Merge remote-tracking branch 'upstream/master'

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

doc/src/Eqs/cnp_cutoff.tex

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

doc/src/Eqs/cnp_cutoff2.tex

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

doc/src/Eqs/cnp_eq.tex

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

doc/src/Eqs/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="4 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
-4 May 2017 version :c,h4
+6 Jul 2017 version :c,h4
 
 Version info: :h4
 

doc/src/Section_commands.txt

@@ -618,6 +618,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "press/berendsen"_fix_press_berendsen.html,
 "print"_fix_print.html,
 "property/atom"_fix_property_atom.html,
+"python"_fix_python.html,
 "qeq/comb (o)"_fix_qeq_comb.html,
 "qeq/dynamic"_fix_qeq.html,
 "qeq/fire"_fix_qeq.html,
@@ -716,7 +717,7 @@ package"_Section_start.html#start_3.
 "phonon"_fix_phonon.html,
 "pimd"_fix_pimd.html,
 "qbmsst"_fix_qbmsst.html,
-"qeq/reax"_fix_qeq_reax.html,
+"qeq/reax (ko)"_fix_qeq_reax.html,
 "qmmm"_fix_qmmm.html,
 "qtb"_fix_qtb.html,
 "reax/c/bonds"_fix_reax_bonds.html,
@@ -830,6 +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,
@@ -931,6 +933,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 "gran/hertz/history (o)"_pair_gran.html,
 "gran/hooke (o)"_pair_gran.html,
 "gran/hooke/history (o)"_pair_gran.html,
+"gw"_pair_gw.html,
+"gw/zbl"_pair_gw.html,
 "hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,
 "hbond/dreiding/morse (o)"_pair_hbond_dreiding.html,
 "kim"_pair_kim.html,
@@ -960,7 +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,
@@ -982,6 +986,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "peri/pmb (o)"_pair_peri.html,
 "peri/ves"_pair_peri.html,
 "polymorphic"_pair_polymorphic.html,
+"python"_pair_python.html,
 "reax"_pair_reax.html,
 "rebo (o)"_pair_airebo.html,
 "resquared (go)"_pair_resquared.html,
@@ -1016,6 +1021,7 @@ package"_Section_start.html#start_3.
 "dpd/fdt/energy"_pair_dpd_fdt.html,
 "eam/cd (o)"_pair_eam.html,
 "edip (o)"_pair_edip.html,
+"edip/multi"_pair_edip.html,
 "eff/cut"_pair_eff.html,
 "exp6/rx"_pair_exp6_rx.html,
 "gauss/cut"_pair_gauss.html,
@@ -1033,7 +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,
@@ -1052,7 +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,
@@ -1220,7 +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
+See the read_data command for info on using the "extra/angle/per/atom",
-atom", etc header values to allow for additional angles, etc to be
+(or dihedral, improper) keywords to allow for additional
-formed. :dd
+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
+See the read_data command for info on using the "extra/bond/per/atom"
-atom" header value to allow for additional bonds to be formed. :dd
+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
+See the read_data command for info on using the "extra/bond/per/atom"
-atom" header value to allow for additional bonds to be formed. :dd
+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
+See the "special_bonds extra" command
-the special bonds list to allow for additional bonds to be formed. :dd
+(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
+See the special_bonds extra command
-atom" header value to allow for additional special values to be
+(or the read_data extra/special/per/atom command)
-stored. :dd
+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
+See the extra/angle/per/atom keyword for the create_box
-atom" header value to set this limit larger. :dd
+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
+See the extra/bond/per/atom keyword for the create_box
-atom" header value to set this limit larger. :dd
+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
+See the extra/dihedral/per/atom keyword for the create_box
-dihedral per atom" header value to set this limit larger. :dd
+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
+See the extra/improper/per/atom keyword for the create_box
-improper per atom" header value to set this limit larger. :dd
+or the read_data command to set this limit larger :dd
 
 {Substitution for illegal variable} :dt
 

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
@@ -1502,7 +1503,7 @@ 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:]
 
@@ -2027,8 +2028,8 @@ 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
+[Author:] Stefan Paquay (until 2017: Eindhoven University of Technology (TU/e), The
-Netherlands)
+Netherlands; since 2017: Brandeis University, Waltham, MA, USA)
 
 [Install or un-install:]
 
@@ -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:]

doc/src/Section_python.txt

@@ -118,13 +118,21 @@ check which version of Python you have installed, by simply typing
 
 11.2 Overview of using Python from a LAMMPS script :link(py_2),h4
 
-LAMMPS has a "python"_python.html command which can be used in an
+LAMMPS has several commands which can be used to invoke Python
-input script to define and execute a Python function that you write
+code directly from an input script:
-the code for.  The Python function can also be assigned to a LAMMPS
+
-python-style variable via the "variable"_variable.html command.  Each
+"python"_python.html
-time the variable is evaluated, either in the LAMMPS input script
+"variable python"_variable.html
-itself, or by another LAMMPS command that uses the variable, this will
+"fix python"_fix_python.html
-trigger the Python function to be invoked.
+"pair_style python"_pair_python.html :ul
+
+The "python"_python.html command which can be used to define and
+execute a Python function that you write the code for.  The Python
+function can also be assigned to a LAMMPS python-style variable via
+the "variable"_variable.html command.  Each time the variable is
+evaluated, either in the LAMMPS input script itself, or by another
+LAMMPS command that uses the variable, this will trigger the Python
+function to be invoked.
 
 The Python code for the function can be included directly in the input
 script or in an auxiliary file.  The function can have arguments which
@@ -155,11 +163,18 @@ commands.
 See the "python"_python.html doc page and the "variable"_variable.html
 doc page for its python-style variables for more info, including
 examples of Python code you can write for both pure Python operations
-and callbacks to LAMMPS. See "fix python"_fix_python.html to learn about
+and callbacks to LAMMPS.
-possibilities to execute Python code during each time step.
 
-To run pure Python code from LAMMPS, you only need to build LAMMPS
+The "fix python"_fix_python.html command can execute
-with the PYTHON package installed:
+Python code at selected timesteps during a simulation run.
+
+The "pair_style python"_pair_python command allows you to define
+pairwise potentials as python code which encodes a single pairwise
+interaction.  This is useful for rapid-developement and debugging of a
+new potential.
+
+To use any of these commands, you only need to build LAMMPS with the
+PYTHON package installed:
 
 make yes-python
 make machine :pre

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
+charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long, sw, tersoff :l
-K-Space Styles: pppm :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
+the src/USER-INTEL/TEST directory with the provided run script.
-results given are with 512K particles (524K for Liquid Crystal).
+These are scalable in size; the results given are with 512K
-Most of the simulations are standard LAMMPS benchmarks (indicated
+particles (524K for Liquid Crystal). Most of the simulations are
-by the filename extension in parenthesis) with modifications to the
+standard LAMMPS benchmarks (indicated by the filename extension in
-run length and to add a warmup run (for use with offload
+parenthesis) with modifications to the run length and to add a
-benchmarks).
+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
+(code-named Knights Landing) with "June 2017" LAMMPS built with
-Intel Parallel Studio 2016 update 3. Results are with 1 MPI task
+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
+Set the environment variable KMP_BLOCKTIME=0 :l
-performance.  Cutoff should be roughly the neighbor list cutoff.  By
+"-pk intel 0 omp $t -sf intel" added to LAMMPS command-line :l
-default the binsize is half the neighbor list cutoff.  :l
+$t should be 2 for Intel Xeon CPUs and 2 or 4 for Intel Xeon Phi :l
-"-pk intel 0 omp 2 -sf intel" added to LAMMPS command-line :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
+For Intel Xeon Phi CPUs:
-pppm} in the input script :
 
-Edit src/MAKE/OPTIONS/Makefile.knl as necessary. :ulb,l
+Runs should be performed using MCDRAM. :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
 :ule
 
-For Intel Xeon Phi CPUs for simulations with {kspace_style
+For simulations using {kspace_style pppm} on Intel CPUs
-pppm} in the input script:
+supporting AVX-512:
 
-Edit src/MAKE/OPTIONS/Makefile.knl as necessary. :ulb,l
+Add "kspace_modify diff ad" to the input script :ulb,l
-Runs should be performed using MCDRAM. :l
+The command-line option should be changed to
-Add "neigh_modify binsize 3" to the input script for better
+"-pk intel 0 omp $r lrt yes -sf intel" where $r is the number of
-performance. :l
+threads minus 1. :l
-Add "kspace_modify diff ad" to the input script for better
+Do not use thread affinity (set KMP_AFFINITY=none) :l
-performance. :l
+The "newton off" setting may provide better scalability :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
 :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
+"kspace_modify diff ad"_kspace_modify.html should be added to the
-3"_neigh_modify.html should be added to the input script.
+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/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:
+H:       He:      Li:      Be:       B:
-         C:       N:       O:       F:      Ne:
+C:        N:       O:       F:      Ne:
-        Na:      Mg:      Al:      Si:       P:
+Na:      Mg:      Al:      Si:       P:
-         S:      Cl:      Ar:       K:      Ca:
+S:       Cl:      Ar:       K:      Ca:
-        Sc:      Ti:       V:      Cr:      Mn:
+Sc:      Ti:       V:      Cr:      Mn:
-        Fe:      Co:      Ni:      Cu:      Zn:
+Fe:      Co:      Ni:      Cu:      Zn:
-        Ga:      Ge:      As:      Se:      Br:
+Ga:      Ge:      As:      Se:      Br:
-        Kr:      Rb:      Sr:       Y:      Zr:
+Kr:      Rb:      Sr:       Y:      Zr:
-        Nb:      Mo:      Tc:      Ru:      Rh:
+Nb:      Mo:      Tc:      Ru:      Rh:
-        Pd:      Ag:      Cd:      In:      Sn:
+Pd:      Ag:      Cd:      In:      Sn:
-        Sb:      Te:       I:      Xe:      Cs:
+Sb:      Te:       I:      Xe:      Cs:
-        Ba:      La:      Ce:      Pr:      Nd:
+Ba:      La:      Ce:      Pr:      Nd:
-        Pm:      Sm:      Eu:      Gd:      Tb:
+Pm:      Sm:      Eu:      Gd:      Tb:
-        Dy:      Ho:      Er:      Tm:      Yb:
+Dy:      Ho:      Er:      Tm:      Yb:
-        Lu:      Hf:      Ta:       W:      Re:
+Lu:      Hf:      Ta:       W:      Re:
-        Os:      Ir:      Pt:      Au:      Hg:
+Os:      Ir:      Pt:      Au:      Hg:
-        Tl:      Pb:      Bi:      Po:      At:
+Tl:      Pb:      Bi:      Po:      At:
-        Rn:      Fr:      Ra:      Ac:      Th:
+Rn:      Fr:      Ra:      Ac:      Th:
-        Pa:       U:      Np:      Pu:      Am:
+Pa:       U:      Np:      Pu:      Am:
-        Cm:      Bk:      Cf:tb(c=5,s=:)
+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
+the products of all distinct pairs of  bispectrum components. If the
-number of bispectrum components is {K}, then the number of matrix elements
+number of bispectrum components is {K}, then the number of distinct pairs
-is {K}^2. These are output in subblocks of {K}^2 columns, using the same
+is  {K}({K}+1)/2. These are output in subblocks of  {K}({K}+1)/2 columns, using the same
-ordering of columns and sub-blocks as was used for the bispectrum
+ordering of sub-blocks as was used for the bispectrum
-components.
+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
+style = {many} or {single/bond} or {single/angle} or {single/dihedral} :ule,l
-group2-ID = ID of second group, bonds will be between atoms in the 2 groups
+  {many} args = group-ID group2-ID btype rmin rmax
-btype = bond type of created bonds
+    group-ID = ID of first group
-rmin = minimum distance between pair of atoms to bond together
+    group2-ID = ID of second group, bonds will be between atoms in the 2 groups
-rmax = minimum distance between pair of atoms to bond together :ul
+    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 many all all 1 1.0 1.2
-create_bonds surf solvent 3 2.0 2.4 :pre
+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
+Create bonds between pairs of atoms that meet a specified distance
-criteria.  The bond interactions can then be computed during a
+criteria.  Or create a single bond, angle, or dihedral between 2, 3,
-simulation by the bond potential defined by the
+or 4 specified atoms.
-"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.
 
-Note that the flexibility of this command is limited.  It can be used
+The new bond (angle, dihedral) interactions will then be computed
-several times to create different types of bond at different
+during a simulation by the bond (angle, dihedral) potential defined by
-distances.  But it cannot typically create all the bonds that would
+the "bond_style"_bond_style.html, "bond_coeff"_bond_coeff.html,
-normally be defined in a complex system of molecules.  Also note that
+"angle_style"_angle_style.html, "angle_coeff"_angle_coeff.html,
-this command does not add any 3-body or 4-body interactions which,
+"dihedral_style"_dihedral_style.html,
-depending on your model, may be induced by added bonds,
+"dihedral_coeff"_dihedral_coeff.html commands.
-e.g. "angle"_angle_style.html, "dihedral"_dihedral_style.html, or
-"improper"_improper_style.html interactions.
 
-All created bonds will be between pairs of atoms I,J where I is in one
+The {many} style is useful for adding bonds to a system, e.g. between
-of the two specified groups, and J is in the other.  The two groups
+nearest neighbors in a lattice of atoms, without having to enumerate
-can be the same, e.g. group "all".  The created bonds will be of bond
+all the bonds in the data file read by the "read_data"_read_data.html
-type {btype}, where {btype} must be a value between 1 and the number
+command.
-of bond types defined.  This maximum value is set by the "bond types"
+
-field in the header of the data file read by the
+The {single} styles are useful for adding bonds, angles, dihedrals
-"read_data"_read_data.html command, or via the optional "bond/types"
+to a system incrementally, then continuing a simulation.
-argument of the "create_box"_create_box.html command.
+
+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
+The following settings must have been made in an input script before
-script before this command is used:
+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
+An additional requirement for this style is that your system must be
-a simulation.  This means, for example, that all
+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
+:line
-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
+The {single/bond} style creates a single bond of type {btype} between
-set to large enough values.  Otherwise an error may occur when too
+two atoms with IDs {batom1} and {batom2}.  {Btype} must be a value
-many bonds are added to an atom.  If the "read_data"_read_data.html
+between 1 and the number of bond types defined.
-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
+The {single/angle} style creates a single angle of type {atype}
-section of the data file.  If the "create_box"_create_box.html command
+between three atoms with IDs {aatom1}, {aatom2}, and {aatom3}.  The
-is used to define the system, these 2 parameters can be set via its
+ordering of the atoms is the same as in the {Angles} section of a data
-optional "bond/types" and "extra/bond/per/atom" arguments.  See the
+file read by the "read_data"_read_data command.  I.e. the 3 atoms are
-doc pages for the 2 commands for details.
+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

@@ -15,9 +15,10 @@ dihedral_style spherical :pre
 [Examples:]
 
 dihedral_coeff 1 1  286.1  1 124  1    1 90.0 0    1 90.0 0
-dihedral_coeff 1 3  286.1  1 114 1   1 90  0    1 90.0  0  &
+dihedral_coeff 1 3  69.3   1 93.9 1    1 90   0    1 90   0  &
-                    17.3   0 0.0 0   1 158 1    0 0.0   0  &
+                    49.1   0 0.00 0    1 74.4 1    0 0.00 0  &
-                    15.1   0 0.0 0   0 0.0 0    1 167.3 1   :pre
+                    25.2   0 0.00 0    0 0.00 0    1 48.1 1
+:pre
 
 [Description:]
 
@@ -35,13 +36,14 @@ the dihedral interaction even if it requires adding additional terms to
 the expansion (as was done in the second example).  A careful choice of
 parameters can prevent singularities that occur with traditional
 force-fields whenever theta1 or theta2 approach 0 or 180 degrees.
+
 The last example above corresponds to an interaction with a single energy
-minima located at phi=114, theta1=158, theta2=167.3 degrees, and it remains
+minima located near phi=93.9, theta1=74.4, theta2=48.1 degrees, and it remains
 numerically stable at all angles (phi, theta1, theta2). In this example,
-the coefficients 17.3, and 15.1 can be physically interpreted as the
+the coefficients 49.1, and 25.2 can be physically interpreted as the
 harmonic spring constants for theta1 and theta2 around their minima.
-The coefficient 286.1 is the harmonic spring constant for phi after
+The coefficient 69.3 is the harmonic spring constant for phi after
-division by sin(158)*sin(167.3) (the minima positions for theta1 and theta2).
+division by sin(74.4)*sin(48.1) (the minima positions for theta1 and theta2).
 
 The following coefficients must be defined for each dihedral type via the
 "dihedral_coeff"_dihedral_coeff.html command as in the example above, or in

doc/src/dump_modify.txt

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

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_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
+This fix will restore the initial box settings from "binary restart
-files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+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_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_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_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
+The keyword {tscale} is a factor between 0 and 1 that determines what
-thermal kinetic energy is converted to compressive strain kinetic
+fraction of thermal kinetic energy is converted to compressive strain
-energy at the start of the simulation.  Setting this parameter to a
+kinetic energy at the start of the simulation.  Setting this parameter
-non-zero value may assist in compression at the start of simulations
+to a non-zero value may assist in compression at the start of
-where it is slow to occur.
+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 fix computes a temperature and pressure and potential energy each
-this, the fix creates its own computes of style "temp" and "pressure",
+timestep. To do this, the fix creates its own computes of style "temp"
-as if these commands had been issued:
+"pressure", and "pe", as if these commands had been issued:
 
-compute fix-ID_temp group-ID temp
+compute fix-ID_MSST_temp all temp
-compute fix-ID_press group-ID pressure fix-ID_temp :pre
+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
+IDs of the new computes are the fix-ID + "_MSST_temp" or "_MSST_press"
-+ underscore + "press".  The group for the new computes is "all".
+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
+The keyword defaults are q = 10, mu = 0, tscale = 0.01, dftb = no,
-are calculated on the first step.
+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
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
-neb = style name of this fix command
+neb = style name of this fix command :l
-Kspring = inter-replica spring constant (force/distance units) :ul
+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
+elastic band (NEB) calculation for finding the transition state.
-explanations of NEB are given with the "neb"_neb.html command and in
+Hi-level explanations of NEB are given with the "neb"_neb.html command
-"Section 6.5"_Section_howto.html#howto_5 of the manual.  The fix
+and in "Section_howto 5"_Section_howto.html#howto_5 of the manual.
-neb command must be used with the "neb" command to define how
+The fix neb command must be used with the "neb" command and defines
-inter-replica forces are computed.
+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.
+A key purpose of the nudging forces is to keep the replicas equally
-Atoms in the two end-point replicas do not experience these forces,
+spaced.  During the NEB calculation, the 3N-length vector of
-but those in intermediate replicas do.  During the initial stage of
+interatomic force Fi = -Grad(V) for each replica I is altered.  For
-NEB, the 3N-length vector of interatomic forces Fi = -Grad(V) acting
+all intermediate replicas (i.e. for 1 < I < N, except the climbing
-on the atoms of each intermediate replica I is altered, as described
+replica) the force vector becomes:
-in the "(Henkelman1)"_#Henkelman1 paper, to become:
 
-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
+T' is the unit "tangent" vector for replica I and is a function of Ri,
-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,
 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
+In the second stage of the NEB calculation, the interatomic force Fi
-interatomic forces perpendicular to the tangent vector.  The last term
+for the climbing replica (the replica of highest energy after the
-is a spring force between replica I and its neighbors, parallel to the
+first stage) is changed to:
-tangent vector direction with the specified spring constant {Kspring}.
 
-The effect of the first two terms is to push the atoms of each replica
+Fi = -Grad(V) + 2 (Grad(V) dot T') T' :pre
-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.
 
-The effect of the last term is to push each replica away from its two
+and the relaxation procedure is continued to a new converged MEP.
-neighbors in a direction along the MEP, so that the final set of
-states are equidistant from each other.
 
-During the second stage of NEB, the forces on the N atoms in the
+:line
-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:
 
-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
+Fnudge_parallel = {Kspring} * (|Ri+1 - Ri| - |Ri - Ri-1|) :pre
-first equation.
+
+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_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_reax_bonds.txt

@@ -34,7 +34,20 @@ written to {filename} on timesteps that are multiples of {Nevery},
 including timestep 0.  For time-averaged chemical species analysis,
 please see the "fix reaxc/c/species"_fix_reaxc_species.html command.
 
-The format of the output file should be self-explanatory.
+The format of the output file should be reasonably self-explanatory.
+The meaning of the column header abbreviations is as follows:
+
+id = atom id
+type = atom type
+nb = number of bonds
+id_1 = atom id of first bond
+id_nb = atom id of Nth bond
+mol = molecule id
+bo_1 = bond order of first bond
+bo_nb = bond order of Nth bond
+abo = atom bond order (sum of all bonds)
+nlp = number of lone pairs
+q = atomic charge :ul
 
 If the filename ends with ".gz", the output file is written in gzipped
 format.  A gzipped dump file will be about 3x smaller than the text

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
+nvt"_fix_nh.html, "fix npt"_fix_nh.html, "fix move"_fix_move.html),
-their motion more than once each timestep.  When performing a hybrid
+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
+IMPORTANT NOTE: The aggregate properties of each rigid body are
-time at the start of the first simulation run after these fixes are
+calculated at the start of a simulation run and are maintained in
-specified.  The properties include the position and velocity of the
+internal data structures. The properties include the position and
-center-of-mass of the body, its moments of inertia, and its angular
+velocity of the center-of-mass of the body, its moments of inertia, and
-momentum.  This is done using the properties of the constituent atoms
+its angular momentum.  This is done using the properties of the
-of the body at that point in time (or see the {infile} keyword
+constituent atoms of the body at that point in time (or see the {infile}
-option).  Thereafter, changing properties of individual atoms in the
+keyword option).  Thereafter, changing these properties of individual
-body will have no effect on a rigid body's dynamics, unless they
+atoms in the body will have no effect on a rigid body's dynamics, unless
-affect the "pair_style"_pair_style.html interactions that individual
+they effect any computation of per-atom forces or torques. If the
-particles are part of.  For example, you might think you could
+keyword {reinit} is set to {yes} (the default), the rigid body data
-displace the atoms in a body or add a large velocity to each atom in a
+structures will be recreated at the beginning of each {run} command;
-body to make it move in a desired direction before a 2nd run is
+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
+commands.  But these commands will not affect the internal attributes
-of the body, and the position and velocity of individual atoms in the
+of the body unless {reinit} is set to {yes}. With {reinit} set to {no}
-body will be reset when time integration starts.
+(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_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
+The {fftbench} keyword applies only to PPPM. It is off by default. If
-this option is turned off, LAMMPS will not take the time at the end
+this option is turned on, LAMMPS will perform a short FFT benchmark
-of a run to give FFT benchmark timings, and will finish a few seconds
+computation and report its timings, and will thus finish a some seconds
-faster than it would if this option were on.
+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

@@ -237,6 +237,7 @@ fix_pour.html
 fix_press_berendsen.html
 fix_print.html
 fix_property_atom.html
+fix_python.html
 fix_qbmsst.html
 fix_qeq.html
 fix_qeq_comb.html
@@ -300,6 +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
@@ -432,6 +434,7 @@ pair_gauss.html
 pair_gayberne.html
 pair_gran.html
 pair_gromacs.html
+pair_gw.html
 pair_hbond_dreiding.html
 pair_hybrid.html
 pair_kim.html
@@ -444,7 +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
@@ -467,6 +469,7 @@ pair_oxdna.html
 pair_oxdna2.html
 pair_peri.html
 pair_polymorphic.html
+pair_python.html
 pair_quip.html
 pair_reax.html
 pair_reaxc.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 @ 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_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
+    filename = unique filename for each replica (except first)
-  {none} arg = no argument
+      with its initial coords
-    all replicas assumed to already have their initial coords :pre
+  {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,
+follows the discussion in these 4 papers: "(HenkelmanA)"_#HenkelmanA,
-"(HenkelmanB)"_#HenkelmanB, and "(Nakano)"_#Nakano3.
+"(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
+In a NEB calculation each replica is connected to other replicas by
-atom in adjacent replicas by springs, which induce inter-replica
+inter-replica nudging forces.  These forces are imposed by the "fix
-forces.  These forces are imposed by the "fix neb"_fix_neb.html
+neb"_fix_neb.html command, which must be used in conjunction with the
-command, which must be used in conjunction with the neb command.  The
+neb command.  The group used to define the fix neb command defines the
-group used to define the fix neb command defines the NEB atoms which
+NEB atoms which are the only ones that inter-replica springs are
-are the only ones that inter-replica springs are applied to.  If the
+applied to.  If the group does not include all atoms, then non-NEB
-group does not include all atoms, then non-NEB atoms have no
+atoms have no inter-replica springs and the forces they feel and their
-inter-replica springs and the forces they feel and their motion is
+motion is computed in the usual way due only to other atoms within
-computed in the usual way due only to other atoms within their
+their replica.  Conceptually, the non-NEB atoms provide a background
-replica.  Conceptually, the non-NEB atoms provide a background force
+force field for the NEB atoms.  They can be allowed to move during the
-field for the NEB atoms.  They can be allowed to move during the NEB
+NEB minimization procedure (which will typically induce different
-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
+Conceptually, the initial and final configurations for the first
-be a state with all the atoms (NEB and non-NEB) having coordinates on
+replica should be states on either side of an energy barrier.
-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.
 
 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
+from such an initial path.  In this case, you will want to generate
-generate initial states for the intermediate replicas that are
+initial states for the intermediate replicas that are geometrically
-geometrically closer to the MEP and read them in.
+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
+the line.  Note that for this procedure to produce consistent
-across all the replicas, the current coordinates need to be the same
+coordinates across all the replicas, the current coordinates need to
-in all replicas.  LAMMPS does not check for this, but invalid initial
+be the same in all replicas.  LAMMPS does not check for this, but
-configurations will likely result if it is not the case.
+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
+assumed to be unique to each replica.  This can be done by using a
-using a variable in the filename, e.g.
+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
+nudging forces, since these are non-conservative.  A non-zero {ftol}
-that the NEB calculation will terminate if the force criterion is met
+means that the NEB calculation will terminate if the force criterion
-by every replica.  The forces being compared to {ftol} include the
+is met by every replica.  The forces being compared to {ftol} include
-inter-replica forces between an atom and its images in adjacent
+the inter-replica nudging forces.
-replicas.
 
 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
+a minimum energy path (MEP) of conformational states that transition
-over the barrier.  The MEP for a barrier is defined as a sequence of
+over a barrier.  The MEP for a transition is defined as a sequence of
-3N-dimensional states that cross the barrier at its saddle point, each
+3N-dimensional states, each of which has a potential energy gradient
-of which has a potential energy gradient parallel to the MEP itself.
+parallel to the MEP itself.  The configuration of highest energy along
-The replica states will also be roughly equally spaced along the MEP
+a MEP corresponds to a saddle point.  The replica states will also be
-due to the inter-replica spring force added by the "fix
+roughly equally spaced along the MEP due to the inter-replica nugding
-neb"_fix_neb.html command.
+force added by the "fix neb"_fix_neb.html command.
 
-In the second stage of NEB, the replica with the highest energy
+In the second stage of NEB, the replica with the highest energy is
-is selected and the inter-replica forces on it are converted to a
+selected and the inter-replica forces on it are converted to a force
-force that drives its atom coordinates to the top or saddle point of
+that drives its atom coordinates to the top or saddle point of the
-the barrier, via the barrier-climbing calculation described in
+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
+the configurations of the replicas should be along (close to) the MEP
-saddle point of the barrier, the potential energies for the set of
+and the replica with the highest energy should be an atomic
-replicas should represent the energy profile of the barrier along the
+configuration at (close to) the saddle point of the transition. The
-MEP, and the configurations of the replicas should be a sequence of
+potential energies for the set of replicas represents the energy
-configurations along the MEP.
+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 fields are the atom ID, followed by the x,y,z coordinates.  The
-The lines can be listed in any order.  Additional trailing information
+lines can be listed in any order.  Additional trailing information on
-on the line is OK, such as a comment.
+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,
+final, and climbing replicas, the forward and backward energy
-the total reaction coordinate (RDT), and the normalized reaction
+barriers, the total reaction coordinate (RDT), and the normalized
-coordinate and potential energy of each replica.
+reaction coordinate and potential energy of each replica.
 
-The "maximum force per replica" is
+The "maximum force per replica" is the two-norm of the 3N-length force
-the two-norm of the 3N-length force vector for the atoms in each
+vector for the atoms in each replica, maximized across replicas, which
-replica, maximized across replicas, which is what the {ftol} setting
+is what the {ftol} setting is checking against.  In this case, N is
-is checking against.  In this case, N is all the atoms in each
+all the atoms in each replica.  The "maximum force per atom" is the
-replica.  The "maximum force per atom" is the maximum force component
+maximum force component of any atom in any replica.  The potential
-of any atom in any replica.  The potential gradients are the two-norm
+gradients are the two-norm of the 3N-length force vector solely due to
-of the 3N-length force vector solely due to the interaction potential i.e.
+the interaction potential i.e.  without adding in inter-replica
-without adding in inter-replica forces. Note that inter-replica forces
+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 "reaction coordinate" (RD) for each
+The "reaction coordinate" (RD) for each replica is the two-norm of the
-replica is the two-norm of the 3N-length vector of distances between
+3N-length vector of distances between its atoms and the preceding
-its atoms and the preceding replica's atoms, added to the RD of the
+replica's atoms, added to the RD of the preceding replica. The RD of
-preceding replica. The RD of the first replica RD1 = 0.0;
+the first replica RD1 = 0.0; the RD of the final replica RDN = RDT,
-the RD of the final replica RDN = RDT, the total reaction coordinate.
+the total reaction coordinate.  The normalized RDs are divided by RDT,
-The normalized RDs are divided by RDT,
+so that they form a monotonically increasing sequence from zero to
-so that they form a monotonically increasing sequence
+one. When computing RD, N only includes the atoms being operated on by
-from zero to one. When computing RD, N only includes the atoms
+the fix neb command.
-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
+"prd"_prd.html, "temper"_temper.html, "fix langevin"_fix_langevin.html,
-langevin"_fix_langevin.html, "fix viscous"_fix_viscous.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
+For the KOKKOS package, the option defaults neigh = full,
- = full, newton = off, binsize = 0.0, and comm = device.  These settings
+neigh/qeq = full, newton = off, binsize = 0.0, and comm = device.
- are made automatically by the required "-k on" "command-line
+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_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_edip.txt

@@ -7,11 +7,13 @@
 :line
 
 pair_style edip command :h3
+pair_style edip/multi command :h3
 
 [Syntax:]
 
-pair_style edip :pre
+pair_style style :pre
-pair_style edip/omp :pre
+
+style = {edip} or {edip/multi} :ul
 
 [Examples:]
 
@@ -20,11 +22,14 @@ pair_coeff * * Si.edip Si
 
 [Description:]
 
-The {edip} style computes a 3-body "EDIP"_#EDIP potential which is
+The {edip} and {edip/multi} styles compute a 3-body "EDIP"_#EDIP
-popular for modeling silicon materials where it can have advantages
+potential which is popular for modeling silicon materials where
-over other models such as the "Stillinger-Weber"_pair_sw.html or
+it can have advantages over other models such as the
-"Tersoff"_pair_tersoff.html potentials.  In EDIP, the energy E of a
+"Stillinger-Weber"_pair_sw.html or "Tersoff"_pair_tersoff.html
-system of atoms is
+potentials. The {edip} style has been programmed for single element
+potentials, while {edip/multi} supports multi-element EDIP runs.
+
+In EDIP, the energy E of a system of atoms is
 
 :c,image(Eqs/pair_edip.jpg)
 
@@ -142,7 +147,7 @@ This pair style can only be used via the {pair} keyword of the
 
 [Restrictions:]
 
-This angle style can only be used if LAMMPS was built with the
+This pair style can only be used if LAMMPS was built with the
 USER-MISC package.  See the "Making LAMMPS"_Section_start.html#start_3
 section for more info on packages.
 
@@ -151,7 +156,7 @@ for pair interactions.
 
 The EDIP potential files provided with LAMMPS (see the potentials directory)
 are parameterized for metal "units"_units.html.
-You can use the SW potential with any LAMMPS units, but you would need
+You can use the EDIP potential with any LAMMPS units, but you would need
 to create your own EDIP potential file with coefficients listed in the
 appropriate units if your simulation doesn't use "metal" units.
 
@@ -164,4 +169,4 @@ appropriate units if your simulation doesn't use "metal" units.
 :line
 
 :link(EDIP)
-[(EDIP)] J. F. Justo et al., Phys. Rev. B 58, 2539 (1998).
+[(EDIP)] J F Justo et al, Phys Rev B 58, 2539 (1998).

doc/src/pair_gauss.txt

@@ -128,7 +128,7 @@ The B parameter is converted to a distance (sigma), before mixing
 afterwards (using B=sigma^2).
 Negative A values are converted to positive A values (using abs(A))
 before mixing, and converted back after mixing
-(by multiplying by sign(Ai)*sign(Aj)).
+(by multiplying by min(sign(Ai),sign(Aj))).
 This way, if either particle is repulsive (if Ai<0 or Aj<0),
 then the default interaction between both particles will be repulsive.
 

doc/src/pair_gw.txt

@@ -0,0 +1,120 @@
+"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 gw command :h3
+pair_style gw/zbl command :h3
+
+[Syntax:]
+
+pair_style style :pre
+
+style = {gw} or {gw/zbl} :ul
+
+[Examples:]
+
+pair_style gw
+pair_coeff * * SiC.gw Si C C
+
+pair_style gw/zbl
+pair_coeff * * SiC.gw.zbl C Si :pre
+
+[Description:]
+
+The {gw} style computes a 3-body "Gao-Weber"_#Gao potential;
+similarly {gw/zbl} combines this potential with a modified
+repulsive ZBL core function in a similar fashion as implemented
+in the "tersoff/zbl"_pair_tersoff_zbl.html pair style.
+
+Unfortunately the author of this contributed code has not been
+able to submit a suitable documentation explaining the details
+of the potentials. The LAMMPS developers thus have finally decided
+to release the code anyway with only the technical explanations.
+For details of the model and the parameters, please refer to the
+linked publication.
+
+Only a single pair_coeff command is used with the {gw} and {gw/zbl}
+styles which specifies a Gao-Weber potential file with parameters
+for all 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
+N element names = mapping of GW elements to atom types :ul
+
+See the "pair_coeff"_pair_coeff.html doc page for alternate ways
+to specify the path for the potential file.
+
+As an example, imagine a file SiC.gw has Gao-Weber values for Si and C.
+If your LAMMPS simulation has 4 atoms types and you want the first 3 to
+be Si, and the 4th to be C, you would use the following pair_coeff command:
+
+pair_coeff * * SiC.gw Si Si Si C :pre
+
+The first 2 arguments must be * * so as to span all LAMMPS atom types.
+The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
+element in the GW file.  The final C argument maps LAMMPS atom type 4
+to the C element in the GW file.  If a mapping value is specified as
+NULL, the mapping is not performed.  This can be used when a {gw}
+potential is used as part of the {hybrid} pair style.  The NULL values
+are placeholders for atom types that will be used with other
+potentials.
+
+Gao-Weber files in the {potentials} directory of the LAMMPS
+distribution have a ".gw" suffix.  Gao-Weber with ZBL files
+have a ".gz.zbl" suffix. The structure of the potential files
+is similar to other many-body potentials supported by LAMMPS.
+You have to refer to the comments in the files and the literature
+to learn more details.
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS as
+described above from values in the potential file.
+
+This pair style does not support the "pair_modify"_pair_modify.html
+shift, table, and tail options.
+
+This pair style does not write its information to "binary restart
+files"_restart.html, since it is stored in potential files.  Thus, you
+need to re-specify the pair_style and pair_coeff commands 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.
+
+This pair style requires the "newton"_newton.html setting to be "on"
+for pair interactions.
+
+The Gao-Weber potential files provided with LAMMPS (see the
+potentials directory) are parameterized for metal "units"_units.html.
+You can use the GW potential with any LAMMPS units, but you would need
+to create your own GW potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "metal" units.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html
+
+[Default:] none
+
+:line
+
+:link(Gao)
+[(Gao)] Gao and Weber, Nuclear Instruments and Methods in Physics Research B 191 (2012) 504.

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_style lj/smooth/linear 2.5
-pair_coeff * * 0.7242785984051078 2.598146797350056
+pair_coeff * * 1.0 1.0
-pair_coeff 1 1 20.0 1.3 9.0 :pre
+pair_coeff 1 1 0.3 3.0 9.0 :pre
 
 [Description:]
 
-Style {lj/smooth/linear} computes a LJ interaction that combines the
+Style {lj/smooth/linear} computes a truncated and force-shifted LJ
-standard 12/6 Lennard-Jones function and subtracts a linear term that
+interaction (aka Shifted Force Lennard-Jones) that combines the
-includes the cutoff distance Rc, as in this formula:
+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
+The last coefficient is optional. If not specified, the global
-for Rc is used.
+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
+The "pair_modify"_pair_modify.html table option is not relevant
-this pair style.
+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
+built and linked with LAMMPS.
-LAMMPS"_Section_start.html#start_3 section for more info.
+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_meam_spline.txt

@@ -33,7 +33,7 @@ atoms J, I, and K centered on atom I. The five functions Phi, U, rho,
 f, and g are represented by cubic splines.
 
 The {meam/spline} style also supports a new style multicomponent
-modified embedded-atom method (MEAM) potential "(Zhang)"_#Zhang1, where
+modified embedded-atom method (MEAM) potential "(Zhang)"_#Zhang4, where
 the total energy E is given by
 
 :c,image(Eqs/pair_meam_spline_multicomponent.jpg)
@@ -164,5 +164,5 @@ for more info.
 Kress, Modelling Simulation Materials Science Engineering, 8, 825
 (2000).
 
-:link(Zhang1)
+:link(Zhang4)
 [(Zhang)] Zhang and Trinkle, Computational Materials Science, 124, 204-210 (2016).

doc/src/pair_morse.txt

@@ -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_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
+It is required that the potential file contains entries for {all}
-of the elements listed in the pair_coeff command.  It can also contain
+permutations of the elements listed in the pair_coeff command.
-entries for additional elements not being used in a particular
+If certain combinations are not parameterized the corresponding
-simulation; LAMMPS ignores those entries.
+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_python.txt

@@ -0,0 +1,217 @@
+"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 python command :h3
+
+[Syntax:]
+
+pair_style python cutoff :pre
+
+cutoff = global cutoff for interactions in python potential classes
+
+[Examples:]
+
+pair_style python 2.5
+pair_coeff * * py_pot.LJCutMelt lj :pre
+
+pair_style hybrid/overlay coul/long 12.0 python 12.0
+pair_coeff * * coul/long
+pair_coeff * * python py_pot.LJCutSPCE OW NULL :pre
+
+[Description:]
+
+The {python} pair style provides a way to define pairwise additive
+potential functions as python script code that is loaded into LAMMPS
+from a python file which must contain specific python class definitions.
+This allows to rapidly evaluate different potential functions without
+having to modify and recompile LAMMPS. Due to python being an
+interpreted language, however, the performance of this pair style is
+going to be significantly slower (often between 20x and 100x) than
+corresponding compiled code. This penalty can be significantly reduced
+through generating tabulations from the python code through the
+"pair_write"_pair_write.html command, which is supported by this style.
+
+Only a single pair_coeff command is used with the {python} pair style
+which specifies a python class inside a python module or file that
+LAMMPS will look up in the current directory, the folder pointed to by
+the LAMMPS_POTENTIALS environment variable or somewhere in your python
+path.  A single python module can hold multiple python pair class
+definitions. The class definitions itself have to follow specific
+rules that are explained below.
+
+Atom types in the python class are specified through symbolic
+constants, typically strings. These are mapped to LAMMPS atom types by
+specifying N additional arguments after the class name in the
+pair_coeff command, where N must be the number of currently defined
+atom types:
+
+As an example, imagine a file {py_pot.py} has a python potential class
+names {LJCutMelt} with parameters and potential functions for a two
+Lennard-Jones atom types labeled as 'LJ1' and 'LJ2'. In your LAMMPS
+input and you would have defined 3 atom types, out of which the first
+two are supposed to be using the 'LJ1' parameters and the third the
+'LJ2' parameters, then you would use the following pair_coeff command:
+
+pair_coeff * * py_pot.LJCutMelt LJ1 LJ1 LJ2 :pre
+
+The first two arguments [must] be * * so as to span all LAMMPS atom
+types.  The first two LJ1 arguments map LAMMPS atom types 1 and 2 to
+the LJ1 atom type in the LJCutMelt class of the py_pot.py file.  The
+final LJ2 argument maps LAMMPS atom type 3 to the LJ2 atom type the
+python file.  If a mapping value is specified as NULL, the mapping is
+not performed, any pair interaction with this atom type will be
+skipped. This can be used when a {python} potential is used as part of
+the {hybrid} or {hybrid/overlay} pair style. The NULL values are then
+placeholders for atom types that will be used with other potentials.
+
+:line
+
+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()
+        self.units='lj'
+    def map_coeff(self,name,ltype):
+        self.pmap\[ltype\]=name
+    def check_units(self,units):
+        if (units != self.units):
+           raise Exception("Conflicting units: %s vs. %s" % (self.units,units))
+:pre
+
+Any classes with definitions of specific potentials have to be derived
+from this class and should be initialize in a similar fashion to the
+example given below.
+
+NOTE: The class constructor has to set up a data structure containing
+the potential parameters supported by this class.  It should also
+define a variable {self.units} containing a string matching one of the
+options of LAMMPS' "units"_units.html command, which is used to
+verify, that the potential definition in the python class and in the
+LAMMPS input match.
+
+Here is an example for a single type Lennard-Jones potential class
+{LJCutMelt} in reducted units, which defines an atom type {lj} for
+which the parameters epsilon and sigma are both 1.0:
+
+class LJCutMelt(LAMMPSPairPotential):
+    def __init__(self):
+        super(LJCutMelt,self).__init__()
+        # set coeffs: 48*eps*sig**12, 24*eps*sig**6,
+        #              4*eps*sig**12,  4*eps*sig**6
+        self.units = 'lj'
+        self.coeff = \{'lj'  : \{'lj'  : (48.0,24.0,4.0,4.0)\}\}
+:pre
+
+The class also has to provide two methods for the computation of the
+potential energy and forces, which have be named {compute_force},
+and {compute_energy}, which both take 3 numerical arguments:
+
+  rsq   = the square of the distance between a pair of atoms (float) :l
+  itype = the (numerical) type of the first atom :l
+  jtype = the (numerical) type of the second atom :ul
+
+This functions need to compute the force and the energy, respectively,
+and use the result as return value. The functions need to use the
+{pmap} dictionary to convert the LAMMPS atom type number to the symbolic
+value of the internal potential parameter data structure. Following
+the {LJCutMelt} example, here are the two functions:
+
+   def compute_force(self,rsq,itype,jtype):
+        coeff = self.coeff\[self.pmap\[itype\]\]\[self.pmap\[jtype\]\]
+        r2inv  = 1.0/rsq
+        r6inv  = r2inv*r2inv*r2inv
+        lj1 = coeff\[0\]
+        lj2 = coeff\[1\]
+        return (r6inv * (lj1*r6inv - lj2))*r2inv :pre
+
+    def compute_energy(self,rsq,itype,jtype):
+        coeff = self.coeff\[self.pmap\[itype\]\]\[self.pmap\[jtype\]\]
+        r2inv  = 1.0/rsq
+        r6inv  = r2inv*r2inv*r2inv
+        lj3 = coeff\[2\]
+        lj4 = coeff\[3\]
+        return (r6inv * (lj3*r6inv - lj4)) :pre
+
+NOTE: for consistency with the C++ pair styles in LAMMPS, the
+{compute_force} function follows the conventions of the Pair::single()
+methods and does not return the full force, but the force scaled by
+the distance between the two atoms, so this value only needs to be
+multiplied by delta x, delta y, and delta z to conveniently obtain the
+three components of the force vector between these two atoms.
+
+:line
+
+NOTE: The evaluation of scripted python code will slow down the
+computation pair-wise interactions quite significantly. However, this
+can be largely worked around through using the python pair style not
+for the actual simulation, but to generate tabulated potentials on the
+fly using the "pair_write"_pair_write.html command. Please see below
+for an example LAMMPS input of how to build a table file:
+
+pair_style python 2.5
+pair_coeff * * py_pot.LJCutMelt lj
+shell rm -f melt.table
+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, 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:
+
+pair_style      table linear 2000
+pair_coeff      1  1  melt.table lj :pre
+
+This can also be done for more complex systems.  Please see the
+{examples/python} folders for a few more examples.
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+Mixing of potential parameters has to be handled inside the provided
+python module. The python pair style simply assumes that force and
+energy computation can be correctly performed for all pairs of atom
+types as they are mapped to the atom type labels inside the python
+potential class.
+
+This pair style does not support the "pair_modify"_pair_modify.html
+shift, table, and tail options.
+
+This pair style does not write its information to "binary restart
+files"_restart.html, since it is stored in potential files.  Thus, you
+need to re-specify the pair_style and pair_coeff commands 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 PYTHON 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, "pair_write"_pair_write.html,
+"pair style table"_pair_table.html
+
+[Default:] none
+
+

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_tersoff.txt

@@ -18,7 +18,7 @@ pair_style tersoff/table/omp command :h3
 
 pair_style style :pre
 
-style = {tersoff} or {tersoff/table} or {tersoff/gpu} or {tersoff/omp} or {tersoff/table/omp}
+style = {tersoff} or {tersoff/table} or {tersoff/gpu} or {tersoff/omp} or {tersoff/table/omp} :ul
 
 [Examples:]
 

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_yukawa_colloid.txt

@@ -35,7 +35,7 @@ cutoff.
 In contrast to "pair_style yukawa"_pair_yukawa.html, this functional
 form arises from the Coulombic interaction between two colloid
 particles, screened due to the presence of an electrolyte, see the
-book by "Safran"_#Safran for a derivation in the context of DVLO
+book by "Safran"_#Safran for a derivation in the context of DLVO
 theory.  "Pair_style yukawa"_pair_yukawa.html is a screened Coulombic
 potential between two point-charges and uses no such approximation.
 

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

@@ -36,6 +36,7 @@ Pair Styles :h1
    pair_gayberne
    pair_gran
    pair_gromacs
+   pair_gw
    pair_hbond_dreiding
    pair_hybrid
    pair_kim
@@ -48,7 +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
@@ -71,6 +71,7 @@ Pair Styles :h1
    pair_oxdna2
    pair_peri
    pair_polymorphic
+   pair_python
    pair_quip
    pair_reax
    pair_reaxc

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 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
+{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
+{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
+{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
+{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
+bond/create"_fix_bond_create.html command. Using this header flag
-space in LAMMPS data structures for storing the new bonds (angles,
+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
+will be added to the system, e.g. by using the
-deposit"_fix_deposit.html or "fix pour"_fix_pour.html commands, which
+"fix deposit"_fix_deposit.html or "fix pour"_fix_pour.html commands,
-will have more special 1-2,1-3,1-4 neighbors than any other molecules
+which will have more special 1-2,1-3,1-4 neighbors than any other
-defined in the data file.  Using this setting will pre-allocate space
+molecules defined in the data file.  Using this header flag is
-in the LAMMPS data structures for storing these neighbors.  See the
+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
+NOTE: All of the "extra" settings are only applied in the first data
-first data file read; see the description of the {add} keyword above
+file read and when no simulation box has yet been created; as soon as
-for reading multiple data files.  If they appear in later data files,
+the simulation box is created (and read_data implies that), these
-they are ignored.
+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/rerun.txt

@@ -15,7 +15,7 @@ rerun file1 file2 ... keyword args ... :pre
 file1,file2,... = dump file(s) to read :ulb,l
 one or more keywords may be appended, keyword {dump} must appear and be last :l
 keyword = {first} or {last} or {every} or {skip} or {start} or {stop} or {dump}
- {first} args = Nfirts
+ {first} args = Nfirst
    Nfirst = dump timestep to start on
  {last} args = Nlast
    Nlast = dumptimestep to stop on

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
+nx,ny,nz, then the current image value for that dimension is unchanged.
-unchanged.  For non-periodic dimensions only a value of 0 can be
+For non-periodic dimensions only a value of 0 can be specified.
-specified.  This keyword does not allow use of atom-style variables.
 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_pylammps.txt

@@ -10,6 +10,7 @@ PyLammps Tutorial :h1
 
 <!-- RST
 .. contents::
+
 END_RST -->
 
 Overview :h2

doc/src/velocity.txt

@@ -61,7 +61,7 @@ keyword/value parameters.  Not all options are used by each style.
 Each option has a default as listed below.
 
 The {create} style generates an ensemble of velocities using a random
-number generator with the specified seed as the specified temperature.
+number generator with the specified seed at the specified temperature.
 
 The {set} style sets the velocities of all atoms in the group to the
 specified values.  If any component is specified as NULL, then it is

examples/ASPHERE/poly/in.poly

@@ -62,6 +62,7 @@ pair_coeff	3 3 1.0 1.5
 pair_coeff	1 4 0.0 1.0 0.5
 pair_coeff	2 4 0.0 1.0 1.0
 pair_coeff	3 4 0.0 1.0 0.75
+pair_coeff	4 4 0.0 1.0 0.0
 
 delete_atoms	overlap 1.0 small big
 

examples/ASPHERE/poly/in.poly.mp

@@ -62,6 +62,7 @@ pair_coeff	3 3 1.0 1.5
 pair_coeff	1 4 0.0 1.0 0.5
 pair_coeff	2 4 0.0 1.0 1.0
 pair_coeff	3 4 0.0 1.0 0.75
+pair_coeff	4 4 0.0 1.0 0.0
 
 delete_atoms	overlap 1.0 small big
 

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
+
+

examples/COUPLE/simple/simple.cpp

@@ -153,7 +153,7 @@ int main(int narg, char **arg)
     for (int i = 0; i < natoms; i++) type[i] = 1;
 
     lmp->input->one("delete_atoms group all");
-    lammps_create_atoms(lmp,natoms,NULL,type,x,v);
+    lammps_create_atoms(lmp,natoms,NULL,type,x,v,NULL,0);
     lmp->input->one("run 10");
   }
 

examples/USER/cgdna/util/generate.py

@@ -14,7 +14,7 @@
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
-   Contributing author: Oliver Henrich (EPCC, University of Edinburgh)
+   Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
 ------------------------------------------------------------------------- */
 """
 

examples/USER/misc/cnp/in.cnp

@@ -0,0 +1,51 @@
+# Generation and relaxation of a partial dislocation in Cu perfect FCC crystal
+
+# Initialization
+units           metal
+boundary        p p p
+atom_style      atomic
+
+# create simulation box and system
+lattice         fcc 3.615  origin 0.01 0.01 0.01 orient x -1 -1 2 orient y 1 1 1 orient z -1 1 0 
+region          mdbox  block 0 3 0.0 14.0 0 84 units lattice
+region          system block 0 3 1.1 13.1 0 84 units lattice
+create_box      2 mdbox
+create_atoms    1 region system
+
+# Define atoms mass and force field
+mass            *  63.54                     
+pair_style      eam/alloy
+pair_coeff      * * Cu_Mishin1.eam Cu Cu
+
+# Delete a plane of atoms along the z direction to generate a partial dislocation
+region          dislocation_atoms block 0 3 7 14 41.9 42.1 units lattice
+delete_atoms    region dislocation_atoms
+region          quarter_up block 0 3 7 11 0 84 units lattice
+group           middle region quarter_up
+
+# specify simulation parameters
+timestep        0.004
+
+# Relax configuration using conjugate gradient
+#min_style cg
+#minimize 1.0e-4 1.0e-6 100 1000
+
+# Setup calculations 
+compute         1 all cnp/atom 3.086
+compute         2 all cna/atom 3.086
+compute         3 all centro/atom fcc
+compute         4 all coord/atom cutoff 3.086
+dump            1 all custom 100 dump.lammpstrj id type xu yu zu c_1 c_2 c_3 c_4 
+
+### Set up thermo display
+thermo          10
+thermo_style    custom step atoms temp press pe ke etotal
+
+# Relax the system performing a langevin dynamics (freeze motion along y 111 direction)
+fix             1 all nve
+fix             2 all langevin 50 1 0.1 699483
+fix             3 all setforce NULL 0.0 NULL
+fix             4 middle setforce 0.0  0.0 0.0
+run             100
+unfix           4
+run             200

examples/USER/misc/cnp/log.31May17.cnp.g++.4

@@ -0,0 +1,185 @@
+LAMMPS (19 May 2017)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# Generation and relaxation of a partial dislocation in Cu perfect FCC crystal
+
+# Initialization
+units           metal
+boundary        p p p
+atom_style      atomic
+
+# create simulation box and system
+lattice         fcc 3.615  origin 0.01 0.01 0.01 orient x -1 -1 2 orient y 1 1 1 orient z -1 1 0
+Lattice spacing in x,y,z = 5.90327 6.26136 5.11238
+region          mdbox  block 0 3 0.0 14.0 0 84 units lattice
+region          system block 0 3 1.1 13.1 0 84 units lattice
+create_box      2 mdbox
+Created orthogonal box = (0 0 0) to (17.7098 87.6591 429.44)
+  1 by 1 by 4 MPI processor grid
+create_atoms    1 region system
+Created 48384 atoms
+
+# Define atoms mass and force field
+mass            *  63.54
+pair_style      eam/alloy
+pair_coeff      * * Cu_Mishin1.eam Cu Cu
+
+# Delete a plane of atoms along the z direction to generate a partial dislocation
+region          dislocation_atoms block 0 3 7 14 41.9 42.1 units lattice
+delete_atoms    region dislocation_atoms
+Deleted 76 atoms, new total = 48308
+region          quarter_up block 0 3 7 11 0 84 units lattice
+group           middle region quarter_up
+16080 atoms in group middle
+
+# specify simulation parameters
+timestep        0.004
+
+# Relax configuration using conjugate gradient
+#min_style cg
+#minimize 1.0e-4 1.0e-6 100 1000
+
+# Setup calculations
+compute         1 all cnp/atom 3.086
+compute         2 all cna/atom 3.086
+compute         3 all centro/atom fcc
+compute         4 all coord/atom cutoff 3.086
+dump            1 all custom 100 dump.lammpstrj id type xu yu zu c_1 c_2 c_3 c_4
+
+### Set up thermo display
+thermo          10
+thermo_style    custom step atoms temp press pe ke etotal
+
+# Relax the system performing a langevin dynamics (freeze motion along y 111 direction)
+fix             1 all nve
+fix             2 all langevin 50 1 0.1 699483
+fix             3 all setforce NULL 0.0 NULL
+fix             4 middle setforce 0.0  0.0 0.0
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.50679
+  ghost atom cutoff = 7.50679
+  binsize = 3.75339, bins = 5 24 115
+  5 neighbor lists, perpetual/occasional/extra = 1 4 0
+  (1) pair eam/alloy, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) compute cnp/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) compute cna/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (4) compute centro/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (5) compute coord/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 45.41 | 45.41 | 45.41 Mbytes
+Step Atoms Temp Press PotEng KinEng TotEng 
+       0    48308            0   -3388.0911   -169746.07            0   -169746.07 
+      10    48308      7.35092   -3091.0864   -169715.96    45.900393   -169670.05 
+      20    48308    9.9162268   -2822.7045   -169678.51    61.918604   -169616.59 
+      30    48308    12.351316   -2726.7195   -169666.35    77.123716   -169589.23 
+      40    48308    13.302856    -2703.586    -169662.9     83.06529   -169579.83 
+      50    48308    12.782228   -2706.8662   -169662.36    79.814401   -169582.55 
+      60    48308    12.198179   -2772.4206   -169670.02    76.167503   -169593.86 
+      70    48308    10.663322   -2841.3384   -169677.48    66.583595    -169610.9 
+      80    48308    9.1169804   -2932.3896   -169687.85    56.927974   -169630.92 
+      90    48308    7.2905076   -3029.9433   -169699.09    45.523167   -169653.56 
+     100    48308    5.4063635   -3139.4496   -169711.65    33.758252   -169677.89 
+Loop time of 10.9003 on 4 procs for 100 steps with 48308 atoms
+
+Performance: 3.171 ns/day, 7.570 hours/ns, 9.174 timesteps/s
+31.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 9.8764     | 9.9587     | 10.021     |   1.6 | 91.36
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.1232     | 0.18385    | 0.26683    |  12.1 |  1.69
+Output  | 0.45385    | 0.45451    | 0.45634    |   0.2 |  4.17
+Modify  | 0.25026    | 0.2537     | 0.25744    |   0.5 |  2.33
+Other   |            | 0.04949    |            |       |  0.45
+
+Nlocal:    12077 ave 12096 max 12020 min
+Histogram: 1 0 0 0 0 0 0 0 0 3
+Nghost:    14204 ave 14261 max 14109 min
+Histogram: 1 0 0 0 0 1 0 0 0 2
+Neighs:    814050 ave 818584 max 809212 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+FullNghs:  1.6281e+06 ave 1.63296e+06 max 1.61808e+06 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+
+Total # of neighbors = 6512400
+Ave neighs/atom = 134.81
+Neighbor list builds = 0
+Dangerous builds = 0
+unfix           4
+run             200
+Per MPI rank memory allocation (min/avg/max) = 45.41 | 45.41 | 45.41 Mbytes
+Step Atoms Temp Press PotEng KinEng TotEng 
+     100    48308    5.4063635   -3139.4496   -169711.65    33.758252   -169677.89 
+     110    48308    15.260795    -2793.119   -169677.24    95.290993   -169581.95 
+     120    48308    18.548656   -2433.1584   -169624.79    115.82096   -169508.97 
+     130    48308     22.15831    -2276.626   -169604.28    138.36025   -169465.92 
+     140    48308    24.393841   -2208.1771   -169596.16    152.31929   -169443.84 
+     150    48308    24.797558   -2173.3145   -169591.43    154.84016   -169436.59 
+     160    48308     24.73371    -2188.909   -169593.08    154.44148   -169438.64 
+     170    48308    24.128467   -2220.3404   -169596.96    150.66225   -169446.29 
+     180    48308    22.975708   -2275.1244   -169602.72    143.46422   -169459.26 
+     190    48308    21.936324   -2348.3762   -169610.59    136.97413   -169473.61 
+     200    48308    20.516249   -2432.8447   -169619.98    128.10694   -169491.87 
+     210    48308    19.000566   -2510.2915   -169628.58    118.64276   -169509.93 
+     220    48308    17.490407    -2597.299   -169638.24    109.21307   -169529.03 
+     230    48308    16.062482   -2684.1203   -169648.31    100.29687   -169548.01 
+     240    48308    14.360342   -2768.2313    -169657.7    89.668411   -169568.03 
+     250    48308    12.802315   -2852.6965   -169666.99    79.939831   -169587.05 
+     260    48308    11.258205   -2944.4533   -169677.52    70.298142   -169607.23 
+     270    48308    9.6159129   -3038.6304   -169688.06    60.043393   -169628.02 
+     280    48308     7.972425   -3129.0826   -169698.03    49.781176   -169648.25 
+     290    48308    6.3752377   -3219.2054   -169708.23    39.808067   -169668.42 
+     300    48308    4.7374688   -3306.1468   -169718.27     29.58156   -169688.69 
+Loop time of 23.0164 on 4 procs for 200 steps with 48308 atoms
+
+Performance: 3.003 ns/day, 7.992 hours/ns, 8.689 timesteps/s
+31.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 20.221     | 20.423     | 20.57      |   3.1 | 88.73
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.27748    | 0.42603    | 0.62832    |  21.4 |  1.85
+Output  | 1.5454     | 1.5473     | 1.5529     |   0.3 |  6.72
+Modify  | 0.48886    | 0.49773    | 0.50842    |   1.1 |  2.16
+Other   |            | 0.1221     |            |       |  0.53
+
+Nlocal:    12077 ave 12096 max 12020 min
+Histogram: 1 0 0 0 0 0 0 0 0 3
+Nghost:    14204 ave 14261 max 14109 min
+Histogram: 1 0 0 0 0 1 0 0 0 2
+Neighs:    814094 ave 818584 max 809212 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+FullNghs:  1.62852e+06 ave 1.63296e+06 max 1.61892e+06 min
+Histogram: 1 0 0 0 0 0 0 1 0 2
+
+Total # of neighbors = 6514094
+Ave neighs/atom = 134.845
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:35

examples/USER/misc/edip/Si.edip

@@ -0,0 +1,26 @@
+# DATE: 2011-09-15 CONTRIBUTOR: Unknown CITATION: Justo, Bazant, Kaxiras, Bulatov and Yip, Phys Rev B, 58, 2539 (1998)
+
+# EDIP parameters for various elements and mixtures
+# multiple entries can be added to this file, LAMMPS reads the ones it needs
+# these entries are in LAMMPS "metal" units
+
+# format of a single entry (one or more lines)
+#
+#   element 1, element 2, element 3, 
+#     A   B   cutoffA   cutoffC   alpha   beta   eta 
+#     gamma   lambda    mu   rho   sigma   Q0 
+#     u1   u2   u3   u4
+#
+# units for each parameters:
+#     A , lambda are in eV  
+#     B, cutoffA, cutoffC, gamma, sigma are in Angstrom
+#     alpha, beta, eta, mu, rho, Q0, u1-u4 are pure numbers 
+
+# Here are the original parameters in metal units, for Silicon from:
+# J. F. Justo, M. Z. Bazant, E. Kaxiras, V. V. Bulatov, S. Yip
+#       Phys. Rev. B 58, 2539 (1998)
+#
+
+Si Si Si 7.9821730 1.5075463 3.1213820 2.5609104 3.1083847 0.0070975 0.2523244
+         1.1247945 1.4533108 0.6966326 1.2085196 0.5774108 312.1341346
+         -0.165799 32.557 0.286198 0.66

examples/USER/misc/edip/SiC.edip

@@ -0,0 +1,38 @@
+# DATE: 2017-05-16 CONTRIBUTOR: Laurent Pizzagalli CITATION: G. Lucas, M. Bertolus, and L. Pizzagalli, J. Phys. : Condens. Matter 22, 035802 (2010)
+#   element 1, element 2, element 3, 
+#     A   B   cutoffA   cutoffC   alpha   beta   eta 
+#     gamma   lambda    mu   rho   sigma   Q0 
+#     u1   u2   u3   u4
+#
+Si Si Si 5.488043 1.446435 2.941586 2.540193 3.066580 0.008593 0.589390
+         1.135256 2.417497 0.629131 1.343679 0.298443 208.924548
+         -0.165799 32.557 0.286198 0.66
+
+C C C    10.222599 0.959814 2.212263 1.741598 1.962090 0.025661 0.275605
+         1.084183 3.633621 0.594236 2.827634 0.536561 289.305617
+         -0.165799 32.557 0.286198 0.66
+
+C Si Si  7.535967 1.177019 2.534972 1.973974 2.507738 0.015347 0.432497
+         1.191567 3.025559 0.611684 2.061835 0.423863 249.115082
+         -0.165799 32.557000 0.286198 0.660000
+
+Si C C   7.535967 1.177019 2.534972 1.973974 2.507738 0.015347 0.432497
+         1.191567 3.025559 0.611684 2.061835 0.423863 249.115082
+         -0.165799 32.557000 0.286198 0.660000
+
+Si Si C  5.488043 1.446435 2.941586 2.540193 3.066580 0.008593 0.510944
+         1.135256 2.721528 0.620407 1.343679 0.298443 229.019815
+         -0.165799 32.557000 0.286198 0.660000
+
+Si C Si  7.535967 1.177019 2.534972 1.973974 2.507738 0.015347 0.510944
+         1.191567 2.721528 0.620407 2.061835 0.423863 229.019815
+         -0.165799 32.557000 0.286198 0.660000
+
+C C Si   10.222599 0.959814 2.212263 1.741598 1.962090 0.025661 0.354051
+         1.084183 3.329590 0.602960 2.827634 0.536561 269.210350
+         -0.165799 32.557000 0.286198 0.660000
+
+C Si C   7.535967 1.177019 2.534972 1.973974 2.507738 0.015347 0.354051
+         1.191567 3.329590 0.602960 2.061835 0.423863 269.210350
+         -0.165799 32.557000 0.286198 0.660000
+

examples/USER/misc/edip/data.SiC

@@ -0,0 +1,138 @@
+Position data for Silicon-Carbon system
+
+	128 	atoms
+	2 	atom types
+  -6.00 	5.97232152 	xlo xhi
+  -6.00		5.97232152 	ylo yhi
+  -6.00 	5.97232152 	zlo zhi
+
+ Atoms
+
+1	2       -2.9378454      -4.4592615      -4.8109196
+2	2        5.6222143      -2.7335026      -1.7157569
+3	2       -2.6614623      -5.5431059       1.6353686
+4	2       -5.4326838      -4.6174577       5.9452279
+5	2        5.8679239      -0.1120535      -3.5839373
+6	2       -3.7174621      -0.6623311      -0.3714789
+7	2       -5.0724728      -2.5671623       4.4103461
+8	2       -3.3951436       0.9341126       4.9310702
+9	2       -5.4347593       1.9523767      -5.6180938
+10	2       -4.5884719       2.2904528      -1.0597739
+11	2       -5.9058662       0.6212406       2.0127574
+12	2       -4.7680660       0.1965740       4.3267764
+13	2       -5.4228882       5.2569673      -4.5162920
+14	2       -5.2683965      -5.9193658      -2.8648668
+15	2       -2.8610884       1.0484664       2.0299077
+16	2       -4.0711084       5.3133026       3.8009514
+17	2       -0.1947147      -4.1677696      -5.6950931
+18	2       -2.9892710      -3.1647368      -1.6173910
+19	2       -0.9129311      -4.3819066      -0.1601859
+20	2       -2.4513693      -5.2466501       4.8882912
+21	2       -2.8879952      -0.1633446      -3.3401150
+22	1       -4.6738762      -1.3807254      -2.2946777
+23	2       -0.6973948      -1.4885343       0.6005156
+24	1       -2.7392164      -2.4774843       0.2387186
+25	2       -2.6551254      -2.7229952       2.6350264
+26	1       -3.4644263      -4.6028144       3.3817786
+27	2        0.7227614      -2.0709446       2.9214737
+28	1       -2.1000577      -3.2131296       5.7273437
+29	2       -3.1057649       2.3204819      -2.2725622
+30	1       -2.2298751       0.7168389      -1.3107201
+31	2       -1.8698261       1.4006751       0.7265108
+32	1       -4.1103409      -0.7093340       1.9341753
+33	2       -0.3505581       3.2707182      -0.2880656
+34	1       -3.4045407      -1.4383961       4.3903527
+35	2       -3.0940529       1.4132478      -5.3635505
+36	1       -4.4560663       1.2072875      -3.7310176
+37	2       -2.6061002       4.6373499      -4.6903941
+38	1       -3.3477444       4.6768137      -2.6284678
+39	2        0.8121697       4.8602418      -4.6710946
+40	1       -2.5756922       3.3740738      -0.2136350
+41	2       -0.3867976       5.8745611      -2.1119905
+42	1       -1.6766249       1.3374292       3.8741477
+43	2       -0.8770613       3.3735941       4.3846975
+44	1       -1.8609254       3.3158245      -5.9786556
+45	1       -5.2732321      -4.6073253      -0.9581754
+46	1       -2.7888697      -5.6910152      -0.7922023
+47	1       -2.4717165       4.5801880       2.5083210
+48	1       -3.8819950       5.8456589      -5.7563384
+49	2        2.2314782      -2.7729214      -5.2356862
+50	2        0.2981976      -3.1385279      -3.1608167
+51	2        2.8810785      -3.4658695      -0.5823196
+52	2        0.2509625      -5.7595229       2.7389761
+53	2       -0.2934120      -0.8029431      -3.3698507
+54	1       -1.0075690      -2.0481922      -1.9419298
+55	2        2.0729069       1.4922441      -2.3898096
+56	1        1.1110944      -3.2004208       0.9491078
+57	2        1.6774298      -0.7901860       2.5158773
+58	1       -0.8342297      -4.3342518       2.0971458
+59	2        3.2747406      -1.3107897       4.7884706
+60	1        1.7126246      -3.3691471       4.5581012
+61	2        0.4770605       1.7769008      -5.3339915
+62	1        0.2944391       0.5892781      -2.2030106
+63	2        2.2039275       3.1557557      -2.0276796
+64	1       -0.0404494       0.4767818       1.0396418
+65	2        1.1395867       2.3763443       2.3481007
+66	1       -0.9738374      -1.6325161       3.7538567
+67	2       -0.3291998       0.2996990       5.2770809
+68	1       -1.6185604      -0.3964274      -5.1771220
+69	2        2.5999949      -5.1977715       5.8230717
+70	1       -1.6270675       2.3210900      -3.6299941
+71	2        3.6532700       4.9282597      -5.4319276
+72	1        0.0788934       4.0241037      -2.5011530
+73	2        2.8556507       2.6168653       2.1125546
+74	1        0.9738989       2.6255364       4.3412121
+75	2        3.7452938       3.4521356       4.5946426
+76	1        2.0805182       4.7039015       5.3280260
+77	1       -1.0324174      -5.8155041      -4.3265820
+78	1        0.7622442      -4.3631629      -1.3156572
+79	1        0.3263684       3.9937357       1.6172321
+80	1       -0.4350105      -5.7997058       4.5959134
+81	2        3.9161132      -4.6052788      -3.3191717
+82	2        1.9240657       5.7345079      -1.9754251
+83	2       -5.9794488      -4.2369359       1.8646522
+84	2        4.3339975      -4.4845227       5.3737440
+85	2        2.2755456      -0.6327737      -5.7931837
+86	1        1.8728190      -1.5504906      -3.4560010
+87	2        3.4558100      -1.1054068      -1.8333071
+88	1        4.3788172      -1.9466494      -0.3284637
+89	2        2.5999235      -3.7548996       2.5740569
+90	1        3.9983910      -4.4856603       1.1968663
+91	2       -5.7295580      -2.1475672      -5.9963645
+92	1        4.2664051      -2.6988975      -5.8005478
+93	2        4.5254685       2.2906832      -3.4765798
+94	1        2.3603088       1.3416442      -4.4173836
+95	2        4.7767057       1.4061217      -0.7524620
+96	1        1.8072666      -0.7835973      -0.4581995
+97	2        4.4745018       0.3736224       2.1068274
+98	1        3.6081170      -1.7315713       2.4019053
+99	2        4.6281423      -0.2865409       4.4756524
+100	1        1.7975239       0.2893530       4.2330830
+101	2        5.8341452       4.4986472      -5.9664541
+102	1        3.2401308       4.1655227      -3.5070029
+103	2        4.8720339       4.8709982      -2.3364366
+104	1        3.5526476       1.2262752       0.6926826
+105	2       -5.8173342       4.5420479       1.5578881
+106	1        3.9683224       1.5441137       3.8284375
+107	2       -5.5349308       1.9067049       3.7504113
+108	1        4.4728615       2.6415574      -5.5952809
+109	1        1.7000950      -4.8115440      -4.1953920
+110	1        1.7221527       4.1878404      -0.3712681
+111	1        3.9218156       4.5935583       1.3263407
+112	1        3.1310195      -5.8922481       3.6001155
+113	1        4.7558719      -2.2877771      -3.4742052
+114	1       -5.5050300      -2.7027381       0.8748867
+115	1        5.8418594      -4.6064370       3.8714113
+116	1       -4.7516868      -3.1691984      -4.4099768
+117	1        3.9404971       0.7188702      -2.2898786
+118	1       -5.6869740       0.2042380      -0.1916738
+119	1        5.8949589      -1.2422560       3.1201292
+120	1        5.9675804      -0.0712572       5.8964022
+121	1       -5.6208517       3.3600036      -2.9493510
+122	1        5.2065263       3.4517912      -0.3800894
+123	1       -4.6994522       2.5489583       1.8297431
+124	1       -4.0758407       3.0726196       5.0647973
+125	1        4.1587591      -5.0896820      -1.1443498
+126	1       -4.6963753      -5.7429833       1.1357818
+127	1        5.5994192       4.6887008       3.5948264
+128	1        5.0988369      -5.3774409      -4.9051267

examples/USER/misc/edip/in.edip-Si

@@ -0,0 +1,72 @@
+
+units           metal
+
+atom_style      atomic
+atom_modify     map array
+boundary        p p p
+atom_modify	sort 0 0.0
+
+# temperature
+
+variable t equal 1800.0
+
+# coordination number cutoff
+
+variable r equal 2.835
+
+# minimization parameters
+
+variable etol equal 1.0e-5
+variable ftol equal 1.0e-5
+variable maxiter equal 100
+variable maxeval equal 100
+variable dmax equal 1.0e-1
+
+# diamond unit cell
+
+variable a equal 5.431
+lattice         custom $a               &
+                a1 1.0 0.0 0.0          &
+                a2 0.0 1.0 0.0          &
+                a3 0.0 0.0 1.0          &
+                basis 0.0 0.0 0.0       &
+                basis 0.0 0.5 0.5       &
+                basis 0.5 0.0 0.5       &
+                basis 0.5 0.5 0.0       &
+                basis 0.25 0.25 0.25    &
+                basis 0.25 0.75 0.75    &
+                basis 0.75 0.25 0.75    &
+                basis 0.75 0.75 0.25
+
+region          myreg block     0 4 &
+                                0 4 &
+                                0 4
+create_box      1 myreg
+create_atoms    1 region myreg
+
+mass            1       28.06
+
+group Si type 1
+
+velocity all create $t 5287287 mom yes rot yes dist gaussian
+
+# make a vacancy
+
+group del id 300
+delete_atoms group del
+
+pair_style      edip
+pair_coeff * * Si.edip Si
+
+thermo          10
+
+fix             1 all nvt temp $t $t 0.1
+
+timestep        1.0e-3
+neighbor        1.0 bin
+neigh_modify    every 1 delay 10 check yes
+
+# equilibrate
+
+run             500
+

examples/USER/misc/edip/in.edip-Si-multi

@@ -0,0 +1,72 @@
+
+units           metal
+
+atom_style      atomic
+atom_modify     map array
+boundary        p p p
+atom_modify	sort 0 0.0
+
+# temperature
+
+variable t equal 1800.0
+
+# coordination number cutoff
+
+variable r equal 2.835
+
+# minimization parameters
+
+variable etol equal 1.0e-5
+variable ftol equal 1.0e-5
+variable maxiter equal 100
+variable maxeval equal 100
+variable dmax equal 1.0e-1
+
+# diamond unit cell
+
+variable a equal 5.431
+lattice         custom $a               &
+                a1 1.0 0.0 0.0          &
+                a2 0.0 1.0 0.0          &
+                a3 0.0 0.0 1.0          &
+                basis 0.0 0.0 0.0       &
+                basis 0.0 0.5 0.5       &
+                basis 0.5 0.0 0.5       &
+                basis 0.5 0.5 0.0       &
+                basis 0.25 0.25 0.25    &
+                basis 0.25 0.75 0.75    &
+                basis 0.75 0.25 0.75    &
+                basis 0.75 0.75 0.25
+
+region          myreg block     0 4 &
+                                0 4 &
+                                0 4
+create_box      1 myreg
+create_atoms    1 region myreg
+
+mass            1       28.06
+
+group Si type 1
+
+velocity all create $t 5287287 mom yes rot yes dist gaussian
+
+# make a vacancy
+
+group del id 300
+delete_atoms group del
+
+pair_style      edip/multi
+pair_coeff * * Si.edip Si
+
+thermo          10
+
+fix             1 all nvt temp $t $t 0.1
+
+timestep        1.0e-3
+neighbor        1.0 bin
+neigh_modify    every 1 delay 10 check yes
+
+# equilibrate
+
+run             500
+

examples/USER/misc/edip/in.edip-SiC

@@ -0,0 +1,33 @@
+# Test of MEAM potential for SiC system
+
+units		metal
+boundary	p p p
+
+atom_style	atomic
+
+read_data	data.SiC
+
+pair_style	edip/multi
+pair_coeff	* * SiC.edip Si C
+
+mass 1 28.085
+mass 2 12.001
+
+neighbor	1.0 bin
+neigh_modify	delay 1
+
+fix		1 all nve
+thermo		10
+timestep	0.001
+
+#dump		1 all atom 50 dump.meam
+
+#dump		2 all image 10 image.*.jpg element element &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	2 pad 3 element Si C
+
+#dump		3 all movie 10 movie.mpg element element &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	3 pad 3 element Si C
+
+run		100

examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.1

@@ -0,0 +1,167 @@
+LAMMPS (4 May 2017)
+  using 1 OpenMP thread(s) per MPI task
+
+units           metal
+
+atom_style      atomic
+atom_modify     map array
+boundary        p p p
+atom_modify	sort 0 0.0
+
+# temperature
+
+variable t equal 1800.0
+
+# coordination number cutoff
+
+variable r equal 2.835
+
+# minimization parameters
+
+variable etol equal 1.0e-5
+variable ftol equal 1.0e-5
+variable maxiter equal 100
+variable maxeval equal 100
+variable dmax equal 1.0e-1
+
+# diamond unit cell
+
+variable a equal 5.431
+lattice         custom $a                               a1 1.0 0.0 0.0                          a2 0.0 1.0 0.0                          a3 0.0 0.0 1.0                          basis 0.0 0.0 0.0                       basis 0.0 0.5 0.5                       basis 0.5 0.0 0.5                       basis 0.5 0.5 0.0                       basis 0.25 0.25 0.25                    basis 0.25 0.75 0.75                    basis 0.75 0.25 0.75                    basis 0.75 0.75 0.25
+lattice         custom 5.431                               a1 1.0 0.0 0.0                          a2 0.0 1.0 0.0                          a3 0.0 0.0 1.0                          basis 0.0 0.0 0.0                       basis 0.0 0.5 0.5                       basis 0.5 0.0 0.5                       basis 0.5 0.5 0.0                       basis 0.25 0.25 0.25                    basis 0.25 0.75 0.75                    basis 0.75 0.25 0.75                    basis 0.75 0.75 0.25
+Lattice spacing in x,y,z = 5.431 5.431 5.431
+
+region          myreg block     0 4                                 0 4                                 0 4
+create_box      1 myreg
+Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 region myreg
+Created 512 atoms
+
+mass            1       28.06
+
+group Si type 1
+512 atoms in group Si
+
+velocity all create $t 5287287 mom yes rot yes dist gaussian
+velocity all create 1800 5287287 mom yes rot yes dist gaussian
+
+# make a vacancy
+
+group del id 300
+1 atoms in group del
+delete_atoms group del
+Deleted 1 atoms, new total = 511
+
+pair_style      edip/multi
+pair_coeff * * Si.edip Si
+Reading potential file Si.edip with DATE: 2011-09-15
+
+thermo          10
+
+fix             1 all nvt temp $t $t 0.1
+fix             1 all nvt temp 1800 $t 0.1
+fix             1 all nvt temp 1800 1800 0.1
+
+timestep        1.0e-3
+neighbor        1.0 bin
+neigh_modify    every 1 delay 10 check yes
+
+# equilibrate
+
+run             500
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.12138
+  ghost atom cutoff = 4.12138
+  binsize = 2.06069, bins = 11 11 11
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair edip/multi, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.979 | 2.979 | 2.979 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0    1802.5039   -2372.6618            0   -2253.8359    12261.807 
+      10    952.62744    -2316.428            0   -2253.6283    723.08194 
+      20    549.13801    -2289.442            0   -2253.2413   -2444.5204 
+      30    1047.0106   -2321.1523            0   -2252.1305     9013.201 
+      40    663.46141   -2294.2083            0   -2250.4711    2942.5348 
+      50    504.74535    -2282.849            0   -2249.5748   -461.44909 
+      60    1019.2173   -2315.5639            0   -2248.3744    7706.4286 
+      70    844.51195   -2302.5251            0   -2246.8526    3116.8302 
+      80    814.90407   -2299.3372            0   -2245.6166    794.77455 
+      90    1269.5636   -2327.4775            0   -2243.7845    7729.3968 
+     100    977.61563   -2306.1118            0   -2241.6647    2969.9939 
+     110    843.08539   -2295.6547            0   -2240.0763    1393.4039 
+     120    1161.6968   -2314.6587            0   -2238.0766    7398.3492 
+     130    918.19451   -2296.4321            0   -2235.9022    2537.3997 
+     140    881.42548   -2292.2768            0   -2234.1709    1550.3339 
+     150    1231.1005   -2313.1054            0   -2231.9479    8112.7566 
+     160    967.01862    -2293.332            0   -2229.5836    3422.9627 
+     170    833.51248   -2282.7489            0   -2227.8015    43.991459 
+     180    1240.8488   -2307.3633            0   -2225.5632    6557.8651 
+     190    1126.4621   -2297.1922            0   -2222.9328    4289.0067 
+     200    947.59571     -2283.29            0    -2220.822     586.2811 
+     210     1228.153   -2299.4702            0   -2218.5071    5315.0425 
+     220    1215.4104   -2295.9408            0   -2215.8176    4870.3417 
+     230     1112.436   -2286.7552            0   -2213.4204    2527.1879 
+     240     1300.081   -2296.6013            0   -2210.8965    5738.3708 
+     250    1192.5738   -2286.8463            0   -2208.2286      4076.49 
+     260    1004.7055   -2272.1753            0   -2205.9424    359.37589 
+     270    1241.2018   -2285.3632            0   -2203.5399    4160.5763 
+     280    1360.1974    -2290.325            0   -2200.6572    5802.3902 
+     290    1151.9365   -2273.9467            0    -2198.008    1418.8887 
+     300    1174.3518   -2273.0089            0   -2195.5925     1998.229 
+     310    1329.2727   -2280.5049            0   -2192.8757    4721.7297 
+     320    1284.4414   -2274.7519            0   -2190.0781    2985.4674 
+     330    1328.3761   -2274.9545            0   -2187.3844    4543.2109 
+     340    1446.3847   -2279.8693            0   -2184.5198    6254.4059 
+     350    1366.2165   -2271.7475            0   -2181.6828    3637.8335 
+     360    1358.9609   -2268.5982            0   -2179.0118    3049.5798 
+     370     1552.208   -2278.4802            0   -2176.1545    6334.0058 
+     380    1562.5295   -2276.1793            0   -2173.1732    5787.5547 
+     390    1415.5498   -2263.7824            0   -2170.4655    3438.5766 
+     400    1323.1568   -2255.1641            0    -2167.938    2427.2294 
+     410    1260.7186   -2248.5373            0   -2165.4273    1208.6299 
+     420    1282.1118   -2247.3718            0   -2162.8516    462.65374 
+     430     1451.944   -2255.7551            0   -2160.0391    2037.8025 
+     440    1568.9415    -2260.417            0   -2156.9882    3531.1602 
+     450    1565.8262   -2257.2396            0   -2154.0162    2586.7886 
+     460    1677.7143   -2261.7214            0    -2151.122    4112.9756 
+     470    1762.9071   -2264.4244            0   -2148.2089    5053.2139 
+     480    1704.5898   -2257.8678            0   -2145.4967    4077.4626 
+     490    1731.2619   -2257.1048            0   -2142.9753    4710.5263 
+     500    1723.9777    -2254.161            0   -2140.5118    4760.7295 
+Loop time of 0.679564 on 1 procs for 500 steps with 511 atoms
+
+Performance: 63.570 ns/day, 0.378 hours/ns, 735.765 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.65181    | 0.65181    | 0.65181    |   0.0 | 95.92
+Neigh   | 0.013857   | 0.013857   | 0.013857   |   0.0 |  2.04
+Comm    | 0.0033884  | 0.0033884  | 0.0033884  |   0.0 |  0.50
+Output  | 0.00070739 | 0.00070739 | 0.00070739 |   0.0 |  0.10
+Modify  | 0.0083694  | 0.0083694  | 0.0083694  |   0.0 |  1.23
+Other   |            | 0.001432   |            |       |  0.21
+
+Nlocal:    511 ave 511 max 511 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    845 ave 845 max 845 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  7902 ave 7902 max 7902 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7902
+Ave neighs/atom = 15.4638
+Neighbor list builds = 19
+Dangerous builds = 0
+
+Total wall time: 0:00:00

examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.4

@@ -0,0 +1,167 @@
+LAMMPS (4 May 2017)
+  using 1 OpenMP thread(s) per MPI task
+
+units           metal
+
+atom_style      atomic
+atom_modify     map array
+boundary        p p p
+atom_modify	sort 0 0.0
+
+# temperature
+
+variable t equal 1800.0
+
+# coordination number cutoff
+
+variable r equal 2.835
+
+# minimization parameters
+
+variable etol equal 1.0e-5
+variable ftol equal 1.0e-5
+variable maxiter equal 100
+variable maxeval equal 100
+variable dmax equal 1.0e-1
+
+# diamond unit cell
+
+variable a equal 5.431
+lattice         custom $a                               a1 1.0 0.0 0.0                          a2 0.0 1.0 0.0                          a3 0.0 0.0 1.0                          basis 0.0 0.0 0.0                       basis 0.0 0.5 0.5                       basis 0.5 0.0 0.5                       basis 0.5 0.5 0.0                       basis 0.25 0.25 0.25                    basis 0.25 0.75 0.75                    basis 0.75 0.25 0.75                    basis 0.75 0.75 0.25
+lattice         custom 5.431                               a1 1.0 0.0 0.0                          a2 0.0 1.0 0.0                          a3 0.0 0.0 1.0                          basis 0.0 0.0 0.0                       basis 0.0 0.5 0.5                       basis 0.5 0.0 0.5                       basis 0.5 0.5 0.0                       basis 0.25 0.25 0.25                    basis 0.25 0.75 0.75                    basis 0.75 0.25 0.75                    basis 0.75 0.75 0.25
+Lattice spacing in x,y,z = 5.431 5.431 5.431
+
+region          myreg block     0 4                                 0 4                                 0 4
+create_box      1 myreg
+Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
+  1 by 2 by 2 MPI processor grid
+create_atoms    1 region myreg
+Created 512 atoms
+
+mass            1       28.06
+
+group Si type 1
+512 atoms in group Si
+
+velocity all create $t 5287287 mom yes rot yes dist gaussian
+velocity all create 1800 5287287 mom yes rot yes dist gaussian
+
+# make a vacancy
+
+group del id 300
+1 atoms in group del
+delete_atoms group del
+Deleted 1 atoms, new total = 511
+
+pair_style      edip/multi
+pair_coeff * * Si.edip Si
+Reading potential file Si.edip with DATE: 2011-09-15
+
+thermo          10
+
+fix             1 all nvt temp $t $t 0.1
+fix             1 all nvt temp 1800 $t 0.1
+fix             1 all nvt temp 1800 1800 0.1
+
+timestep        1.0e-3
+neighbor        1.0 bin
+neigh_modify    every 1 delay 10 check yes
+
+# equilibrate
+
+run             500
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.12138
+  ghost atom cutoff = 4.12138
+  binsize = 2.06069, bins = 11 11 11
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair edip/multi, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.955 | 2.955 | 2.955 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0    1802.3816   -2372.6618            0    -2253.844    12260.967 
+      10    938.75954   -2315.5185            0   -2253.6329    558.21646 
+      20    534.27233   -2288.4721            0   -2253.2514    -2710.768 
+      30    1043.7796   -2320.9485            0   -2252.1398    8679.4381 
+      40     658.0916   -2293.8597            0   -2250.4765    2165.3742 
+      50    517.93009   -2283.7238            0   -2249.5805   -1124.9373 
+      60    1063.3594   -2318.4409            0   -2248.3414    7277.8526 
+      70    868.14006   -2304.0134            0   -2246.7832    2050.2848 
+      80    826.37805   -2300.0187            0   -2245.5416    91.099408 
+      90    1289.6772   -2328.7151            0   -2243.6961    8180.7423 
+     100    976.36208   -2305.9371            0   -2241.5727    3614.0499 
+     110    810.81713   -2293.4705            0   -2240.0193     1359.368 
+     120     1165.707   -2314.9026            0    -2238.056      7336.45 
+     130    929.81245    -2297.139            0   -2235.8432    2793.8451 
+     140    804.47874   -2287.2074            0    -2234.174    704.92455 
+     150    1182.4141   -2310.0266            0   -2232.0787    7822.2337 
+     160    979.92391   -2294.2969            0   -2229.6977    3206.7458 
+     170    830.14748   -2282.6079            0   -2227.8824   -296.87377 
+     180    1271.1133   -2309.4274            0   -2225.6322     7199.614 
+     190    1209.6006   -2302.6407            0   -2222.9006    5528.3784 
+     200    954.67693   -2283.6621            0   -2220.7273     47.02795 
+     210     1260.814   -2301.5582            0    -2218.442     4829.788 
+     220    1274.9954   -2299.7285            0   -2215.6774    5518.0597 
+     230    1048.0074    -2282.398            0   -2213.3106    1754.4144 
+     240    1261.7072   -2294.1108            0   -2210.9356    5233.2712 
+     250    1272.6178   -2292.0793            0   -2208.1849    4795.9325 
+     260    989.14205   -2271.0278            0   -2205.8209    -820.1828 
+     270    1212.0445   -2283.4212            0     -2203.52    3395.8634 
+     280    1391.9572   -2292.3809            0   -2200.6194    6666.2451 
+     290    1093.1204   -2270.0421            0   -2197.9807    206.94523 
+     300    1159.4831    -2272.102            0   -2195.6657    778.53806 
+     310    1407.3528   -2285.6228            0   -2192.8463     5223.048 
+     320    1236.7163   -2271.5389            0   -2190.0113    1865.3943 
+     330    1258.8275   -2270.4611            0   -2187.4758    2333.3209 
+     340    1507.9519   -2283.9906            0   -2184.5824    6775.5456 
+     350    1366.5116   -2271.7287            0   -2181.6446     3432.115 
+     360    1305.2829   -2265.1092            0   -2179.0614    1498.4073 
+     370    1581.4335   -2280.4645            0   -2176.2122    6518.5597 
+     380    1589.5319   -2277.9428            0   -2173.1567    6334.6506 
+     390    1402.6781   -2262.9323            0    -2170.464    3278.3038 
+     400    1374.9587   -2258.5717            0   -2167.9307    3608.7284 
+     410    1295.7416   -2250.7752            0   -2165.3565    1877.5222 
+     420    1278.6727   -2247.1099            0   -2162.8164    1599.4181 
+     430    1508.1328   -2259.4245            0   -2160.0044    4300.2224 
+     440    1624.2957   -2263.9806            0   -2156.9026     4432.625 
+     450    1597.3356    -2259.263            0   -2153.9624    3370.3816 
+     460    1772.0922   -2267.9106            0   -2151.0895    5788.3214 
+     470    1806.4047    -2267.304            0    -2148.221    5950.1166 
+     480    1593.0406   -2250.7469            0   -2145.7294    2518.0576 
+     490    1660.9767    -2252.894            0    -2143.398    4282.1643 
+     500     1714.283   -2253.9295            0   -2140.9194    5740.0247 
+Loop time of 0.205398 on 4 procs for 500 steps with 511 atoms
+
+Performance: 210.324 ns/day, 0.114 hours/ns, 2434.304 timesteps/s
+99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.16285    | 0.1688     | 0.17446    |   1.1 | 82.18
+Neigh   | 0.0035172  | 0.0036234  | 0.0038214  |   0.2 |  1.76
+Comm    | 0.018727   | 0.024851   | 0.030996   |   2.9 | 12.10
+Output  | 0.0013061  | 0.0014012  | 0.0015635  |   0.3 |  0.68
+Modify  | 0.0046582  | 0.0048603  | 0.0050988  |   0.2 |  2.37
+Other   |            | 0.001861   |            |       |  0.91
+
+Nlocal:    127.75 ave 131 max 124 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+Nghost:    433.75 ave 441 max 426 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  1979.5 ave 2040 max 1895 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+
+Total # of neighbors = 7918
+Ave neighs/atom = 15.4951
+Neighbor list builds = 19
+Dangerous builds = 0
+
+Total wall time: 0:00:00