom
+  {extra/angle/per/atom} arg = leave space for this many new angles per atom
+  {extra/dihedral/per/atom} arg = leave space for this many new dihedrals per atom
+  {extra/improper/per/atom} arg = leave space for this many new impropers per atom
+  {extra/special/per/atom} arg = leave space for extra 1-2,1-3,1-4 interactions per atom
   {group} args = groupID
     groupID = add atoms in data file to this group
   {nocoeff} = ignore force field parameters
@@ -264,11 +269,11 @@ is different than the default.
 {angle types} = # of angle types in system
 {dihedral types} = # of dihedral types in system
 {improper types} = # of improper types in system
-{extra bond per atom} = leave space for this many new bonds per atom
-{extra angle per atom} = leave space for this many new angles per atom
-{extra dihedral per atom} = leave space for this many new dihedrals per atom
-{extra improper per atom} = leave space for this many new impropers per atom
-{extra special per atom} = leave space for this many new special bonds per atom
+{extra bond per atom} = leave space for this many new bonds per atom (deprecated, use extra/bond/per/atom keyword)
+{extra angle per atom} = leave space for this many new angles per atom (deprecated, use extra/angle/per/atom keyword)
+{extra dihedral per atom} = leave space for this many new dihedrals per atom (deprecated, use extra/dihedral/per/atom keyword)
+{extra improper per atom} = leave space for this many new impropers per atom (deprecated, use extra/improper/per/atom keyword)
+{extra special per atom} = leave space for this many new special bonds per atom (deprecated, use extra/special/per/atom keyword)
 {ellipsoids} = # of ellipsoids in system
 {lines} = # of line segments in system
 {triangles} = # of triangles in system
@@ -367,25 +372,32 @@ read_data command will generate an error in this case.
 The "extra bond per atom" setting (angle, dihedral, improper) is only
 needed if new bonds (angles, dihedrals, impropers) will be added to
 the system when a simulation runs, e.g. by using the "fix
-bond/create"_fix_bond_create.html command.  This will pre-allocate
-space in LAMMPS data structures for storing the new bonds (angles,
+bond/create"_fix_bond_create.html command. Using this header flag
+is deprecated; please use the {extra/bond/per/atom} keyword (and
+correspondingly for angles, dihedrals and impropers) in the
+read_data command instead. Either will pre-allocate space in LAMMPS
+ data structures for storing the new bonds (angles,
 dihedrals, impropers).
 
 The "extra special per atom" setting is typically only needed if new
 bonds/angles/etc will be added to the system, e.g. by using the "fix
 bond/create"_fix_bond_create.html command.  Or if entire new molecules
-will be added to the system, e.g. by using the "fix
-deposit"_fix_deposit.html or "fix pour"_fix_pour.html commands, which
-will have more special 1-2,1-3,1-4 neighbors than any other molecules
-defined in the data file.  Using this setting will pre-allocate space
-in the LAMMPS data structures for storing these neighbors.  See the
+will be added to the system, e.g. by using the
+"fix deposit"_fix_deposit.html or "fix pour"_fix_pour.html commands,
+which will have more special 1-2,1-3,1-4 neighbors than any other
+molecules defined in the data file.  Using this header flag is
+deprecated; please use the {extra/special/per/atom} keyword instead.
+Using this setting will pre-allocate space in the LAMMPS data
+structures for storing these neighbors.  See the
 "special_bonds"_special_bonds.html and "molecule"_molecule.html doc
 pages for more discussion of 1-2,1-3,1-4 neighbors.
 
-NOTE: All of the "extra" settings are only used if they appear in the
-first data file read; see the description of the {add} keyword above
-for reading multiple data files.  If they appear in later data files,
-they are ignored.
+NOTE: All of the "extra" settings are only applied in the first data
+file read and when no simulation box has yet been created; as soon as
+the simulation box is created (and read_data implies that), these
+settings are {locked} and cannot be changed anymore. Please see the
+description of the {add} keyword above for reading multiple data files.
+If they appear in later data files, they are ignored.
 
 The "ellipsoids" and "lines" and "triangles" and "bodies" settings are
 only used with "atom_style ellipsoid or line or tri or

doc/src/run_style.txt

@@ -17,7 +17,7 @@ style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l
   {verlet/split} args = none
   {respa} args = N n1 n2 ... keyword values ...
     N = # of levels of rRESPA
-    n1, n2, ... = loop factor between rRESPA levels (N-1 values)
+    n1, n2, ... = loop factors between rRESPA levels (N-1 values)
     zero or more keyword/value pairings may be appended to the loop factors
     keyword = {bond} or {angle} or {dihedral} or {improper} or
               {pair} or {inner} or {middle} or {outer} or {hybrid} or {kspace}
@@ -55,7 +55,7 @@ style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l
 
 run_style verlet
 run_style respa 4 2 2 2 bond 1 dihedral 2 pair 3 kspace 4
-run_style respa 4 2 2 2 bond 1 dihedral 2 inner 3 5.0 6.0 outer 4 kspace 4 :pre
+run_style respa 4 2 2 2 bond 1 dihedral 2 inner 3 5.0 6.0 outer 4 kspace 4
 run_style respa 3 4 2 bond 1 hybrid 2 2 1 kspace 3 :pre
 
 [Description:]

doc/src/set.txt

@@ -80,6 +80,7 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
     value can be an atom-style variable (see below)
   {image} nx ny nz
     nx,ny,nz = which periodic image of the simulation box the atom is in
+    any of nx,ny,nz can be an atom-style variable (see below)
   {bond} value = bond type for all bonds between selected atoms
   {angle} value = angle type for all angles between selected atoms
   {dihedral} value = dihedral type for all dihedrals between selected atoms
@@ -363,9 +364,8 @@ A value of -1 means subtract 1 box length to get the true value.
 LAMMPS updates these flags as atoms cross periodic boundaries during
 the simulation.  The flags can be output with atom snapshots via the
 "dump"_dump.html command.  If a value of NULL is specified for any of
-nx,ny,nz, then the current image value for that dimension is
-unchanged.  For non-periodic dimensions only a value of 0 can be
-specified.  This keyword does not allow use of atom-style variables.
+nx,ny,nz, then the current image value for that dimension is unchanged.
+For non-periodic dimensions only a value of 0 can be specified.
 This command can be useful after a system has been equilibrated and
 atoms have diffused one or more box lengths in various directions.
 This command can then reset the image values for atoms so that they

doc/src/special_bonds.txt

@@ -65,7 +65,13 @@ sense to define permanent bonds between atoms that interact via these
 potentials, though such bonds may exist elsewhere in your system,
 e.g. when using the "pair_style hybrid"_pair_hybrid.html command.
 Thus LAMMPS ignores special_bonds settings when manybody potentials
-are calculated.
+are calculated.  Please note, that the existence of explicit bonds
+for atoms that are described by a manybody potential will alter the
+neigborlist and thus can render the computation of those interactions
+invalid, since those pairs are not only used to determine direct
+pairwise interactions but also neighbors of neighbors and more.
+The recommended course of action is to remove such bonds, or - if
+that is not possible - use a special bonds setting of 1.0 1.0 1.0.
 
 NOTE: Unlike some commands in LAMMPS, you cannot use this command
 multiple times in an incremental fashion: e.g. to first set the LJ

doc/src/tutorial_github.txt

@@ -86,7 +86,7 @@ machine via HTTPS:
 or, if you have set up your GitHub account for using SSH keys, via SSH:
 
   $ git clone git@github.com:<your user name>/lammps.git :pre
-  
+
 You can find the proper URL by clicking the "Clone or download"-button:
 
 :c,image(JPG/tutorial_https_block.png)

doc/src/tutorial_pylammps.txt

@@ -10,6 +10,7 @@ PyLammps Tutorial :h1
 
 <!-- RST
 .. contents::
+
 END_RST -->
 
 Overview :h2
@@ -35,7 +36,7 @@ lammps.PyLammps :h4
 
 higher-level abstraction built on top of original C-Types interface
 manipulation of Python objects
-communication with LAMMPS is hidden from API user 
+communication with LAMMPS is hidden from API user
 shorter, more concise Python
 better IPython integration, designed for quick prototyping :ul
 
@@ -327,7 +328,7 @@ IPyLammps Examples :h2
 
 Examples of IPython notebooks can be found in the python/examples/pylammps
 subdirectory. To open these notebooks launch {jupyter notebook} inside this
-directory and navigate to one of them. If you compiled and installed 
+directory and navigate to one of them. If you compiled and installed
 a LAMMPS shared library with exceptions, PNG, JPEG and FFMPEG support
 you should be able to rerun all of these notebooks.
 
@@ -398,19 +399,19 @@ natoms = L.system.natoms :pre
 for i in range(niterations):
     iatom = random.randrange(0, natoms)
     current_atom = L.atoms\[iatom\] :pre
-    
+
     x0, y0 = current_atom.position :pre
-    
+
     dx = deltamove * random.uniform(-1, 1)
     dy = deltamove * random.uniform(-1, 1) :pre
-    
+
     current_atom.position = (x0+dx, y0+dy) :pre
-    
+
     L.run(1, "pre no post no") :pre
-    
+
     e = L.eval("pe")
     energies.append(e) :pre
-    
+
     if e <= elast:
         naccept += 1
         elast = e
@@ -459,4 +460,4 @@ Feedback and Contributing :h2
 If you find this Python interface useful, please feel free to provide feedback
 and ideas on how to improve it to Richard Berger (richard.berger@temple.edu). We also
 want to encourage people to write tutorial style IPython notebooks showcasing LAMMPS usage
-and maybe their latest research results. 
+and maybe their latest research results.

examples/COUPLE/README

@@ -41,5 +41,8 @@ fortran             a simple wrapper on the LAMMPS library API that
  		      can be called from Fortran
 fortran2            a more sophisticated wrapper on the LAMMPS library API that
  		      can be called from Fortran
+fortran3            wrapper written by Nir Goldman (LLNL), as an
+                      extension to fortran2, used for calling LAMMPS
+                      from Fortran DFTB+ code
 
-Each sub-directory has its own README.
+Each sub-directory has its own README with more details.

examples/COUPLE/fortran3/LAMMPS-wrapper.cpp

@@ -0,0 +1,236 @@
+/* -----------------------------------------------------------------------
+    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+    www.cs.sandia.gov/~sjplimp/lammps.html
+    Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
+ 
+    Copyright (2003) Sandia Corporation.  Under the terms of Contract
+    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+    certain rights in this software.  This software is distributed under 
+    the GNU General Public License.
+ 
+    See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ------------------------------------------------------------------------
+    Contributing author:  Karl D. Hammond <karlh@ugcs.caltech.edu>
+                          University of Tennessee, Knoxville (USA), 2012
+------------------------------------------------------------------------- */
+
+/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself
+   provides a (I hope) robust Fortran interface to library.cpp and
+   library.h.  All functions herein COULD be added to library.cpp instead of
+   including this as a separate file. See the README for instructions. */
+
+#include <mpi.h>
+#include "LAMMPS-wrapper.h"
+#include <library.h>
+#include <lammps.h>
+#include <atom.h>
+#include <fix.h>
+#include <compute.h>
+#include <modify.h>
+#include <error.h>
+#include <cstdlib>
+
+using namespace LAMMPS_NS;
+
+void lammps_open_fortran_wrapper (int argc, char **argv,
+      MPI_Fint communicator, void **ptr)
+{
+   MPI_Comm C_communicator = MPI_Comm_f2c (communicator);
+   lammps_open (argc, argv, C_communicator, ptr);
+}
+
+int lammps_get_ntypes (void *ptr)
+{
+  class LAMMPS *lmp = (class LAMMPS *) ptr;
+  int ntypes = lmp->atom->ntypes;
+  return ntypes;
+}
+
+void lammps_error_all (void *ptr, const char *file, int line, const char *str)
+{
+   class LAMMPS *lmp = (class LAMMPS *) ptr;
+   lmp->error->all (file, line, str);
+}
+
+int lammps_extract_compute_vectorsize (void *ptr, char *id, int style)
+{
+   class LAMMPS *lmp = (class LAMMPS *) ptr;
+   int icompute = lmp->modify->find_compute(id);
+   if ( icompute < 0 ) return 0;
+   class Compute *compute = lmp->modify->compute[icompute];
+
+   if ( style == 0 )
+   {
+      if ( !compute->vector_flag )
+         return 0;
+      else
+         return compute->size_vector;
+   }
+   else if ( style == 1 )
+   {
+      return lammps_get_natoms (ptr);
+   }
+   else if ( style == 2 )
+   {
+      if ( !compute->local_flag )
+         return 0;
+      else
+         return compute->size_local_rows;
+   }
+   else
+      return 0;
+}
+
+void lammps_extract_compute_arraysize (void *ptr, char *id, int style,
+      int *nrows, int *ncols)
+{
+   class LAMMPS *lmp = (class LAMMPS *) ptr;
+   int icompute = lmp->modify->find_compute(id);
+   if ( icompute < 0 )
+   {
+      *nrows = 0;
+      *ncols = 0;
+   }
+   class Compute *compute = lmp->modify->compute[icompute];
+
+   if ( style == 0 )
+   {
+      if ( !compute->array_flag )
+      {
+         *nrows = 0;
+         *ncols = 0;
+      }
+      else
+      {
+         *nrows = compute->size_array_rows;
+         *ncols = compute->size_array_cols;
+      }
+   }
+   else if ( style == 1 )
+   {
+      if ( !compute->peratom_flag )
+      {
+         *nrows = 0;
+         *ncols = 0;
+      }
+      else
+      {
+         *nrows = lammps_get_natoms (ptr);
+         *ncols = compute->size_peratom_cols;
+      }
+   }
+   else if ( style == 2 )
+   {
+      if ( !compute->local_flag )
+      {
+         *nrows = 0;
+         *ncols = 0;
+      }
+      else
+      {
+         *nrows = compute->size_local_rows;
+         *ncols = compute->size_local_cols;
+      }
+   }
+   else
+   {
+      *nrows = 0;
+      *ncols = 0;
+   }
+
+   return;
+}
+
+int lammps_extract_fix_vectorsize (void *ptr, char *id, int style)
+{
+   class LAMMPS *lmp = (class LAMMPS *) ptr;
+   int ifix = lmp->modify->find_fix(id);
+   if ( ifix < 0 ) return 0;
+   class Fix *fix = lmp->modify->fix[ifix];
+
+   if ( style == 0 )
+   {
+      if ( !fix->vector_flag )
+         return 0;
+      else
+         return fix->size_vector;
+   }
+   else if ( style == 1 )
+   {
+      return lammps_get_natoms (ptr);
+   }
+   else if ( style == 2 )
+   {
+      if ( !fix->local_flag )
+         return 0;
+      else
+         return fix->size_local_rows;
+   }
+   else
+      return 0;
+}
+
+void lammps_extract_fix_arraysize (void *ptr, char *id, int style,
+      int *nrows, int *ncols)
+{
+   class LAMMPS *lmp = (class LAMMPS *) ptr;
+   int ifix = lmp->modify->find_fix(id);
+   if ( ifix < 0 )
+   {
+      *nrows = 0;
+      *ncols = 0;
+   }
+   class Fix *fix = lmp->modify->fix[ifix];
+
+   if ( style == 0 )
+   {
+      if ( !fix->array_flag )
+      {
+         *nrows = 0;
+         *ncols = 0;
+      }
+      else
+      {
+         *nrows = fix->size_array_rows;
+         *ncols = fix->size_array_cols;
+      }
+   }
+   else if ( style == 1 )
+   {
+      if ( !fix->peratom_flag )
+      {
+         *nrows = 0;
+         *ncols = 0;
+      }
+      else
+      {
+         *nrows = lammps_get_natoms (ptr);
+         *ncols = fix->size_peratom_cols;
+      }
+   }
+   else if ( style == 2 )
+   {
+      if ( !fix->local_flag )
+      {
+         *nrows = 0;
+         *ncols = 0;
+      }
+      else
+      {
+         *nrows = fix->size_local_rows;
+         *ncols = fix->size_local_cols;
+      }
+   }
+   else
+   {
+      *nrows = 0;
+      *ncols = 0;
+   }
+
+   return;
+
+}
+
+/* vim: set ts=3 sts=3 expandtab: */

examples/COUPLE/fortran3/LAMMPS-wrapper.h

@@ -0,0 +1,40 @@
+/* -----------------------------------------------------------------------
+    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+    www.cs.sandia.gov/~sjplimp/lammps.html
+    Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
+ 
+    Copyright (2003) Sandia Corporation.  Under the terms of Contract
+    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+    certain rights in this software.  This software is distributed under 
+    the GNU General Public License.
+ 
+    See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ------------------------------------------------------------------------
+    Contributing author:  Karl D. Hammond <karlh@ugcs.caltech.edu>
+                          University of Tennessee, Knoxville (USA), 2012
+------------------------------------------------------------------------- */
+
+/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself
+   provides a (I hope) robust Fortran interface to library.cpp and
+   library.h.  All prototypes herein COULD be added to library.h instead of
+   including this as a separate file. See the README for instructions. */
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* Prototypes for auxiliary functions */
+void lammps_open_fortran_wrapper (int, char**, MPI_Fint, void**);
+int lammps_get_ntypes (void*);
+int lammps_extract_compute_vectorsize (void*, char*, int);
+void lammps_extract_compute_arraysize (void*, char*, int, int*, int*);
+int lammps_extract_fix_vectorsize (void*, char*, int);
+void lammps_extract_fix_arraysize (void*, char*, int, int*, int*);
+void lammps_error_all (void*, const char*, int, const char*);
+
+#ifdef __cplusplus
+}
+#endif
+
+/* vim: set ts=3 sts=3 expandtab: */

examples/COUPLE/fortran3/LAMMPS-wrapper2.cpp

@@ -0,0 +1,57 @@
+/* -----------------------------------------------------------------------
+    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+    www.cs.sandia.gov/~sjplimp/lammps.html
+    Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
+ 
+    Copyright (2003) Sandia Corporation.  Under the terms of Contract
+    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+    certain rights in this software.  This software is distributed under 
+    the GNU General Public License.
+ 
+    See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ------------------------------------------------------------------------
+    Contributing author:  Karl D. Hammond <karlh@ugcs.caltech.edu>
+                          University of Tennessee, Knoxville (USA), 2012
+------------------------------------------------------------------------- */
+
+/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself
+   provides a (I hope) robust Fortran interface to library.cpp and
+   library.h.  All functions herein COULD be added to library.cpp instead of
+   including this as a separate file. See the README for instructions. */
+
+#include <mpi.h>
+#include "LAMMPS-wrapper2.h"
+#include <library.h>
+#include <lammps.h>
+#include <atom.h>
+#include <input.h>
+#include <modify.h>
+#include <fix.h>
+#include <fix_external.h>
+#include <compute.h>
+#include <modify.h>
+#include <error.h>
+#include <cstdlib>
+
+using namespace LAMMPS_NS;
+
+extern "C" void f_callback(void *, bigint, int, tagint *, double **, double **);
+
+void lammps_set_callback (void *ptr) {
+  class LAMMPS *lmp = (class LAMMPS *) ptr;
+  int ifix = lmp->modify->find_fix_by_style("external");
+  FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix];
+  fix->set_callback(f_callback, ptr);
+  return;
+}
+
+void lammps_set_user_energy (void *ptr, double energy) {
+  class LAMMPS *lmp = (class LAMMPS *) ptr;
+  int ifix = lmp->modify->find_fix_by_style("external");
+  FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix];
+  fix->set_energy(energy);
+  return;
+}
+

examples/COUPLE/fortran3/LAMMPS-wrapper2.h

@@ -0,0 +1,34 @@
+/* -----------------------------------------------------------------------
+    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+    www.cs.sandia.gov/~sjplimp/lammps.html
+    Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
+ 
+    Copyright (2003) Sandia Corporation.  Under the terms of Contract
+    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+    certain rights in this software.  This software is distributed under 
+    the GNU General Public License.
+ 
+    See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ------------------------------------------------------------------------
+    Contributing author:  Nir Goldman, ngoldman@llnl.gov, Oct. 19th, 2016
+------------------------------------------------------------------------- */
+
+/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself
+   provides a (I hope) robust Fortran interface to library.cpp and
+   library.h.  All prototypes herein COULD be added to library.h instead of
+   including this as a separate file. See the README for instructions. */
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* Prototypes for auxiliary functions */
+void lammps_set_callback (void *); 
+void lammps_set_user_energy (void*, double); 
+
+#ifdef __cplusplus
+}
+#endif
+
+/* vim: set ts=3 sts=3 expandtab: */

examples/COUPLE/fortran3/LAMMPS.F90

@@ -0,0 +1,956 @@
+!! -----------------------------------------------------------------------
+!   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+!   www.cs.sandia.gov/~sjplimp/lammps.html
+!   Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
+!
+!   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+!   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+!   certain rights in this software.  This software is distributed under 
+!   the GNU General Public License.
+!
+!   See the README file in the top-level LAMMPS directory.
+!--------------------------------------------------------------------------
+
+!! ------------------------------------------------------------------------
+!   Contributing author:  Karl D. Hammond <karlh@ugcs.caltech.edu>
+!                         University of Tennessee, Knoxville (USA), 2012
+!--------------------------------------------------------------------------
+
+!! LAMMPS, a Fortran 2003 module containing an interface between Fortran
+!! programs and the C-style functions in library.cpp that ship with LAMMPS.
+!! This file should be accompanied by LAMMPS-wrapper.cpp and LAMMPS-wrapper.h,
+!! which define wrapper functions that ease portability and enforce array
+!! dimensions.
+!!
+!! Everything in this module should be 100% portable by way of Fortran 2003's
+!! ISO_C_BINDING intrinsic module.  See the README for instructions for
+!! compilation and use.
+!!
+!! Here are the PUBLIC functions and subroutines included in this module.
+!!    subroutine lammps_open (command_line, communicator, ptr)
+!!    subroutine lammps_open_no_mpi (command_line, ptr)
+!!    subroutine lammps_close (ptr)
+!!    subroutine lammps_file (ptr, str)
+!!    subroutine lammps_command (ptr, str)
+!!    subroutine lammps_free (ptr)
+!!    subroutine lammps_extract_global (global, ptr, name)
+!!    subroutine lammps_extract_atom (atom, ptr, name)
+!!    subroutine lammps_extract_fix (fix, ptr, id, style, type, i, j)
+!!    subroutine lammps_extract_compute (compute, ptr, id, style, type)
+!!    subroutine lammps_extract_variable (variable, ptr, name, group)
+!!    function lammps_get_natoms (ptr)
+!!    subroutine lammps_gather_atoms (ptr, name, count, data)
+!!    subroutine lammps_scatter_atoms (ptr, name, data)
+
+#define FLERR __FILE__,__LINE__
+! The above line allows for similar error checking as is done with standard
+! LAMMPS files.
+
+module LAMMPS
+
+   use, intrinsic :: ISO_C_binding, only : C_double, C_int, C_ptr, C_char, &
+      C_NULL_CHAR, C_loc, C_F_pointer, lammps_instance => C_ptr
+   implicit none
+   private
+   public :: lammps_open, lammps_open_no_mpi, lammps_close, lammps_file, &
+      lammps_command, lammps_free, lammps_extract_global, &
+      lammps_extract_atom, lammps_extract_compute, lammps_extract_fix, &
+      lammps_extract_variable, lammps_get_natoms, lammps_gather_atoms, &
+      lammps_scatter_atoms, lammps_set_callback, lammps_set_user_energy
+   public :: lammps_instance, C_ptr, C_double, C_int
+
+   !! Functions supplemental to the prototypes in library.h. {{{1
+   !! The function definitions (in C++) are contained in LAMMPS-wrapper.cpp.
+   !! I would have written the first in Fortran, but the MPI libraries (which
+   !! were written in C) have C-based functions to convert from Fortran MPI
+   !! handles to C MPI handles, and there is no Fortran equivalent for those
+   !! functions.
+   interface
+      subroutine lammps_open_wrapper (argc, argv, communicator, ptr) &
+      bind (C, name='lammps_open_fortran_wrapper')
+         import :: C_int, C_ptr
+         integer (C_int), value :: argc
+         type (C_ptr), dimension(*) :: argv
+         integer, value :: communicator
+         type (C_ptr) :: ptr
+      end subroutine lammps_open_wrapper
+      subroutine lammps_actual_error_all (ptr, file, line, str) &
+      bind (C, name='lammps_error_all')
+         import :: C_int, C_char, C_ptr
+         type (C_ptr), value :: ptr
+         character (kind=C_char), dimension(*), intent(in) :: file, str
+         integer (C_int), value :: line
+      end subroutine lammps_actual_error_all
+      function lammps_get_ntypes (ptr) result (ntypes) &
+      bind (C, name='lammps_get_ntypes')
+         import :: C_int, C_ptr
+         type (C_ptr), value :: ptr
+         integer (C_int) :: ntypes
+      end function lammps_get_ntypes
+      function lammps_actual_extract_compute_vectorsize (ptr, id, style) &
+      result (vectorsize) bind (C, name='lammps_extract_compute_vectorsize')
+         import :: C_int, C_char, C_ptr
+         integer (C_int) :: vectorsize
+         type (C_ptr), value :: ptr
+         character (kind=C_char), dimension(*) :: id
+         integer (C_int), value :: style
+      end function lammps_actual_extract_compute_vectorsize
+      subroutine lammps_actual_extract_compute_arraysize (ptr, id, style, &
+            nrows, ncols) bind (C, name='lammps_extract_compute_arraysize')
+         import :: C_int, C_char, C_ptr
+         integer (C_int) :: arraysize
+         type (C_ptr), value :: ptr
+         character (kind=C_char), dimension(*) :: id
+         integer (C_int), value :: style
+         integer (C_int) :: nrows, ncols
+      end subroutine lammps_actual_extract_compute_arraysize
+      function lammps_actual_extract_fix_vectorsize (ptr, id, style) &
+      result (vectorsize) bind (C, name='lammps_extract_fix_vectorsize')
+         import :: C_int, C_char, C_ptr
+         integer (C_int) :: vectorsize
+         type (C_ptr), value :: ptr
+         character (kind=C_char), dimension(*) :: id
+         integer (C_int), value :: style
+      end function lammps_actual_extract_fix_vectorsize
+      subroutine lammps_actual_extract_fix_arraysize (ptr, id, style, &
+            nrows, ncols) bind (C, name='lammps_extract_fix_arraysize')
+         import :: C_int, C_char, C_ptr
+         type (C_ptr), value :: ptr
+         character (kind=C_char), dimension(*) :: id
+         integer (C_int), value :: style
+         integer (C_int) :: nrows, ncols
+      end subroutine lammps_actual_extract_fix_arraysize
+   end interface
+
+   !! Functions/subroutines defined in library.h and library.cpp {{{1
+   interface
+      subroutine lammps_actual_open_no_mpi (argc, argv, ptr) &
+      bind (C, name='lammps_open_no_mpi')
+         import :: C_int, C_ptr
+         integer (C_int), value :: argc
+         type (C_ptr), dimension(*) :: argv
+         type (C_ptr) :: ptr
+      end subroutine lammps_actual_open_no_mpi
+
+      subroutine lammps_close (ptr) bind (C, name='lammps_close')
+         import :: C_ptr
+         type (C_ptr), value :: ptr
+      end subroutine lammps_close
+
+      subroutine lammps_actual_file (ptr, str) bind (C, name='lammps_file')
+         import :: C_ptr, C_char
+         type (C_ptr), value :: ptr
+         character (kind=C_char), dimension(*) :: str
+      end subroutine lammps_actual_file
+
+      function lammps_actual_command (ptr, str) result (command) &
+      bind (C, name='lammps_command')
+         import :: C_ptr, C_char
+         type (C_ptr), value :: ptr
+         character (kind=C_char), dimension(*) :: str
+         type (C_ptr) :: command
+      end function lammps_actual_command
+
+      subroutine lammps_free (ptr) bind (C, name='lammps_free')
+         import :: C_ptr
+         type (C_ptr), value :: ptr
+      end subroutine lammps_free
+
+      function lammps_actual_extract_global (ptr, name) &
+      bind (C, name='lammps_extract_global') result (global)
+         import :: C_ptr, C_char
+         type (C_ptr), value :: ptr
+         character (kind=C_char), dimension(*) :: name
+         type (C_ptr) :: global
+      end function lammps_actual_extract_global
+
+      function lammps_actual_extract_atom (ptr, name) &
+      bind (C, name='lammps_extract_atom') result (atom)
+         import :: C_ptr, C_char
+         type (C_ptr), value :: ptr
+         character (kind=C_char), dimension(*) :: name
+         type (C_ptr) :: atom
+      end function lammps_actual_extract_atom
+
+      function lammps_actual_extract_compute (ptr, id, style, type) &
+      result (compute) bind (C, name='lammps_extract_compute')
+         import :: C_ptr, C_char, C_int
+         type (C_ptr), value :: ptr
+         character (kind=C_char), dimension(*) :: id
+         integer (C_int), value :: style, type
+         type (C_ptr) :: compute
+      end function lammps_actual_extract_compute
+
+      function lammps_actual_extract_fix (ptr, id, style, type, i, j) &
+      result (fix) bind (C, name='lammps_extract_fix')
+         import :: C_ptr, C_char, C_int
+         type (C_ptr), value :: ptr
+         character (kind=C_char), dimension(*) :: id
+         integer (C_int), value :: style, type, i, j
+         type (C_ptr) :: fix
+      end function lammps_actual_extract_fix
+
+      function lammps_actual_extract_variable (ptr, name, group) &
+      result (variable) bind (C, name='lammps_extract_variable')
+         import :: C_ptr, C_char
+         type (C_ptr), value :: ptr
+         character (kind=C_char), dimension(*) :: name, group
+         type (C_ptr) :: variable
+      end function lammps_actual_extract_variable
+
+      function lammps_get_natoms (ptr) result (natoms) &
+      bind (C, name='lammps_get_natoms')
+         import :: C_ptr, C_int
+         type (C_ptr), value :: ptr
+         integer (C_int) :: natoms
+      end function lammps_get_natoms
+ 
+      subroutine lammps_set_callback (ptr) &
+      bind (C, name='lammps_set_callback')
+        import :: C_ptr
+        type (C_ptr), value :: ptr
+      end subroutine lammps_set_callback
+
+      subroutine lammps_set_user_energy (ptr, energy) &
+      bind (C, name='lammps_set_user_energy')
+        import :: C_ptr, C_double 
+        type (C_ptr), value :: ptr
+        real(C_double), value :: energy
+      end subroutine lammps_set_user_energy 
+
+      subroutine lammps_actual_gather_atoms (ptr, name, type, count, data) &
+      bind (C, name='lammps_gather_atoms')
+         import :: C_ptr, C_int, C_char
+         type (C_ptr), value :: ptr, data
+         character (kind=C_char), dimension(*) :: name
+         integer (C_int), value :: type, count
+      end subroutine lammps_actual_gather_atoms
+
+      subroutine lammps_actual_scatter_atoms (ptr, name, type, count, data) &
+      bind (C, name='lammps_scatter_atoms')
+         import :: C_ptr, C_int, C_char
+         type (C_ptr), value :: ptr, data
+         character (kind=C_char), dimension(*) :: name
+         integer (C_int), value :: type, count
+      end subroutine lammps_actual_scatter_atoms
+   end interface
+
+   ! Generic functions for the wrappers below {{{1
+
+   interface lammps_extract_global
+      module procedure lammps_extract_global_i, &
+         lammps_extract_global_dp
+   end interface lammps_extract_global
+
+   interface lammps_extract_atom
+      module procedure lammps_extract_atom_ia, &
+         lammps_extract_atom_dpa, &
+         lammps_extract_atom_dp2a
+   end interface lammps_extract_atom
+
+   interface lammps_extract_compute
+      module procedure lammps_extract_compute_dp, &
+         lammps_extract_compute_dpa, &
+         lammps_extract_compute_dp2a
+   end interface lammps_extract_compute
+
+   interface lammps_extract_fix
+      module procedure lammps_extract_fix_dp, &
+         lammps_extract_fix_dpa, &
+         lammps_extract_fix_dp2a
+   end interface lammps_extract_fix
+
+   interface lammps_extract_variable
+      module procedure lammps_extract_variable_dp, &
+         lammps_extract_variable_dpa
+   end interface lammps_extract_variable
+
+   interface lammps_gather_atoms
+      module procedure lammps_gather_atoms_ia, lammps_gather_atoms_dpa
+   end interface lammps_gather_atoms
+
+   interface lammps_scatter_atoms
+      module procedure lammps_scatter_atoms_ia, lammps_scatter_atoms_dpa
+   end interface lammps_scatter_atoms
+
+contains !! Wrapper functions local to this module {{{1
+
+   subroutine lammps_open (command_line, communicator, ptr)
+      character (len=*), intent(in) :: command_line
+      integer, intent(in) :: communicator
+      type (C_ptr) :: ptr
+      integer (C_int) :: argc
+      type (C_ptr), dimension(:), allocatable :: argv
+      character (kind=C_char), dimension(len_trim(command_line)+1), target :: &
+         c_command_line
+      c_command_line = string2Cstring (command_line)
+      call Cstring2argcargv (c_command_line, argc, argv)
+      call lammps_open_wrapper (argc, argv, communicator, ptr)
+      deallocate (argv)
+   end subroutine lammps_open
+
+!-----------------------------------------------------------------------------
+
+   subroutine lammps_open_no_mpi (command_line, ptr)
+      character (len=*), intent(in) :: command_line
+      type (C_ptr) :: ptr
+      integer (C_int) :: argc
+      type (C_ptr), dimension(:), allocatable :: argv
+      character (kind=C_char), dimension(len_trim(command_line)+1), target :: &
+         c_command_line
+      c_command_line = string2Cstring (command_line)
+      call Cstring2argcargv (c_command_line, argc, argv)
+      call lammps_actual_open_no_mpi (argc, argv, ptr)
+      deallocate (argv)
+   end subroutine lammps_open_no_mpi
+
+!-----------------------------------------------------------------------------
+
+   subroutine lammps_file (ptr, str)
+      type (C_ptr) :: ptr
+      character (len=*) :: str
+      character (kind=C_char), dimension(len_trim(str)+1) :: Cstr
+      Cstr = string2Cstring (str)
+      call lammps_actual_file (ptr, Cstr)
+   end subroutine lammps_file
+
+!-----------------------------------------------------------------------------
+
+   subroutine lammps_command (ptr, str)
+      type (C_ptr) :: ptr
+      character (len=*) :: str
+      character (kind=C_char), dimension(len_trim(str)+1) :: Cstr
+      type (C_ptr) :: dummy
+      Cstr = string2Cstring (str)
+      dummy = lammps_actual_command (ptr, Cstr)
+   end subroutine lammps_command
+
+!-----------------------------------------------------------------------------
+
+! lammps_extract_global {{{2
+   function lammps_extract_global_Cptr (ptr, name) result (global)
+      type (C_ptr) :: global
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: name
+      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
+      Cname = string2Cstring (name)
+      global = lammps_actual_extract_global (ptr, Cname)
+   end function lammps_extract_global_Cptr
+   subroutine lammps_extract_global_i (global, ptr, name)
+      integer (C_int), pointer, intent(out) :: global
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: name
+      type (C_ptr) :: Cptr
+      Cptr = lammps_extract_global_Cptr (ptr, name)
+      call C_F_pointer (Cptr, global)
+   end subroutine lammps_extract_global_i
+   subroutine lammps_extract_global_dp (global, ptr, name)
+      real (C_double), pointer, intent(out) :: global
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: name
+      type (C_ptr) :: Cptr
+      Cptr = lammps_extract_global_Cptr (ptr, name)
+      call C_F_pointer (Cptr, global)
+   end subroutine lammps_extract_global_dp
+
+!-----------------------------------------------------------------------------
+
+! lammps_extract_atom {{{2
+   function lammps_extract_atom_Cptr (ptr, name) result (atom)
+      type (C_ptr) :: atom
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: name
+      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
+      Cname = string2Cstring (name)
+      atom = lammps_actual_extract_atom (ptr, Cname)
+   end function lammps_extract_atom_Cptr
+   subroutine lammps_extract_atom_ia (atom, ptr, name)
+      integer (C_int), dimension(:), pointer, intent(out) :: atom
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: name
+      type (C_ptr) :: Cptr
+      integer (C_int), pointer :: nelements
+      call lammps_extract_global_i (nelements, ptr, 'nlocal')
+      Cptr = lammps_extract_atom_Cptr (ptr, name)
+      call C_F_pointer (Cptr, atom, (/nelements/))
+   end subroutine lammps_extract_atom_ia
+   subroutine lammps_extract_atom_dpa (atom, ptr, name)
+      real (C_double), dimension(:), pointer, intent(out) :: atom
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: name
+      type (C_ptr) :: Cptr
+      integer (C_int), pointer :: nlocal
+      integer :: nelements
+      real (C_double), dimension(:), pointer :: Fptr
+      if ( name == 'mass' ) then
+         nelements = lammps_get_ntypes (ptr) + 1
+      else if ( name == 'x' .or. name == 'v' .or. name == 'f' .or. &
+                name == 'mu' .or. name == 'omega' .or. name == 'torque' .or. &
+                name == 'angmom' ) then
+         ! We should not be getting a rank-2 array here!
+         call lammps_error_all (ptr, FLERR, 'You cannot extract those atom&
+            & data (' // trim(name) // ') into a rank 1 array.')
+         return
+      else
+         ! Everything else we can get is probably nlocal units long
+         call lammps_extract_global_i (nlocal, ptr, 'nlocal')
+         nelements = nlocal
+      end if
+      Cptr = lammps_extract_atom_Cptr (ptr, name)
+      call C_F_pointer (Cptr, Fptr, (/nelements/))
+      if ( name == 'mass' ) then
+         !atom(0:) => Fptr
+         atom => Fptr
+      else
+         atom => Fptr
+      end if
+   end subroutine lammps_extract_atom_dpa
+   subroutine lammps_extract_atom_dp2a (atom, ptr, name)
+      real (C_double), dimension(:,:), pointer, intent(out) :: atom
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: name
+      type (C_ptr) :: Cptr
+      type (C_ptr), pointer, dimension(:) :: Catom
+      integer (C_int), pointer :: nelements
+      if ( name /= 'x' .and. name /= 'v' .and. name /= 'f' .and. &
+           name /= 'mu' .and. name /= 'omega' .and. name /= 'tandque' .and. &
+           name /= 'angmom' .and. name /= 'fexternal' ) then
+         ! We should not be getting a rank-2 array here!
+         call lammps_error_all (ptr, FLERR, 'You cannot extract those atom&
+            & data (' // trim(name) // ') into a rank 2 array.')
+         return
+      end if
+      Cptr = lammps_extract_atom_Cptr (ptr, name)
+      call lammps_extract_global_i (nelements, ptr, 'nlocal')
+      ! Catom will now be the array of void* pointers that the void** pointer
+      ! pointed to.  Catom(1) is now the pointer to the first element.
+      call C_F_pointer (Cptr, Catom, (/nelements/))
+      ! Now get the actual array, which has its shape transposed from what we
+      ! might think of it in C
+      call C_F_pointer (Catom(1), atom, (/3, nelements/))
+   end subroutine lammps_extract_atom_dp2a
+
+!-----------------------------------------------------------------------------
+
+! lammps_extract_compute {{{2
+   function lammps_extract_compute_Cptr (ptr, id, style, type) result (compute)
+      type (C_ptr) :: compute
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: id
+      integer, intent(in) :: style, type
+      integer (kind=C_int) :: Cstyle, Ctype
+      character (kind=C_char), dimension(len_trim(id)+1) :: Cid
+      Cid = string2Cstring (id)
+      Cstyle = style
+      Ctype = type
+      compute = lammps_actual_extract_compute (ptr, Cid, Cstyle, Ctype)
+   end function lammps_extract_compute_Cptr
+   subroutine lammps_extract_compute_dp (compute, ptr, id, style, type)
+      real (C_double), pointer, intent(out) :: compute
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: id
+      integer, intent(in) :: style, type
+      type (C_ptr) :: Cptr
+      ! The only valid values of (style,type) are (0,0) for scalar 'compute'
+      if ( style /= 0 ) then
+         call lammps_error_all (ptr, FLERR, 'You cannot pack per-atom/local&
+            & data into a scalar.')
+         return
+      end if
+      if ( type == 1 ) then
+         call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
+            & vector (rank 1) into a scalar.')
+         return
+      else if ( type == 2 ) then
+         call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
+            & array (rank 2) into a scalar.')
+         return
+      end if
+      Cptr = lammps_extract_compute_Cptr (ptr, id, style, type)
+      call C_F_pointer (Cptr, compute)
+   end subroutine lammps_extract_compute_dp
+   subroutine lammps_extract_compute_dpa (compute, ptr, id, style, type)
+      real (C_double), dimension(:), pointer, intent(out) :: compute
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: id
+      integer, intent(in) :: style, type
+      type (C_ptr) :: Cptr
+      integer :: nelements
+      ! Check for the correct dimensionality
+      if ( type == 0 ) then
+         call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
+            & scalar (rank 0) into a rank 1 variable.')
+         return
+      else if ( type == 2 ) then
+         call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
+            & array (rank 2) into a rank 1 variable.')
+         return
+      end if
+      nelements = lammps_extract_compute_vectorsize (ptr, id, style)
+      Cptr = lammps_extract_compute_Cptr (ptr, id, style, type)
+      call C_F_pointer (Cptr, compute, (/nelements/))
+   end subroutine lammps_extract_compute_dpa
+   subroutine lammps_extract_compute_dp2a (compute, ptr, id, style, type)
+      real (C_double), dimension(:,:), pointer, intent(out) :: compute
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: id
+      integer, intent(in) :: style, type
+      type (C_ptr) :: Cptr
+      type (C_ptr), pointer, dimension(:) :: Ccompute
+      integer :: nr, nc
+      ! Check for the correct dimensionality
+      if ( type == 0 ) then
+         call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
+            & scalar (rank 0) into a rank 2 variable.')
+         return
+      else if ( type == 1 ) then
+         call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
+            & array (rank 1) into a rank 2 variable.')
+         return
+      end if
+      call lammps_extract_compute_arraysize (ptr, id, style, nr, nc)
+      Cptr = lammps_extract_compute_Cptr (ptr, id, style, type)
+      call C_F_pointer (Cptr, Ccompute, (/nr/))
+      ! Note that the matrix is transposed, from Fortran's perspective
+      call C_F_pointer (Ccompute(1), compute, (/nc, nr/))
+   end subroutine lammps_extract_compute_dp2a
+
+!-----------------------------------------------------------------------------
+
+! lammps_extract_fix {{{2
+   function lammps_extract_fix_Cptr (ptr, id, style, type, i, j) &
+   result (fix)
+      type (C_ptr) :: fix
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: id
+      integer, intent(in) :: style, type, i, j
+      character (kind=C_char), dimension(len_trim(id)+1) :: Cid
+      integer (kind=C_int) :: Cstyle, Ctype, Ci, Cj
+      Cid = string2Cstring (id)
+      Cstyle = style
+      Ctype = type
+      Ci = i - 1  ! This is for consistency with the values from f_ID[i],
+      Cj = j - 1  ! which is different from what library.cpp uses!
+      if ( (type >= 1 .and. Ci < 0) .or. &
+           (type == 2 .and. (Ci < 0 .or. Cj < 0) ) ) then
+         call lammps_error_all (ptr, FLERR, 'Index out of range in&
+            & lammps_extract_fix')
+      end if
+      fix = lammps_actual_extract_fix (ptr, Cid, Cstyle, Ctype, Ci, Cj)
+   end function lammps_extract_fix_Cptr
+   subroutine lammps_extract_fix_dp (fix, ptr, id, style, type, i, j)
+      real (C_double), intent(out) :: fix
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: id
+      integer, intent(in) :: style, type, i, j
+      type (C_ptr) :: Cptr
+      real (C_double), pointer :: Fptr
+      ! Check for the correct dimensionality
+      if ( style /= 0 ) then
+         select case (type)
+         case (0)
+            call lammps_error_all (ptr, FLERR, 'There is no per-atom or local&
+               & scalar data available from fixes.')
+         case (1)
+            call lammps_error_all (ptr, FLERR, 'You cannot extract a fix''s &
+               &per-atom/local vector (rank 1) into a scalar.')
+         case (2)
+            call lammps_error_all (ptr, FLERR, 'You cannot extract a fix''s &
+               &per-atom/local array (rank 2) into a scalar.')
+         case default
+            call lammps_error_all (ptr, FLERR, 'Invalid extract_fix style/&
+               &type combination.')
+         end select
+         return
+      end if
+      Cptr = lammps_extract_fix_Cptr (ptr, id, style, type, i, j)
+      call C_F_pointer (Cptr, Fptr)
+      fix = Fptr
+      nullify (Fptr)
+      ! Memory is only allocated for "global" fix variables
+      if ( style == 0 ) call lammps_free (Cptr)
+   end subroutine lammps_extract_fix_dp
+   subroutine lammps_extract_fix_dpa (fix, ptr, id, style, type, i, j)
+      real (C_double), dimension(:), pointer, intent(out) :: fix
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: id
+      integer, intent(in) :: style, type, i, j
+      type (C_ptr) :: Cptr
+      integer :: fix_len
+      ! Check for the correct dimensionality
+      if ( style == 0 ) then
+         call lammps_error_all (ptr, FLERR, 'You can''t extract the&
+            & whole vector from global fix data')
+         return
+      else if ( type == 0 ) then
+         call lammps_error_all (ptr, FLERR, 'You can''t extract a fix&
+            & scalar into a rank 1 variable')
+         return
+      else if ( type == 2 ) then
+         call lammps_error_all (ptr, FLERR, 'You cannot extract a fix&
+            & array into a rank 1 variable.')
+         return
+      else if ( type /= 1 ) then
+         call lammps_error_all (ptr, FLERR, 'Invalid type for fix extraction.')
+         return
+      end if
+      fix_len = lammps_extract_fix_vectorsize (ptr, id, style)
+      call C_F_pointer (Cptr, fix, (/fix_len/))
+      ! Memory is only allocated for "global" fix variables, which we should
+      ! never get here, so no need to call lammps_free!
+   end subroutine lammps_extract_fix_dpa
+   subroutine lammps_extract_fix_dp2a (fix, ptr, id, style, type, i, j)
+      real (C_double), dimension(:,:), pointer, intent(out) :: fix
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: id
+      integer, intent(in) :: style, type, i, j
+      type (C_ptr) :: Cptr
+      type (C_ptr), pointer, dimension(:) :: Cfix
+      integer :: nr, nc
+      ! Check for the correct dimensionality
+      if ( style == 0 ) then
+         call lammps_error_all (ptr, FLERR, 'It is not possible to extract the&
+            & entire array from global fix data.')
+         return
+      else if ( type == 0 ) then
+         call lammps_error_all (ptr, FLERR, 'You cannot extract a fix&
+            & scalar (rank 0) into a rank 2 variable.')
+         return
+      else if ( type == 1 ) then
+         call lammps_error_all (ptr, FLERR, 'You cannot extract a fix&
+            & vector (rank 1) into a rank 2 variable.')
+         return
+      end if
+      call lammps_extract_fix_arraysize (ptr, id, style, nr, nc)
+      ! Extract pointer to first element as Cfix(1)
+      call C_F_pointer (Cptr, Cfix, (/nr/))
+      ! Now extract the array, which is transposed
+      call C_F_pointer (Cfix(1), fix, (/nc, nr/))
+   end subroutine lammps_extract_fix_dp2a
+
+!-----------------------------------------------------------------------------
+
+! lammps_extract_variable {{{2
+   function lammps_extract_variable_Cptr (ptr, name, group) result (variable)
+      type (C_ptr) :: ptr, variable
+      character (len=*) :: name
+      character (len=*), optional :: group
+      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
+      character (kind=C_char), dimension(:), allocatable :: Cgroup
+      Cname = string2Cstring (name)
+      if ( present(group) ) then
+         allocate (Cgroup(len_trim(group)+1))
+         Cgroup = string2Cstring (group)
+      else
+         allocate (Cgroup(1))
+         Cgroup(1) = C_NULL_CHAR
+      end if
+      variable = lammps_actual_extract_variable (ptr, Cname, Cgroup)
+      deallocate (Cgroup)
+   end function lammps_extract_variable_Cptr
+   subroutine lammps_extract_variable_dp (variable, ptr, name, group)
+      real (C_double), intent(out) :: variable
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: name
+      character (len=*), intent(in), optional :: group
+      type (C_ptr) :: Cptr
+      real (C_double), pointer :: Fptr
+      if ( present(group) ) then
+         Cptr = lammps_extract_variable_Cptr (ptr, name, group)
+      else
+         Cptr = lammps_extract_variable_Cptr (ptr, name)
+      end if
+      call C_F_pointer (Cptr, Fptr)
+      variable = Fptr
+      nullify (Fptr)
+      call lammps_free (Cptr)
+   end subroutine lammps_extract_variable_dp
+   subroutine lammps_extract_variable_dpa (variable, ptr, name, group)
+      real (C_double), dimension(:), allocatable, intent(out) :: variable
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: name
+      character (len=*), intent(in), optional :: group
+      type (C_ptr) :: Cptr
+      real (C_double), dimension(:), pointer :: Fptr
+      integer :: natoms
+      if ( present(group) ) then
+         Cptr = lammps_extract_variable_Cptr (ptr, name, group)
+      else
+         Cptr = lammps_extract_variable_Cptr (ptr, name)
+      end if
+      natoms = lammps_get_natoms (ptr)
+      allocate (variable(natoms))
+      call C_F_pointer (Cptr, Fptr, (/natoms/))
+      variable = Fptr
+      nullify (Fptr)
+      call lammps_free (Cptr)
+   end subroutine lammps_extract_variable_dpa
+
+!-------------------------------------------------------------------------2}}}
+
+   subroutine lammps_gather_atoms_ia (ptr, name, count, data)
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: name
+      integer, intent(in) :: count
+      integer, dimension(:), allocatable, intent(out) :: data
+      type (C_ptr) :: Cdata
+      integer (C_int), dimension(:), pointer :: Fdata
+      integer (C_int) :: natoms
+      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
+      integer (C_int), parameter :: Ctype = 0_C_int
+      integer (C_int) :: Ccount
+      natoms = lammps_get_natoms (ptr)
+      Cname = string2Cstring (name)
+      if ( count /= 1 .and. count /= 3 ) then
+         call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
+            & count to be either 1 or 3')
+      else
+         Ccount = count
+      end if
+      allocate ( Fdata(count*natoms) )
+      allocate ( data(count*natoms) )
+      Cdata = C_loc (Fdata(1))
+      call lammps_actual_gather_atoms (ptr, Cname, Ctype, Ccount, Cdata)
+      data = Fdata
+      deallocate (Fdata)
+   end subroutine lammps_gather_atoms_ia
+   subroutine lammps_gather_atoms_dpa (ptr, name, count, data)
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: name
+      integer, intent(in) :: count
+      double precision, dimension(:), allocatable, intent(out) :: data
+      type (C_ptr) :: Cdata
+      real (C_double), dimension(:), pointer :: Fdata
+      integer (C_int) :: natoms
+      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
+      integer (C_int), parameter :: Ctype = 1_C_int
+      integer (C_int) :: Ccount
+      natoms = lammps_get_natoms (ptr)
+      Cname = string2Cstring (name)
+      if ( count /= 1 .and. count /= 3 ) then
+         call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
+            & count to be either 1 or 3')
+      else
+         Ccount = count
+      end if
+      allocate ( Fdata(count*natoms) )
+      allocate ( data(count*natoms) )
+      Cdata = C_loc (Fdata(1))
+      call lammps_actual_gather_atoms (ptr, Cname, Ctype, Ccount, Cdata)
+      data = Fdata(:)
+      deallocate (Fdata)
+   end subroutine lammps_gather_atoms_dpa
+
+!-----------------------------------------------------------------------------
+
+   subroutine lammps_scatter_atoms_ia (ptr, name, data)
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: name
+      integer, dimension(:), intent(in) :: data
+      integer (kind=C_int) :: natoms, Ccount
+      integer (kind=C_int), parameter :: Ctype = 0_C_int
+      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
+      integer (C_int), dimension(size(data)), target :: Fdata
+      type (C_ptr) :: Cdata
+      natoms = lammps_get_natoms (ptr)
+      Cname = string2Cstring (name)
+      Ccount = size(data) / natoms
+      if ( Ccount /= 1 .and. Ccount /= 3 ) &
+         call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
+            & count to be either 1 or 3')
+      Fdata = data
+      Cdata = C_loc (Fdata(1))
+      call lammps_actual_scatter_atoms (ptr, Cname, Ctype, Ccount, Cdata)
+   end subroutine lammps_scatter_atoms_ia
+   subroutine lammps_scatter_atoms_dpa (ptr, name, data)
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: name
+      double precision, dimension(:), intent(in) :: data
+      integer (kind=C_int) :: natoms, Ccount
+      integer (kind=C_int), parameter :: Ctype = 1_C_int
+      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
+      real (C_double), dimension(size(data)), target :: Fdata
+      type (C_ptr) :: Cdata
+      natoms = lammps_get_natoms (ptr)
+      Cname = string2Cstring (name)
+      Ccount = size(data) / natoms
+      if ( Ccount /= 1 .and. Ccount /= 3 ) &
+         call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
+            & count to be either 1 or 3')
+      Fdata = data
+      Cdata = C_loc (Fdata(1))
+      call lammps_actual_scatter_atoms (ptr, Cname, Ctype, Ccount, Cdata)
+   end subroutine lammps_scatter_atoms_dpa
+
+!-----------------------------------------------------------------------------
+
+   function lammps_extract_compute_vectorsize (ptr, id, style) &
+   result (vectorsize)
+      integer :: vectorsize
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: id
+      integer, intent(in) :: style
+      integer (C_int) :: Cvectorsize, Cstyle
+      character (kind=C_char), dimension(len_trim(id)+1) :: Cid
+      Cid = string2Cstring (id)
+      Cstyle = int(style, C_int)
+      Cvectorsize = lammps_actual_extract_compute_vectorsize (ptr, Cid, Cstyle)
+      vectorsize = int(Cvectorsize, kind(vectorsize))
+   end function lammps_extract_compute_vectorsize
+
+!-----------------------------------------------------------------------------
+
+   function lammps_extract_fix_vectorsize (ptr, id, style) &
+   result (vectorsize)
+      integer :: vectorsize
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: id
+      integer, intent(in) :: style
+      integer (C_int) :: Cvectorsize, Cstyle
+      character (kind=C_char), dimension(len_trim(id)+1) :: Cid
+      Cid = string2Cstring (id)
+      Cstyle = int(style, C_int)
+      Cvectorsize = lammps_actual_extract_fix_vectorsize (ptr, Cid, Cstyle)
+      vectorsize = int(Cvectorsize, kind(vectorsize))
+   end function lammps_extract_fix_vectorsize
+
+!-----------------------------------------------------------------------------
+
+   subroutine lammps_extract_compute_arraysize (ptr, id, style, nrows, ncols)
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: id
+      integer, intent(in) :: style
+      integer, intent(out) :: nrows, ncols
+      integer (C_int) :: Cstyle, Cnrows, Cncols
+      character (kind=C_char), dimension(len_trim(id)+1) :: Cid
+      Cid = string2Cstring (id)
+      Cstyle = int (style, C_int)
+      call lammps_actual_extract_compute_arraysize (ptr, Cid, Cstyle, &
+         Cnrows, Cncols)
+      nrows = int (Cnrows, kind(nrows))
+      ncols = int (Cncols, kind(ncols))
+   end subroutine lammps_extract_compute_arraysize
+
+!-----------------------------------------------------------------------------
+
+   subroutine lammps_extract_fix_arraysize (ptr, id, style, nrows, ncols)
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: id
+      integer, intent(in) :: style
+      integer, intent(out) :: nrows, ncols
+      integer (C_int) :: Cstyle, Cnrows, Cncols
+      character (kind=C_char), dimension(len_trim(id)+1) :: Cid
+      Cid = string2Cstring (id)
+      Cstyle = int (style, kind(Cstyle))
+      call lammps_actual_extract_fix_arraysize (ptr, Cid, Cstyle, &
+         Cnrows, Cncols)
+      nrows = int (Cnrows, kind(nrows))
+      ncols = int (Cncols, kind(ncols))
+   end subroutine lammps_extract_fix_arraysize
+
+!-----------------------------------------------------------------------------
+
+   subroutine lammps_error_all (ptr, file, line, str)
+      type (C_ptr), intent(in) :: ptr
+      character (len=*), intent(in) :: file, str
+      integer, intent(in) :: line
+      character (kind=C_char), dimension(len_trim(file)+1) :: Cfile
+      character (kind=C_char), dimension(len_trim(str)+1) :: Cstr
+      integer (C_int) :: Cline
+      Cline = int(line, kind(Cline))
+      Cfile = string2Cstring (file)
+      Cstr = string2Cstring (str)
+      call lammps_actual_error_all (ptr, Cfile, Cline, Cstr)
+   end subroutine lammps_error_all
+
+!-----------------------------------------------------------------------------
+
+! Locally defined helper functions {{{1
+
+   pure function string2Cstring (string) result (C_string)
+      use, intrinsic :: ISO_C_binding, only : C_char, C_NULL_CHAR
+      character (len=*), intent(in) :: string
+      character (len=1, kind=C_char) :: C_string (len_trim(string)+1)
+      integer :: i, n
+      n = len_trim (string)
+      forall (i = 1:n)
+         C_string(i) = string(i:i)
+      end forall
+      C_string(n+1) = C_NULL_CHAR
+   end function string2Cstring
+
+!-----------------------------------------------------------------------------
+
+   subroutine Cstring2argcargv (Cstring, argc, argv)
+   !! Converts a C-style string to argc and argv, that is, words in Cstring
+   !! become C-style strings in argv.  IMPORTANT:  Cstring is modified by
+   !! this routine!  I would make Cstring local TO this routine and accept
+   !! a Fortran-style string instead, but we run into scoping and
+   !! allocation problems that way.  This routine assumes the string is
+   !! null-terminated, as all C-style strings must be.
+
+      character (kind=C_char), dimension(*), target, intent(inout) :: Cstring
+      integer (C_int), intent(out) :: argc
+      type (C_ptr), dimension(:), allocatable, intent(out) :: argv
+
+      integer :: StringStart, SpaceIndex, strlen, argnum
+
+      argc = 1_C_int
+
+      ! Find the length of the string
+      strlen = 1
+      do while ( Cstring(strlen) /= C_NULL_CHAR )
+         strlen = strlen + 1
+      end do
+
+      ! Find the number of non-escaped spaces
+      SpaceIndex = 2
+      do while ( SpaceIndex < strlen )
+         if ( Cstring(SpaceIndex) == ' ' .and. &
+              Cstring(SpaceIndex-1) /= '\' ) then
+            argc = argc + 1_C_int
+            ! Find the next non-space character
+            do while ( Cstring(SpaceIndex+1) == ' ')
+               SpaceIndex = SpaceIndex + 1
+            end do
+         end if
+         SpaceIndex = SpaceIndex + 1
+      end do
+
+      ! Now allocate memory for argv
+      allocate (argv(argc))
+
+      ! Now find the string starting and ending locations
+      StringStart = 1
+      SpaceIndex = 2
+      argnum = 1
+      do while ( SpaceIndex < strlen )
+         if ( Cstring(SpaceIndex) == ' ' .and. &
+              Cstring(SpaceIndex-1) /= '\' ) then
+            ! Found a real space => split strings and store this one
+            Cstring(Spaceindex) = C_NULL_CHAR ! Replaces space with NULL
+            argv(argnum) = C_loc(Cstring(StringStart))
+            argnum = argnum + 1
+            ! Find the next non-space character
+            do while ( Cstring(SpaceIndex+1) == ' ')
+               SpaceIndex = SpaceIndex + 1
+            end do
+            StringStart = SpaceIndex + 1
+         else if ( Cstring(SpaceIndex) == ' ' .and. &
+              Cstring(SpaceIndex-1) == '\' ) then
+            ! Escaped space => remove backslash and move rest of array
+            Cstring(SpaceIndex-1:strlen-1) = Cstring(SpaceIndex:strlen)
+            strlen = strlen - 1 ! Last character is still C_NULL_CHAR
+         end if
+         SpaceIndex = SpaceIndex + 1
+      end do
+      ! Now handle the last argument
+      argv(argnum) = C_loc(Cstring(StringStart))
+
+   end subroutine Cstring2argcargv
+
+! 1}}}
+
+end module LAMMPS
+
+! vim: foldmethod=marker tabstop=3 softtabstop=3 shiftwidth=3 expandtab

examples/COUPLE/fortran3/README

@@ -0,0 +1,33 @@
+This directory has an example of using a callback function to obtain
+forces from a fortran code for a LAMMPS simulation.  The reader should
+refer to the README file in COUPLE/fortran2 before proceeding. Here,
+the LAMMPS.F90 file has been modified slightly and additional files
+named LAMMPS-wrapper2.h and LAMMPS-wrapper2.cpp have been included in
+order to supply wrapper functions to set the LAMMPS callback function
+and total energy.
+
+In this example, the callback function is set to run the
+semi-empirical quantum code DFTB+ in serial and then read in the total
+energy, forces, and stress tensor from file.  In this case, nlocal =
+the total number of atoms in the system, so particle positions can be
+read from the pos array directly, and DFTB+ forces can simply be
+included via the fext array. The user should take care in the case of
+a parallel calculation, where LAMMPS can assign different particules
+to each processor. For example, the user should use functions such as
+lammps_gather_atoms() and lammps_scatter_atoms() in the case where the
+fortran force calculating code requires the positions of all atoms,
+etc.
+
+A few more important notes: 
+
+-The stress tensor from DFTB+ is passed in to LAMMPS via pointer.
+-Calling the subroutine lammps_set_callback() is required in order to set
+       a pointer to the callback function in LAMMPS.
+-The subroutine lammps_set_user_energy() passes in the potential energy
+       from DFTB+ to LAMMPS.
+
+This example was created by Nir Goldman, whom you can contact with
+questions:
+
+Nir Goldman, LLNL
+ngoldman@llnl.gov

examples/COUPLE/fortran3/data.diamond

@@ -0,0 +1,148 @@
+# Position data file
+
+64 atoms
+1 atom types
+
+0 7.134 xlo xhi
+0 7.134 ylo yhi
+0 7.134 zlo zhi
+
+0.00000000 0.00000000 0.00000000 xy xz yz
+
+Masses
+
+1 12.010000
+
+Atoms
+
+     1 1 0     0 0 0
+     2 1 0     0.89175 0.89175 0.89175
+     3 1 0     1.7835 1.7835 0
+     4 1 0     2.67525 2.67525 0.89175
+     5 1 0     0 1.7835 1.7835
+     6 1 0     0.89175 2.67525 2.67525
+     7 1 0     1.7835 0 1.7835
+     8 1 0     2.67525 0.89175 2.67525
+     9 1 0     0 0 3.567
+     10 1 0     0.89175 0.89175 4.45875
+     11 1 0     1.7835 1.7835 3.567
+     12 1 0     2.67525 2.67525 4.45875
+     13 1 0     0 1.7835 5.3505
+     14 1 0     0.89175 2.67525 6.24225
+     15 1 0     1.7835 0 5.3505
+     16 1 0     2.67525 0.89175 6.24225
+     17 1 0     0 3.567 0
+     18 1 0     0.89175 4.45875 0.89175
+     19 1 0     1.7835 5.3505 0
+     20 1 0     2.67525 6.24225 0.89175
+     21 1 0     0 5.3505 1.7835
+     22 1 0     0.89175 6.24225 2.67525
+     23 1 0     1.7835 3.567 1.7835
+     24 1 0     2.67525 4.45875 2.67525
+     25 1 0     0 3.567 3.567
+     26 1 0     0.89175 4.45875 4.45875
+     27 1 0     1.7835 5.3505 3.567
+     28 1 0     2.67525 6.24225 4.45875
+     29 1 0     0 5.3505 5.3505
+     30 1 0     0.89175 6.24225 6.24225
+     31 1 0     1.7835 3.567 5.3505
+     32 1 0     2.67525 4.45875 6.24225
+     33 1 0     3.567 0 0
+     34 1 0     4.45875 0.89175 0.89175
+     35 1 0     5.3505 1.7835 0
+     36 1 0     6.24225 2.67525 0.89175
+     37 1 0     3.567 1.7835 1.7835
+     38 1 0     4.45875 2.67525 2.67525
+     39 1 0     5.3505 0 1.7835
+     40 1 0     6.24225 0.89175 2.67525
+     41 1 0     3.567 0 3.567
+     42 1 0     4.45875 0.89175 4.45875
+     43 1 0     5.3505 1.7835 3.567
+     44 1 0     6.24225 2.67525 4.45875
+     45 1 0     3.567 1.7835 5.3505
+     46 1 0     4.45875 2.67525 6.24225
+     47 1 0     5.3505 0 5.3505
+     48 1 0     6.24225 0.89175 6.24225
+     49 1 0     3.567 3.567 0
+     50 1 0     4.45875 4.45875 0.89175
+     51 1 0     5.3505 5.3505 0
+     52 1 0     6.24225 6.24225 0.89175
+     53 1 0     3.567 5.3505 1.7835
+     54 1 0     4.45875 6.24225 2.67525
+     55 1 0     5.3505 3.567 1.7835
+     56 1 0     6.24225 4.45875 2.67525
+     57 1 0     3.567 3.567 3.567
+     58 1 0     4.45875 4.45875 4.45875
+     59 1 0     5.3505 5.3505 3.567
+     60 1 0     6.24225 6.24225 4.45875
+     61 1 0     3.567 5.3505 5.3505
+     62 1 0     4.45875 6.24225 6.24225
+     63 1 0     5.3505 3.567 5.3505
+     64 1 0     6.24225 4.45875 6.24225
+
+Velocities
+
+1 -0.00733742 -0.0040297 -0.00315229 
+2 -0.00788609 -0.00567535 -0.00199152 
+3 -0.00239042 0.00710139 -0.00335049 
+4 0.00678551 0.0019976 0.00219289 
+5 0.00413717 0.00275709 0.000937637 
+6 -0.00126313 0.00485636 0.00727862 
+7 0.00337547 -0.00234623 -0.000922223 
+8 -0.00792183 -0.00509186 -0.00104168 
+9 0.00414091 0.00390285 0.000845961 
+10 -0.000284543 0.0010771 -0.00458404 
+11 -0.00394968 -0.00446363 -0.00361688 
+12 0.00067088 -0.00655175 -0.00752464 
+13 0.00306632 -0.00245545 -0.00183867 
+14 -0.0082145 -0.00564127 0.000281191 
+15 0.00504454 0.0045835 0.000495763 
+16 0.0035767 0.00320441 -0.00486426 
+17 0.00420597 0.00262005 -0.0049459 
+18 0.00440579 -1.76783e-05 0.00449311 
+19 -0.00406463 0.00613304 0.00285599 
+20 0.00171215 -0.00517887 0.00124326 
+21 0.0011118 0.00334129 -0.0015222 
+22 -0.00838394 -0.00112906 -0.00353379 
+23 -0.00578527 -0.00415501 0.00297043 
+24 -0.00211466 0.000964108 -0.00716523 
+25 -0.000204107 -0.00380986 0.00681648 
+26 0.00677838 0.00540935 0.0044354 
+27 -0.00266809 -0.00358382 -0.00241889 
+28 -0.0003973 0.00236566 0.00558871 
+29 0.000754103 0.00457797 0.000105531 
+30 -0.00246049 0.00110428 0.00511088 
+31 0.00248891 0.00623314 0.00461597 
+32 -0.00509423 0.000570503 0.00720856 
+33 -0.00244427 -0.00374384 0.00618767 
+34 -0.000360752 -8.10558e-05 0.00314052 
+35 0.00435313 -0.00630587 -0.0070309 
+36 0.00651087 -0.00389833 3.72525e-05 
+37 0.00631828 -0.00316064 0.00231522 
+38 -0.00579624 -0.00345068 -0.000277486 
+39 0.00483974 0.000715028 0.000206355 
+40 -0.00388164 -0.00189242 -0.00554862 
+41 0.00398115 0.00152915 0.00756919 
+42 -0.000552263 0.00352025 -0.000246143 
+43 -0.00800284 0.00555703 0.00425716 
+44 -0.00734405 -0.00752512 0.00667173 
+45 -0.00545636 0.00421035 0.00399552 
+46 0.00480246 0.00621147 -0.00492715 
+47 -0.00424168 0.00621818 -9.37733e-05 
+48 -0.00649561 0.00612908 -0.0020753 
+49 -0.0075007 -0.00384737 -0.00687913 
+50 -0.00203903 -0.00764372 0.0023883 
+51 0.00442642 0.00744072 -0.0049344 
+52 -0.00280486 -0.00509128 -0.00678045 
+53 0.00679491 0.00583493 0.00333875 
+54 0.00574665 -0.00521074 0.00523475 
+55 0.00305618 -0.00320094 0.00341297 
+56 0.004304 0.000615544 -0.00668787 
+57 0.00564532 0.00327373 0.00388611 
+58 0.000676899 0.00210326 0.00495295 
+59 0.000160781 -0.00744313 -0.00279828 
+60 0.00623521 0.00371301 0.00178015 
+61 0.00520759 0.000642669 0.00207913 
+62 0.00398042 0.0046438 -0.00359978 
+63 -0.00478071 -0.00304932 -0.00765125 
+64 0.00282671 -0.00548392 -0.00692691 

examples/COUPLE/fortran3/in.simple

@@ -0,0 +1,16 @@
+units real
+atom_style	charge
+atom_modify map array
+atom_modify sort 0 0.0
+read_data data.diamond
+neighbor        1.0 bin
+neigh_modify    delay 0 every 5 check no
+fix 1 all nve
+fix 2 all external pf/callback 1 1
+
+fix_modify 2 energy yes 
+thermo_style custom step temp etotal ke pe lx ly lz pxx pyy pzz press 
+
+thermo          1
+timestep        0.5
+

examples/COUPLE/fortran3/makefile

@@ -0,0 +1,45 @@
+SHELL = /bin/sh
+
+# Path to LAMMPS extraction directory
+LAMMPS_ROOT = ../../..
+LAMMPS_SRC = $(LAMMPS_ROOT)/src
+
+# Uncomment the line below if using the MPI stubs library
+MPI_STUBS = #-I$(LAMMPS_SRC)/STUBS
+
+FC = mpif90 # replace with your Fortran compiler
+CXX = mpicc # replace with your C++ compiler
+
+# Flags for Fortran compiler, C++ compiler, and C preprocessor, respectively
+FFLAGS = -O2 -fPIC 
+CXXFLAGS = -O2 -fPIC
+CPPFLAGS = -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX
+
+all : liblammps_fortran.a liblammps_fortran.so simpleF.x
+
+liblammps_fortran.so : LAMMPS.o LAMMPS-wrapper.o LAMMPS-wrapper2.o
+	$(FC) $(FFLAGS) -shared -o $@ $^
+
+simpleF.x: simple.o LAMMPS.o LAMMPS-wrapper.o LAMMPS-wrapper2.o
+	$(FC) $(FFLAGS) simple.o -o simpleF.x liblammps_fortran.a $(LAMMPS_SRC)/liblammps_mvapich.a -lstdc++ /usr/local/tools/fftw/lib/libfftw.a
+
+liblammps_fortran.a : LAMMPS.o LAMMPS-wrapper.o LAMMPS-wrapper2.o
+	$(AR) rs $@ $^
+
+LAMMPS.o lammps.mod : LAMMPS.F90
+	$(FC) $(CPPFLAGS) $(FFLAGS) -c $<
+
+simple.o : simple.f90
+	$(FC) $(FFLAGS) -c $<
+
+LAMMPS-wrapper.o : LAMMPS-wrapper.cpp LAMMPS-wrapper.h
+	$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c $< -I$(LAMMPS_SRC) $(MPI_STUBS)
+
+LAMMPS-wrapper2.o : LAMMPS-wrapper2.cpp LAMMPS-wrapper2.h
+	$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c $< -I$(LAMMPS_SRC) $(MPI_STUBS)
+
+clean :
+	$(RM) *.o *.mod liblammps_fortran.a liblammps_fortran.so
+
+dist :
+	tar -czvf fortran-interface-callback.tar.gz LAMMPS-wrapper.h LAMMPS-wrapper.cpp LAMMPS-wrapper2.h LAMMPS-wrapper2.cpp LAMMPS.F90 makefile README simple.f90

examples/COUPLE/fortran3/simple.f90

@@ -0,0 +1,114 @@
+   module callback
+     implicit none
+     contains
+       subroutine fortran_callback(lmp, timestep, nlocal, ids, c_pos, c_fext) & 
+     & bind(C, name='f_callback')
+       use, intrinsic :: ISO_C_binding
+       use LAMMPS
+       implicit none
+       type (C_ptr), value :: lmp
+       integer(C_int64_t), intent(in), value :: timestep
+       integer(C_int), intent(in), value :: nlocal
+       real (C_double), dimension(:,:), pointer :: x
+       type(c_ptr) :: c_pos, c_fext, c_ids
+       double precision, pointer :: fext(:,:), pos(:,:)
+       integer, intent(in) :: ids(nlocal)
+       real (C_double), dimension(:), pointer :: virial => NULL()
+       real (C_double) :: etot
+       real(C_double), pointer :: ts_lmp
+       double precision :: stress(3,3), ts_dftb
+       integer :: natom , i
+       real (C_double), parameter :: econv = 627.4947284155114 ! converts from Ha to
+       double precision, parameter :: fconv = 1185.793095983065 ! converts from Ha/bohr to
+       double precision, parameter :: autoatm = 2.9037166638E8
+       double precision lx, ly, lz
+       real (C_double), pointer :: boxxlo, boxxhi
+       real (C_double), pointer :: boxylo, boxyhi
+       real (C_double), pointer :: boxzlo, boxzhi
+       double precision, parameter :: nktv2p = 68568.4149999999935972
+       double precision :: volume
+       type (C_ptr) :: Cptr
+       type (C_ptr), pointer, dimension(:) :: Catom
+
+       call c_f_pointer(c_pos, pos, [3,nlocal])
+       call c_f_pointer(c_fext, fext, [3,nlocal])
+       call lammps_extract_global(boxxlo, lmp, 'boxxlo')
+       call lammps_extract_global(boxxhi, lmp, 'boxxhi')
+       call lammps_extract_global(boxylo, lmp, 'boxylo')
+       call lammps_extract_global(boxyhi, lmp, 'boxyhi')
+       call lammps_extract_global(boxzlo, lmp, 'boxzlo')
+       call lammps_extract_global(boxzhi, lmp, 'boxzhi')
+       lx = boxxhi - boxxlo
+       ly = boxyhi - boxylo
+       lz = boxzhi - boxzlo
+       volume = lx*ly*lz
+       open (unit = 10, status = 'replace', action = 'write', file='lammps.gen')
+       write(10,*)nlocal,"S"
+       write(10,*) "C"
+       do i = 1, nlocal
+         write(10,'(2I,3F15.6)')i,1,pos(:,ids(i))
+       enddo
+       write(10,*)"0.0 0.0 0.0"
+       write(10,*)lx,0,0
+       write(10,*)0,ly,0
+       write(10,*)0,0,lz
+       close(10)
+       call system("./dftb+ > dftb.out")
+       open (unit = 10, status = 'old', file = 'results.out')
+       read(10,*)etot
+       read(10,*)ts_dftb
+       do i = 1, 3
+         read(10,*)stress(i,:)
+       enddo
+       stress (:,:) = stress(:,:)*autoatm
+       etot = etot*econv
+       call lammps_extract_global(ts_lmp, lmp, 'TS_dftb')
+       ts_lmp = ts_dftb
+       do i = 1, nlocal
+         read(10,*)fext(:,ids(i))
+         fext(:,ids(i)) = fext(:,ids(i))*fconv
+       enddo
+       close(10)
+       call lammps_set_user_energy (lmp, etot)
+       call lammps_extract_atom (virial, lmp, 'virial')
+       if (.not. associated(virial)) then
+         print*,'virial pointer not associated.'
+         STOP
+       endif
+       virial(1) = stress(1,1)/(nktv2p/volume)
+       virial(2) = stress(2,2)/(nktv2p/volume)
+       virial(3) = stress(3,3)/(nktv2p/volume)
+       virial(4) = stress(1,2)/(nktv2p/volume)
+       virial(5) = stress(1,3)/(nktv2p/volume)
+       virial(6) = stress(2,3)/(nktv2p/volume)
+
+       end  subroutine
+    end module callback
+
+
+program simple_fortran_callback
+
+   use MPI
+   use LAMMPS
+   use callback
+   use, intrinsic :: ISO_C_binding, only : C_double, C_ptr, C_int, C_FUNPTR
+   implicit none
+   type (C_ptr) :: lmp
+   integer :: error, narg, me, nprocs
+
+   call MPI_Init (error)
+   call MPI_Comm_rank (MPI_COMM_WORLD, me, error)
+   call MPI_Comm_size (MPI_COMM_WORLD, nprocs, error)
+
+   call lammps_open_no_mpi ('lmp -log log.simple', lmp)
+   call lammps_file (lmp, 'in.simple')
+   call lammps_set_callback(lmp)
+
+   call lammps_command (lmp, 'run 10')
+   call lammps_close (lmp)
+   call MPI_Finalize (error)
+
+
+end program simple_fortran_callback
+
+