patch 6Jul17

bugfix for fix msst

.github/CONTRIBUTING.md

@@ -0,0 +1,112 @@
+# Contributing to LAMMPS via GitHub
+
+Thank your for considering to contribute to the LAMMPS software project.
+
+The following is a set of guidelines as well as explanations of policies and workflows for contributing to the LAMMPS molecular dynamics software project. These guidelines focus on submitting issues or pull requests on the LAMMPS GitHub project.
+
+Thus please also have a look at:
+* [The Section on submitting new features for inclusion in LAMMPS of the Manual](http://lammps.sandia.gov/doc/Section_modify.html#mod-15)
+* [The LAMMPS GitHub Tutorial in the Manual](http://lammps.sandia.gov/doc/tutorial_github.html)
+
+## Table of Contents
+
+[I don't want to read this whole thing, I just have a question!](#i-dont-want-to-read-this-whole-thing-i-just-have-a-question)
+
+[How Can I Contribute?](#how-can-i-contribute)
+* [Discussing How To Use LAMMPS](#discussing-how-to-use-lammps)
+* [Reporting Bugs](#reporting-bugs)
+* [Suggesting Enhancements](#suggesting-enhancements)
+* [Contributing Code](#contributing-code)
+
+[GitHub Workflows](#github-workflows)
+* [Issues](#issues)
+* [Pull Requests](#pull-requests)
+
+__
+
+## I don't want to read this whole thing I just have a question!
+
+> **Note:** Please do not file an issue to ask a general question about LAMMPS, its features, how to use specific commands, or how perform simulations or analysis in LAMMPS. Instead post your question to the ['lammps-users' mailing list](http://lammps.sandia.gov/mail.html). You do not need to be subscribed to post to the list (but a mailing list subscription avoids having your post delayed until it is approved by a mailing list moderator). Most posts to the mailing list receive a response within less than 24 hours. Before posting to the mailing list, please read the [mailing list guidelines](http://lammps.sandia.gov/guidelines.html). Following those guidelines will help greatly to get a helpful response. Always mention which LAMMPS version you are using.
+
+## How Can I Contribute?
+
+There are several ways how you can actively contribute to the LAMMPS project: you can discuss compiling and using LAMMPS, and solving LAMMPS related problems with other LAMMPS users on the lammps-users mailing list, you can report bugs or suggest enhancements by creating issues on GitHub (or posting them to the lammps-users mailing list), and you can contribute by submitting pull requests on GitHub or e-mail your code
+to one of the [LAMMPS core developers](http://lammps.sandia.gov/authors.html). As you may see from the aforementioned developer page, the LAMMPS software package includes the efforts of a very large number of contributors beyond the principal authors and maintainers.
+
+### Discussing How To Use LAMMPS
+
+The LAMMPS mailing list is hosted at SourceForge. The mailing list began in 2005, and now includes tens of thousands of messages in thousands of threads. LAMMPS developers try to respond to posted questions in a timely manner, but there are no guarantees. Please consider that people live in different timezone and may not have time to answer e-mails outside of their work hours.
+You can post to list by sending your email to lammps-users at lists.sourceforge.net (no subscription required), but before posting, please read the [mailing list guidelines](http://lammps.sandia.gov/guidelines.html) to maximize your chances to receive a helpful response.
+
+Anyone can browse/search previous questions/answers in the archives. You do not have to subscribe to the list to post questions, receive answers (to your questions), or browse/search the archives. You **do** need to subscribe to the list if you want emails for **all** the posts (as individual messages or in digest form), or to answer questions yourself. Feel free to sign up and help us out! Answering questions from fellow LAMMPS users is a great way to pay back the community for providing you a useful tool for free, and to pass on the advice you have received yourself to others. It improves your karma and helps you understand your own research better.
+
+If you post a message and you are a subscriber, your message will appear immediately. If you are not a subscriber, your message will be moderated, which typically takes one business day. Either way, when someone replies the reply will usually be sent to both, your personal email address and the mailing list. When replying to people, that responded to your post to the list, please always included the mailing list in your replies (i.e. use "Reply All" and **not** "Reply"). Responses will appear on the list in a few minutes, but it can take a few hours for postings and replies to show up in the SourceForge archive. Sending replies also to the mailing list is important, so that responses are archived and people with a similar issue can search for possible solutions in the mailing list archive.
+
+### Reporting Bugs
+
+While developers writing code for LAMMPS are careful to test their code, LAMMPS is such a large and complex software, that it is impossible to test for all combinations of features under all normal and not so normal circumstances. Thus bugs do happen, and if you suspect, that you have encountered one, please try to document it and report it as an [Issue](https://github.com/lammps/lammps/issues) on the LAMMPS GitHub project web page. However, before reporting a bug, you need to check whether this is something that may have already been corrected. The [Latest Features and Bug Fixes in LAMMPS](http://lammps.sandia.gov/bug.html) web page lists all significant changes to LAMMPS over the years. It also tells you what the current latest development version of LAMMPS is, and you should test whether your issue still applies to that version.
+
+When you click on the green "New Issue" button, you will be provided with a text field, where you can enter your message. That text field with contain a template with several headlines and some descriptions. Keep the headlines that are relevant to your reported potential bug and replace the descriptions with the information as suggested by the descriptions.
+You can also attach small text files (please add the file name extension `.txt` or it will be rejected), images, or small compressed text files (using gzip, do not use RAR or 7-ZIP or similar tools that are uncommon outside of Windows machines). In many cases, bugs are best illustrated by providing a small input deck (do **not** attach your entire production input, but remove everything that is not required to reproduce the issue, and scale down your system size, that the resulting calculation runs fast and can be run on small desktop quickly).
+
+To be able to submit an issue on GitHub, you have to register for an account (for GitHub in general). If you do not want to do that, or have other reservations against submitting an issue there, you can - as an alternative and in decreasing preference - either send an e-mail to the lammps-users mailing list, the original authors of the feature that you suspect to be affected, or one or more of the core LAMMPS developers.
+
+### Suggesting Enhancements
+
+The LAMMPS developers welcome suggestions for enhancements or new features. These should be submitted using the [GitHub Issue Tracker](https://github.com/lammps/lammps/issues) of the LAMMPS project. This is particularly recommended, when you plan to implement the feature or enhancement yourself, as this allows to coordinate in case there are other similar or conflicting ongoing developments.
+The LAMMPS developers will review your submission and consider implementing it. Whether this will actually happen depends on many factors: how difficult it would be, how much effort it would take, how many users would benefit from it, how well the individual developer would understand the underlying physics of the feature, and whether this is a feature that would fit into a software like LAMMPS, or would be better implemented as a separate tool. Because of these factors, it matters how well the suggested enhancement is formulated and the overall benefit is argued convincingly.
+
+To be able to submit an issue on GitHub, you have to register for an account (for GitHub in general). If you do not want to do that, or have other reservations against submitting an issue there, you can - as an alternative - send an e-mail to the lammps-users mailing list.
+
+### Contributing Code
+
+We encourage users to submit new features or modifications for LAMMPS to the core developers so they can be added to the LAMMPS distribution. The preferred way to manage and coordinate this is by submitting a pull request at the LAMMPS project on GitHub. For any larger modifications or programming project, you are encouraged to contact the LAMMPS developers ahead of time, in order to discuss implementation strategies and coding guidelines, that will make it easier to integrate your contribution and result in less work for everybody involved. You are also encouraged to search through the list of open issues on GitHub and submit a new issue for a planned feature, so you would not duplicate the work of others (and possibly get scooped by them) or have your work duplicated by others.
+
+How quickly your contribution will be integrated depends largely on how much effort it will cause to integrate and test it, how much it requires changes to the core code base, and of how much interest it is to the larger LAMMPS community. Please see below for a checklist of typical requirements. Once you have prepared everything, see [this tutorial](http://lammps.sandia.gov/doc/tutorial_github.html)
+ for instructions on how to submit your changes or new files through a GitHub pull request
+
+Here is a checklist of steps you need to follow to submit a single file or user package for our consideration. Following these steps will save both you and us time. See existing files in packages in the source directory for examples. If you are uncertain, please ask on the lammps-users mailing list.
+
+* All source files you provide must compile with the most current version of LAMMPS with multiple configurations. In particular you need to test compiling LAMMPS from scratch with `-DLAMMPS_BIGBIG` set in addition to the default `-DLAMMPS_SMALLBIG` setting. Your code will need to work correctly in serial and in parallel using MPI.
+* For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no lines over 80 characters. I/O is done via the C-style stdio library, class header files should not import any system headers outside <stdio.h>, STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. Header files must not import namespaces with using. This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages.
+* If you want your contribution to be added as a user-contributed feature, and it is a single file (actually a `<name>.cpp` and `<name>.h` file) it can be rapidly added to the USER-MISC directory. Include the one-line entry to add to the USER-MISC/README file in that directory, along with the 2 source files. You can do this multiple times if you wish to contribute several individual features.
+* If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like USER-FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this USER-FOO directory.
+* Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code.
+* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are simple text files with a specific markup language, that are then auto-converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.txt` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. A description of the markup can also be found in `lammps/doc/utils/txt2html/README.html` As appropriate, the text files can include links to equations (see doc/Eqs/*.tex for examples, we auto-create the associated JPG files), or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.txt for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv, the requirement for generating the PDF format manual is the htmldoc software. Please run at least "make html" and carefully inspect and proofread the resulting HTML format doc page before submitting your code.
+* For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/USER for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind
+* If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the *.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide.
+
+Finally, as a general rule-of-thumb, the more clear and self-explanatory you make your documentation and README files, and the easier you make it for people to get started, e.g. by providing example scripts, the more likely it is that users will try out your new feature.
+
+If the new features/files are broadly useful we may add them as core files to LAMMPS or as part of a standard package. Else we will add them as a user-contributed file or package. Examples of user packages are in src sub-directories that start with USER. The USER-MISC package is simply a collection of (mostly) unrelated single files, which is the simplest way to have your contribution quickly added to the LAMMPS distribution. You can see a list of the both standard and user packages by typing "make package" in the LAMMPS src directory.
+
+Note that by providing us files to release, you are agreeing to make them open-source, i.e. we can release them under the terms of the GPL, used as a license for the rest of LAMMPS. See Section 1.4 for details.
+
+With user packages and files, all we are really providing (aside from the fame and fortune that accompanies having your name in the source code and on the Authors page of the LAMMPS WWW site), is a means for you to distribute your work to the LAMMPS user community, and a mechanism for others to easily try out your new feature. This may help you find bugs or make contact with new collaborators. Note that you are also implicitly agreeing to support your code which means answer questions, fix bugs, and maintain it if LAMMPS changes in some way that breaks it (an unusual event).
+
+To be able to submit an issue on GitHub, you have to register for an account (for GitHub in general). If you do not want to do that, or have other reservations or difficulties to submit a pull request, you can - as an alternative - contact one or more of the core LAMMPS developers and ask if one of them would be interested in manually merging your code into LAMMPS and send them your source code. Since the effort to merge a pull request is a small fraction of the effort of integrating source code manually (which would usually be done by converting the contribution into a pull request), your chances to have your new code included quickly are the best with a pull request.
+
+If you prefer to submit patches or full files, you should first make certain, that your code works correctly with the latest patch-level version of LAMMPS and contains all bug fixes from it. Then create a gzipped tar file of all changed or added files or a corresponding patch file using 'diff -u' or 'diff -c' and compress it with gzip. Please only use gzip compression, as this works well on all platforms.
+
+## GitHub Workflows
+
+This section briefly summarizes the steps that will happen **after** you have submitted either an issue or a pull request on the LAMMPS GitHub project page. 
+
+### Issues
+
+After submitting an issue, one or more of the LAMMPS developers will review it and categorize it by assigning labels. Confirmed bug reports will be labeled `bug`; if the bug report also contains a suggestion for how to fix it, it will be labeled `bugfix`; if the issue is a feature request, it will be labeled `enhancement`. Other labels may be attached as well, depending on which parts of the LAMMPS code are affected. If the assessment is, that the issue does not warrant any changes, the `wontfix` label will be applied and if the submission is incorrect or something that should not be submitted as an issue, the `invalid` label will be applied. In both of the last two cases, the issue will then be closed without further action.
+
+For feature requests, what happens next is that developers may comment on the viability or relevance of the request, discuss and make suggestions for how to implement it. If a LAMMPS developer or user is planning to implement the feature, the issue will be assigned to that developer. For developers, that are not yet listed as LAMMPS project collaborators, they will receive an invitation to be added to the LAMMPS project as a collaborator so they can get assigned. If the requested feature or enhancement is implemented, it will usually be submitted as a pull request, which will contain a reference to the issue number. And once the pull request is reviewed and accepted for inclusion into LAMMPS, the issue will be closed. For details on how pull requests are processed, please see below.
+
+For bug reports, the next step is that one of the core LAMMPS developers will self-assign to the issue and try to confirm the bug. If confirmed, the `bug` label and potentially other labels are added to classify the issue and its impact to LAMMPS. Before confirming, further questions may be asked or requests for providing additional input files or details about the steps required to reproduce the issue. Any bugfix is likely to be submitted as a pull request (more about that below) and since most bugs require only local changes, the bugfix may be included in a pull request specifically set up to collect such local bugfixes or small enhancements. Once the bugfix is included in the master branch, the issue will be closed.
+
+### Pull Requests
+
+For submitting pull requests, there is a [detailed tutorial](http://lammps.sandia.gov/doc/tutorial_github.html) in the LAMMPS manual. Thus only a brief breakdown of the steps is presented here.
+Immediately after the submission, the LAMMPS continuing integration server at ci.lammps.org will download your submitted branch and perform a simple compilation test, i.e. will test whether your submitted code can be compiled under various conditions. It will also do a check on whether your included documentation translates cleanly. Whether these tests are successful or fail will be recorded. If a test fails, please inspect the corresponding output on the CI server and take the necessary steps, if needed, so that the code can compile cleanly again. The test will be re-run each the pull request is updated with a push to the remote branch on GitHub.
+Next a LAMMPS core developer will self-assign and do an overall technical assessment of the submission. If you are not yet registered as a LAMMPS collaborator, you will receive an invitation for that.
+You may also receive comments and suggestions on the overall submission or specific details. If permitted, additional changes may be pushed into your pull request branch or a pull request may be filed in your LAMMPS fork on GitHub to include those changes.
+The LAMMPS developer may then decide to assign the pull request to another developer (e.g. when that developer is more knowledgeable about the submitted feature or enhancement or has written the modified code). It may also happen, that additional developers are requested to provide a review and approve the changes. For submissions, that may change the general behavior of LAMMPS, or where a possibility of unwanted side effects exists, additional tests may be requested by the assigned developer.
+If the assigned developer is satisfied and considers the submission ready for inclusion into LAMMPS, the pull request will be assigned to the LAMMPS lead developer, Steve Plimpton (@sjplimp), who will then have the final decision on whether the submission will be included, additional changes are required or it will be ultimately rejected. After the pull request is merged, you may delete the pull request branch in your personal LAMMPS fork.
+Since the learning curve for git is quite steep for efficiently managing remote repositories, local and remote branches, pull requests and more, do not hesitate to ask questions, if you are not sure about how to do certain steps that are asked of you. Even if the changes asked of you do not make sense to you, they may be important for the LAMMPS developers. Please also note, that these all are guidelines and not set in stone.
+

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,31 @@
+## Summary
+
+_Please provide a brief description of the issue_
+
+## Type of Issue
+
+_Is this a 'Bug Report' or a 'Suggestion for an Enhancement'?_
+
+## Detailed Description (Enhancement Suggestion)
+
+_Explain how you would like to see LAMMPS enhanced, what feature(s) you are looking for, provide references to relevant background information, and whether you are willing to implement the enhancement yourself or would like to participate in the implementation_
+
+## LAMMPS Version (Bug Report)
+
+_Please specify which LAMMPS version this issue was detected with. If this is not the latest development version, please stop and test that version, too, and report it here if the bug persists_
+
+## Expected Behavior (Bug Report)
+
+_Describe the expected behavior. Quote from the LAMMPS manual where needed or explain why the expected behavior is meaningful, especially when it differs from the manual_
+
+## Actual Behavior (Bug Report)
+
+_Describe the actual behavior, how it differs from the expected behavior, and how this can be observed. Try to be specific and do **not* use vague terms like "doesn't work" or "wrong result". Do not assume that the person reading this has any experience with or knowledge of your specific research._
+
+## Steps to Reproduce (Bug Report)
+
+_Describe the steps required to quickly reproduce the issue. You can attach (small) files to the section below or add URLs where to download an archive with all necessary files. Please try to create input that are as small as possible and run as fast as possible. NOTE: the less effort and time it takes to reproduce your issue, the more likely, that somebody will look into it._
+
+## Further Information, Files, and Links
+
+_Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications_

.github/PULL_REQUEST_TEMPLATE.md

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

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="20 Jun 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
-20 Jun 2017 version :c,h4
+6 Jul 2017 version :c,h4
 
 Version info: :h4
 

doc/src/Section_commands.txt

@@ -1039,6 +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,
+"meam/c"_pair_meam.html,
 "meam/spline (o)"_pair_meam_spline.html,
 "meam/sw/spline"_pair_meam_sw_spline.html,
 "mgpt"_pair_mgpt.html,
@@ -1073,7 +1074,7 @@ package"_Section_start.html#start_3.
 "table/rx"_pair_table_rx.html,
 "tersoff/table (o)"_pair_tersoff.html,
 "thole"_pair_thole.html,
-"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c) 
+"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)
 
 :line
 

doc/src/Section_errors.txt

@@ -4696,9 +4696,9 @@ Self-explanatory. :dd
 
 {Fix bond/create induced too many angles/dihedrals/impropers per atom} :dt
 
-See the read_data command for info on setting the "extra angle per
-atom", etc header values to allow for additional angles, etc to be
-formed. :dd
+See the read_data command for info on using the "extra/angle/per/atom",
+(or dihedral, improper) keywords to allow for additional
+angles, dihedrals, and impropers to be formed. :dd
 
 {Fix bond/create needs ghost atoms from further away} :dt
 
@@ -7876,18 +7876,20 @@ See the setting for tagint in the src/lmptype.h file. :dd
 
 {New bond exceeded bonds per atom in create_bonds} :dt
 
-See the read_data command for info on setting the "extra bond per
-atom" header value to allow for additional bonds to be formed. :dd
+See the read_data command for info on using the "extra/bond/per/atom"
+keyword to allow for additional bonds to be formed
 
 {New bond exceeded bonds per atom in fix bond/create} :dt
 
-See the read_data command for info on setting the "extra bond per
-atom" header value to allow for additional bonds to be formed. :dd
+See the read_data command for info on using the "extra/bond/per/atom"
+keyword to allow for additional bonds to be formed :dd
 
 {New bond exceeded special list size in fix bond/create} :dt
 
-See the special_bonds extra command for info on how to leave space in
-the special bonds list to allow for additional bonds to be formed. :dd
+See the "special_bonds extra" command
+(or the "read_data extra/special/per/atom" command)
+for info on how to leave space in the special bonds
+list to allow for additional bonds to be formed. :dd
 
 {Newton bond change after simulation box is defined} :dt
 
@@ -9664,9 +9666,10 @@ you are running. :dd
 
 {Special list size exceeded in fix bond/create} :dt
 
-See the read_data command for info on setting the "extra special per
-atom" header value to allow for additional special values to be
-stored. :dd
+See the special_bonds extra command
+(or the read_data extra/special/per/atom command)
+for info on how to leave space in the special bonds
+list to allow for additional bonds to be formed. :dd
 
 {Specified processors != physical processors} :dt
 
@@ -9683,23 +9686,23 @@ Self-explanatory. :dd
 
 {Subsequent read data induced too many angles per atom} :dt
 
-See the create_box extra/angle/per/atom or read_data "extra angle per
-atom" header value to set this limit larger. :dd
+See the extra/angle/per/atom keyword for the create_box
+or the read_data command to set this limit larger :dd
 
 {Subsequent read data induced too many bonds per atom} :dt
 
-See the create_box extra/bond/per/atom or read_data "extra bond per
-atom" header value to set this limit larger. :dd
+See the extra/bond/per/atom keyword for the create_box
+or the read_data command to set this limit larger :dd
 
 {Subsequent read data induced too many dihedrals per atom} :dt
 
-See the create_box extra/dihedral/per/atom or read_data "extra
-dihedral per atom" header value to set this limit larger. :dd
+See the extra/dihedral/per/atom keyword for the create_box
+or the read_data command to set this limit larger :dd
 
 {Subsequent read data induced too many impropers per atom} :dt
 
-See the create_box extra/improper/per/atom or read_data "extra
-improper per atom" header value to set this limit larger. :dd
+See the extra/improper/per/atom keyword for the create_box
+or the read_data command to set this limit larger :dd
 
 {Substitution for illegal variable} :dt
 

doc/src/Section_howto.txt

@@ -1938,7 +1938,7 @@ documentation in the src/library.cpp file for details, including
 which quantities can be queried by name:
 
 void *lammps_extract_global(void *, char *)
-void lammps_extract_box(void *, double *, double *, 
+void lammps_extract_box(void *, double *, double *,
                         double *, double *, double *, int *, int *)
 void *lammps_extract_atom(void *, char *)
 void *lammps_extract_compute(void *, char *, int, int)
@@ -2682,14 +2682,14 @@ bond_coeff      2 25.724 0.0 :pre
 
 When running dynamics with the adiabatic core/shell model, the
 following issues should be considered.  The relative motion of
-the core and shell particles corresponds to the polarization, 
-hereby an instantaneous relaxation of the shells is approximated 
+the core and shell particles corresponds to the polarization,
+hereby an instantaneous relaxation of the shells is approximated
 and a fast core/shell spring frequency ensures a nearly constant
-internal kinetic energy during the simulation. 
+internal kinetic energy during the simulation.
 Thermostats can alter this polarization behaviour, by scaling the
-internal kinetic energy, meaning the shell will not react freely to 
-its electrostatic environment. 
-Therefore it is typically desirable to decouple the relative motion of 
+internal kinetic energy, meaning the shell will not react freely to
+its electrostatic environment.
+Therefore it is typically desirable to decouple the relative motion of
 the core/shell pair, which is an imaginary degree of freedom, from the
 real physical system.  To do that, the "compute
 temp/cs"_compute_temp_cs.html command can be used, in conjunction with
@@ -2721,13 +2721,13 @@ fix thermostatequ all nve                               # integrator as needed f
 fix_modify thermoberendsen temp CSequ
 thermo_modify temp CSequ                                # output of center-of-mass derived temperature :pre
 
-The pressure for the core/shell system is computed via the regular 
-LAMMPS convention by "treating the cores and shells as individual 
-particles"_#MitchellFincham2. For the thermo output of the pressure 
-as well as for the application of a barostat, it is necessary to 
-use an additional "pressure"_compute_pressure compute based on the 
-default "temperature"_compute_temp and specifying it as a second 
-argument in "fix modify"_fix_modify.html and 
+The pressure for the core/shell system is computed via the regular
+LAMMPS convention by "treating the cores and shells as individual
+particles"_#MitchellFincham2. For the thermo output of the pressure
+as well as for the application of a barostat, it is necessary to
+use an additional "pressure"_compute_pressure compute based on the
+default "temperature"_compute_temp and specifying it as a second
+argument in "fix modify"_fix_modify.html and
 "thermo_modify"_thermo_modify.html resulting in:
 
 (...)
@@ -2757,18 +2757,18 @@ temp/cs"_compute_temp_cs.html command to the {temp} keyword of the
 velocity all create 1427 134 bias yes temp CSequ
 velocity all scale 1427 temp CSequ :pre
 
-To maintain the correct polarizability of the core/shell pairs, the 
-kinetic energy of the internal motion shall remain nearly constant. 
-Therefore the choice of spring force and mass ratio need to ensure 
-much faster relative motion of the 2 atoms within the core/shell pair 
-than their center-of-mass velocity. This allows the shells to 
-effectively react instantaneously to the electrostatic environment and 
+To maintain the correct polarizability of the core/shell pairs, the
+kinetic energy of the internal motion shall remain nearly constant.
+Therefore the choice of spring force and mass ratio need to ensure
+much faster relative motion of the 2 atoms within the core/shell pair
+than their center-of-mass velocity. This allows the shells to
+effectively react instantaneously to the electrostatic environment and
 limits energy transfer to or from the core/shell oscillators.
 This fast movement also dictates the timestep that can be used.
 
 The primary literature of the adiabatic core/shell model suggests that
 the fast relative motion of the core/shell pairs only allows negligible
-energy transfer to the environment. 
+energy transfer to the environment.
 The mentioned energy transfer will typically lead to a small drift
 in total energy over time.  This internal energy can be monitored
 using the "compute chunk/atom"_compute_chunk_atom.html and "compute
@@ -2790,7 +2790,7 @@ pairs as chunks.
 
 For example if core/shell pairs are the only molecules:
 
-read_data NaCl_CS_x0.1_prop.data 
+read_data NaCl_CS_x0.1_prop.data
 compute prop all property/atom molecule
 compute cs_chunk all chunk/atom c_prop
 compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0     # note the chosen degrees of freedom for the core/shell pairs

doc/src/Section_packages.txt

@@ -121,6 +121,7 @@ Package, Description, Doc page, Example, Library
 "USER-INTEL"_#USER-INTEL, optimized Intel CPU and KNL styles,"Section 5.3.2"_accelerate_intel.html, WWW bench, -
 "USER-LB"_#USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, -
 "USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, -
+"USER-MEAMC"_#USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, -
 "USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -
 "USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, -
 "USER-MOLFILE"_#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
@@ -585,7 +586,7 @@ do not recommend building with other acceleration packages installed
 
 make yes-kokkos
 make machine :pre
- 
+
 make no-kokkos
 make machine :pre
 
@@ -839,13 +840,13 @@ written and read in parallel.
 Note that MPIIO is part of the standard message-passing interface
 (MPI) library, so you should not need any additional compiler or link
 settings, beyond what LAMMPS normally uses for MPI on your system.
- 
+
 make yes-mpiio
 make machine :pre
- 
+
 make no-mpiio
 make machine :pre
- 
+
 [Supporting info:]
 
 src/MPIIO: filenames -> commands
@@ -855,7 +856,7 @@ src/MPIIO: filenames -> commands
 "read_restart"_read_restart.html :ul
 
 :line
- 
+
 MSCG package :link(mscg),h4
 
 [Contents:]
@@ -914,7 +915,7 @@ lib/mscg/README
 examples/mscg :ul
 
 :line
- 
+
 OPT package :link(OPT),h4
 
 [Contents:]
@@ -1387,7 +1388,7 @@ atomic information to continuum fields.
 [Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).
 
 [Install or un-install:]
-  
+
 Before building LAMMPS with this package, you must first build the ATC
 library in lib/atc.  You can do this manually if you prefer; follow
 the instructions in lib/atc/README.  You can also do it in one step
@@ -1420,10 +1421,10 @@ usual manner:
 
 make yes-user-atc
 make machine :pre
- 
+
 make no-user-atc
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-ATC: filenames -> commands
@@ -1446,7 +1447,7 @@ model.
 [Author:] Ilya Valuev (JIHT, Russia).
 
 [Install or un-install:]
-  
+
 Before building LAMMPS with this package, you must first build the
 AWPMD library in lib/awpmd.  You can do this manually if you prefer;
 follow the instructions in lib/awpmd/README.  You can also do it in
@@ -1479,10 +1480,10 @@ usual manner:
 
 make yes-user-awpmd
 make machine :pre
- 
+
 make no-user-awpmd
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-AWPMD: filenames -> commands
@@ -1505,13 +1506,13 @@ stability.
 [Author:] Oliver Henrich (University of Strathclyde, Glasgow).
 
 [Install or un-install:]
-  
+
 make yes-user-cgdna
 make machine :pre
- 
+
 make no-user-cgdna
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-CGDNA: filenames -> commands
@@ -1536,13 +1537,13 @@ acids.
 [Author:] Axel Kohlmeyer (Temple U).
 
 [Install or un-install:]
-  
+
 make yes-user-cgsdk
 make machine :pre
- 
+
 make no-user-cgsdk
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-CGSDK: filenames -> commands
@@ -1570,7 +1571,7 @@ by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and
 Jerome Henin (LISM, CNRS, Marseille, France).
 
 [Install or un-install:]
-  
+
 Before building LAMMPS with this package, you must first build the
 COLVARS library in lib/colvars.  You can do this manually if you
 prefer; follow the instructions in lib/colvars/README.  You can also
@@ -1594,10 +1595,10 @@ usual manner:
 
 make yes-user-colvars
 make machine :pre
- 
+
 make no-user-colvars
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-COLVARS: filenames -> commands
@@ -1619,13 +1620,13 @@ intensities based on kinematic diffraction theory.
 [Author:] Shawn Coleman while at the U Arkansas.
 
 [Install or un-install:]
-  
+
 make yes-user-diffraction
 make machine :pre
- 
+
 make no-user-diffraction
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-DIFFRACTION: filenames -> commands
@@ -1654,13 +1655,13 @@ algorithm.
 Brennan (ARL).
 
 [Install or un-install:]
-  
+
 make yes-user-dpd
 make machine :pre
- 
+
 make no-user-dpd
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-DPD: filenames -> commands
@@ -1696,13 +1697,13 @@ tools/drude.
 Devemy (CNRS), and Agilio Padua (U Blaise Pascal).
 
 [Install or un-install:]
-  
+
 make yes-user-drude
 make machine :pre
- 
+
 make no-user-drude
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-DRUDE: filenames -> commands
@@ -1734,13 +1735,13 @@ tools/eff; see its README file.
 [Author:] Andres Jaramillo-Botero (CalTech).
 
 [Install or un-install:]
-  
+
 make yes-user-eff
 make machine :pre
- 
+
 make no-user-eff
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-EFF: filenames -> commands
@@ -1773,13 +1774,13 @@ for using this package in tools/fep; see its README file.
 [Author:] Agilio Padua (Universite Blaise Pascal Clermont-Ferrand)
 
 [Install or un-install:]
-  
+
 make yes-user-fep
 make machine :pre
- 
+
 make no-user-fep
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-FEP: filenames -> commands
@@ -1836,13 +1837,13 @@ file.
 
 You can then install/un-install the package and build LAMMPS in the
 usual manner:
-  
+
 make yes-user-h5md
 make machine :pre
- 
+
 make no-user-h5md
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-H5MD: filenames -> commands
@@ -1908,7 +1909,7 @@ explained in "Section 5.3.2"_accelerate_intel.html.
 
 make yes-user-intel yes-user-omp
 make machine :pre
- 
+
 make no-user-intel no-user-omp
 make machine :pre
 
@@ -1938,13 +1939,13 @@ can be used to model MD particles influenced by hydrodynamic forces.
 Ontario).
 
 [Install or un-install:]
-  
+
 make yes-user-lb
 make machine :pre
- 
+
 make no-user-lb
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-LB: filenames -> commands
@@ -1972,13 +1973,13 @@ matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL.
 [Authors:] Tomas Oppelstrup and John Moriarty (LLNL).
 
 [Install or un-install:]
-  
+
 make yes-user-mgpt
 make machine :pre
- 
+
 make no-user-mgpt
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-MGPT: filenames -> commands
@@ -2000,13 +2001,13 @@ dihedral, improper, or command style.
 src/USER-MISC/README file.
 
 [Install or un-install:]
-  
+
 make yes-user-misc
 make machine :pre
- 
+
 make no-user-misc
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-MISC: filenames -> commands
@@ -2031,13 +2032,13 @@ n = grad(g).
 Netherlands; since 2017: Brandeis University, Waltham, MA, USA)
 
 [Install or un-install:]
-  
+
 make yes-user-manifold
 make machine :pre
- 
+
 make no-user-manifold
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-MANIFOLD: filenames -> commands
@@ -2051,6 +2052,37 @@ http://lammps.sandia.gov/movies.html#manifold :ul
 
 :line
 
+USER-MEAMC package :link(USER-MEAMC),h4
+
+[Contents:]
+
+A pair style for the modified embedded atom (MEAM) potential
+translated from the Fortran version in the "MEAM"_MEAM package
+to plain C++. In contrast to the MEAM package, no library
+needs to be compiled and the pair style can be instantiated
+multiple times.
+
+[Author:] Sebastian Huetter, (Otto-von-Guericke University Magdeburg)
+based on the Fortran version of Greg Wagner (Northwestern U) while at
+Sandia.
+
+[Install or un-install:]
+  
+make yes-user-meamc
+make machine :pre
+ 
+make no-user-meamc
+make machine :pre
+ 
+[Supporting info:]
+
+src/USER-MEAMC: filenames -> commands
+src/USER-MEAMC/README
+"pair meam/c"_pair_meam.html
+examples/meam :ul
+
+:line
+
 USER-MOLFILE package :link(USER-MOLFILE),h4
 
 [Contents:]
@@ -2080,7 +2112,7 @@ at
 [Author:] Axel Kohlmeyer (Temple U).
 
 [Install or un-install:]
-  
+
 Note that the lib/molfile/Makefile.lammps file has a setting for a
 dynamic loading library libdl.a that should is typically present on
 all systems, which is required for LAMMPS to link with this package.
@@ -2090,10 +2122,10 @@ lib/molfile/Makefile.lammps for details.
 
 make yes-user-molfile
 make machine :pre
- 
+
 make no-user-molfile
 make machine :pre
- 
+
 [Supporting info:]
 
 src/USER-MOLFILE: filenames -> commands
@@ -2128,7 +2160,7 @@ tools:
 [Author:] Lars Pastewka (Karlsruhe Institute of Technology).
 
 [Install or un-install:]
-   
+
 Note that to follow these steps, you need the standard NetCDF software
 package installed on your system.  The lib/netcdf/Makefile.lammps file
 has settings for NetCDF include and library files that LAMMPS needs to
@@ -2138,7 +2170,7 @@ lib/netcdf/README for details.
 
 make yes-user-netcdf
 make machine :pre
-  
+
 make no-user-netcdf
 make machine :pre
 
@@ -2178,10 +2210,10 @@ Once you have an appropriate Makefile.machine, you can
 install/un-install the package and build LAMMPS in the usual manner:
 
 [Install or un-install:]
-  
+
 make yes-user-omp
 make machine :pre
- 
+
 make no-user-omp
 make machine :pre
 
@@ -2213,13 +2245,13 @@ relations, directly from molecular dynamics simulations.
 [Author:] Ling-Ti Kong (Shanghai Jiao Tong University).
 
 [Install or un-install:]
-   
+
 make yes-user-phonon
 make machine :pre
-  
+
 make no-user-phonon
 make machine :pre
-  
+
 [Supporting info:]
 
 src/USER-PHONON: filenames -> commands
@@ -2235,7 +2267,7 @@ USER-QMMM package :link(USER-QMMM),h4
 
 A "fix qmmm"_fix_qmmm.html command which allows LAMMPS to be used in a
 QM/MM simulation, currently only in combination with the "Quantum
-ESPRESSO"_espresso package.  
+ESPRESSO"_espresso package.
 
 :link(espresso,http://www.quantum-espresso.org)
 
@@ -2275,7 +2307,7 @@ usual manner:
 
 make yes-user-qmmm
 make machine :pre
-  
+
 make no-user-qmmm
 make machine :pre
 
@@ -2284,7 +2316,7 @@ for a QM/MM simulation.  You must also build Quantum ESPRESSO and
 create a new executable which links LAMMPS and Quanutm ESPRESSO
 together.  These are steps 3 and 4 described in the lib/qmmm/README
 file.
-  
+
 [Supporting info:]
 
 src/USER-QMMM: filenames -> commands
@@ -2312,13 +2344,13 @@ simulation.
 [Author:] Yuan Shen (Stanford U).
 
 [Install or un-install:]
-   
+
 make yes-user-qtb
 make machine :pre
-  
+
 make no-user-qtb
 make machine :pre
-  
+
 [Supporting info:]
 
 src/USER-QTB: filenames -> commands
@@ -2362,10 +2394,10 @@ usual manner:
 
 make yes-user-quip
 make machine :pre
-  
+
 make no-user-quip
 make machine :pre
-  
+
 [Supporting info:]
 
 src/USER-QUIP: filenames -> commands
@@ -2388,13 +2420,13 @@ for monitoring molecules as bonds are created and destroyed.
 [Author:] Hasan Metin Aktulga (MSU) while at Purdue University.
 
 [Install or un-install:]
-   
+
 make yes-user-reaxc
 make machine :pre
-  
+
 make no-user-reaxc
 make machine :pre
-  
+
 [Supporting info:]
 
 src/USER-REAXC: filenames -> commands
@@ -2451,10 +2483,10 @@ usual manner:
 
 make yes-user-smd
 make machine :pre
-  
+
 make no-user-smd
 make machine :pre
-  
+
 [Supporting info:]
 
 src/USER-SMD: filenames -> commands
@@ -2477,13 +2509,13 @@ ionocovalent bonds in oxides.
 Tetot (LAAS-CNRS, France).
 
 [Install or un-install:]
-   
+
 make yes-user-smtbq
 make machine :pre
-  
+
 make no-user-smtbq
 make machine :pre
-  
+
 [Supporting info:]
 
 src/USER-SMTBQ: filenames -> commands
@@ -2516,13 +2548,13 @@ property/atom"_compute_property_atom.html command.
 Dynamics, Ernst Mach Institute, Germany).
 
 [Install or un-install:]
-   
+
 make yes-user-sph
 make machine :pre
-  
+
 make no-user-sph
 make machine :pre
-  
+
 [Supporting info:]
 
 src/USER-SPH: filenames -> commands
@@ -2544,13 +2576,13 @@ stress, etc) about individual interactions.
 [Author:] Axel Kohlmeyer (Temple U).
 
 [Install or un-install:]
-   
+
 make yes-user-tally
 make machine :pre
-  
+
 make no-user-tally
 make machine :pre
-  
+
 [Supporting info:]
 
 src/USER-TALLY: filenames -> commands
@@ -2577,7 +2609,7 @@ system.
 [Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing).
 
 [Install or un-install:]
-   
+
 The lib/vtk/Makefile.lammps file has settings for accessing VTK files
 and its library, which are required for LAMMPS to build and link with
 this package.  If the settings are not valid for your system, check if
@@ -2590,10 +2622,10 @@ usual manner:
 
 make yes-user-vtk
 make machine :pre
-  
+
 make no-user-vtk
 make machine :pre
-  
+
 [Supporting info:]
 
 src/USER-VTK: filenames -> commands

doc/src/Section_python.txt

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

doc/src/accelerate_intel.txt

@@ -42,11 +42,11 @@ 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 with the provided run script. 
-These are scalable in size; the results given are with 512K 
-particles (524K for Liquid Crystal). Most of the simulations are 
+the src/USER-INTEL/TEST directory with the provided run script.
+These are scalable in size; the results given are with 512K
+particles (524K for Liquid Crystal). Most of the simulations are
 standard LAMMPS benchmarks (indicated by the filename extension in
-parenthesis) with modifications to the run length and to add a 
+parenthesis) with modifications to the run length and to add a
 warmup run (for use with offload benchmarks).
 
 :c,image(JPG/user_intel.png)
@@ -64,30 +64,30 @@ simulation rates and instructions to reproduce.
 
 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 
+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 
+{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 
+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 
+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 
+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.
 
@@ -106,7 +106,9 @@ $t should be 2 for Intel Xeon CPUs and 2 or 4 for Intel Xeon Phi :l
 For some of the simple 2-body potentials without long-range
 electrostatics, performance and scalability can be better with
 the "newton off" setting added to the input script :l
-If using {kspace_style pppm} in the input script, add 
+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
 
@@ -115,12 +117,12 @@ For Intel Xeon Phi CPUs:
 Runs should be performed using MCDRAM. :ulb,l
 :ule
 
-For simulations using {kspace_style pppm} on Intel CPUs 
+For simulations using {kspace_style pppm} on Intel CPUs
 supporting AVX-512:
 
 Add "kspace_modify diff ad" to the input script :ulb,l
-The command-line option should be changed to 
-"-pk intel 0 omp $r lrt yes -sf intel" where $r is the number of 
+The command-line option should be changed to
+"-pk intel 0 omp $r lrt yes -sf intel" where $r is the number of
 threads minus 1. :l
 Do not use thread affinity (set KMP_AFFINITY=none) :l
 The "newton off" setting may provide better scalability :l
@@ -352,7 +354,7 @@ 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 should be added to the 
+"kspace_modify diff ad"_kspace_modify.html should be added to the
 input script.
 
 Long-Range Thread (LRT) mode is an option to the "package
@@ -392,6 +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

doc/src/bond_oxdna.txt

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

doc/src/compute_cnp_atom.txt

@@ -42,7 +42,7 @@ 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. 
+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

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/create_bonds.txt

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

doc/src/dihedral_charmm.txt

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

doc/src/dump_vtk.txt

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

doc/src/fix_box_relax.txt

@@ -245,7 +245,7 @@ appear the system is converging to your specified pressure.  The
 solution for this is to either (a) zero the velocities of all atoms
 before performing the minimization, or (b) make sure you are
 monitoring the pressure without its kinetic component.  The latter can
-be done by outputting the pressure from the pressure compute this 
+be done by outputting the pressure from the pressure compute this
 command creates (see below) or a pressure compute you define yourself.
 
 NOTE: Because pressure is often a very sensitive function of volume,

doc/src/fix_eos_table_rx.txt

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

doc/src/fix_filter_corotate.txt

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

doc/src/fix_gcmc.txt

@@ -406,7 +406,7 @@ the user for each subsequent fix gcmc command.
 [Default:]
 
 The option defaults are mol = no, maxangle = 10, overlap_cutoff = 0.0,
-fugacity_coeff = 1, and full_energy = no, 
+fugacity_coeff = 1, and full_energy = no,
 except for the situations where full_energy is required, as
 listed above.
 

doc/src/fix_grem.txt

@@ -85,13 +85,13 @@ No information about this fix is written to "binary restart
 files"_restart.html.
 
 The "thermo_modify"_thermo_modify.html {press} option is supported
-by this fix to add the rescaled kinetic pressure as part of 
+by this fix to add the rescaled kinetic pressure as part of
 "thermodynamic output"_thermo_style.html.
 
 [Restrictions:]
 
-This fix is part of the USER-MISC package. It is only enabled if 
-LAMMPS was built with that package. See the "Making 
+This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 
 [Related commands:]

doc/src/fix_ipi.txt

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

doc/src/fix_mscg.txt

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

doc/src/fix_msst.txt

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

doc/src/fix_nve_dot.txt

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

doc/src/fix_nve_dotc_langevin.txt

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

doc/src/fix_nvk.txt

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

doc/src/fix_spring.txt

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

doc/src/fix_ti_spring.txt

@@ -144,7 +144,11 @@ this fix.
 
 "fix spring"_fix_spring.html, "fix adapt"_fix_adapt.html
 
-[Restrictions:] none
+[Restrictions:]
+
+This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
 
 [Default:]
 

doc/src/kspace_modify.txt

@@ -219,10 +219,10 @@ instead of using the virial equation. This option cannot be used to access
 individual components of the pressure tensor, to compute per-atom virial,
 or with suffix kspace/pair styles of MSM, like OMP or GPU.
 
-The {fftbench} keyword applies only to PPPM. It is on by default. If
-this option is turned off, LAMMPS will not take the time at the end
-of a run to give FFT benchmark timings, and will finish a few seconds
-faster than it would if this option were on.
+The {fftbench} keyword applies only to PPPM. It is off by default. If
+this option is turned on, LAMMPS will perform a short FFT benchmark
+computation and report its timings, and will thus finish a some seconds
+later than it would if this option were off.
 
 The {collective} keyword applies only to PPPM.  It is set to {no} by
 default, except on IBM BlueGene machines.  If this option is set to
@@ -306,7 +306,7 @@ 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. For pppm/intel, order =
 order/disp = 7.

doc/src/neb.txt

@@ -344,7 +344,7 @@ 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.
- 
+
 
 When running on multiple partitions, LAMMPS produces additional log
 files for each partition, e.g. log.lammps.0, log.lammps.1, etc.  For a

doc/src/pair_agni.txt

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

doc/src/pair_buck.txt

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

doc/src/pair_charmm.txt

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

doc/src/pair_dipole.txt

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

doc/src/pair_exp6_rx.txt

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

doc/src/pair_kolmogorov_crespi_z.txt

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

doc/src/pair_meam.txt

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

doc/src/pair_multi_lucy_rx.txt

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

doc/src/pair_nb3b_harmonic.txt

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

doc/src/pair_oxdna.txt

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

doc/src/pair_oxdna2.txt

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

doc/src/pair_table_rx.txt

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

doc/src/python.txt

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

doc/src/read_data.txt

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

doc/src/run_style.txt

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

doc/src/tutorial_github.txt

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

doc/src/tutorial_pylammps.txt

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

examples/COUPLE/README

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

examples/COUPLE/fortran3/LAMMPS-wrapper.cpp

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

examples/COUPLE/fortran3/LAMMPS-wrapper.h

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

examples/COUPLE/fortran3/LAMMPS-wrapper2.cpp

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

examples/COUPLE/fortran3/LAMMPS-wrapper2.h

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

examples/COUPLE/fortran3/LAMMPS.F90

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

examples/COUPLE/fortran3/README

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

examples/COUPLE/fortran3/data.diamond

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

examples/COUPLE/fortran3/in.simple

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

examples/COUPLE/fortran3/makefile

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

examples/COUPLE/fortran3/simple.f90

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

examples/USER/misc/filter_corotate/in.bpti

@@ -28,7 +28,7 @@ thermo          100
 thermo_style    multi
 timestep	8
 
-run_style respa 3 2 8 bond 1 pair 2 kspace 3
+run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
 
 velocity        all create 200.0 12345678 dist uniform
 #dump            dump1 all atom 100 4pti.dump

examples/USER/misc/filter_corotate/in.peptide

@@ -20,7 +20,7 @@ thermo          50
 
 timestep        8
 
-run_style respa 3 2 8 bond 1 pair 2 kspace 3
+run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
 
 fix             1 all nvt temp 250.0 250.0 100.0 tchain 1
 fix             cor all filter/corotate m 1.0

examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.1

@@ -1,240 +0,0 @@
-LAMMPS (10 Mar 2017)
-  using 1 OpenMP thread(s) per MPI task
-
-units           real
-
-atom_style      full
-bond_style      harmonic
-angle_style     charmm
-dihedral_style  charmm
-improper_style  harmonic
-
-pair_style      lj/charmm/coul/long 8 10
-pair_modify     mix arithmetic
-kspace_style    pppm 1e-4
-
-read_data       data.bpti
-  orthogonal box = (-10 -10 -30) to (50 50 30)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  892 atoms
-  scanning bonds ...
-  4 = max bonds/atom
-  scanning angles ...
-  6 = max angles/atom
-  scanning dihedrals ...
-  18 = max dihedrals/atom
-  scanning impropers ...
-  2 = max impropers/atom
-  reading bonds ...
-  906 bonds
-  reading angles ...
-  1626 angles
-  reading dihedrals ...
-  2501 dihedrals
-  reading impropers ...
-  137 impropers
-  4 = max # of 1-2 neighbors
-  9 = max # of 1-3 neighbors
-  19 = max # of 1-4 neighbors
-  21 = max # of special neighbors
-
-special_bonds   charmm
-neigh_modify    delay 2 every 1
-
-
-# ------------- MINIMIZE ----------
-
-minimize 	1e-4 1e-6 1000 10000
-WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
-PPPM initialization ...
-WARNING: System is not charge neutral, net charge = 6 (../kspace.cpp:302)
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
-  G vector (1/distance) = 0.203272
-  grid = 16 16 16
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0316399
-  estimated relative force accuracy = 9.52826e-05
-  using double precision FFTs
-  3d grid and FFT values/proc = 9261 4096
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 12
-  ghost atom cutoff = 12
-  binsize = 6, bins = 10 10 10
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/charmm/coul/long, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory usage (min/avg/max) = 17.8596/1/0 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0            0   -3075.6498    943.91164   -2131.7381   -380.67776 
-     241            0    -4503.313    749.58662   -3753.7264   -29.045104 
-Loop time of 3.35722 on 1 procs for 241 steps with 892 atoms
-
-99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-Minimization stats:
-  Stopping criterion = energy tolerance
-  Energy initial, next-to-last, final = 
-        -2131.73812515     -3753.43984087     -3753.72636847
-  Force two-norm initial, final = 1086.21 26.3688
-  Force max component initial, final = 310.811 3.92748
-  Final line search alpha, max atom move = 0.00596649 0.0234333
-  Iterations, force evaluations = 241 463
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 2.5003     | 2.5003     | 2.5003     |   0.0 | 74.48
-Bond    | 0.24287    | 0.24287    | 0.24287    |   0.0 |  7.23
-Kspace  | 0.53428    | 0.53428    | 0.53428    |   0.0 | 15.91
-Neigh   | 0.069765   | 0.069765   | 0.069765   |   0.0 |  2.08
-Comm    | 0.00065374 | 0.00065374 | 0.00065374 |   0.0 |  0.02
-Output  | 0          | 0          | 0          |   0.0 |  0.00
-Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 0.009358   |            |       |  0.28
-
-Nlocal:    892 ave 892 max 892 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    31 ave 31 max 31 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    148891 ave 148891 max 148891 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 148891
-Ave neighs/atom = 166.918
-Ave special neighs/atom = 10.9395
-Neighbor list builds = 15
-Dangerous builds = 0
-reset_timestep  0
-
-# ------------- RUN ---------------
-
-thermo          100
-thermo_style    multi
-timestep	8
-
-run_style respa 3 2 8 bond 1 pair 2 kspace 3
-Respa levels:
-  1 = bond angle dihedral improper
-  2 = pair
-  3 = kspace
-
-velocity        all create 200.0 12345678 dist uniform
-#dump            dump1 all atom 100 4pti.dump
-
-fix             1 all nvt temp 200 300 25
-fix             cor all filter/corotate m 1.0
-  163 = # of size 2 clusters
-  0 = # of size 3 clusters
-  25 = # of size 4 clusters
-  0 = # of size 5 clusters
-  100 = # of frozen angles
-
-run             1000
-PPPM initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
-  G vector (1/distance) = 0.203272
-  grid = 16 16 16
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0316399
-  estimated relative force accuracy = 9.52826e-05
-  using double precision FFTs
-  3d grid and FFT values/proc = 9261 4096
-Per MPI rank memory usage (min/avg/max) = 19.5425/1/0 Mbytes
----------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
-TotEng   =     -3220.3378 KinEng   =       531.1804 Temp     =       200.0000 
-PotEng   =     -3751.5181 E_bond   =        42.2810 E_angle  =       345.2592 
-E_dihed  =       337.8361 E_impro  =        24.2103 E_vdwl   =      -288.5339 
-E_coul   =      -886.3622 E_long   =     -3326.2088 Press    =        83.2283 
----------------- Step      100 ----- CPU =      3.9414 (sec) ----------------
-TotEng   =     -2718.8970 KinEng   =       538.6206 Temp     =       202.8014 
-PotEng   =     -3257.5176 E_bond   =       203.3367 E_angle  =       566.5317 
-E_dihed  =       397.6202 E_impro  =        34.6623 E_vdwl   =      -248.7451 
-E_coul   =      -874.5122 E_long   =     -3336.4111 Press    =       135.8662 
----------------- Step      200 ----- CPU =      7.9028 (sec) ----------------
-TotEng   =     -2660.1406 KinEng   =       626.3319 Temp     =       235.8265 
-PotEng   =     -3286.4725 E_bond   =       209.5147 E_angle  =       591.7773 
-E_dihed  =       388.9591 E_impro  =        29.4992 E_vdwl   =      -243.5808 
-E_coul   =      -923.5115 E_long   =     -3339.1306 Press    =        88.9000 
----------------- Step      300 ----- CPU =     11.8246 (sec) ----------------
-TotEng   =     -2673.8090 KinEng   =       616.7924 Temp     =       232.2346 
-PotEng   =     -3290.6014 E_bond   =       202.8254 E_angle  =       568.6860 
-E_dihed  =       378.4182 E_impro  =        38.2399 E_vdwl   =      -221.3236 
-E_coul   =      -915.3004 E_long   =     -3342.1468 Press    =        78.8527 
----------------- Step      400 ----- CPU =     15.7990 (sec) ----------------
-TotEng   =     -2614.9416 KinEng   =       649.3474 Temp     =       244.4922 
-PotEng   =     -3264.2890 E_bond   =       211.6116 E_angle  =       617.2026 
-E_dihed  =       399.8744 E_impro  =        40.2678 E_vdwl   =      -211.7790 
-E_coul   =      -978.1624 E_long   =     -3343.3041 Press    =        -4.1958 
----------------- Step      500 ----- CPU =     19.8146 (sec) ----------------
-TotEng   =     -2588.6772 KinEng   =       660.1424 Temp     =       248.5568 
-PotEng   =     -3248.8196 E_bond   =       218.4786 E_angle  =       620.8605 
-E_dihed  =       390.3220 E_impro  =        41.6794 E_vdwl   =      -226.3657 
-E_coul   =      -953.1676 E_long   =     -3340.6269 Press    =        99.3200 
----------------- Step      600 ----- CPU =     23.8587 (sec) ----------------
-TotEng   =     -2550.4618 KinEng   =       693.3384 Temp     =       261.0557 
-PotEng   =     -3243.8002 E_bond   =       232.3563 E_angle  =       606.2922 
-E_dihed  =       396.2469 E_impro  =        37.1980 E_vdwl   =      -235.8425 
-E_coul   =      -937.1208 E_long   =     -3342.9303 Press    =       -21.7737 
----------------- Step      700 ----- CPU =     27.8381 (sec) ----------------
-TotEng   =     -2554.4355 KinEng   =       692.8951 Temp     =       260.8888 
-PotEng   =     -3247.3306 E_bond   =       216.3395 E_angle  =       637.7785 
-E_dihed  =       391.5940 E_impro  =        43.1426 E_vdwl   =      -187.6159 
-E_coul   =     -1008.1694 E_long   =     -3340.3998 Press    =        75.1484 
----------------- Step      800 ----- CPU =     31.8039 (sec) ----------------
-TotEng   =     -2508.3551 KinEng   =       699.0766 Temp     =       263.2163 
-PotEng   =     -3207.4317 E_bond   =       241.9936 E_angle  =       641.3631 
-E_dihed  =       386.2198 E_impro  =        43.7793 E_vdwl   =      -217.7523 
-E_coul   =      -964.6070 E_long   =     -3338.4282 Press    =      -127.7337 
----------------- Step      900 ----- CPU =     35.7700 (sec) ----------------
-TotEng   =     -2452.7644 KinEng   =       762.1842 Temp     =       286.9776 
-PotEng   =     -3214.9485 E_bond   =       243.9191 E_angle  =       649.8664 
-E_dihed  =       382.4351 E_impro  =        39.0029 E_vdwl   =      -221.3389 
-E_coul   =      -970.8965 E_long   =     -3337.9366 Press    =       122.7720 
----------------- Step     1000 ----- CPU =     39.7695 (sec) ----------------
-TotEng   =     -2386.6805 KinEng   =       799.0253 Temp     =       300.8490 
-PotEng   =     -3185.7058 E_bond   =       265.3649 E_angle  =       661.7543 
-E_dihed  =       374.6843 E_impro  =        38.6877 E_vdwl   =      -229.2030 
-E_coul   =      -960.7041 E_long   =     -3336.2899 Press    =       -17.9910 
-Loop time of 39.7695 on 1 procs for 1000 steps with 892 atoms
-
-Performance: 17.380 ns/day, 1.381 hours/ns, 25.145 timesteps/s
-99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 29.169     | 29.169     | 29.169     |   0.0 | 73.34
-Bond    | 7.6249     | 7.6249     | 7.6249     |   0.0 | 19.17
-Kspace  | 1.1525     | 1.1525     | 1.1525     |   0.0 |  2.90
-Neigh   | 0.87606    | 0.87606    | 0.87606    |   0.0 |  2.20
-Comm    | 0.01563    | 0.01563    | 0.01563    |   0.0 |  0.04
-Output  | 0.00048423 | 0.00048423 | 0.00048423 |   0.0 |  0.00
-Modify  | 0.80446    | 0.80446    | 0.80446    |   0.0 |  2.02
-Other   |            | 0.1266     |            |       |  0.32
-
-Nlocal:    892 ave 892 max 892 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    27 ave 27 max 27 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    146206 ave 146206 max 146206 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 146206
-Ave neighs/atom = 163.908
-Ave special neighs/atom = 10.9395
-Neighbor list builds = 186
-Dangerous builds = 0
-
-unfix           cor
-unfix           1
-
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:43

examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.4

@@ -1,240 +0,0 @@
-LAMMPS (10 Mar 2017)
-  using 1 OpenMP thread(s) per MPI task
-
-units           real
-
-atom_style      full
-bond_style      harmonic
-angle_style     charmm
-dihedral_style  charmm
-improper_style  harmonic
-
-pair_style      lj/charmm/coul/long 8 10
-pair_modify     mix arithmetic
-kspace_style    pppm 1e-4
-
-read_data       data.bpti
-  orthogonal box = (-10 -10 -30) to (50 50 30)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  892 atoms
-  scanning bonds ...
-  4 = max bonds/atom
-  scanning angles ...
-  6 = max angles/atom
-  scanning dihedrals ...
-  18 = max dihedrals/atom
-  scanning impropers ...
-  2 = max impropers/atom
-  reading bonds ...
-  906 bonds
-  reading angles ...
-  1626 angles
-  reading dihedrals ...
-  2501 dihedrals
-  reading impropers ...
-  137 impropers
-  4 = max # of 1-2 neighbors
-  9 = max # of 1-3 neighbors
-  19 = max # of 1-4 neighbors
-  21 = max # of special neighbors
-
-special_bonds   charmm
-neigh_modify    delay 2 every 1
-
-
-# ------------- MINIMIZE ----------
-
-minimize 	1e-4 1e-6 1000 10000
-WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
-PPPM initialization ...
-WARNING: System is not charge neutral, net charge = 6 (../kspace.cpp:302)
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
-  G vector (1/distance) = 0.203272
-  grid = 16 16 16
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0316399
-  estimated relative force accuracy = 9.52826e-05
-  using double precision FFTs
-  3d grid and FFT values/proc = 3549 1024
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 12
-  ghost atom cutoff = 12
-  binsize = 6, bins = 10 10 10
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/charmm/coul/long, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory usage (min/avg/max) = 16.9693/0.981879/0 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0            0   -3075.6498    943.91164   -2131.7381   -380.67776 
-     241            0   -4503.3131    749.58666   -3753.7264   -29.045153 
-Loop time of 1.26594 on 4 procs for 241 steps with 892 atoms
-
-99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-Minimization stats:
-  Stopping criterion = energy tolerance
-  Energy initial, next-to-last, final = 
-        -2131.73812515     -3753.43983927     -3753.72640137
-  Force two-norm initial, final = 1086.21 26.3688
-  Force max component initial, final = 310.811 3.92751
-  Final line search alpha, max atom move = 0.00596649 0.0234334
-  Iterations, force evaluations = 241 463
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.34267    | 0.63792    | 0.90268    |  25.2 | 50.39
-Bond    | 0.025776   | 0.063318   | 0.095631   |  10.8 |  5.00
-Kspace  | 0.21904    | 0.51601    | 0.84895    |  31.3 | 40.76
-Neigh   | 0.023185   | 0.023363   | 0.023538   |   0.1 |  1.85
-Comm    | 0.012025   | 0.014189   | 0.016335   |   1.4 |  1.12
-Output  | 0          | 0          | 0          |   0.0 |  0.00
-Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 0.01114    |            |       |  0.88
-
-Nlocal:    223 ave 323 max 89 min
-Histogram: 1 0 0 0 1 0 0 0 1 1
-Nghost:    613 ave 675 max 557 min
-Histogram: 1 0 0 1 0 1 0 0 0 1
-Neighs:    37222.8 ave 50005 max 20830 min
-Histogram: 1 0 0 0 1 0 0 1 0 1
-
-Total # of neighbors = 148891
-Ave neighs/atom = 166.918
-Ave special neighs/atom = 10.9395
-Neighbor list builds = 15
-Dangerous builds = 0
-reset_timestep  0
-
-# ------------- RUN ---------------
-
-thermo          100
-thermo_style    multi
-timestep	8
-
-run_style respa 3 2 8 bond 1 pair 2 kspace 3
-Respa levels:
-  1 = bond angle dihedral improper
-  2 = pair
-  3 = kspace
-
-velocity        all create 200.0 12345678 dist uniform
-#dump            dump1 all atom 100 4pti.dump
-
-fix             1 all nvt temp 200 300 25
-fix             cor all filter/corotate m 1.0
-  163 = # of size 2 clusters
-  0 = # of size 3 clusters
-  25 = # of size 4 clusters
-  0 = # of size 5 clusters
-  100 = # of frozen angles
-
-run             1000
-PPPM initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
-  G vector (1/distance) = 0.203272
-  grid = 16 16 16
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0316399
-  estimated relative force accuracy = 9.52826e-05
-  using double precision FFTs
-  3d grid and FFT values/proc = 3549 1024
-Per MPI rank memory usage (min/avg/max) = 17.142/0.97212/0 Mbytes
----------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
-TotEng   =     -3220.3378 KinEng   =       531.1804 Temp     =       200.0000 
-PotEng   =     -3751.5182 E_bond   =        42.2810 E_angle  =       345.2592 
-E_dihed  =       337.8361 E_impro  =        24.2103 E_vdwl   =      -288.5339 
-E_coul   =      -886.3622 E_long   =     -3326.2088 Press    =        83.2282 
----------------- Step      100 ----- CPU =      1.5457 (sec) ----------------
-TotEng   =     -2718.9184 KinEng   =       538.6205 Temp     =       202.8014 
-PotEng   =     -3257.5389 E_bond   =       203.3365 E_angle  =       566.5311 
-E_dihed  =       397.6202 E_impro  =        34.6621 E_vdwl   =      -248.7451 
-E_coul   =      -874.5326 E_long   =     -3336.4111 Press    =       135.8435 
----------------- Step      200 ----- CPU =      3.0720 (sec) ----------------
-TotEng   =     -2660.1146 KinEng   =       626.3474 Temp     =       235.8323 
-PotEng   =     -3286.4620 E_bond   =       209.5168 E_angle  =       591.7735 
-E_dihed  =       388.9615 E_impro  =        29.5000 E_vdwl   =      -243.5840 
-E_coul   =      -923.4998 E_long   =     -3339.1299 Press    =        88.8857 
----------------- Step      300 ----- CPU =      4.5597 (sec) ----------------
-TotEng   =     -2669.7442 KinEng   =       619.3625 Temp     =       233.2023 
-PotEng   =     -3289.1067 E_bond   =       203.4405 E_angle  =       569.5281 
-E_dihed  =       378.3314 E_impro  =        38.2880 E_vdwl   =      -221.1904 
-E_coul   =      -915.3396 E_long   =     -3342.1646 Press    =        79.3780 
----------------- Step      400 ----- CPU =      5.9808 (sec) ----------------
-TotEng   =     -2618.9975 KinEng   =       644.6145 Temp     =       242.7102 
-PotEng   =     -3263.6119 E_bond   =       209.5864 E_angle  =       618.8954 
-E_dihed  =       401.3798 E_impro  =        39.9064 E_vdwl   =      -212.1271 
-E_coul   =      -977.1589 E_long   =     -3344.0940 Press    =        -7.8938 
----------------- Step      500 ----- CPU =      7.4159 (sec) ----------------
-TotEng   =     -2579.7486 KinEng   =       666.4643 Temp     =       250.9371 
-PotEng   =     -3246.2129 E_bond   =       219.2549 E_angle  =       620.3474 
-E_dihed  =       388.4395 E_impro  =        41.4499 E_vdwl   =      -225.9686 
-E_coul   =      -949.3689 E_long   =     -3340.3672 Press    =       113.2543 
----------------- Step      600 ----- CPU =      8.9252 (sec) ----------------
-TotEng   =     -2535.8235 KinEng   =       708.5919 Temp     =       266.7990 
-PotEng   =     -3244.4154 E_bond   =       243.9451 E_angle  =       606.0866 
-E_dihed  =       400.0562 E_impro  =        33.9708 E_vdwl   =      -223.1319 
-E_coul   =      -964.9940 E_long   =     -3340.3482 Press    =      -102.4475 
----------------- Step      700 ----- CPU =     10.4022 (sec) ----------------
-TotEng   =     -2552.6681 KinEng   =       702.3080 Temp     =       264.4330 
-PotEng   =     -3254.9761 E_bond   =       250.8834 E_angle  =       639.0977 
-E_dihed  =       386.4014 E_impro  =        42.3004 E_vdwl   =      -224.4816 
-E_coul   =     -1011.8551 E_long   =     -3337.3222 Press    =        10.6424 
----------------- Step      800 ----- CPU =     11.8699 (sec) ----------------
-TotEng   =     -2423.5415 KinEng   =       772.1254 Temp     =       290.7206 
-PotEng   =     -3195.6670 E_bond   =       238.5831 E_angle  =       640.9180 
-E_dihed  =       377.7994 E_impro  =        40.3135 E_vdwl   =      -216.5705 
-E_coul   =      -935.1087 E_long   =     -3341.6019 Press    =       -38.2479 
----------------- Step      900 ----- CPU =     13.3548 (sec) ----------------
-TotEng   =     -2394.4779 KinEng   =       766.6895 Temp     =       288.6739 
-PotEng   =     -3161.1673 E_bond   =       284.8428 E_angle  =       671.0959 
-E_dihed  =       380.3406 E_impro  =        51.2975 E_vdwl   =      -219.5211 
-E_coul   =      -990.6305 E_long   =     -3338.5925 Press    =       -15.2279 
----------------- Step     1000 ----- CPU =     14.7908 (sec) ----------------
-TotEng   =     -2340.1471 KinEng   =       799.0198 Temp     =       300.8469 
-PotEng   =     -3139.1669 E_bond   =       271.0389 E_angle  =       683.8278 
-E_dihed  =       407.0795 E_impro  =        39.6209 E_vdwl   =      -230.5355 
-E_coul   =      -974.2981 E_long   =     -3335.9003 Press    =       -94.3420 
-Loop time of 14.7909 on 4 procs for 1000 steps with 892 atoms
-
-Performance: 46.732 ns/day, 0.514 hours/ns, 67.609 timesteps/s
-99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 4.4184     | 7.5543     | 10.133     |  74.2 | 51.07
-Bond    | 0.94027    | 1.9781     | 2.7492     |  54.4 | 13.37
-Kspace  | 0.45487    | 0.45887    | 0.46343    |   0.4 |  3.10
-Neigh   | 0.28145    | 0.28339    | 0.28539    |   0.3 |  1.92
-Comm    | 0.7515     | 4.1484     | 8.3861     | 135.5 | 28.05
-Output  | 0.00049973 | 0.00055474 | 0.00066924 |   0.0 |  0.00
-Modify  | 0.26165    | 0.31142    | 0.35023    |   6.7 |  2.11
-Other   |            | 0.05572    |            |       |  0.38
-
-Nlocal:    223 ave 313 max 122 min
-Histogram: 1 0 0 1 0 0 0 1 0 1
-Nghost:    584.5 ave 605 max 553 min
-Histogram: 1 0 0 0 0 1 0 0 0 2
-Neighs:    35448 ave 42093 max 25175 min
-Histogram: 1 0 0 0 0 0 1 1 0 1
-
-Total # of neighbors = 141792
-Ave neighs/atom = 158.96
-Ave special neighs/atom = 10.9395
-Neighbor list builds = 186
-Dangerous builds = 0
-
-unfix           cor
-unfix           1
-
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:16

examples/USER/misc/filter_corotate/log.10Mar2017.peptide.g++.1

@@ -1,146 +0,0 @@
-LAMMPS (10 Mar 2017)
-  using 1 OpenMP thread(s) per MPI task
-# Solvated 5-mer peptide, run for 8ps in NVT
-
-units           real
-atom_style      full
-
-pair_style      lj/charmm/coul/long 8.0 10.0 10.0
-bond_style      harmonic
-angle_style     charmm
-dihedral_style  charmm
-improper_style  harmonic
-kspace_style    pppm 0.0001
-
-read_data       data.peptide
-  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  2004 atoms
-  reading velocities ...
-  2004 velocities
-  scanning bonds ...
-  3 = max bonds/atom
-  scanning angles ...
-  6 = max angles/atom
-  scanning dihedrals ...
-  14 = max dihedrals/atom
-  scanning impropers ...
-  1 = max impropers/atom
-  reading bonds ...
-  1365 bonds
-  reading angles ...
-  786 angles
-  reading dihedrals ...
-  207 dihedrals
-  reading impropers ...
-  12 impropers
-  4 = max # of 1-2 neighbors
-  7 = max # of 1-3 neighbors
-  14 = max # of 1-4 neighbors
-  18 = max # of special neighbors
-
-neighbor        2.0 bin
-neigh_modify    delay 5
-
-thermo          50
-#dump            dump1 all atom 100 peptide.dump
-
-timestep        8
-
-run_style respa 3 2 8 bond 1 pair 2 kspace 3
-Respa levels:
-  1 = bond angle dihedral improper
-  2 = pair
-  3 = kspace
-
-fix             1 all nvt temp 250.0 250.0 100.0 tchain 1
-fix             cor all filter/corotate m 1.0
-  19 = # of size 2 clusters
-  0 = # of size 3 clusters
-  3 = # of size 4 clusters
-  0 = # of size 5 clusters
-  646 = # of frozen angles
-run             1000
-PPPM initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
-  G vector (1/distance) = 0.268725
-  grid = 15 15 15
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0228209
-  estimated relative force accuracy = 6.87243e-05
-  using double precision FFTs
-  3d grid and FFT values/proc = 10648 3375
-Neighbor list info ...
-  update every 1 steps, delay 5 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 12
-  ghost atom cutoff = 12
-  binsize = 6, bins = 5 5 5
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/charmm/coul/long, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory usage (min/avg/max) = 22.6706/1/0 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0     190.0857   -6785.6785    70.391457   -5580.3684    19434.821 
-      50    239.46028   -7546.5667    1092.8874   -5023.9668   -24643.891 
-     100    242.81799   -7125.5527     416.0788   -5259.7139    15525.465 
-     150    235.97108   -7531.9334    932.35464   -5190.6987   -14838.489 
-     200    252.06415   -7195.6011    568.02993   -5122.6064     8841.332 
-     250    249.99431   -7586.5092    881.83491   -5212.0676    -9330.345 
-     300     240.3382   -7333.0933    633.29951   -5264.8395    5137.9757 
-     350    255.34529   -7568.2413    856.46371   -5187.2226    -6206.063 
-     400    242.99276   -7419.9031    713.23943   -5255.8602    2447.0091 
-     450    251.10653    -7622.061    844.20584   -5278.6079   -4906.6559 
-     500    255.59314    -7439.253    710.84907   -5202.3691    1571.0032 
-     550     253.2025   -7660.5101    823.05373    -5325.695    -4551.399 
-     600    249.05313   -7509.6729    741.48104   -5281.2046       992.87 
-     650    251.75984   -7593.6589    847.08244   -5243.4286   -3510.1176 
-     700    249.25027   -7601.9112     794.0912   -5319.6557    305.76021 
-     750      255.415   -7602.2674    822.98524   -5254.3109    -2333.421 
-     800    241.99621   -7643.8878    796.53352   -5402.5008   -298.66565 
-     850     253.6428   -7598.3764    816.45457   -5267.5316   -1905.3478 
-     900    247.20231   -7690.2806    789.75999   -5424.5838   -1331.7228 
-     950    255.92583   -7634.7505    831.18272   -5275.5466   -2186.5117 
-    1000     253.2126   -7647.9526    823.93602    -5312.195   -1189.9659 
-Loop time of 150.664 on 1 procs for 1000 steps with 2004 atoms
-
-Performance: 4.588 ns/day, 5.231 hours/ns, 6.637 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    | 135.81     | 135.81     | 135.81     |   0.0 | 90.14
-Bond    | 2.5889     | 2.5889     | 2.5889     |   0.0 |  1.72
-Kspace  | 2.0379     | 2.0379     | 2.0379     |   0.0 |  1.35
-Neigh   | 5.893      | 5.893      | 5.893      |   0.0 |  3.91
-Comm    | 1.6998     | 1.6998     | 1.6998     |   0.0 |  1.13
-Output  | 0.00077915 | 0.00077915 | 0.00077915 |   0.0 |  0.00
-Modify  | 2          | 2          | 2          |   0.0 |  1.33
-Other   |            | 0.6352     |            |       |  0.42
-
-Nlocal:    2004 ave 2004 max 2004 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    11197 ave 11197 max 11197 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    707779 ave 707779 max 707779 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 707779
-Ave neighs/atom = 353.183
-Ave special neighs/atom = 2.34032
-Neighbor list builds = 200
-Dangerous builds = 200
-unfix           cor
-unfix           1
-
-
-
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:02:30

examples/USER/misc/filter_corotate/log.10Mar2017.peptide.g++.4

@@ -1,146 +0,0 @@
-LAMMPS (10 Mar 2017)
-  using 1 OpenMP thread(s) per MPI task
-# Solvated 5-mer peptide, run for 8ps in NVT
-
-units           real
-atom_style      full
-
-pair_style      lj/charmm/coul/long 8.0 10.0 10.0
-bond_style      harmonic
-angle_style     charmm
-dihedral_style  charmm
-improper_style  harmonic
-kspace_style    pppm 0.0001
-
-read_data       data.peptide
-  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  2004 atoms
-  reading velocities ...
-  2004 velocities
-  scanning bonds ...
-  3 = max bonds/atom
-  scanning angles ...
-  6 = max angles/atom
-  scanning dihedrals ...
-  14 = max dihedrals/atom
-  scanning impropers ...
-  1 = max impropers/atom
-  reading bonds ...
-  1365 bonds
-  reading angles ...
-  786 angles
-  reading dihedrals ...
-  207 dihedrals
-  reading impropers ...
-  12 impropers
-  4 = max # of 1-2 neighbors
-  7 = max # of 1-3 neighbors
-  14 = max # of 1-4 neighbors
-  18 = max # of special neighbors
-
-neighbor        2.0 bin
-neigh_modify    delay 5
-
-thermo          50
-#dump            dump1 all atom 100 peptide.dump
-
-timestep        8
-
-run_style respa 3 2 8 bond 1 pair 2 kspace 3
-Respa levels:
-  1 = bond angle dihedral improper
-  2 = pair
-  3 = kspace
-
-fix             1 all nvt temp 250.0 250.0 100.0 tchain 1
-fix             cor all filter/corotate m 1.0
-  19 = # of size 2 clusters
-  0 = # of size 3 clusters
-  3 = # of size 4 clusters
-  0 = # of size 5 clusters
-  646 = # of frozen angles
-run             1000
-PPPM initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
-  G vector (1/distance) = 0.268725
-  grid = 15 15 15
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0228209
-  estimated relative force accuracy = 6.87243e-05
-  using double precision FFTs
-  3d grid and FFT values/proc = 4312 960
-Neighbor list info ...
-  update every 1 steps, delay 5 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 12
-  ghost atom cutoff = 12
-  binsize = 6, bins = 5 5 5
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/charmm/coul/long, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory usage (min/avg/max) = 16.8394/0.98826/0 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0     190.0857   -6785.6785    70.391457   -5580.3684    19434.821 
-      50    239.46028   -7546.5668    1092.8874   -5023.9668   -24643.891 
-     100    242.81819   -7125.5629    416.08082   -5259.7209    15525.244 
-     150    235.94928   -7531.9186    932.50658   -5190.6621   -14842.431 
-     200    255.85551   -7254.4065     568.8803   -5157.9249    8936.8651 
-     250     247.8705   -7607.4583    858.06087   -5269.4711   -9926.0442 
-     300    257.64176    -7267.424     618.5573   -5110.6004    5173.3307 
-     350    251.65439   -7572.3806    821.15745   -5248.7049    -7092.327 
-     400    256.87927   -7414.2145    655.33178    -5225.169    4119.4095 
-     450    257.12393   -7576.5541    853.39773   -5187.9819   -5224.8823 
-     500    242.42371    -7524.705    705.75357   -5371.5455    2111.3878 
-     550    248.97188    -7541.076    792.86994   -5261.7038   -2278.4185 
-     600    249.81862   -7592.0499    767.17722   -5333.3149   -1149.4759 
-     650    253.31349   -7578.2665    813.75975   -5252.0827   -2915.5706 
-     700    256.61152   -7588.1475    761.03356   -5294.9988   -747.88089 
-     750     248.3606    -7660.457    837.71615   -5339.8883   -3072.8311 
-     800    253.81464   -7638.6089     782.4229   -5340.7698    -1025.909 
-     850    245.69185   -7660.9036    795.66792   -5398.3172   -2717.5851 
-     900    249.13156   -7589.4769    806.43464   -5295.5867   -761.63361 
-     950    251.11482   -7691.4981    869.34937    -5322.852   -3282.3031 
-    1000     241.9195   -7630.9899    828.59107   -5358.0033   -95.962685 
-Loop time of 45.5507 on 4 procs for 1000 steps with 2004 atoms
-
-Performance: 15.174 ns/day, 1.582 hours/ns, 21.954 timesteps/s
-99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 35.545     | 36.674     | 38.004     |  15.8 | 80.51
-Bond    | 0.51302    | 0.67796    | 0.86345    |  18.6 |  1.49
-Kspace  | 0.66031    | 0.68459    | 0.70506    |   2.1 |  1.50
-Neigh   | 1.5605     | 1.5627     | 1.5649     |   0.1 |  3.43
-Comm    | 3.4611     | 4.9841     | 6.294      |  47.2 | 10.94
-Output  | 0.00079799 | 0.00086641 | 0.0010369  |   0.0 |  0.00
-Modify  | 0.67341    | 0.69059    | 0.71186    |   1.7 |  1.52
-Other   |            | 0.2762     |            |       |  0.61
-
-Nlocal:    501 ave 523 max 473 min
-Histogram: 1 0 0 0 0 0 2 0 0 1
-Nghost:    6643.25 ave 6708 max 6566 min
-Histogram: 1 1 0 0 0 0 0 0 0 2
-Neighs:    176977 ave 185765 max 164931 min
-Histogram: 1 0 0 0 1 0 0 0 1 1
-
-Total # of neighbors = 707908
-Ave neighs/atom = 353.248
-Ave special neighs/atom = 2.34032
-Neighbor list builds = 200
-Dangerous builds = 200
-unfix           cor
-unfix           1
-
-
-
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:45

examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.1

@@ -0,0 +1,241 @@
+LAMMPS (20 Jun 2017)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+
+units           real
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+
+pair_style      lj/charmm/coul/long 8 10
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data       data.bpti
+  orthogonal box = (-10 -10 -30) to (50 50 30)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  892 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  906 bonds
+  reading angles ...
+  1626 angles
+  reading dihedrals ...
+  2501 dihedrals
+  reading impropers ...
+  137 impropers
+  4 = max # of 1-2 neighbors
+  9 = max # of 1-3 neighbors
+  19 = max # of 1-4 neighbors
+  21 = max # of special neighbors
+
+special_bonds   charmm
+neigh_modify    delay 2 every 1
+
+
+# ------------- MINIMIZE ----------
+
+minimize 	1e-4 1e-6 1000 10000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+PPPM initialization ...
+WARNING: System is not charge neutral, net charge = 6 (../kspace.cpp:302)
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.203272
+  grid = 16 16 16
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0316399
+  estimated relative force accuracy = 9.52826e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 9261 4096
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 10 10 10
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 17.86 | 17.86 | 17.86 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -3075.6498    943.91164   -2131.7381   -380.67776 
+     241            0    -4503.313    749.58662   -3753.7264   -29.045104 
+Loop time of 7.63279 on 1 procs for 241 steps with 892 atoms
+
+32.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+  Stopping criterion = energy tolerance
+  Energy initial, next-to-last, final = 
+        -2131.73812515     -3753.43984087     -3753.72636847
+  Force two-norm initial, final = 1086.21 26.3688
+  Force max component initial, final = 310.811 3.92748
+  Final line search alpha, max atom move = 0.00596649 0.0234333
+  Iterations, force evaluations = 241 463
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.8395     | 5.8395     | 5.8395     |   0.0 | 76.51
+Bond    | 0.46414    | 0.46414    | 0.46414    |   0.0 |  6.08
+Kspace  | 1.1535     | 1.1535     | 1.1535     |   0.0 | 15.11
+Neigh   | 0.14908    | 0.14908    | 0.14908    |   0.0 |  1.95
+Comm    | 0.001932   | 0.001932   | 0.001932   |   0.0 |  0.03
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.02465    |            |       |  0.32
+
+Nlocal:    892 ave 892 max 892 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    31 ave 31 max 31 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    148891 ave 148891 max 148891 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 148891
+Ave neighs/atom = 166.918
+Ave special neighs/atom = 10.9395
+Neighbor list builds = 15
+Dangerous builds = 0
+reset_timestep  0
+
+# ------------- RUN ---------------
+
+thermo          100
+thermo_style    multi
+timestep	8
+
+run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
+Respa levels:
+  1 = bond angle
+  2 = dihedral improper pair
+  3 = kspace
+
+velocity        all create 200.0 12345678 dist uniform
+#dump            dump1 all atom 100 4pti.dump
+
+fix             1 all nvt temp 200 300 25
+fix             cor all filter/corotate m 1.0
+  163 = # of size 2 clusters
+  0 = # of size 3 clusters
+  25 = # of size 4 clusters
+  0 = # of size 5 clusters
+  100 = # of frozen angles
+
+run             1000
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.203272
+  grid = 16 16 16
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0316399
+  estimated relative force accuracy = 9.52826e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 9261 4096
+Per MPI rank memory allocation (min/avg/max) = 19.55 | 19.55 | 19.55 Mbytes
+---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
+TotEng   =     -3220.3378 KinEng   =       531.1804 Temp     =       200.0000 
+PotEng   =     -3751.5181 E_bond   =        42.2810 E_angle  =       345.2592 
+E_dihed  =       337.8361 E_impro  =        24.2103 E_vdwl   =      -288.5339 
+E_coul   =      -886.3622 E_long   =     -3326.2088 Press    =        83.2283 
+---------------- Step      100 ----- CPU =      8.4380 (sec) ----------------
+TotEng   =     -2718.4258 KinEng   =       539.6265 Temp     =       203.1802 
+PotEng   =     -3258.0524 E_bond   =       203.2307 E_angle  =       566.1893 
+E_dihed  =       397.6759 E_impro  =        34.7696 E_vdwl   =      -248.6577 
+E_coul   =      -874.8466 E_long   =     -3336.4135 Press    =       135.8640 
+---------------- Step      200 ----- CPU =     16.9012 (sec) ----------------
+TotEng   =     -2661.9611 KinEng   =       625.0674 Temp     =       235.3503 
+PotEng   =     -3287.0285 E_bond   =       208.1804 E_angle  =       590.8462 
+E_dihed  =       389.1482 E_impro  =        30.5882 E_vdwl   =      -240.5448 
+E_coul   =      -926.3091 E_long   =     -3338.9378 Press    =       103.4738 
+---------------- Step      300 ----- CPU =     25.3046 (sec) ----------------
+TotEng   =     -2662.4139 KinEng   =       622.2647 Temp     =       234.2951 
+PotEng   =     -3284.6785 E_bond   =       202.4210 E_angle  =       573.6793 
+E_dihed  =       382.8919 E_impro  =        41.8973 E_vdwl   =      -218.9895 
+E_coul   =      -924.8414 E_long   =     -3341.7372 Press    =        40.6746 
+---------------- Step      400 ----- CPU =     33.8063 (sec) ----------------
+TotEng   =     -2604.9431 KinEng   =       662.9890 Temp     =       249.6286 
+PotEng   =     -3267.9321 E_bond   =       195.9116 E_angle  =       616.1383 
+E_dihed  =       407.8502 E_impro  =        43.3560 E_vdwl   =      -219.0377 
+E_coul   =      -966.3118 E_long   =     -3345.8387 Press    =       -91.8856 
+---------------- Step      500 ----- CPU =     42.3470 (sec) ----------------
+TotEng   =     -2609.3867 KinEng   =       657.0939 Temp     =       247.4090 
+PotEng   =     -3266.4806 E_bond   =       236.4955 E_angle  =       570.6256 
+E_dihed  =       390.5111 E_impro  =        41.9250 E_vdwl   =      -223.9927 
+E_coul   =      -939.5249 E_long   =     -3342.5201 Press    =       236.7471 
+---------------- Step      600 ----- CPU =     50.9590 (sec) ----------------
+TotEng   =     -2564.7161 KinEng   =       701.8494 Temp     =       264.2603 
+PotEng   =     -3266.5655 E_bond   =       223.5820 E_angle  =       582.7722 
+E_dihed  =       394.6196 E_impro  =        43.8581 E_vdwl   =      -201.7759 
+E_coul   =      -967.4136 E_long   =     -3342.2079 Press    =        26.6595 
+---------------- Step      700 ----- CPU =     59.4791 (sec) ----------------
+TotEng   =     -2510.1142 KinEng   =       689.5931 Temp     =       259.6455 
+PotEng   =     -3199.7072 E_bond   =       254.6476 E_angle  =       611.9715 
+E_dihed  =       403.0624 E_impro  =        44.1360 E_vdwl   =      -205.6377 
+E_coul   =      -964.7455 E_long   =     -3343.1416 Press    =        60.5789 
+---------------- Step      800 ----- CPU =     67.9330 (sec) ----------------
+TotEng   =     -2452.7408 KinEng   =       777.5962 Temp     =       292.7805 
+PotEng   =     -3230.3370 E_bond   =       250.4950 E_angle  =       656.6738 
+E_dihed  =       382.4702 E_impro  =        39.5378 E_vdwl   =      -225.0375 
+E_coul   =      -994.4519 E_long   =     -3340.0244 Press    =       -19.6463 
+---------------- Step      900 ----- CPU =     76.3690 (sec) ----------------
+TotEng   =     -2339.9766 KinEng   =       808.7116 Temp     =       304.4961 
+PotEng   =     -3148.6883 E_bond   =       247.7657 E_angle  =       679.0658 
+E_dihed  =       398.2984 E_impro  =        43.7890 E_vdwl   =      -230.2498 
+E_coul   =      -945.8152 E_long   =     -3341.5422 Press    =       -64.4343 
+---------------- Step     1000 ----- CPU =     84.8757 (sec) ----------------
+TotEng   =     -2329.1819 KinEng   =       822.9820 Temp     =       309.8691 
+PotEng   =     -3152.1639 E_bond   =       264.9609 E_angle  =       691.7104 
+E_dihed  =       385.9914 E_impro  =        40.5525 E_vdwl   =      -230.5182 
+E_coul   =      -954.6203 E_long   =     -3350.2405 Press    =      -146.6649 
+Loop time of 84.8758 on 1 procs for 1000 steps with 892 atoms
+
+Performance: 8.144 ns/day, 2.947 hours/ns, 11.782 timesteps/s
+32.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 68.548     | 68.548     | 68.548     |   0.0 | 80.76
+Bond    | 10.263     | 10.263     | 10.263     |   0.0 | 12.09
+Kspace  | 2.4528     | 2.4528     | 2.4528     |   0.0 |  2.89
+Neigh   | 1.9041     | 1.9041     | 1.9041     |   0.0 |  2.24
+Comm    | 0.044126   | 0.044126   | 0.044126   |   0.0 |  0.05
+Output  | 0.000983   | 0.000983   | 0.000983   |   0.0 |  0.00
+Modify  | 1.4113     | 1.4113     | 1.4113     |   0.0 |  1.66
+Other   |            | 0.2516     |            |       |  0.30
+
+Nlocal:    892 ave 892 max 892 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    38 ave 38 max 38 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    144068 ave 144068 max 144068 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 144068
+Ave neighs/atom = 161.511
+Ave special neighs/atom = 10.9395
+Neighbor list builds = 190
+Dangerous builds = 0
+
+unfix           cor
+unfix           1
+
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:01:32

examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.4

@@ -0,0 +1,241 @@
+LAMMPS (20 Jun 2017)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+
+units           real
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+
+pair_style      lj/charmm/coul/long 8 10
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data       data.bpti
+  orthogonal box = (-10 -10 -30) to (50 50 30)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  892 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  906 bonds
+  reading angles ...
+  1626 angles
+  reading dihedrals ...
+  2501 dihedrals
+  reading impropers ...
+  137 impropers
+  4 = max # of 1-2 neighbors
+  9 = max # of 1-3 neighbors
+  19 = max # of 1-4 neighbors
+  21 = max # of special neighbors
+
+special_bonds   charmm
+neigh_modify    delay 2 every 1
+
+
+# ------------- MINIMIZE ----------
+
+minimize 	1e-4 1e-6 1000 10000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+PPPM initialization ...
+WARNING: System is not charge neutral, net charge = 6 (../kspace.cpp:302)
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.203272
+  grid = 16 16 16
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0316399
+  estimated relative force accuracy = 9.52826e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 3549 1024
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 10 10 10
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 16.97 | 17.2 | 17.52 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -3075.6498    943.91164   -2131.7381   -380.67776 
+     241            0   -4503.3131    749.58665   -3753.7264   -29.044989 
+Loop time of 3.06327 on 4 procs for 241 steps with 892 atoms
+
+31.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+  Stopping criterion = energy tolerance
+  Energy initial, next-to-last, final = 
+        -2131.73812515      -3753.4398752     -3753.72640446
+  Force two-norm initial, final = 1086.21 26.3687
+  Force max component initial, final = 310.811 3.92765
+  Final line search alpha, max atom move = 0.0059665 0.0234343
+  Iterations, force evaluations = 241 463
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.91458    | 1.6235     | 2.2701     |  38.2 | 53.00
+Bond    | 0.055164   | 0.13173    | 0.19487    |  15.1 |  4.30
+Kspace  | 0.48966    | 1.1993     | 1.9847     |  48.7 | 39.15
+Neigh   | 0.053297   | 0.053442   | 0.053576   |   0.0 |  1.74
+Comm    | 0.031677   | 0.035006   | 0.038061   |   1.5 |  1.14
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.02021    |            |       |  0.66
+
+Nlocal:    223 ave 323 max 89 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Nghost:    613 ave 675 max 557 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Neighs:    37222.8 ave 50005 max 20830 min
+Histogram: 1 0 0 0 1 0 0 1 0 1
+
+Total # of neighbors = 148891
+Ave neighs/atom = 166.918
+Ave special neighs/atom = 10.9395
+Neighbor list builds = 15
+Dangerous builds = 0
+reset_timestep  0
+
+# ------------- RUN ---------------
+
+thermo          100
+thermo_style    multi
+timestep	8
+
+run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
+Respa levels:
+  1 = bond angle
+  2 = dihedral improper pair
+  3 = kspace
+
+velocity        all create 200.0 12345678 dist uniform
+#dump            dump1 all atom 100 4pti.dump
+
+fix             1 all nvt temp 200 300 25
+fix             cor all filter/corotate m 1.0
+  163 = # of size 2 clusters
+  0 = # of size 3 clusters
+  25 = # of size 4 clusters
+  0 = # of size 5 clusters
+  100 = # of frozen angles
+
+run             1000
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.203272
+  grid = 16 16 16
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0316399
+  estimated relative force accuracy = 9.52826e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 3549 1024
+Per MPI rank memory allocation (min/avg/max) = 17.14 | 17.63 | 18.14 Mbytes
+---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
+TotEng   =     -3220.3378 KinEng   =       531.1804 Temp     =       200.0000 
+PotEng   =     -3751.5182 E_bond   =        42.2810 E_angle  =       345.2593 
+E_dihed  =       337.8361 E_impro  =        24.2103 E_vdwl   =      -288.5339 
+E_coul   =      -886.3622 E_long   =     -3326.2088 Press    =        83.2284 
+---------------- Step      100 ----- CPU =      3.4639 (sec) ----------------
+TotEng   =     -2718.4266 KinEng   =       539.6246 Temp     =       203.1794 
+PotEng   =     -3258.0513 E_bond   =       203.2306 E_angle  =       566.1887 
+E_dihed  =       397.6756 E_impro  =        34.7695 E_vdwl   =      -248.6577 
+E_coul   =      -874.8446 E_long   =     -3336.4135 Press    =       135.8653 
+---------------- Step      200 ----- CPU =      6.8898 (sec) ----------------
+TotEng   =     -2662.0450 KinEng   =       625.0178 Temp     =       235.3317 
+PotEng   =     -3287.0628 E_bond   =       208.1691 E_angle  =       590.8259 
+E_dihed  =       389.1424 E_impro  =        30.5879 E_vdwl   =      -240.5397 
+E_coul   =      -926.3110 E_long   =     -3338.9375 Press    =       103.4843 
+---------------- Step      300 ----- CPU =     10.2791 (sec) ----------------
+TotEng   =     -2661.8829 KinEng   =       623.0352 Temp     =       234.5852 
+PotEng   =     -3284.9181 E_bond   =       203.0274 E_angle  =       573.6583 
+E_dihed  =       383.0124 E_impro  =        41.9015 E_vdwl   =      -218.0696 
+E_coul   =      -926.5806 E_long   =     -3341.8675 Press    =        45.6868 
+---------------- Step      400 ----- CPU =     13.5874 (sec) ----------------
+TotEng   =     -2594.5220 KinEng   =       672.8693 Temp     =       253.3487 
+PotEng   =     -3267.3914 E_bond   =       201.3378 E_angle  =       612.7099 
+E_dihed  =       410.1920 E_impro  =        44.0201 E_vdwl   =      -217.9714 
+E_coul   =      -971.6203 E_long   =     -3346.0595 Press    =      -121.1015 
+---------------- Step      500 ----- CPU =     16.9047 (sec) ----------------
+TotEng   =     -2603.9306 KinEng   =       668.2122 Temp     =       251.5952 
+PotEng   =     -3272.1428 E_bond   =       238.1081 E_angle  =       578.3310 
+E_dihed  =       399.1305 E_impro  =        41.4314 E_vdwl   =      -216.9664 
+E_coul   =      -969.4047 E_long   =     -3342.7729 Press    =       156.7851 
+---------------- Step      600 ----- CPU =     20.1970 (sec) ----------------
+TotEng   =     -2531.1096 KinEng   =       728.1698 Temp     =       274.1705 
+PotEng   =     -3259.2794 E_bond   =       232.8396 E_angle  =       621.3323 
+E_dihed  =       398.1952 E_impro  =        37.0914 E_vdwl   =      -241.6350 
+E_coul   =      -963.1540 E_long   =     -3343.9488 Press    =        58.6784 
+---------------- Step      700 ----- CPU =     23.4360 (sec) ----------------
+TotEng   =     -2499.9495 KinEng   =       742.1211 Temp     =       279.4234 
+PotEng   =     -3242.0705 E_bond   =       240.5622 E_angle  =       582.9270 
+E_dihed  =       396.6246 E_impro  =        36.6510 E_vdwl   =      -228.4925 
+E_coul   =      -926.8734 E_long   =     -3343.4695 Press    =       -60.7458 
+---------------- Step      800 ----- CPU =     26.6709 (sec) ----------------
+TotEng   =     -2426.0217 KinEng   =       760.1083 Temp     =       286.1959 
+PotEng   =     -3186.1300 E_bond   =       266.5863 E_angle  =       652.3401 
+E_dihed  =       380.7407 E_impro  =        34.6861 E_vdwl   =      -225.3729 
+E_coul   =      -953.2382 E_long   =     -3341.8721 Press    =       -57.9824 
+---------------- Step      900 ----- CPU =     29.8152 (sec) ----------------
+TotEng   =     -2419.4636 KinEng   =       780.8361 Temp     =       294.0004 
+PotEng   =     -3200.2996 E_bond   =       269.3237 E_angle  =       665.7171 
+E_dihed  =       408.3527 E_impro  =        43.7811 E_vdwl   =      -254.0696 
+E_coul   =     -1002.0694 E_long   =     -3331.3352 Press    =       -52.0169 
+---------------- Step     1000 ----- CPU =     32.8748 (sec) ----------------
+TotEng   =     -2398.7244 KinEng   =       811.9856 Temp     =       305.7288 
+PotEng   =     -3210.7099 E_bond   =       258.2207 E_angle  =       639.3671 
+E_dihed  =       379.3353 E_impro  =        41.7602 E_vdwl   =      -207.2654 
+E_coul   =      -983.9330 E_long   =     -3338.1948 Press    =        89.4870 
+Loop time of 32.8751 on 4 procs for 1000 steps with 892 atoms
+
+Performance: 21.025 ns/day, 1.141 hours/ns, 30.418 timesteps/s
+31.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 12.449     | 19.023     | 24.612     |  99.6 | 57.86
+Bond    | 1.4547     | 2.8768     | 3.9098     |  61.4 |  8.75
+Kspace  | 1.0537     | 1.0778     | 1.0992     |   2.1 |  3.28
+Neigh   | 0.67542    | 0.67994    | 0.68323    |   0.3 |  2.07
+Comm    | 1.8602     | 8.4515     | 16.516     | 182.9 | 25.71
+Output  | 0.000839   | 0.00147    | 0.003293   |   2.7 |  0.00
+Modify  | 0.56658    | 0.63186    | 0.69304    |   6.8 |  1.92
+Other   |            | 0.133      |            |       |  0.40
+
+Nlocal:    223 ave 339 max 136 min
+Histogram: 1 1 0 0 0 1 0 0 0 1
+Nghost:    590 ave 626 max 552 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+Neighs:    36488.2 ave 41965 max 29054 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+
+Total # of neighbors = 145953
+Ave neighs/atom = 163.624
+Ave special neighs/atom = 10.9395
+Neighbor list builds = 189
+Dangerous builds = 0
+
+unfix           cor
+unfix           1
+
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:36

examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.1

@@ -0,0 +1,147 @@
+LAMMPS (20 Jun 2017)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide, run for 8ps in NVT
+
+units           real
+atom_style      full
+
+pair_style      lj/charmm/coul/long 8.0 10.0 10.0
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+kspace_style    pppm 0.0001
+
+read_data       data.peptide
+  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  2004 atoms
+  reading velocities ...
+  2004 velocities
+  scanning bonds ...
+  3 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  14 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  1365 bonds
+  reading angles ...
+  786 angles
+  reading dihedrals ...
+  207 dihedrals
+  reading impropers ...
+  12 impropers
+  4 = max # of 1-2 neighbors
+  7 = max # of 1-3 neighbors
+  14 = max # of 1-4 neighbors
+  18 = max # of special neighbors
+
+neighbor        2.0 bin
+neigh_modify    delay 5
+
+thermo          50
+#dump            dump1 all atom 100 peptide.dump
+
+timestep        8
+
+run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
+Respa levels:
+  1 = bond angle
+  2 = dihedral improper pair
+  3 = kspace
+
+fix             1 all nvt temp 250.0 250.0 100.0 tchain 1
+fix             cor all filter/corotate m 1.0
+  19 = # of size 2 clusters
+  0 = # of size 3 clusters
+  3 = # of size 4 clusters
+  0 = # of size 5 clusters
+  646 = # of frozen angles
+run             1000
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.268725
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0228209
+  estimated relative force accuracy = 6.87243e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 10648 3375
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 22.72 | 22.72 | 22.72 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0     190.0857   -6442.7438    70.391457   -5237.4338    20361.984 
+      50    239.47667   -7205.1006    1092.7664   -4682.5237   -23733.122 
+     100    244.63086   -6788.0793    422.97204   -4904.5234    16458.011 
+     150    240.79042   -7267.0791    966.31411   -4863.1107   -13554.894 
+     200    254.77122   -6868.5713    591.00071   -4756.4431    10532.563 
+     250    241.87417   -7264.9349     856.9357   -4963.8743   -9043.4359 
+     300    251.37775      -6976.8    650.55612   -4825.3773    6986.2021 
+     350    250.81494   -7286.7011    880.11184   -4909.0829   -6392.4665 
+     400    247.55673   -7104.4036    701.89555   -4924.4551    4720.7811 
+     450    258.54988   -7215.3011    832.23692   -4839.3759   -3446.3859 
+     500    246.80928   -7151.2468    715.61007   -4962.0464    2637.5769 
+     550    246.20721   -7159.0464    805.24974   -4883.8011    -2725.227 
+     600    250.62483   -7201.7688    806.10076   -4899.2968    770.22352 
+     650    247.59777   -7260.1607    802.97277   -4978.8899   -430.42309 
+     700    246.86951   -7286.2971    825.99865   -4986.3486   -427.88651 
+     750    252.79268   -7307.8572     833.4822   -4965.0605   -614.74372 
+     800    251.73191   -7315.2457    839.59859    -4972.666    952.56448 
+     850    246.75844   -7303.6221    816.67112   -5013.6642   -2055.2823 
+     900    251.00123   -7317.4219    825.12165   -4993.6817   -356.53166 
+     950    259.20822   -7252.3466    854.62611   -4850.1016   -1719.5267 
+    1000    245.72486   -7347.5547    811.48146   -5068.9576    -717.6136 
+Loop time of 357.523 on 1 procs for 1000 steps with 2004 atoms
+
+Performance: 1.933 ns/day, 12.414 hours/ns, 2.797 timesteps/s
+32.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 328.2      | 328.2      | 328.2      |   0.0 | 91.80
+Bond    | 4.4815     | 4.4815     | 4.4815     |   0.0 |  1.25
+Kspace  | 3.9448     | 3.9448     | 3.9448     |   0.0 |  1.10
+Neigh   | 12.457     | 12.457     | 12.457     |   0.0 |  3.48
+Comm    | 3.2147     | 3.2147     | 3.2147     |   0.0 |  0.90
+Output  | 0.001689   | 0.001689   | 0.001689   |   0.0 |  0.00
+Modify  | 3.937      | 3.937      | 3.937      |   0.0 |  1.10
+Other   |            | 1.289      |            |       |  0.36
+
+Nlocal:    2004 ave 2004 max 2004 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    11191 ave 11191 max 11191 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    708610 ave 708610 max 708610 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 708610
+Ave neighs/atom = 353.598
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 200
+Dangerous builds = 200
+unfix           cor
+unfix           1
+
+
+
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:05:57

examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.4

@@ -0,0 +1,147 @@
+LAMMPS (20 Jun 2017)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide, run for 8ps in NVT
+
+units           real
+atom_style      full
+
+pair_style      lj/charmm/coul/long 8.0 10.0 10.0
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+kspace_style    pppm 0.0001
+
+read_data       data.peptide
+  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  2004 atoms
+  reading velocities ...
+  2004 velocities
+  scanning bonds ...
+  3 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  14 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  1365 bonds
+  reading angles ...
+  786 angles
+  reading dihedrals ...
+  207 dihedrals
+  reading impropers ...
+  12 impropers
+  4 = max # of 1-2 neighbors
+  7 = max # of 1-3 neighbors
+  14 = max # of 1-4 neighbors
+  18 = max # of special neighbors
+
+neighbor        2.0 bin
+neigh_modify    delay 5
+
+thermo          50
+#dump            dump1 all atom 100 peptide.dump
+
+timestep        8
+
+run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
+Respa levels:
+  1 = bond angle
+  2 = dihedral improper pair
+  3 = kspace
+
+fix             1 all nvt temp 250.0 250.0 100.0 tchain 1
+fix             cor all filter/corotate m 1.0
+  19 = # of size 2 clusters
+  0 = # of size 3 clusters
+  3 = # of size 4 clusters
+  0 = # of size 5 clusters
+  646 = # of frozen angles
+run             1000
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.268725
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0228209
+  estimated relative force accuracy = 6.87243e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 4312 960
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 16.87 | 17.05 | 17.26 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0     190.0857   -6442.7438    70.391457   -5237.4338    20361.984 
+      50    239.47667   -7205.1005    1092.7664   -4682.5237   -23733.122 
+     100    244.63889   -6788.1152    422.96733   -4904.5161    16457.756 
+     150    239.36917   -7258.7053    967.87775   -4861.6589   -13526.261 
+     200    255.14702   -6864.0525    604.58036   -4736.1009      11013.1 
+     250    252.72919   -7303.0966    898.11178   -4896.0494   -8480.8766 
+     300    250.66477   -6989.2603    652.83649   -4839.8141    6209.3375 
+     350    243.30794   -7218.8575    838.31977   -4927.8525   -5180.4928 
+     400     256.3573    -7090.677    706.24197   -4853.8377     3302.577 
+     450    246.15776    -7274.574    834.31676    -4970.557    -3427.971 
+     500    256.28473   -7082.1447    735.42828   -4816.5524     2846.086 
+     550    251.32327    -7341.739    812.64934   -5028.5484   -1786.9277 
+     600    254.57737   -7152.3448    740.52534   -4891.8494    825.91675 
+     650    244.95305   -7207.1136    790.67659   -4953.9295   -520.79769 
+     700     249.4984   -7204.2699    779.06969   -4935.5544   -940.75384 
+     750    248.46962   -7232.1037     791.6642   -4956.9361   -548.12171 
+     800     260.2974   -7293.1982    793.23282   -4945.8435     -1171.26 
+     850    249.79023   -7258.3759    823.56789   -4943.4198   -499.76275 
+     900    249.97237   -7267.0584    784.57992   -4990.0028   -271.33531 
+     950    251.29018   -7261.0642      823.467   -4937.2534    -538.7168 
+    1000    246.05777   -7285.0948    847.90892   -4968.0826   -2613.1854 
+Loop time of 94.6835 on 4 procs for 1000 steps with 2004 atoms
+
+Performance: 7.300 ns/day, 3.288 hours/ns, 10.562 timesteps/s
+37.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 33.389     | 78.508     | 94.639     | 294.1 | 82.92
+Bond    | 0.39957    | 1.104      | 1.4443     |  40.6 |  1.17
+Kspace  | 0.53324    | 1.2631     | 1.5137     |  37.5 |  1.33
+Neigh   | 1.2668     | 3.011      | 3.5942     |  58.0 |  3.18
+Comm    | 3.4563     | 8.8707     | 11.494     | 107.9 |  9.37
+Output  | 0.000435   | 0.0017425  | 0.004136   |   3.4 |  0.00
+Modify  | 0.59335    | 1.4123     | 1.6921     |  39.8 |  1.49
+Other   |            | 0.5129     |            |       |  0.54
+
+Nlocal:    501 ave 515 max 476 min
+Histogram: 1 0 0 0 0 0 0 1 1 1
+Nghost:    6681.5 ave 6740 max 6634 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Neighs:    176872 ave 182642 max 168464 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+
+Total # of neighbors = 707486
+Ave neighs/atom = 353.037
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 200
+Dangerous builds = 200
+unfix           cor
+unfix           1
+
+
+
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:01:53

examples/balance/in.balance.bond.fast

@@ -32,7 +32,7 @@ bond_coeff      1 10.0 1.2
 # need to preserve 1-3, 1-4 pairwise interactions during hard collisions
 
 special_bonds   lj/coul 0 1 1
-create_bonds    all all 1 1.0 1.5
+create_bonds    many all all 1 1.0 1.5
 
 neighbor	0.3 bin
 neigh_modify	delay 0 every 1 check yes

examples/balance/in.balance.bond.slow

@@ -32,7 +32,7 @@ pair_coeff	1 1 10.0 1.0 2.5
 bond_style      harmonic
 bond_coeff      1 10.0 1.2
 
-create_bonds    all all 1 1.0 1.5
+create_bonds    many all all 1 1.0 1.5
 
 neighbor	0.3 bin
 neigh_modify	delay 0 every 1 check yes

examples/meam/in.meamc

@@ -0,0 +1,30 @@
+# Test of MEAM potential for SiC system
+
+units		metal
+boundary	p p p
+
+atom_style	atomic
+
+read_data	data.meam
+
+pair_style	meam/c
+pair_coeff	* * library.meam Si C SiC.meam Si C
+
+neighbor	0.3 bin
+neigh_modify	delay 10
+
+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/meam/in.meamc.shear

@@ -0,0 +1,79 @@
+# 3d metal shear simulation
+
+units		metal
+boundary	s s p
+
+atom_style	atomic
+lattice		fcc 3.52
+region		box block 0 16.0 0 10.0 0 2.828427
+create_box	3 box
+
+lattice		fcc 3.52 orient	x 1 0 0 orient y 0 1 1 orient z 0 -1 1 &
+		origin 0.5 0 0 
+create_atoms	1 box
+
+pair_style	meam/c
+pair_coeff	* * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
+
+neighbor	0.3 bin
+neigh_modify	delay 5
+
+region		lower block INF INF INF 0.9 INF INF
+region		upper block INF INF 6.1 INF INF INF
+group		lower region lower
+group		upper region upper
+group		boundary union lower upper
+group		mobile subtract all boundary
+
+set		group lower type 2
+set		group upper type 3
+
+# void
+
+#region		void cylinder z 8 5 2.5 INF INF
+#delete_atoms	region void
+
+# temp controllers
+
+compute		new3d mobile temp
+compute		new2d mobile temp/partial 0 1 1
+
+# equilibrate
+
+velocity	mobile create 300.0 5812775 temp new3d
+fix		1 all nve
+fix		2 boundary setforce 0.0 0.0 0.0
+
+fix		3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify	3 temp new3d
+
+thermo		25
+thermo_modify	temp new3d
+
+timestep	0.001
+run		100
+
+# shear
+
+velocity	upper set 1.0 0 0
+velocity	mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
+
+unfix		3
+fix		3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify	3 temp new2d
+
+#dump		1 all atom 500 dump.meam.shear
+
+#dump		2 all image 100 image.*.jpg type type &
+#		axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
+#dump_modify	2 pad 4
+
+#dump		3 all movie 100 movie.mpg type type &
+#		axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
+#dump_modify	3 pad 4
+
+thermo		100
+thermo_modify	temp new2d
+
+reset_timestep	0
+run		3000

examples/meam/log.19May17.meam.g++.1

@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (19 May 2017)
+  using 1 OpenMP thread(s) per MPI task
 # Test of MEAM potential for SiC system
 
 units		metal
@@ -34,13 +35,23 @@ timestep	0.001
 
 run		100
 Neighbor list info ...
-  2 neighbor list requests
   update every 1 steps, delay 10 steps, check yes
   max neighbors/atom: 2000, page size: 100000
   master list distance cutoff = 4.3
   ghost atom cutoff = 4.3
-  binsize = 2.15 -> bins = 6 6 6
-Memory usage per processor = 7.39054 Mbytes
+  binsize = 2.15, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair meam, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair meam, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 8.103 | 8.103 | 8.103 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0            0   -636.38121            0   -636.38121   -76571.819 
       10    1807.8862   -666.21959            0   -636.54126   -150571.49 
@@ -53,20 +64,20 @@ Step Temp E_pair E_mol TotEng Press
       80    2126.0903   -671.43755            0   -636.53557   -97475.831 
       90     2065.755    -670.4349            0   -636.52338   -95858.837 
      100    2051.4553   -670.20799            0   -636.53122    -107068.9 
-Loop time of 0.094512 on 1 procs for 100 steps with 128 atoms
+Loop time of 0.0864418 on 1 procs for 100 steps with 128 atoms
 
-Performance: 91.417 ns/day, 0.263 hours/ns, 1058.067 timesteps/s
-99.4% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 99.952 ns/day, 0.240 hours/ns, 1156.848 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.091268   | 0.091268   | 0.091268   |   0.0 | 96.57
-Neigh   | 0.0021861  | 0.0021861  | 0.0021861  |   0.0 |  2.31
-Comm    | 0.00059438 | 0.00059438 | 0.00059438 |   0.0 |  0.63
-Output  | 9.0837e-05 | 9.0837e-05 | 9.0837e-05 |   0.0 |  0.10
-Modify  | 0.00024438 | 0.00024438 | 0.00024438 |   0.0 |  0.26
-Other   |            | 0.000128   |            |       |  0.14
+Pair    | 0.082592   | 0.082592   | 0.082592   |   0.0 | 95.55
+Neigh   | 0.0028124  | 0.0028124  | 0.0028124  |   0.0 |  3.25
+Comm    | 0.00049043 | 0.00049043 | 0.00049043 |   0.0 |  0.57
+Output  | 0.00014329 | 0.00014329 | 0.00014329 |   0.0 |  0.17
+Modify  | 0.00025415 | 0.00025415 | 0.00025415 |   0.0 |  0.29
+Other   |            | 0.0001497  |            |       |  0.17
 
 Nlocal:    128 ave 128 max 128 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

examples/meam/log.19May17.meam.g++.4

@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (19 May 2017)
+  using 1 OpenMP thread(s) per MPI task
 # Test of MEAM potential for SiC system
 
 units		metal
@@ -34,13 +35,23 @@ timestep	0.001
 
 run		100
 Neighbor list info ...
-  2 neighbor list requests
   update every 1 steps, delay 10 steps, check yes
   max neighbors/atom: 2000, page size: 100000
   master list distance cutoff = 4.3
   ghost atom cutoff = 4.3
-  binsize = 2.15 -> bins = 6 6 6
-Memory usage per processor = 7.319 Mbytes
+  binsize = 2.15, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair meam, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair meam, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 8.024 | 8.026 | 8.027 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0            0   -636.38121            0   -636.38121   -76571.819 
       10    1807.8862   -666.21959            0   -636.54126   -150571.49 
@@ -53,20 +64,20 @@ Step Temp E_pair E_mol TotEng Press
       80    2126.0903   -671.43755            0   -636.53557   -97475.831 
       90     2065.755    -670.4349            0   -636.52338   -95858.837 
      100    2051.4553   -670.20799            0   -636.53122    -107068.9 
-Loop time of 0.0350628 on 4 procs for 100 steps with 128 atoms
+Loop time of 0.0389078 on 4 procs for 100 steps with 128 atoms
 
-Performance: 246.415 ns/day, 0.097 hours/ns, 2852.026 timesteps/s
-98.4% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 222.063 ns/day, 0.108 hours/ns, 2570.177 timesteps/s
+99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.030952   | 0.031776   | 0.032203   |   0.3 | 90.63
-Neigh   | 0.00058937 | 0.00061423 | 0.00063896 |   0.1 |  1.75
-Comm    | 0.0018125  | 0.0022421  | 0.0030777  |   1.1 |  6.39
-Output  | 0.00018525 | 0.00019765 | 0.00021911 |   0.1 |  0.56
-Modify  | 8.0585e-05 | 9.0539e-05 | 9.7752e-05 |   0.1 |  0.26
-Other   |            | 0.0001422  |            |       |  0.41
+Pair    | 0.031958   | 0.033267   | 0.034691   |   0.6 | 85.50
+Neigh   | 0.00079155 | 0.00086409 | 0.00098801 |   0.0 |  2.22
+Comm    | 0.0025704  | 0.0041765  | 0.005573   |   1.9 | 10.73
+Output  | 0.0002749  | 0.00029588 | 0.00033569 |   0.0 |  0.76
+Modify  | 9.4891e-05 | 0.00010347 | 0.00011587 |   0.0 |  0.27
+Other   |            | 0.000201   |            |       |  0.52
 
 Nlocal:    32 ave 36 max 30 min
 Histogram: 1 2 0 0 0 0 0 0 0 1

examples/meam/log.19May17.meam.shear.g++.1

@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (19 May 2017)
+  using 1 OpenMP thread(s) per MPI task
 # 3d metal shear simulation
 
 units		metal
@@ -62,38 +63,48 @@ fix_modify	3 temp new3d
 
 thermo		25
 thermo_modify	temp new3d
-WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489)
 
 timestep	0.001
 run		100
 Neighbor list info ...
-  2 neighbor list requests
   update every 1 steps, delay 5 steps, check yes
   max neighbors/atom: 2000, page size: 100000
   master list distance cutoff = 4.3
   ghost atom cutoff = 4.3
-  binsize = 2.15 -> bins = 27 17 5
-Memory usage per processor = 8.55725 Mbytes
+  binsize = 2.15, bins = 27 17 5
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair meam, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair meam, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 9.788 | 9.788 | 9.788 Mbytes
 Step Temp E_pair E_mol TotEng Press Volume 
        0          300   -8232.7767            0   -8179.1466    1386.6643     19547.02 
       25    222.78953   -8188.1215            0   -8148.2941    9095.9008     19547.02 
       50          300   -8149.7654            0   -8096.1353    10633.141    19684.382 
       75    304.80657   -8163.4557            0   -8108.9665     7045.457    19759.745 
      100          300   -8173.6884            0   -8120.0584     5952.521    19886.589 
-Loop time of 1.72323 on 1 procs for 100 steps with 1912 atoms
+Loop time of 1.58103 on 1 procs for 100 steps with 1912 atoms
 
-Performance: 5.014 ns/day, 4.787 hours/ns, 58.031 timesteps/s
-99.8% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 5.465 ns/day, 4.392 hours/ns, 63.250 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 1.7026     | 1.7026     | 1.7026     |   0.0 | 98.80
-Neigh   | 0.014496   | 0.014496   | 0.014496   |   0.0 |  0.84
-Comm    | 0.0015783  | 0.0015783  | 0.0015783  |   0.0 |  0.09
-Output  | 6.0081e-05 | 6.0081e-05 | 6.0081e-05 |   0.0 |  0.00
-Modify  | 0.0034628  | 0.0034628  | 0.0034628  |   0.0 |  0.20
-Other   |            | 0.00101    |            |       |  0.06
+Pair    | 1.5561     | 1.5561     | 1.5561     |   0.0 | 98.42
+Neigh   | 0.018544   | 0.018544   | 0.018544   |   0.0 |  1.17
+Comm    | 0.0013864  | 0.0013864  | 0.0013864  |   0.0 |  0.09
+Output  | 0.00011396 | 0.00011396 | 0.00011396 |   0.0 |  0.01
+Modify  | 0.0038245  | 0.0038245  | 0.0038245  |   0.0 |  0.24
+Other   |            | 0.001096   |            |       |  0.07
 
 Nlocal:    1912 ave 1912 max 1912 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -128,11 +139,11 @@ fix_modify	3 temp new2d
 
 thermo		100
 thermo_modify	temp new2d
-WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489)
 
 reset_timestep	0
 run		3000
-Memory usage per processor = 8.73384 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 9.964 | 9.964 | 9.964 Mbytes
 Step Temp E_pair E_mol TotEng Press Volume 
        0    300.39988   -8173.6884            0   -8137.8874    4992.9811    19894.297 
      100    292.06374   -8177.7096            0   -8142.9021    2568.3762     19871.53 
@@ -144,53 +155,53 @@ Step Temp E_pair E_mol TotEng Press Volume
      700          300   -8148.1328            0   -8112.3794    3506.9234    20435.302 
      800          300   -8139.1821            0   -8103.4288    3628.3957    20509.519 
      900    305.03425   -8126.7734            0   -8090.4201    5316.2206    20638.992 
-    1000    304.00321   -8112.1616            0   -8075.9311    7441.9639    20767.243 
-    1100    304.14051   -8096.5041            0   -8060.2573     9646.698    20888.167 
-    1200    302.78461   -8080.5931            0   -8044.5079     11516.21    20995.917 
-    1300    308.67046   -8061.6724            0   -8024.8857    11496.487    21130.013 
-    1400    309.83019   -8046.2701            0   -8009.3452    12926.847    21247.271 
-    1500          300   -8035.0322            0   -7999.2789    15346.188    21370.637 
-    1600          300   -8030.6678            0   -7994.9144    14802.342    21496.446 
-    1700          300   -8024.5988            0   -7988.8454    13177.445    21611.262 
-    1800          300    -8023.045            0   -7987.2916    10240.041    21740.735 
-    1900          300   -8028.2797            0   -7992.5263    6912.1441    21866.544 
-    2000          300   -8036.4487            0   -8000.6953    3561.8365    21977.695 
-    2100          300   -8037.8249            0   -8002.0715    2879.2618    22109.611 
-    2200          300   -8033.6682            0   -7997.9148    4936.3695    22224.427 
-    2300    304.49349   -8033.4561            0   -7997.1673    5593.0915    22356.343 
-    2400          300   -8033.2969            0   -7997.5436    7537.0891    22473.601 
-    2500          300   -8033.1874            0   -7997.4341    11476.447    22598.189 
-    2600    307.77395   -8026.9234            0   -7990.2436     15758.81    22720.333 
-    2700          300   -8021.1736            0   -7985.4203    17948.896    22832.706 
-    2800          300   -8017.0863            0   -7981.3329    17154.618    22957.293 
-    2900          300   -8012.0514            0    -7976.298    13224.292    23089.209 
-    3000    304.58031   -8008.1654            0   -7971.8661    8572.9227    23211.354 
-Loop time of 55.136 on 1 procs for 3000 steps with 1912 atoms
+    1000    304.00321   -8112.1616            0   -8075.9311    7441.9638    20767.243 
+    1100    304.14047   -8096.5041            0   -8060.2573    9646.6976    20888.167 
+    1200    302.78457   -8080.5931            0   -8044.5079    11516.209    20995.917 
+    1300    308.67054   -8061.6724            0   -8024.8857    11496.479    21130.013 
+    1400     309.8301     -8046.27            0   -8009.3452    12926.835    21247.271 
+    1500          300   -8035.0321            0   -7999.2788    15346.455    21370.637 
+    1600          300   -8030.6657            0   -7994.9123    14802.869    21496.446 
+    1700          300   -8024.5251            0   -7988.7718    13176.923    21611.262 
+    1800          300   -8022.9963            0    -7987.243    10260.665    21741.956 
+    1900          300   -8028.0522            0   -7992.2988    6955.1367    21867.765 
+    2000          300   -8037.2708            0   -8001.5175    3520.3749    21987.467 
+    2100          300   -8035.9945            0   -8000.2412    3237.6121    22109.611 
+    2200          300   -8036.1882            0   -8000.4348    4295.1386    22223.205 
+    2300          300   -8032.7689            0   -7997.0155    6231.2346    22355.121 
+    2400          300   -8034.6621            0   -7998.9088    8585.3799    22468.716 
+    2500          300   -8031.7774            0   -7996.0241    11627.871    22587.196 
+    2600          300    -8024.032            0   -7988.2786     16254.69    22716.669 
+    2700    308.64215    -8017.407            0   -7980.6237    18440.226    22835.149 
+    2800          300   -8015.7348            0   -7979.9814    17601.716    22957.293 
+    2900    305.82558   -8013.7448            0   -7977.2972    14123.494    23089.209 
+    3000          300   -8011.0289            0   -7975.2755    9957.2884    23205.247 
+Loop time of 51.9315 on 1 procs for 3000 steps with 1912 atoms
 
-Performance: 4.701 ns/day, 5.105 hours/ns, 54.411 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 4.991 ns/day, 4.808 hours/ns, 57.768 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    | 54.317     | 54.317     | 54.317     |  -nan | 98.51
-Neigh   | 0.63189    | 0.63189    | 0.63189    |   0.0 |  1.15
-Comm    | 0.051245   | 0.051245   | 0.051245   |   0.0 |  0.09
-Output  | 0.0005548  | 0.0005548  | 0.0005548  |   0.0 |  0.00
-Modify  | 0.10452    | 0.10452    | 0.10452    |   0.0 |  0.19
-Other   |            | 0.03128    |            |       |  0.06
+Pair    | 50.918     | 50.918     | 50.918     |   0.0 | 98.05
+Neigh   | 0.81033    | 0.81033    | 0.81033    |   0.0 |  1.56
+Comm    | 0.047331   | 0.047331   | 0.047331   |   0.0 |  0.09
+Output  | 0.0011976  | 0.0011976  | 0.0011976  |   0.0 |  0.00
+Modify  | 0.11889    | 0.11889    | 0.11889    |   0.0 |  0.23
+Other   |            | 0.03606    |            |       |  0.07
 
 Nlocal:    1912 ave 1912 max 1912 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    1667 ave 1667 max 1667 min
+Nghost:    1672 ave 1672 max 1672 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    23365 ave 23365 max 23365 min
+Neighs:    23557 ave 23557 max 23557 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  46730 ave 46730 max 46730 min
+FullNghs:  47114 ave 47114 max 47114 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
-Total # of neighbors = 46730
-Ave neighs/atom = 24.4404
+Total # of neighbors = 47114
+Ave neighs/atom = 24.6412
 Neighbor list builds = 221
 Dangerous builds = 0
-Total wall time: 0:00:56
+Total wall time: 0:00:53

examples/meam/log.19May17.meam.shear.g++.4

@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (19 May 2017)
+  using 1 OpenMP thread(s) per MPI task
 # 3d metal shear simulation
 
 units		metal
@@ -62,38 +63,48 @@ fix_modify	3 temp new3d
 
 thermo		25
 thermo_modify	temp new3d
-WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489)
 
 timestep	0.001
 run		100
 Neighbor list info ...
-  2 neighbor list requests
   update every 1 steps, delay 5 steps, check yes
   max neighbors/atom: 2000, page size: 100000
   master list distance cutoff = 4.3
   ghost atom cutoff = 4.3
-  binsize = 2.15 -> bins = 27 17 5
-Memory usage per processor = 7.74146 Mbytes
+  binsize = 2.15, bins = 27 17 5
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair meam, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair meam, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 8.954 | 8.957 | 8.959 Mbytes
 Step Temp E_pair E_mol TotEng Press Volume 
        0          300   -8232.7767            0   -8179.1466    1386.6643     19547.02 
       25    221.59546   -8187.6813            0   -8148.0673    9100.4509     19547.02 
       50          300   -8150.0685            0   -8096.4384    10317.407    19685.743 
       75    307.76021   -8164.6669            0   -8109.6496    6289.7138    19757.814 
      100          300   -8176.5141            0    -8122.884    4162.2559    19873.327 
-Loop time of 0.469502 on 4 procs for 100 steps with 1912 atoms
+Loop time of 0.482293 on 4 procs for 100 steps with 1912 atoms
 
-Performance: 18.402 ns/day, 1.304 hours/ns, 212.992 timesteps/s
-99.7% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 17.914 ns/day, 1.340 hours/ns, 207.343 timesteps/s
+98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.44052    | 0.45213    | 0.45813    |   1.0 | 96.30
-Neigh   | 0.0036478  | 0.0037832  | 0.003854   |   0.1 |  0.81
-Comm    | 0.0055377  | 0.011533   | 0.02316    |   6.5 |  2.46
-Output  | 9.0837e-05 | 9.8228e-05 | 0.00011325 |   0.1 |  0.02
-Modify  | 0.00098062 | 0.0010158  | 0.0010564  |   0.1 |  0.22
-Other   |            | 0.0009408  |            |       |  0.20
+Pair    | 0.44374    | 0.45604    | 0.46922    |   1.4 | 94.56
+Neigh   | 0.0047338  | 0.0049097  | 0.0051899  |   0.2 |  1.02
+Comm    | 0.0054841  | 0.019044   | 0.031472   |   6.9 |  3.95
+Output  | 0.00012755 | 0.00013644 | 0.00015831 |   0.0 |  0.03
+Modify  | 0.0011139  | 0.0011852  | 0.0012643  |   0.2 |  0.25
+Other   |            | 0.0009753  |            |       |  0.20
 
 Nlocal:    478 ave 492 max 465 min
 Histogram: 2 0 0 0 0 0 0 0 1 1
@@ -128,11 +139,11 @@ fix_modify	3 temp new2d
 
 thermo		100
 thermo_modify	temp new2d
-WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489)
 
 reset_timestep	0
 run		3000
-Memory usage per processor = 7.78572 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 8.999 | 9.002 | 9.005 Mbytes
 Step Temp E_pair E_mol TotEng Press Volume 
        0    295.32113   -8176.5141            0   -8141.3183    3169.3113     19886.93 
      100    292.00251   -8176.5358            0   -8141.7356   -825.04802    19918.765 
@@ -144,53 +155,53 @@ Step Temp E_pair E_mol TotEng Press Volume
      700    296.44479   -8149.7914            0   -8114.4618    1985.4155    20421.046 
      800    307.75738   -8139.1649            0    -8102.487     4319.078    20513.183 
      900    304.61422   -8126.9246            0   -8090.6214    6654.0963    20640.213 
-    1000          300   -8113.8464            0   -8078.0931    7760.1242    20768.465 
-    1100    300.17874   -8097.7469            0   -8061.9722    8438.1263    20874.731 
-    1200    306.01444   -8083.3367            0   -8046.8665    10835.585    20994.432 
+    1000          300   -8113.8464            0   -8078.0931    7760.1239    20768.465 
+    1100    300.17873   -8097.7469            0   -8061.9722     8438.126    20874.731 
+    1200    306.01441   -8083.3367            0   -8046.8665    10835.586    20994.432 
     1300          300    -8067.022            0   -8031.2686    11216.067    21126.348 
-    1400          300    -8053.223            0   -8017.4697     10570.21    21253.378 
-    1500          300   -8043.4848            0   -8007.7314    11360.829    21375.523 
-    1600          300   -8034.6216            0   -7998.8683    11371.642    21498.889 
-    1700          300   -8028.6774            0    -7992.924    9595.8772    21613.705 
-    1800          300   -8033.0808            0   -7997.3274    8767.6261    21743.178 
-    1900    303.30302   -8035.1958            0   -7999.0488    8059.5152    21859.215 
-    2000          300   -8025.0857            0   -7989.3323    9308.9938    21980.138 
-    2100          300   -8041.5796            0   -8005.8263    6656.0066     22108.39 
-    2200          300   -8039.6315            0   -8003.8781    7532.9687     22226.87 
-    2300          300    -8053.203            0   -8017.4497    8466.9094    22356.343 
-    2400          300   -8050.9154            0    -8015.162    11784.136    22467.494 
-    2500          300   -8037.6394            0    -8001.886    16464.786    22588.417 
-    2600          300   -8030.9221            0   -7995.1688    16807.326    22719.112 
-    2700          300   -8025.2102            0   -7989.4569     13729.61    22837.592 
-    2800          300   -8014.5312            0   -7978.7779    6784.6283    22953.629 
-    2900          300   -8007.4768            0   -7971.7234    1362.3131    23084.324 
-    3000          300   -7994.5614            0    -7958.808   -1726.5273    23194.254 
-Loop time of 14.8108 on 4 procs for 3000 steps with 1912 atoms
+    1400          300    -8053.223            0   -8017.4697    10570.206    21253.378 
+    1500          300   -8043.4849            0   -8007.7315    11360.766    21375.523 
+    1600          300    -8034.621            0   -7998.8676    11371.584    21498.889 
+    1700          300   -8028.6783            0    -7992.925     9596.524    21613.705 
+    1800          300   -8033.0818            0   -7997.3285    8767.2651    21743.178 
+    1900    303.18912    -8035.194            0   -7999.0606    8059.9558    21859.215 
+    2000          300   -8025.0327            0   -7989.2794    9305.7521    21980.138 
+    2100          300   -8041.4626            0   -8005.7092    6623.8789     22108.39 
+    2200          300   -8040.3133            0   -8004.5599    7512.9368    22225.648 
+    2300          300   -8055.6567            0   -8019.9033     8281.354    22344.128 
+    2400    304.05922    -8050.289            0   -8014.0518    11964.826    22476.044 
+    2500    305.75646   -8037.0481            0   -8000.6087    16594.032    22595.746 
+    2600    307.71105   -8031.2253            0   -7994.5529    18381.745    22708.119 
+    2700      307.397   -8026.5338            0   -7989.8988    13944.653    22829.042 
+    2800     309.3455   -8020.2305            0   -7983.3634    7037.4046    22954.851 
+    2900     301.2859   -8010.4731            0   -7974.5665    3843.8972    23072.109 
+    3000    303.29908   -8000.0395            0   -7963.8929    364.90172     23207.69 
+Loop time of 14.5278 on 4 procs for 3000 steps with 1912 atoms
 
-Performance: 17.501 ns/day, 1.371 hours/ns, 202.555 timesteps/s
-99.8% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 17.842 ns/day, 1.345 hours/ns, 206.500 timesteps/s
+99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 14.05      | 14.237     | 14.332     |   2.9 | 96.12
-Neigh   | 0.1592     | 0.16414    | 0.1671     |   0.8 |  1.11
-Comm    | 0.26002    | 0.35589    | 0.54696    |  18.8 |  2.40
-Output  | 0.00061679 | 0.00065172 | 0.0007441  |   0.2 |  0.00
-Modify  | 0.02895    | 0.030174   | 0.03104    |   0.5 |  0.20
-Other   |            | 0.02338    |            |       |  0.16
+Pair    | 13.872     | 13.929     | 13.998     |   1.4 | 95.88
+Neigh   | 0.20891    | 0.21114    | 0.21272    |   0.3 |  1.45
+Comm    | 0.25364    | 0.32377    | 0.37706    |   8.9 |  2.23
+Output  | 0.0011427  | 0.0012097  | 0.0013931  |   0.3 |  0.01
+Modify  | 0.033687   | 0.033991   | 0.034694   |   0.2 |  0.23
+Other   |            | 0.02871    |            |       |  0.20
 
-Nlocal:    478 ave 509 max 448 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost:    799.25 ave 844 max 756 min
-Histogram: 1 1 0 0 0 0 0 1 0 1
-Neighs:    5813.25 ave 6081 max 5602 min
-Histogram: 2 0 0 0 0 0 1 0 0 1
-FullNghs:  11626.5 ave 12151 max 11205 min
-Histogram: 1 1 0 0 0 0 1 0 0 1
+Nlocal:    478 ave 509 max 445 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Nghost:    804 ave 845 max 759 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Neighs:    5827 ave 6177 max 5496 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+FullNghs:  11654 ave 12330 max 11039 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
 
-Total # of neighbors = 46506
-Ave neighs/atom = 24.3232
-Neighbor list builds = 225
+Total # of neighbors = 46616
+Ave neighs/atom = 24.3808
+Neighbor list builds = 223
 Dangerous builds = 0
 Total wall time: 0:00:15

examples/meam/log.19May17.meamc.g++.1

@@ -0,0 +1,95 @@
+LAMMPS (19 May 2017)
+  using 1 OpenMP thread(s) per MPI task
+# Test of MEAM potential for SiC system
+
+units		metal
+boundary	p p p
+
+atom_style	atomic
+
+read_data	data.meam
+  orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  128 atoms
+
+pair_style	meam/c
+pair_coeff	* * library.meam Si C SiC.meam Si C
+Reading potential file library.meam with DATE: 2012-06-29
+Reading potential file SiC.meam with DATE: 2007-06-11
+
+neighbor	0.3 bin
+neigh_modify	delay 10
+
+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
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.3
+  ghost atom cutoff = 4.3
+  binsize = 2.15, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair meam/c, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair meam/c, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 8.103 | 8.103 | 8.103 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -636.38121            0   -636.38121   -76571.819 
+      10    1807.8862   -666.21959            0   -636.54126   -150571.49 
+      20    1932.4467    -668.2581            0   -636.53498   -120223.52 
+      30    1951.3652   -668.58139            0   -636.54771    -100508.4 
+      40    2172.5974   -672.22715            0    -636.5617   -110753.34 
+      50    2056.9149   -670.33108            0   -636.56468   -105418.07 
+      60    1947.9564   -668.52788            0   -636.55015   -111413.04 
+      70    1994.7712   -669.28849            0   -636.54225   -109645.76 
+      80    2126.0903   -671.43755            0   -636.53557   -97475.832 
+      90    2065.7549    -670.4349            0   -636.52338   -95858.836 
+     100    2051.4553   -670.20799            0   -636.53122   -107068.89 
+Loop time of 0.0778153 on 1 procs for 100 steps with 128 atoms
+
+Performance: 111.032 ns/day, 0.216 hours/ns, 1285.094 timesteps/s
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.073801   | 0.073801   | 0.073801   |   0.0 | 94.84
+Neigh   | 0.0029731  | 0.0029731  | 0.0029731  |   0.0 |  3.82
+Comm    | 0.00047708 | 0.00047708 | 0.00047708 |   0.0 |  0.61
+Output  | 0.00015664 | 0.00015664 | 0.00015664 |   0.0 |  0.20
+Modify  | 0.00025702 | 0.00025702 | 0.00025702 |   0.0 |  0.33
+Other   |            | 0.0001504  |            |       |  0.19
+
+Nlocal:    128 ave 128 max 128 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    543 ave 543 max 543 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1526 ave 1526 max 1526 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  3052 ave 3052 max 3052 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3052
+Ave neighs/atom = 23.8438
+Neighbor list builds = 10
+Dangerous builds = 10
+Total wall time: 0:00:00

examples/meam/log.19May17.meamc.g++.4

@@ -0,0 +1,95 @@
+LAMMPS (19 May 2017)
+  using 1 OpenMP thread(s) per MPI task
+# Test of MEAM potential for SiC system
+
+units		metal
+boundary	p p p
+
+atom_style	atomic
+
+read_data	data.meam
+  orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  128 atoms
+
+pair_style	meam/c
+pair_coeff	* * library.meam Si C SiC.meam Si C
+Reading potential file library.meam with DATE: 2012-06-29
+Reading potential file SiC.meam with DATE: 2007-06-11
+
+neighbor	0.3 bin
+neigh_modify	delay 10
+
+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
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.3
+  ghost atom cutoff = 4.3
+  binsize = 2.15, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair meam/c, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair meam/c, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 8.024 | 8.026 | 8.027 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -636.38121            0   -636.38121   -76571.819 
+      10    1807.8862   -666.21959            0   -636.54126   -150571.49 
+      20    1932.4467    -668.2581            0   -636.53498   -120223.52 
+      30    1951.3652   -668.58139            0   -636.54771    -100508.4 
+      40    2172.5974   -672.22715            0    -636.5617   -110753.34 
+      50    2056.9149   -670.33108            0   -636.56468   -105418.07 
+      60    1947.9564   -668.52788            0   -636.55015   -111413.04 
+      70    1994.7712   -669.28849            0   -636.54225   -109645.76 
+      80    2126.0903   -671.43755            0   -636.53557   -97475.832 
+      90    2065.7549    -670.4349            0   -636.52338   -95858.836 
+     100    2051.4553   -670.20799            0   -636.53122   -107068.89 
+Loop time of 0.037066 on 4 procs for 100 steps with 128 atoms
+
+Performance: 233.097 ns/day, 0.103 hours/ns, 2697.887 timesteps/s
+97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.029985   | 0.031596   | 0.033021   |   0.8 | 85.24
+Neigh   | 0.0007906  | 0.00085384 | 0.00088596 |   0.0 |  2.30
+Comm    | 0.0025654  | 0.0040313  | 0.0057514  |   2.2 | 10.88
+Output  | 0.00027013 | 0.00029153 | 0.00033426 |   0.0 |  0.79
+Modify  | 9.5367e-05 | 0.00010639 | 0.00012016 |   0.0 |  0.29
+Other   |            | 0.0001866  |            |       |  0.50
+
+Nlocal:    32 ave 36 max 30 min
+Histogram: 1 2 0 0 0 0 0 0 0 1
+Nghost:    293.75 ave 305 max 285 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Neighs:    381.5 ave 413 max 334 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+FullNghs:  763 ave 866 max 678 min
+Histogram: 1 0 1 0 0 1 0 0 0 1
+
+Total # of neighbors = 3052
+Ave neighs/atom = 23.8438
+Neighbor list builds = 10
+Dangerous builds = 10
+Total wall time: 0:00:00

examples/meam/log.19May17.meamc.shear.g++.1

@@ -0,0 +1,207 @@
+LAMMPS (19 May 2017)
+  using 1 OpenMP thread(s) per MPI task
+# 3d metal shear simulation
+
+units		metal
+boundary	s s p
+
+atom_style	atomic
+lattice		fcc 3.52
+Lattice spacing in x,y,z = 3.52 3.52 3.52
+region		box block 0 16.0 0 10.0 0 2.828427
+create_box	3 box
+Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
+  1 by 1 by 1 MPI processor grid
+
+lattice		fcc 3.52 orient	x 1 0 0 orient y 0 1 1 orient z 0 -1 1 		origin 0.5 0 0
+Lattice spacing in x,y,z = 3.52 4.97803 4.97803
+create_atoms	1 box
+Created 1912 atoms
+
+pair_style	meam/c
+pair_coeff	* * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
+Reading potential file library.meam with DATE: 2012-06-29
+Reading potential file Ni.meam with DATE: 2007-06-11
+
+neighbor	0.3 bin
+neigh_modify	delay 5
+
+region		lower block INF INF INF 0.9 INF INF
+region		upper block INF INF 6.1 INF INF INF
+group		lower region lower
+264 atoms in group lower
+group		upper region upper
+264 atoms in group upper
+group		boundary union lower upper
+528 atoms in group boundary
+group		mobile subtract all boundary
+1384 atoms in group mobile
+
+set		group lower type 2
+  264 settings made for type
+set		group upper type 3
+  264 settings made for type
+
+# void
+
+#region		void cylinder z 8 5 2.5 INF INF
+#delete_atoms	region void
+
+# temp controllers
+
+compute		new3d mobile temp
+compute		new2d mobile temp/partial 0 1 1
+
+# equilibrate
+
+velocity	mobile create 300.0 5812775 temp new3d
+fix		1 all nve
+fix		2 boundary setforce 0.0 0.0 0.0
+
+fix		3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify	3 temp new3d
+
+thermo		25
+thermo_modify	temp new3d
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489)
+
+timestep	0.001
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.3
+  ghost atom cutoff = 4.3
+  binsize = 2.15, bins = 27 17 5
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair meam/c, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair meam/c, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 9.788 | 9.788 | 9.788 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume 
+       0          300   -8232.7767            0   -8179.1466    1386.6643     19547.02 
+      25    222.78953   -8188.1215            0   -8148.2941    9095.9003     19547.02 
+      50          300   -8149.7654            0   -8096.1353    10633.139    19684.382 
+      75    304.80657   -8163.4557            0   -8108.9665    7045.4555    19759.745 
+     100          300   -8173.6884            0   -8120.0584    5952.5197    19886.589 
+Loop time of 1.46986 on 1 procs for 100 steps with 1912 atoms
+
+Performance: 5.878 ns/day, 4.083 hours/ns, 68.034 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.445      | 1.445      | 1.445      |   0.0 | 98.31
+Neigh   | 0.018564   | 0.018564   | 0.018564   |   0.0 |  1.26
+Comm    | 0.0012956  | 0.0012956  | 0.0012956  |   0.0 |  0.09
+Output  | 0.00012612 | 0.00012612 | 0.00012612 |   0.0 |  0.01
+Modify  | 0.0038197  | 0.0038197  | 0.0038197  |   0.0 |  0.26
+Other   |            | 0.001095   |            |       |  0.07
+
+Nlocal:    1912 ave 1912 max 1912 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1672 ave 1672 max 1672 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    23806 ave 23806 max 23806 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  47612 ave 47612 max 47612 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 47612
+Ave neighs/atom = 24.9017
+Neighbor list builds = 5
+Dangerous builds = 0
+
+# shear
+
+velocity	upper set 1.0 0 0
+velocity	mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
+
+unfix		3
+fix		3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify	3 temp new2d
+
+#dump		1 all atom 500 dump.meam.shear
+
+#dump		2 all image 100 image.*.jpg type type #		axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
+#dump_modify	2 pad 4
+
+#dump		3 all movie 100 movie.mpg type type #		axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
+#dump_modify	3 pad 4
+
+thermo		100
+thermo_modify	temp new2d
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489)
+
+reset_timestep	0
+run		3000
+Per MPI rank memory allocation (min/avg/max) = 9.964 | 9.964 | 9.964 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume 
+       0    300.39988   -8173.6884            0   -8137.8874    4992.9799    19894.297 
+     100    292.06374   -8177.7096            0   -8142.9021    2568.3756     19871.53 
+     200    306.69894   -8177.1357            0    -8140.584    874.24118     20047.24 
+     300    295.68216   -8172.9213            0   -8137.6825   -1049.0799    20091.759 
+     400    308.99955   -8169.6355            0   -8132.8096   -1785.9554    20121.698 
+     500    303.85688   -8163.9842            0   -8127.7712   -150.60892    20183.813 
+     600          300   -8157.7627            0   -8122.0093    1492.8514    20279.887 
+     700          300   -8148.1314            0   -8112.3781    3507.1949    20435.297 
+     800          300   -8139.1805            0   -8103.4272    3628.5908    20509.519 
+     900    305.03217   -8126.7741            0    -8090.421    5313.7881    20638.992 
+    1000     303.7648   -8112.1574            0   -8075.9554    7433.3181    20767.243 
+    1100    302.39719   -8096.1399            0   -8060.1009    9681.7685    20888.167 
+    1200    304.04919   -8080.7022            0   -8044.4663    11621.974    21011.532 
+    1300    303.56395   -8062.0984            0   -8025.9203    11410.793    21125.127 
+    1400    309.92338   -8046.0008            0   -8009.0648    12408.158     21246.05 
+    1500          300   -8034.7094            0    -7998.956    14845.312    21363.308 
+    1600          300   -8028.4585            0   -7992.7051    15120.908    21489.117 
+    1700    308.23904   -8015.9618            0   -7979.2265     14714.73    21612.483 
+    1800          300   -8013.5458            0   -7977.7924    11955.065     21737.07 
+    1900          300   -8012.2984            0    -7976.545    6667.1353    21854.329 
+    2000          300   -8025.6019            0   -7989.8485    2006.6545    21981.359 
+    2100          300   -8027.6823            0   -7991.9289     16.47633    22109.611 
+    2200          300   -8029.6905            0   -7993.9372   -603.98293    22224.427 
+    2300          300   -8033.2663            0    -7997.513   -464.68645    22351.457 
+    2400          300   -8040.6863            0   -8004.9329   -640.54641    22467.494 
+    2500          300   -8037.0332            0   -8001.2799    1504.2444    22587.196 
+    2600          300   -8036.0909            0   -8000.3375    4190.2052    22708.119 
+    2700    308.97892   -8028.5269            0   -7991.7035    5755.7418    22832.706 
+    2800    305.27189   -8023.8286            0   -7987.4469    2611.7551    22962.179 
+    2900    301.94251   -8017.4523            0   -7981.4675    358.11928    23078.216 
+    3000    305.67682    -8009.853            0   -7973.4231    -2345.487    23197.918 
+Loop time of 48.351 on 1 procs for 3000 steps with 1912 atoms
+
+Performance: 5.361 ns/day, 4.477 hours/ns, 62.046 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    | 47.356     | 47.356     | 47.356     |   0.0 | 97.94
+Neigh   | 0.79977    | 0.79977    | 0.79977    |   0.0 |  1.65
+Comm    | 0.043133   | 0.043133   | 0.043133   |   0.0 |  0.09
+Output  | 0.0011899  | 0.0011899  | 0.0011899  |   0.0 |  0.00
+Modify  | 0.11648    | 0.11648    | 0.11648    |   0.0 |  0.24
+Other   |            | 0.03404    |            |       |  0.07
+
+Nlocal:    1912 ave 1912 max 1912 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1662 ave 1662 max 1662 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    23143 ave 23143 max 23143 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  46286 ave 46286 max 46286 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 46286
+Ave neighs/atom = 24.2082
+Neighbor list builds = 220
+Dangerous builds = 0
+Total wall time: 0:00:49

examples/meam/log.19May17.meamc.shear.g++.4

@@ -0,0 +1,207 @@
+LAMMPS (19 May 2017)
+  using 1 OpenMP thread(s) per MPI task
+# 3d metal shear simulation
+
+units		metal
+boundary	s s p
+
+atom_style	atomic
+lattice		fcc 3.52
+Lattice spacing in x,y,z = 3.52 3.52 3.52
+region		box block 0 16.0 0 10.0 0 2.828427
+create_box	3 box
+Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
+  2 by 2 by 1 MPI processor grid
+
+lattice		fcc 3.52 orient	x 1 0 0 orient y 0 1 1 orient z 0 -1 1 		origin 0.5 0 0
+Lattice spacing in x,y,z = 3.52 4.97803 4.97803
+create_atoms	1 box
+Created 1912 atoms
+
+pair_style	meam/c
+pair_coeff	* * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
+Reading potential file library.meam with DATE: 2012-06-29
+Reading potential file Ni.meam with DATE: 2007-06-11
+
+neighbor	0.3 bin
+neigh_modify	delay 5
+
+region		lower block INF INF INF 0.9 INF INF
+region		upper block INF INF 6.1 INF INF INF
+group		lower region lower
+264 atoms in group lower
+group		upper region upper
+264 atoms in group upper
+group		boundary union lower upper
+528 atoms in group boundary
+group		mobile subtract all boundary
+1384 atoms in group mobile
+
+set		group lower type 2
+  264 settings made for type
+set		group upper type 3
+  264 settings made for type
+
+# void
+
+#region		void cylinder z 8 5 2.5 INF INF
+#delete_atoms	region void
+
+# temp controllers
+
+compute		new3d mobile temp
+compute		new2d mobile temp/partial 0 1 1
+
+# equilibrate
+
+velocity	mobile create 300.0 5812775 temp new3d
+fix		1 all nve
+fix		2 boundary setforce 0.0 0.0 0.0
+
+fix		3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify	3 temp new3d
+
+thermo		25
+thermo_modify	temp new3d
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489)
+
+timestep	0.001
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.3
+  ghost atom cutoff = 4.3
+  binsize = 2.15, bins = 27 17 5
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair meam/c, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair meam/c, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 8.954 | 8.957 | 8.959 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume 
+       0          300   -8232.7767            0   -8179.1466    1386.6643     19547.02 
+      25    221.59546   -8187.6813            0   -8148.0673    9100.4505     19547.02 
+      50          300   -8150.0685            0   -8096.4384    10317.406    19685.743 
+      75    307.76021   -8164.6669            0   -8109.6496    6289.7123    19757.814 
+     100          300   -8176.5141            0    -8122.884    4162.2548    19873.327 
+Loop time of 0.435874 on 4 procs for 100 steps with 1912 atoms
+
+Performance: 19.822 ns/day, 1.211 hours/ns, 229.424 timesteps/s
+98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.4092     | 0.41563    | 0.42184    |   0.7 | 95.35
+Neigh   | 0.0048575  | 0.004932   | 0.0049984  |   0.1 |  1.13
+Comm    | 0.0069079  | 0.013151   | 0.019513   |   4.2 |  3.02
+Output  | 0.00012398 | 0.00013405 | 0.00015688 |   0.0 |  0.03
+Modify  | 0.0011275  | 0.0011509  | 0.0011735  |   0.1 |  0.26
+Other   |            | 0.0008795  |            |       |  0.20
+
+Nlocal:    478 ave 492 max 465 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost:    809 ave 822 max 795 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Neighs:    5916 ave 6133 max 5658 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+FullNghs:  11832 ave 12277 max 11299 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+
+Total # of neighbors = 47328
+Ave neighs/atom = 24.7531
+Neighbor list builds = 5
+Dangerous builds = 0
+
+# shear
+
+velocity	upper set 1.0 0 0
+velocity	mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
+
+unfix		3
+fix		3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
+fix_modify	3 temp new2d
+
+#dump		1 all atom 500 dump.meam.shear
+
+#dump		2 all image 100 image.*.jpg type type #		axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
+#dump_modify	2 pad 4
+
+#dump		3 all movie 100 movie.mpg type type #		axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
+#dump_modify	3 pad 4
+
+thermo		100
+thermo_modify	temp new2d
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489)
+
+reset_timestep	0
+run		3000
+Per MPI rank memory allocation (min/avg/max) = 8.999 | 9.002 | 9.005 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume 
+       0    295.32113   -8176.5141            0   -8141.3183    3169.3102     19886.93 
+     100     292.0025   -8176.5358            0   -8141.7356   -825.04852    19918.765 
+     200    306.11682   -8176.7718            0   -8140.2895   -1370.6881    19948.878 
+     300          300   -8172.6262            0   -8136.8729   -1735.9794    20085.715 
+     400    306.88504   -8168.4351            0   -8131.8612   -933.05532    20117.008 
+     500    308.99111   -8166.2909            0    -8129.466   -1049.3442    20198.267 
+     600    304.22555   -8158.0946            0   -8121.8377    583.69142    20328.753 
+     700    296.41606   -8149.7777            0   -8114.4515    1986.7982    20421.032 
+     800    307.88628   -8139.1709            0   -8102.4776    4311.4142    20513.183 
+     900    303.37209   -8126.9382            0   -8090.7829    6712.7316    20640.213 
+    1000          300   -8113.7973            0    -8078.044    7630.2594    20750.143 
+    1100    300.07815   -8098.1383            0   -8062.3756    8423.7063    20879.616 
+    1200          300   -8083.3163            0    -8047.563    10772.917    21000.539 
+    1300          300   -8066.6741            0   -8030.9208    10834.336    21128.791 
+    1400          300   -8050.8799            0   -8015.1265    10842.382    21257.043 
+    1500          300   -8040.3206            0   -8004.5673    11852.589    21362.087 
+    1600          300   -8033.2471            0   -7997.4937    11298.745    21492.782 
+    1700          300   -8030.6375            0   -7994.8842     10850.43     21610.04 
+    1800          300   -8035.1631            0   -7999.4097    9985.6107    21734.628 
+    1900    308.56562   -8040.1954            0   -8003.4213    9865.7107    21859.215 
+    2000          300   -8030.1651            0   -7994.4117    11817.502    21980.138 
+    2100          300   -8031.6147            0   -7995.8613    12791.357    22101.061 
+    2200          300   -8033.7793            0   -7998.0259    13823.043    22234.198 
+    2300          300   -8040.5964            0   -8004.8431    16204.549    22350.236 
+    2400    309.42867   -8045.9414            0   -8009.0644    18506.386    22465.051 
+    2500          300   -8054.2629            0   -8018.5095    20099.612    22593.303 
+    2600          300   -8054.9562            0   -8019.2028    20036.318    22721.555 
+    2700          300   -8051.4788            0   -8015.7254    16993.437    22844.921 
+    2800          300   -8050.6908            0   -8014.9374    9048.5896    22964.622 
+    2900    309.90783   -8044.3096            0   -8007.3754    5017.0198    23080.659 
+    3000          300   -8035.8165            0   -8000.0632    2084.8999     23207.69 
+Loop time of 13.4901 on 4 procs for 3000 steps with 1912 atoms
+
+Performance: 19.214 ns/day, 1.249 hours/ns, 222.386 timesteps/s
+99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 12.851     | 12.919     | 12.945     |   1.1 | 95.76
+Neigh   | 0.20449    | 0.20777    | 0.21169    |   0.6 |  1.54
+Comm    | 0.27479    | 0.30264    | 0.36667    |   6.8 |  2.24
+Output  | 0.0010171  | 0.0010971  | 0.0012388  |   0.3 |  0.01
+Modify  | 0.033248   | 0.033878   | 0.034567   |   0.3 |  0.25
+Other   |            | 0.02594    |            |       |  0.19
+
+Nlocal:    478 ave 506 max 450 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    790.5 ave 822 max 751 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+Neighs:    5829.5 ave 6014 max 5672 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+FullNghs:  11659 ave 12027 max 11320 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 46636
+Ave neighs/atom = 24.3912
+Neighbor list builds = 220
+Dangerous builds = 0
+Total wall time: 0:00:13

src/.gitignore

@@ -31,6 +31,11 @@
 /fix_*manifold*.cpp
 /fix_*manifold*.h
 
+/meam*.h
+/meam*.cpp
+/pair_meamc.cpp
+/pair_meamc.h
+
 /fix_qeq*.cpp
 /fix_qeq*.h
 

src/CORESHELL/compute_temp_cs.h

@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    http://lammps.sandia.gov, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov

src/CORESHELL/pair_born_coul_long_cs.h

@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    http://lammps.sandia.gov, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov

src/CORESHELL/pair_buck_coul_long_cs.h

@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    http://lammps.sandia.gov, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov

src/GPU/pair_lj_cubic_gpu.h

@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    http://lammps.sandia.gov, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov

src/GPU/pair_tersoff_gpu.h

@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    http://lammps.sandia.gov, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov

src/GPU/pair_tersoff_mod_gpu.h

@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    http://lammps.sandia.gov, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov

src/GPU/pair_tersoff_zbl_gpu.h

@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    http://lammps.sandia.gov, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov

src/GPU/pair_zbl_gpu.h

@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    http://lammps.sandia.gov, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov

src/KOKKOS/fix_qeq_reax_kokkos.cpp

@@ -218,8 +218,6 @@ void FixQEqReaxKokkos<DeviceType>::pre_force(int vflag)
   d_ilist = k_list->d_ilist;
   inum = list->inum;
 
-  k_list->clean_copy();
-  //cleanup_copy();
   copymode = 1;
 
   int teamsize = TEAMSIZE;

src/KOKKOS/neigh_list_kokkos.cpp

@@ -22,21 +22,14 @@ enum{NSQ,BIN,MULTI};
 /* ---------------------------------------------------------------------- */
 
 template<class Device>
-void NeighListKokkos<Device>::clean_copy()
+NeighListKokkos<Device>::NeighListKokkos(class LAMMPS *lmp):NeighList(lmp)
 {
-  ilist = NULL;
-  numneigh = NULL;
-  firstneigh = NULL;
-  firstdouble = NULL;
-  dnum = 0;
-  iskip = NULL;
-  ijskip = NULL;
-
-  ipage = NULL;
-  dpage = NULL;
-
+  _stride = 1;
+  maxneighs = 16;
+  kokkos = 1;
   maxatoms = 0;
-}
+  execution_space = ExecutionSpaceFromDevice<Device>::space;
+};
 
 /* ---------------------------------------------------------------------- */
 

src/KOKKOS/neigh_list_kokkos.h

@@ -68,18 +68,13 @@ class NeighListKokkos: public NeighList {
 public:
   int maxneighs;
 
-  void clean_copy();
   void grow(int nmax);
   typename ArrayTypes<Device>::t_neighbors_2d d_neighbors;
   typename DAT::tdual_int_1d k_ilist;   // local indices of I atoms
   typename ArrayTypes<Device>::t_int_1d d_ilist;
   typename ArrayTypes<Device>::t_int_1d d_numneigh; // # of J neighs for each I
 
-  NeighListKokkos(class LAMMPS *lmp):
-  NeighList(lmp) {_stride = 1; maxneighs = 16; kokkos = 1; maxatoms = 0;
-                  execution_space = ExecutionSpaceFromDevice<Device>::space;
-  };
-  ~NeighListKokkos() {numneigh = NULL; ilist = NULL;};
+  NeighListKokkos(class LAMMPS *lmp);
 
   KOKKOS_INLINE_FUNCTION
   AtomNeighbors get_neighbors(const int &i) const {

src/KOKKOS/npair_kokkos.h

@@ -265,7 +265,7 @@ class NeighborKokkosExecute
     h_new_maxneighs() = neigh_list.maxneighs;
   };
 
-  ~NeighborKokkosExecute() {neigh_list.clean_copy();};
+  ~NeighborKokkosExecute() {neigh_list.copymode = 1;};
 
   template<int HalfNeigh, int Newton, int Tri>
   KOKKOS_FUNCTION

src/KOKKOS/pair_buck_kokkos.h

@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    http://lammps.sandia.gov, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov

src/KOKKOS/pair_coul_dsf_kokkos.cpp

@@ -120,9 +120,6 @@ void PairCoulDSFKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
 
   int inum = list->inum;
 
-  // Call cleanup_copy which sets allocations NULL which are destructed by the PairStyle
-
-  k_list->clean_copy();
   copymode = 1;
 
   // loop over neighbors of my atoms

src/KOKKOS/pair_coul_wolf_kokkos.cpp

@@ -121,9 +121,6 @@ void PairCoulWolfKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
 
   int inum = list->inum;
 
-  // Call cleanup_copy which sets allocations NULL which are destructed by the PairStyle
-
-  k_list->clean_copy();
   copymode = 1;
 
   // loop over neighbors of my atoms

src/KOKKOS/pair_eam_alloy_kokkos.cpp

@@ -122,9 +122,6 @@ void PairEAMAlloyKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
   d_ilist = k_list->d_ilist;
   int inum = list->inum;
 
-  // Call cleanup_copy which sets allocations NULL which are destructed by the PairStyle
-
-  k_list->clean_copy();
   copymode = 1;
 
   // zero out density

src/KOKKOS/pair_eam_fs_kokkos.cpp

@@ -122,9 +122,6 @@ void PairEAMFSKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
   d_ilist = k_list->d_ilist;
   int inum = list->inum;
 
-  // Call cleanup_copy which sets allocations NULL which are destructed by the PairStyle
-
-  k_list->clean_copy();
   copymode = 1;
 
   // zero out density