git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@16053 f3b2605a-c512-4ea7-a41b-209d697bcdaa

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@16051 f3b2605a-c512-4ea7-a41b-209d697bcdaa

.github/CODEOWNERS

@@ -1,21 +0,0 @@
-# This file contains file patterns that triggers automatic
-# code review requests from users that are owners of these files
-# Order matters, the last match has the highest precedence
-
-# library folders
-lib/colvars/*         @giacomofiorin
-lib/compress/*        @akohlmey
-lib/kokkos/*          @stanmoore1
-lib/molfile/*         @akohlmey
-lib/qmmm/*            @akohlmey
-lib/vtk/*             @rbberger
-
-# packages
-src/KOKKOS            @stanmoore1
-src/USER-CGSDK        @akohlmey
-src/USER-COLVARS      @giacomofiorin
-src/USER-OMP          @akohlmey
-src/USER-QMMM         @akohlmey
-
-# tools
-tools/msi2lmp/*       @akohlmey

.github/CONTRIBUTING.md

@@ -1,112 +0,0 @@
-# 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

@@ -1,31 +0,0 @@
-## 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

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

.gitignore

@@ -1,42 +0,0 @@
-*~
-*.o
-*.so
-*.cu_o
-*.ptx
-*_ptx.h
-*.a
-*.d
-*.x
-*.exe
-*.dll
-*.pyc
-__pycache__
-
-Obj_*
-log.lammps
-log.cite
-*.bz2
-*.gz
-*.tar
-.*.swp
-*.orig
-*.rej
-.vagrant
-\#*#
-.#*
-
-.DS_Store
-.DS_Store?
-._*
-.Spotlight-V100
-.Trashes
-ehthumbs.db
-Thumbs.db
-
-#cmake
-/build*
-/CMakeCache.txt
-/CMakeFiles/
-/Makefile
-/cmake_install.cmake
-/lmp

LICENSE

@@ -3,7 +3,7 @@ GNU GENERAL PUBLIC LICENSE
 Version 2, June 1991 
 
 Copyright (C) 1989, 1991 Free Software Foundation, Inc.  
-51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+59 Temple Place - Suite 330, Boston, MA  02111-1307, USA
 
 Everyone is permitted to copy and distribute verbatim copies of this
 license document, but changing it is not allowed.

bench/FERMI/README

@@ -1,21 +1,55 @@
 These are input scripts used to run versions of several of the
-benchmarks in the top-level bench directory using the GPU accelerator
-package.  The results of running these scripts on two different machines
-(a desktop with 2 Tesla GPUs and the ORNL Titan supercomputer) are shown
-on the "GPU (Fermi)" section of the Benchmark page of the LAMMPS WWW
-site: lammps.sandia.gov/bench.
+benchmarks in the top-level bench directory using the GPU and
+USER-CUDA accelerator packages.  The results of running these scripts
+on two different machines (a desktop with 2 Tesla GPUs and the ORNL
+Titan supercomputer) are shown on the "GPU (Fermi)" section of the
+Benchmark page of the LAMMPS WWW site: lammps.sandia.gov/bench.
 
 Examples are shown below of how to run these scripts.  This assumes
-you have built 3 executables with the GPU package
+you have built 3 executables with both the GPU and USER-CUDA packages
 installed, e.g.
 
 lmp_linux_single
 lmp_linux_mixed
 lmp_linux_double
 
+The precision (single, mixed, double) refers to the GPU and USER-CUDA
+pacakge precision.  See the README files in the lib/gpu and lib/cuda
+directories for instructions on how to build the packages with
+different precisions.  The GPU and USER-CUDA sub-sections of the
+doc/Section_accelerate.html file also describes this process.
+
+Make.py -d ~/lammps -j 16 -p #all orig -m linux -o cpu -a exe
+Make.py -d ~/lammps -j 16 -p #all opt orig -m linux -o opt -a exe
+Make.py -d ~/lammps -j 16 -p #all omp orig -m linux -o omp -a exe
+Make.py -d ~/lammps -j 16 -p #all gpu orig -m linux \
+        -gpu mode=double arch=20 -o gpu_double -a libs exe
+Make.py -d ~/lammps -j 16 -p #all gpu orig -m linux \
+        -gpu mode=mixed arch=20 -o gpu_mixed -a libs exe
+Make.py -d ~/lammps -j 16 -p #all gpu orig -m linux \
+        -gpu mode=single arch=20 -o gpu_single -a libs exe
+Make.py -d ~/lammps -j 16 -p #all cuda orig -m linux \
+        -cuda mode=double arch=20 -o cuda_double -a libs exe
+Make.py -d ~/lammps -j 16 -p #all cuda orig -m linux \
+        -cuda mode=mixed arch=20 -o cuda_mixed -a libs exe
+Make.py -d ~/lammps -j 16 -p #all cuda orig -m linux \
+        -cuda mode=single arch=20 -o cuda_single -a libs exe
+Make.py -d ~/lammps -j 16 -p #all intel orig -m linux -o intel_cpu -a exe
+Make.py -d ~/lammps -j 16 -p #all kokkos orig -m linux -o kokkos_omp -a exe
+Make.py -d ~/lammps -j 16 -p #all kokkos orig -kokkos cuda arch=20 \
+        -m cuda -o kokkos_cuda -a exe
+
+Make.py -d ~/lammps -j 16 -p #all opt omp gpu cuda intel kokkos orig \
+        -gpu mode=double arch=20 -cuda mode=double arch=20 -m linux \
+        -o all -a libs exe
+
+Make.py -d ~/lammps -j 16 -p #all opt omp gpu cuda intel kokkos orig \
+        -kokkos cuda arch=20 -gpu mode=double arch=20 \
+        -cuda mode=double arch=20 -m cuda -o all_cuda -a libs exe
+
 ------------------------------------------------------------------------
 
-To run on just CPUs (without using the GPU styles),
+To run on just CPUs (without using the GPU or USER-CUDA styles),
 do something like the following:
 
 mpirun -np 1 lmp_linux_double -v x 8 -v y 8 -v z 8 -v t 100 < in.lj
@@ -47,5 +81,23 @@ node via a "-ppn" setting.
 
 ------------------------------------------------------------------------
 
+To run with the USER-CUDA package, do something like the following:
+
+mpirun -np 1 lmp_linux_single -c on -sf cuda -v x 16 -v y 16 -v z 16 -v t 100 < in.lj
+mpirun -np 2 lmp_linux_double -c on -sf cuda -pk cuda 2 -v x 32 -v y 64 -v z 64 -v t 100 < in.eam
+
+The "xyz" settings determine the problem size.  The "t" setting
+determines the number of timesteps.  The "np" setting determines how
+many MPI tasks (per node) the problem will run on.  The numeric
+argument to the "-pk" setting is the number of GPUs (per node); 1 GPU
+is the default.  Note that the number of MPI tasks must equal the
+number of GPUs (both per node) with the USER-CUDA package.
+
+These mpirun commands run on a single node.  To run on multiple nodes,
+scale up the "-np" setting, and control the number of MPI tasks per
+node via a "-ppn" setting.
+
+------------------------------------------------------------------------
+
 If the script has "titan" in its name, it was run on the Titan
 supercomputer at ORNL.

bench/README

@@ -71,33 +71,49 @@ integration
 
 ----------------------------------------------------------------------
 
+Here is a src/Make.py command which will perform a parallel build of a
+LAMMPS executable "lmp_mpi" with all the packages needed by all the
+examples.  This assumes you have an MPI installed on your machine so
+that "mpicxx" can be used as the wrapper compiler.  It also assumes
+you have an Intel compiler to use as the base compiler.  You can leave
+off the "-cc mpi wrap=icc" switch if that is not the case.  You can
+also leave off the "-fft fftw3" switch if you do not have the FFTW
+(v3) installed as an FFT package, in which case the default KISS FFT
+library will be used.
+
+cd src
+Make.py -j 16 -p none molecule manybody kspace granular rigid orig \
+  -cc mpi wrap=icc -fft fftw3 -a file mpi
+
+----------------------------------------------------------------------
+
 Here is how to run each problem, assuming the LAMMPS executable is
 named lmp_mpi, and you are using the mpirun command to launch parallel
 runs:
 
 Serial (one processor runs):
 
-lmp_mpi -in in.lj
-lmp_mpi -in in.chain
-lmp_mpi -in in.eam
-lmp_mpi -in in.chute
-lmp_mpi -in in.rhodo
+lmp_mpi < in.lj
+lmp_mpi < in.chain
+lmp_mpi < in.eam
+lmp_mpi < in.chute
+lmp_mpi < in.rhodo
 
 Parallel fixed-size runs (on 8 procs in this case):
 
-mpirun -np 8 lmp_mpi -in in.lj
-mpirun -np 8 lmp_mpi -in in.chain
-mpirun -np 8 lmp_mpi -in in.eam
-mpirun -np 8 lmp_mpi -in in.chute
-mpirun -np 8 lmp_mpi -in in.rhodo
+mpirun -np 8 lmp_mpi < in.lj
+mpirun -np 8 lmp_mpi < in.chain
+mpirun -np 8 lmp_mpi < in.eam
+mpirun -np 8 lmp_mpi < in.chute
+mpirun -np 8 lmp_mpi < in.rhodo
 
 Parallel scaled-size runs (on 16 procs in this case):
 
-mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 -in in.lj
-mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 -in in.chain.scaled
-mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 -in in.eam
-mpirun -np 16 lmp_mpi -var x 4 -var y 4 -in in.chute.scaled
-mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 -in in.rhodo.scaled
+mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 < in.lj
+mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 < in.chain.scaled
+mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 < in.eam
+mpirun -np 16 lmp_mpi -var x 4 -var y 4 < in.chute.scaled
+mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 < in.rhodo.scaled
 
 For each of the scaled-size runs you must set 3 variables as -var
 command line switches.  The variables x,y,z are used in the input

cmake/CMakeLists.txt

@@ -1,717 +0,0 @@
-########################################
-# CMake build system
-# This file is part of LAMMPS
-# Created by Christoph Junghans and Richard Berger
-cmake_minimum_required(VERSION 3.1)
-
-project(lammps)
-set(SOVERSION 0)
-set(LAMMPS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../src)
-set(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib)
-set(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib)
-
-#To not conflict with old Makefile build system, we build everything here
-file(GLOB LIB_SOURCES ${LAMMPS_SOURCE_DIR}/*.cpp)
-file(GLOB LMP_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
-list(REMOVE_ITEM LIB_SOURCES ${LMP_SOURCES})
-
-# Cmake modules/macros are in a subdirectory to keep this file cleaner
-set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules)
-
-if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
-  #release comes with -O3 by default
-  set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
-endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
-
-# remove any style headers in the src dir
-file(GLOB SRC_STYLE_FILES ${LAMMPS_SOURCE_DIR}/style_*.h)
-if(SRC_STYLE_FILES)
-  file(REMOVE ${SRC_STYLE_FILES})
-endif()
-
-enable_language(CXX)
-
-######################################################################
-# compiler tests
-# these need ot be done early (before further tests).
-#####################################################################
-include(CheckCCompilerFlag)
-
-########################################################################
-# User input options                                                   #
-########################################################################
-option(BUILD_SHARED_LIBS "Build shared libs" OFF)
-if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
-  set(CMAKE_POSITION_INDEPENDENT_CODE ON)
-endif()
-include(GNUInstallDirs)
-
-set(LAMMPS_LINK_LIBS)
-set(LAMMPS_DEPS)
-set(LAMMPS_API_DEFINES)
-option(ENABLE_MPI "Build MPI version" OFF)
-if(ENABLE_MPI)
-  find_package(MPI REQUIRED)
-  include_directories(${MPI_C_INCLUDE_PATH})
-  list(APPEND LAMMPS_LINK_LIBS ${MPI_CXX_LIBRARIES})
-  option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
-  if(LAMMPS_LONGLONG_TO_LONG)
-    add_definitions(-DLAMMPS_LONGLONG_TO_LONG)
-  endif()
-else()
-  file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
-  add_library(mpi_stubs STATIC ${MPI_SOURCES})
-  include_directories(${LAMMPS_SOURCE_DIR}/STUBS)
-  list(APPEND LAMMPS_LINK_LIBS mpi_stubs)
-endif()
-
-set(LAMMPS_SIZE_LIMIT "LAMMPS_SMALLBIG" CACHE STRING "Lammps size limit")
-set_property(CACHE LAMMPS_SIZE_LIMIT PROPERTY STRINGS LAMMPS_SMALLBIG LAMMPS_BIGBIG LAMMPS_SMALLSMALL)
-add_definitions(-D${LAMMPS_SIZE_LIMIT})
-set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${LAMMPS_SIZE_LIMIT}")
-
-set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS")
-add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
-
-option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)
-if(LAMMPS_EXCEPTIONS)
-  add_definitions(-DLAMMPS_EXCEPTIONS)
-  set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES -DLAMMPS_EXCEPTIONS")
-endif()
-
-set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary and liblammps (WON'T enable any features automatically")
-mark_as_advanced(LAMMPS_MACHINE)
-if(LAMMPS_MACHINE)
-  set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}")
-endif()
-
-option(CMAKE_VERBOSE_MAKEFILE "Verbose makefile" OFF)
-
-option(ENABLE_TESTING "Enable testing" OFF)
-if(ENABLE_TESTING)
-  enable_testing()
-endif(ENABLE_TESTING)
-
-option(ENABLE_ALL "Build all default packages" OFF)
-set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR
-  KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ
-  REAX REPLICA RIGID SHOCK SNAP SRD)
-set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE
-  USER-ATC USER-AWPMD USER-CGDNA USER-MESO
-  USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
-  USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
-  USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
-  USER-SMTBQ USER-SPH USER-TALLY USER-VTK USER-QUIP USER-QMMM)
-set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
-foreach(PKG ${DEFAULT_PACKAGES})
-  option(ENABLE_${PKG} "Build ${PKG} Package" ${ENABLE_ALL})
-endforeach()
-foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
-  option(ENABLE_${PKG} "Build ${PKG} Package" OFF)
-endforeach()
-
-macro(pkg_depends PKG1 PKG2)
-  if(ENABLE_${PKG1} AND NOT ENABLE_${PKG2})
-    message(FATAL_ERROR "${PKG1} package needs LAMMPS to be build with ${PKG2}")
-  endif()
-endmacro()
-
-pkg_depends(MPIIO MPI)
-pkg_depends(QEQ MANYBODY)
-pkg_depends(USER-ATC MANYBODY)
-pkg_depends(USER-H5MD MPI)
-pkg_depends(USER-LB MPI)
-pkg_depends(USER-MISC MANYBODY)
-pkg_depends(USER-PHONON KSPACE)
-
-if(ENABLE_BODY AND ENABLE_POEMS)
-  message(FATAL_ERROR "BODY and POEMS cannot be enabled at the same time")
-endif()
-
-######################################################
-# packages with special compiler needs or external libs
-######################################################
-if(ENABLE_REAX OR ENABLE_MEAM OR ENABLE_USER-QUIP OR ENABLE_USER-QMMM OR ENABLE_LATTE)
-  enable_language(Fortran)
-  include(CheckFortranCompilerFlag)
-  check_Fortran_compiler_flag("-fno-second-underscore" FC_HAS_NO_SECOND_UNDERSCORE)
-endif()
-
-if(ENABLE_KOKKOS OR ENABLE_MSCG)
-  # starting with CMake 3.1 this is all you have to do to enforce C++11
-  set(CMAKE_CXX_STANDARD 11) # C++11...
-  set(CMAKE_CXX_STANDARD_REQUIRED ON) #...is required...
-  set(CMAKE_CXX_EXTENSIONS OFF) #...without compiler extensions like gnu++11
-endif()
-
-if(ENABLE_USER-OMP OR ENABLE_KOKKOS OR ENABLE_USER-INTEL)
-  find_package(OpenMP REQUIRED)
-  set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
-  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
-endif()
-
-if(ENABLE_KSPACE)
-  set(FFT "KISSFFT" CACHE STRING "FFT library for KSPACE package")
-  set_property(CACHE FFT PROPERTY STRINGS KISSFFT FFTW3 MKL FFTW2)
-  if(NOT FFT STREQUAL "KISSFFT")
-    find_package(${FFT} REQUIRED)
-    add_definitions(-DFFT_${FFT})
-    include_directories(${${FFT}_INCLUDE_DIRS})
-    list(APPEND LAMMPS_LINK_LIBS ${${FFT}_LIBRARIES})
-  endif()
-  set(PACK_OPTIMIZATION "PACK_ARRAY" CACHE STRING "Optimization for FFT")
-  set_property(CACHE PACK_OPTIMIZATION PROPERTY STRINGS PACK_ARRAY PACK_POINTER PACK_MEMCPY)
-  if(NOT PACK_OPTIMIZATION STREQUAL "PACK_ARRAY")
-    add_definitions(-D${PACK_OPTIMIZATION})
-  endif()
-endif()
-
-if(ENABLE_MISC)
-  option(LAMMPS_XDR "include XDR compatibility files for doing particle dumps in XTC format" OFF)
-  if(LAMMPS_XDR)
-    add_definitions(-DLAMMPS_XDR) # for liblammps
-  endif()
-endif()
-
-if(ENABLE_MSCG OR ENABLE_USER-ATC OR ENABLE_USER-AWPMD OR ENABLE_USER-QUIP OR ENABLE_LATTE)
-  find_package(LAPACK)
-  if(NOT LAPACK_FOUND)
-    enable_language(Fortran)
-    file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.f)
-    add_library(linalg STATIC ${LAPACK_SOURCES})
-    include(CheckFortranCompilerFlag)
-    check_Fortran_compiler_flag("-fno-second-underscore" FC_HAS_NO_SECOND_UNDERSCORE)
-    if(FC_HAS_NO_SECOND_UNDERSCORE)
-      target_compile_options(linalg PRIVATE -fno-second-underscore)
-    endif()
-    set(LAPACK_LIBRARIES linalg)
-  endif()
-endif()
-
-if(ENABLE_PYTHON)
-  find_package(PythonInterp REQUIRED)
-  find_package(PythonLibs REQUIRED)
-  add_definitions(-DLMP_PYTHON)
-  include_directories(${PYTHON_INCLUDE_DIR})
-  list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY})
-  if(NOT PYTHON_INSTDIR)
-    execute_process(COMMAND ${PYTHON_EXECUTABLE}
-	  -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
-      OUTPUT_VARIABLE PYTHON_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
-  endif()
-  install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})
-  if(NOT BUILD_SHARED_LIBS)
-    message(FATAL_ERROR "Python package need lammps to be build shared, use -DBUILD_SHARED_LIBS=ON")
-  endif()
-endif()
-
-find_package(JPEG)
-if(JPEG_FOUND)
-  add_definitions(-DLAMMPS_JPEG)
-  include_directories(${JPEG_INCLUDE_DIR})
-  list(APPEND LAMMPS_LINK_LIBS ${JPEG_LIBRARIES})
-endif()
-
-find_package(PNG)
-find_package(ZLIB)
-if(PNG_FOUND AND ZLIB_FOUND)
-  include_directories(${PNG_INCLUDE_DIRS} ${ZLIB_INCLUDE_DIRS})
-  list(APPEND LAMMPS_LINK_LIBS ${PNG_LIBRARIES} ${ZLIB_LIBRARIES})
-  add_definitions(-DLAMMPS_PNG)
-endif()
-
-find_program(GZIP_EXECUTABLE gzip)
-find_package_handle_standard_args(GZIP REQUIRED_VARS GZIP_EXECUTABLE)
-if(GZIP_FOUND)
-  add_definitions(-DLAMMPS_GZIP)
-endif()
-
-find_program(FFMPEG_EXECUTABLE ffmpeg)
-find_package_handle_standard_args(FFMPEG REQUIRED_VARS FFMPEG_EXECUTABLE)
-if(FFMPEG_FOUND)
-  add_definitions(-DLAMMPS_FFMPEG)
-endif()
-
-if(ENABLE_VORONOI)
-  find_package(VORO REQUIRED) #some distros
-  include_directories(${VORO_INCLUDE_DIRS})
-  list(APPEND LAMMPS_LINK_LIBS ${VORO_LIBRARIES})
-endif()
-
-if(ENABLE_LATTE)
-  find_package(LATTE QUIET)
-  if(NOT LATTE_FOUND)
-    message(STATUS "LATTE not found - we will build our own")
-    include(ExternalProject)
-    ExternalProject_Add(latte_build
-      URL https://github.com/lanl/LATTE/archive/v1.0.1.tar.gz
-      URL_MD5 5137e28cb1a64444bd571c98c98a6eee
-      SOURCE_SUBDIR cmake
-      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE}
-      )
-    ExternalProject_get_property(latte_build INSTALL_DIR)
-    set(LATTE_LIBRARIES ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/liblatte.a)
-    list(APPEND LAMMPS_DEPS latte_build)
-  endif()
-  list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
-endif()
-
-if(ENABLE_USER-MOLFILE)
-  add_library(molfile INTERFACE)
-  target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile)
-  target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
-  list(APPEND LAMMPS_LINK_LIBS molfile)
-endif()
-
-if(ENABLE_USER-NETCDF)
-  find_package(NetCDF REQUIRED)
-  include_directories(NETCDF_INCLUDE_DIR)
-  list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARY})
-  add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
-endif()
-
-if(ENABLE_USER-SMD)
-  find_package(Eigen3 REQUIRED)
-  include_directories(${EIGEN3_INCLUDE_DIR})
-endif()
-
-if(ENABLE_USER-QUIP)
-  find_package(QUIP REQUIRED)
-  list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
-endif()
-
-if(ENABLE_USER-QMMM)
-  find_package(QE REQUIRED)
-  include_directories(${QE_INCLUDE_DIRS})
-  list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
-endif()
-
-if(ENABLE_USER-VTK)
-  find_package(VTK REQUIRED NO_MODULE)
-  include(${VTK_USE_FILE})
-  add_definitions(-DLAMMPS_VTK)
-  list(APPEND LAMMPS_LINK_LIBS ${VTK_LIBRARIES})
-endif()
-
-if(ENABLE_KIM)
-  find_package(KIM REQUIRED)
-  list(APPEND LAMMPS_LINK_LIBS ${KIM_LIBRARIES})
-  include_directories(${KIM_INCLUDE_DIRS})
-endif()
-
-if(ENABLE_MSCG)
-  find_package(GSL REQUIRED)
-  set(LAMMPS_LIB_MSCG_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/mscg)
-  set(MSCG_TARBALL ${LAMMPS_LIB_MSCG_BIN_DIR}/MS-CG-master.zip)
-  set(LAMMPS_LIB_MSCG_BIN_DIR ${LAMMPS_LIB_MSCG_BIN_DIR}/MSCG-release-master/src)
-  if(NOT EXISTS ${LAMMPS_LIB_MSCG_BIN_DIR})
-    if(NOT EXISTS ${MSCG_TARBALL})
-      message(STATUS "Downloading ${MSCG_TARBALL}")
-      file(DOWNLOAD
-        https://github.com/uchicago-voth/MSCG-release/archive/master.zip
-        ${MSCG_TARBALL} SHOW_PROGRESS) #EXPECTED_MD5 cannot be due due to master
-    endif()
-    message(STATUS "Unpacking ${MSCG_TARBALL}")
-    execute_process(COMMAND ${CMAKE_COMMAND} -E tar xvf ${MSCG_TARBALL}
-      WORKING_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/mscg)
-  endif()
-  file(GLOB MSCG_SOURCES ${LAMMPS_LIB_MSCG_BIN_DIR}/*.cpp)
-  add_library(mscg STATIC ${MSCG_SOURCES})
-  list(APPEND LAMMPS_LINK_LIBS mscg)
-  target_compile_options(mscg PRIVATE -DDIMENSION=3 -D_exclude_gromacs=1)
-  target_include_directories(mscg PUBLIC ${LAMMPS_LIB_MSCG_BIN_DIR})
-  target_link_libraries(mscg ${GSL_LIBRARIES} ${LAPACK_LIBRARIES})
-endif()
-
-########################################################################
-# Basic system tests (standard libraries, headers, functions, types)   #
-########################################################################
-include(CheckIncludeFile)
-foreach(HEADER math.h)
-  check_include_file(${HEADER} FOUND_${HEADER})
-  if(NOT FOUND_${HEADER})
-    message(FATAL_ERROR "Could not find needed header - ${HEADER}")
-  endif(NOT FOUND_${HEADER})
-endforeach(HEADER)
-
-set(MATH_LIBRARIES "m" CACHE STRING "math library")
-mark_as_advanced( MATH_LIBRARIES )
-include(CheckLibraryExists)
-foreach(FUNC sin cos)
-  check_library_exists(${MATH_LIBRARIES} ${FUNC} "" FOUND_${FUNC}_${MATH_LIBRARIES})
-  if(NOT FOUND_${FUNC}_${MATH_LIBRARIES})
-    message(FATAL_ERROR "Could not find needed math function - ${FUNC}")
-  endif(NOT FOUND_${FUNC}_${MATH_LIBRARIES})
-endforeach(FUNC)
-list(APPEND LAMMPS_LINK_LIBS ${MATH_LIBRARIES})
-
-######################################
-# Generate Basic Style files
-######################################
-include(StyleHeaderUtils)
-RegisterStyles(${LAMMPS_SOURCE_DIR})
-
-##############################################
-# add sources of enabled packages
-############################################
-foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES})
-  set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
-
-  # ignore PKG files which were manually installed in src folder
-  # headers are ignored during RegisterStyles
-  file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp)
-  file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/*.h)
-
-  foreach(PKG_FILE in ${${PKG}_SOURCES})
-      get_filename_component(FNAME ${PKG_FILE} NAME)
-      list(REMOVE_ITEM LIB_SOURCES ${LAMMPS_SOURCE_DIR}/${FNAME})
-  endforeach()
-
-  foreach(PKG_FILE in ${${PKG}_HEADERS})
-      get_filename_component(FNAME ${PKG_FILE} NAME)
-      DetectAndRemovePackageHeader(${LAMMPS_SOURCE_DIR}/${FNAME})
-  endforeach()
-
-  if(ENABLE_${PKG})
-    # detects styles in package and adds them to global list
-    RegisterStyles(${${PKG}_SOURCES_DIR})
-
-    list(APPEND LIB_SOURCES ${${PKG}_SOURCES})
-    include_directories(${${PKG}_SOURCES_DIR})
-  endif()
-endforeach()
-
-##############################################
-# add lib sources of (simple) enabled packages
-############################################
-foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
-  USER-QMMM)
-  if(ENABLE_${SIMPLE_LIB})
-    string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
-    string(TOLOWER "${PKG_LIB}" PKG_LIB)
-    file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.F
-      ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.c ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.cpp)
-    add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
-    list(APPEND LAMMPS_LINK_LIBS ${PKG_LIB})
-    if(PKG_LIB STREQUAL awpmd)
-      target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include)
-    elseif(PKG_LIB STREQUAL h5md)
-      target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include)
-    else()
-      target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB})
-    endif()
-  endif()
-endforeach()
-
-if(ENABLE_USER-AWPMD)
-  target_link_libraries(awpmd ${LAPACK_LIBRARIES})
-endif()
-
-if(ENABLE_USER-ATC)
-  target_link_libraries(atc ${LAPACK_LIBRARIES})
-endif()
-
-if(ENABLE_USER-H5MD)
-  find_package(HDF5 REQUIRED)
-  target_link_libraries(h5md ${HDF5_LIBRARIES})
-  target_include_directories(h5md PRIVATE ${HDF5_INCLUDE_DIRS})
-endif()
-
-if(ENABLE_MEAM AND FC_HAS_NO_SECOND_UNDERSCORE)
-  foreach(FSRC ${meam_SOURCES})
-    string(REGEX REPLACE "^.*\\." "" FEXT "${FSRC}")
-    list(FIND CMAKE_Fortran_SOURCE_FILE_EXTENSIONS "${FEXT}" FINDEX)
-    if(FINDEX GREATER -1)
-      set_property(SOURCE ${FSRC} APPEND PROPERTY COMPILE_FLAGS "-fno-second-underscore")
-    endif()
-  endforeach()
-endif()
-
-if(ENABLE_REAX AND FC_HAS_NO_SECOND_UNDERSCORE)
-  target_compile_options(reax PRIVATE -fno-second-underscore)
-endif()
-
-
-######################################################################
-# packages which selectively include variants based on enabled styles
-# e.g. accelerator packages
-######################################################################
-if(ENABLE_USER-OMP)
-    set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP)
-    set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
-                         ${USER-OMP_SOURCES_DIR}/thr_omp.cpp
-                         ${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp
-                         ${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp)
-    set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}")
-
-    # detects styles which have USER-OMP version
-    RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
-
-    get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
-
-    list(APPEND LIB_SOURCES ${USER-OMP_SOURCES})
-    include_directories(${USER-OMP_SOURCES_DIR})
-endif()
-
-if(ENABLE_KOKKOS)
-  set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
-  set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
-  add_definitions(-DLMP_KOKKOS)
-  add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
-
-  set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
-                          ${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
-                          ${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src
-                          ${LAMMPS_LIB_KOKKOS_BIN_DIR})
-  include_directories(${Kokkos_INCLUDE_DIRS})
-  list(APPEND LAMMPS_LINK_LIBS kokkos)
-
-  set(KOKKOS_PKG_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/KOKKOS)
-  set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/atom_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/neighbor_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/neigh_list_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/neigh_bond_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/fix_nh_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
-  set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
-
-  # detects styles which have KOKKOS version
-  RegisterStylesExt(${KOKKOS_PKG_SOURCES_DIR} kokkos KOKKOS_PKG_SOURCES)
-
-  get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
-
-  list(APPEND LIB_SOURCES ${KOKKOS_PKG_SOURCES})
-  include_directories(${KOKKOS_PKG_SOURCES_DIR})
-endif()
-
-if(ENABLE_OPT)
-    set(OPT_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/OPT)
-    set(OPT_SOURCES)
-    set_property(GLOBAL PROPERTY "OPT_SOURCES" "${OPT_SOURCES}")
-
-    # detects styles which have OPT version
-    RegisterStylesExt(${OPT_SOURCES_DIR} opt OPT_SOURCES)
-
-    get_property(OPT_SOURCES GLOBAL PROPERTY OPT_SOURCES)
-
-    list(APPEND LIB_SOURCES ${OPT_SOURCES})
-    include_directories(${OPT_SOURCES_DIR})
-endif()
-
-if(ENABLE_USER-INTEL)
-    set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
-    set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/intel_preprocess.h
-                           ${USER-INTEL_SOURCES_DIR}/intel_buffers.h
-                           ${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp
-                           ${USER-INTEL_SOURCES_DIR}/math_extra_intel.h
-                           ${USER-INTEL_SOURCES_DIR}/nbin_intel.h
-                           ${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp
-                           ${USER-INTEL_SOURCES_DIR}/npair_intel.h
-                           ${USER-INTEL_SOURCES_DIR}/npair_intel.cpp
-                           ${USER-INTEL_SOURCES_DIR}/intel_simd.h
-                           ${USER-INTEL_SOURCES_DIR}/intel_intrinsics.h)
-
-    set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")
-
-    # detects styles which have USER-INTEL version
-    RegisterStylesExt(${USER-INTEL_SOURCES_DIR} opt USER-INTEL_SOURCES)
-
-    get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES)
-
-    list(APPEND LIB_SOURCES ${USER-INTEL_SOURCES})
-    include_directories(${USER-INTEL_SOURCES_DIR})
-endif()
-
-if(ENABLE_GPU)
-    set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
-    set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
-                    ${GPU_SOURCES_DIR}/fix_gpu.h
-                    ${GPU_SOURCES_DIR}/fix_gpu.cpp)
-
-    set(GPU_API "OpenCL" CACHE STRING "API used by GPU package")
-    set_property(CACHE GPU_API PROPERTY STRINGS OpenCL CUDA)
-
-    set(GPU_PREC "SINGLE_DOUBLE" CACHE STRING "LAMMPS GPU precision size")
-    set_property(CACHE GPU_PREC PROPERTY STRINGS SINGLE_DOUBLE SINGLE_SINGLE DOUBLE_DOUBLE)
-
-    file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cpp)
-    file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
-
-    if(GPU_API STREQUAL "CUDA")
-      find_package(CUDA REQUIRED)
-      find_program(BIN2C bin2c)
-      if(NOT BIN2C)
-        message(FATAL_ERROR "Couldn't find bin2c, use -DBIN2C helping cmake to find it.")
-      endif()
-      option(CUDPP_OPT "Enable CUDPP_OPT" ON)
-
-      set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM architecture")
-      set_property(CACHE GPU_ARCH PROPERTY STRINGS sm_10 sm_20 sm_30 sm_60)
-
-      file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/*.cu)
-      list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
-
-      cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
-
-      if(CUDPP_OPT)
-        cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
-        file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cpp)
-        file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cu)
-      endif()
-
-      cuda_compile_cubin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
-                   -DUNIX -O3 -Xptxas -v --use_fast_math -DNV_KERNEL -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC})
-
-      cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS $<$<BOOL:${BUILD_SHARED_LIBS}>:-Xcompiler=-fPIC>
-                   -DUNIX -O3 -Xptxas -v --use_fast_math -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC})
-
-      foreach(CU_OBJ ${GPU_GEN_OBJS})
-        get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
-        string(REGEX REPLACE "^.*_lal_" "" CU_NAME "${CU_NAME}")
-        add_custom_command(OUTPUT ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
-          COMMAND ${BIN2C} -c -n ${CU_NAME} ${CU_OBJ} > ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
-          DEPENDS ${CU_OBJ}
-          COMMENT "Generating ${CU_NAME}_cubin.h")
-        list(APPEND GPU_LIB_SOURCES ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h)
-      endforeach()
-      set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "${LAMMPS_LIB_BINARY_DIR}/gpu/*_cubin.h")
-
-
-      add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
-      target_link_libraries(gpu ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
-      target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
-      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC} -DMPI_GERYON -DUCL_NO_EXIT)
-      if(CUDPP_OPT)
-        target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
-        target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
-      endif()
-
-      list(APPEND LAMMPS_LINK_LIBS gpu)
-
-      add_executable(nvc_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
-      target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR)
-      target_link_libraries(nvc_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
-      target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
-
-
-    elseif(GPU_API STREQUAL "OpenCL")
-      find_package(OpenCL REQUIRED)
-      set(OCL_TUNE "GENERIC" CACHE STRING "OpenCL Device Tuning")
-      set_property(CACHE OCL_TUNE PROPERTY STRINGS INTEL FERMI KEPLER CYPRESS GENERIC)
-
-      include(OpenCLUtils)
-      set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
-
-      file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu)
-      list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu)
-
-      foreach(GPU_KERNEL ${GPU_LIB_CU})
-          get_filename_component(basename ${GPU_KERNEL} NAME_WE)
-          string(SUBSTRING ${basename} 4 -1 KERNEL_NAME)
-          GenerateOpenCLHeader(${KERNEL_NAME} ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h ${OCL_COMMON_HEADERS} ${GPU_KERNEL})
-          list(APPEND GPU_LIB_SOURCES ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h)
-      endforeach()
-
-      GenerateOpenCLHeader(gayberne ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu)
-      GenerateOpenCLHeader(gayberne_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu)
-      list(APPEND GPU_LIB_SOURCES ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h)
-
-      add_library(gpu STATIC ${GPU_LIB_SOURCES})
-      target_link_libraries(gpu ${OpenCL_LIBRARIES})
-      target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu ${OpenCL_INCLUDE_DIRS})
-      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC} -DMPI_GERYON -DUCL_NO_EXIT)
-      target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
-
-      list(APPEND LAMMPS_LINK_LIBS gpu)
-
-      add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
-      target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL)
-      target_link_libraries(ocl_get_devices PRIVATE ${OpenCL_LIBRARIES})
-      target_include_directories(ocl_get_devices PRIVATE ${OpenCL_INCLUDE_DIRS})
-    endif()
-
-    # GPU package
-    FindStyleHeaders(${GPU_SOURCES_DIR} FIX_CLASS fix_ FIX)
-
-    set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
-
-    # detects styles which have GPU version
-    RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)
-
-    get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
-
-    list(APPEND LIB_SOURCES ${GPU_SOURCES})
-    include_directories(${GPU_SOURCES_DIR})
-endif()
-
-######################################################
-# Generate style headers based on global list of
-# styles registered during package selection
-######################################################
-set(LAMMPS_STYLE_HEADERS_DIR ${CMAKE_CURRENT_BINARY_DIR}/styles)
-
-GenerateStyleHeaders(${LAMMPS_STYLE_HEADERS_DIR})
-
-include_directories(${LAMMPS_SOURCE_DIR})
-include_directories(${LAMMPS_STYLE_HEADERS_DIR})
-
-###########################################
-# Actually add executable and lib to build
-############################################
-add_library(lammps ${LIB_SOURCES})
-target_link_libraries(lammps ${LAMMPS_LINK_LIBS})
-add_dependencies(lammps ${LAMMPS_DEPS})
-set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
-if(BUILD_SHARED_LIBS)
-  set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
-  install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-  install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
-  configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
-  install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
-endif()
-
-add_executable(lmp ${LMP_SOURCES})
-target_link_libraries(lmp lammps)
-set_target_properties(lmp PROPERTIES OUTPUT_NAME lmp${LAMMPS_MACHINE})
-install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
-if(ENABLE_TESTING)
-  add_test(ShowHelp lmp${LAMMPS_MACHINE} -help)
-endif()
-
-##################################
-# Print package summary
-##################################
-foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES} ${ACCEL_PACKAGES})
-  if(ENABLE_${PKG})
-    message(STATUS "Building package: ${PKG}")
-  endif()
-endforeach()
-
-string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
-message(STATUS "<<< Build configuration >>>
-   Build type       ${CMAKE_BUILD_TYPE}
-   Install path     ${CMAKE_INSTALL_PREFIX}
-   Compilers and Flags:
-   C++ Compiler     ${CMAKE_CXX_COMPILER}
-       Type         ${CMAKE_CXX_COMPILER_ID}
-   C++ Flags        ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
-get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
-if(LANGUAGES MATCHES ".*Fortran.*")
-  message(STATUS "Fortran Compiler ${CMAKE_Fortran_COMPILER} 
-           Type     ${CMAKE_Fortran_COMPILER_ID}
-   Fortran Flags    ${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}")
-endif()
-message(STATUS "Linker flags:
-   Executable      ${CMAKE_EXE_LINKER_FLAGS}")
-if(BUILD_SHARED_LIBS)
-  message(STATUS "Shared libries  ${CMAKE_SHARED_LINKER_FLAGS}")
-else()
-  message(STATUS "Static libries  ${CMAKE_STATIC_LINKER_FLAGS}")
-endif()
-message(STATUS "Link libraries: ${LAMMPS_LINK_LIBS}")
-

cmake/Modules/FindFFTW2.cmake

@@ -1,22 +0,0 @@
-# - Find fftw2
-# Find the native FFTW2 headers and libraries.
-#
-#  FFTW2_INCLUDE_DIRS - where to find fftw2.h, etc.
-#  FFTW2_LIBRARIES    - List of libraries when using fftw2.
-#  FFTW2_FOUND        - True if fftw2 found.
-#
-
-find_path(FFTW2_INCLUDE_DIR fftw.h)
-
-find_library(FFTW2_LIBRARY NAMES fftw)
-
-set(FFTW2_LIBRARIES ${FFTW2_LIBRARY})
-set(FFTW2_INCLUDE_DIRS ${FFTW2_INCLUDE_DIR})
-
-include(FindPackageHandleStandardArgs)
-# handle the QUIETLY and REQUIRED arguments and set FFTW2_FOUND to TRUE
-# if all listed variables are TRUE
-
-find_package_handle_standard_args(FFTW2 DEFAULT_MSG FFTW2_LIBRARY FFTW2_INCLUDE_DIR)
-
-mark_as_advanced(FFTW2_INCLUDE_DIR FFTW2_LIBRARY )

cmake/Modules/FindFFTW3.cmake

@@ -1,25 +0,0 @@
-# - Find fftw3
-# Find the native FFTW3 headers and libraries.
-#
-#  FFTW3_INCLUDE_DIRS - where to find fftw3.h, etc.
-#  FFTW3_LIBRARIES    - List of libraries when using fftw3.
-#  FFTW3_FOUND        - True if fftw3 found.
-#
-
-find_package(PkgConfig)
-
-pkg_check_modules(PC_FFTW3 fftw3)
-find_path(FFTW3_INCLUDE_DIR fftw3.h HINTS ${PC_FFTW3_INCLUDE_DIRS})
-
-find_library(FFTW3_LIBRARY NAMES fftw3 HINTS ${PC_FFTW3_LIBRARY_DIRS})
-
-set(FFTW3_LIBRARIES ${FFTW3_LIBRARY})
-set(FFTW3_INCLUDE_DIRS ${FFTW3_INCLUDE_DIR})
-
-include(FindPackageHandleStandardArgs)
-# handle the QUIETLY and REQUIRED arguments and set FFTW3_FOUND to TRUE
-# if all listed variables are TRUE
-
-find_package_handle_standard_args(FFTW3 DEFAULT_MSG FFTW3_LIBRARY FFTW3_INCLUDE_DIR)
-
-mark_as_advanced(FFTW3_INCLUDE_DIR FFTW3_LIBRARY )

cmake/Modules/FindKIM.cmake

@@ -1,22 +0,0 @@
-# - Find kim
-# Find the native KIM headers and libraries.
-#
-#  KIM_INCLUDE_DIRS - where to find kim.h, etc.
-#  KIM_LIBRARIES    - List of libraries when using kim.
-#  KIM_FOUND        - True if kim found.
-#
-
-find_path(KIM_INCLUDE_DIR KIM_API.h PATH_SUFFIXES kim-api-v1)
-
-find_library(KIM_LIBRARY NAMES kim-api-v1)
-
-set(KIM_LIBRARIES ${KIM_LIBRARY})
-set(KIM_INCLUDE_DIRS ${KIM_INCLUDE_DIR})
-
-include(FindPackageHandleStandardArgs)
-# handle the QUIETLY and REQUIRED arguments and set KIM_FOUND to TRUE
-# if all listed variables are TRUE
-
-find_package_handle_standard_args(KIM DEFAULT_MSG KIM_LIBRARY KIM_INCLUDE_DIR)
-
-mark_as_advanced(KIM_INCLUDE_DIR KIM_LIBRARY )

cmake/Modules/FindLATTE.cmake

@@ -1,18 +0,0 @@
-# - Find latte
-# Find the native LATTE libraries.
-#
-#  LATTE_LIBRARIES    - List of libraries when using latte.
-#  LATTE_FOUND        - True if latte found.
-#
-
-find_library(LATTE_LIBRARY NAMES latte)
-
-set(LATTE_LIBRARIES ${LATTE_LIBRARY})
-
-include(FindPackageHandleStandardArgs)
-# handle the QUIETLY and REQUIRED arguments and set LATTE_FOUND to TRUE
-# if all listed variables are TRUE
-
-find_package_handle_standard_args(LATTE DEFAULT_MSG LATTE_LIBRARY)
-
-mark_as_advanced(LATTE_LIBRARY)

cmake/Modules/FindMKL.cmake

@@ -1,22 +0,0 @@
-# - Find mkl
-# Find the native MKL headers and libraries.
-#
-#  MKL_INCLUDE_DIRS - where to find mkl.h, etc.
-#  MKL_LIBRARIES    - List of libraries when using mkl.
-#  MKL_FOUND        - True if mkl found.
-#
-
-find_path(MKL_INCLUDE_DIR mkl_dfti.h HINTS $ENV{MKLROOT}/include)
-
-find_library(MKL_LIBRARY NAMES mkl_rt HINTS $ENV{MKLROOT}/lib $ENV{MKLROOT}/lib/intel64)
-
-set(MKL_LIBRARIES ${MKL_LIBRARY})
-set(MKL_INCLUDE_DIRS ${MKL_INCLUDE_DIR})
-
-include(FindPackageHandleStandardArgs)
-# handle the QUIETLY and REQUIRED arguments and set MKL_FOUND to TRUE
-# if all listed variables are TRUE
-
-find_package_handle_standard_args(MKL DEFAULT_MSG MKL_LIBRARY MKL_INCLUDE_DIR)
-
-mark_as_advanced(MKL_INCLUDE_DIR MKL_LIBRARY )

cmake/Modules/FindNetCDF.cmake

@@ -1,118 +0,0 @@
-# - Find NetCDF
-# Find the native NetCDF includes and library
-#
-#  NETCDF_INCLUDE_DIR  - user modifiable choice of where netcdf headers are
-#  NETCDF_LIBRARY      - user modifiable choice of where netcdf libraries are
-#
-# Your package can require certain interfaces to be FOUND by setting these
-#
-#  NETCDF_CXX         - require the C++ interface and link the C++ library
-#  NETCDF_F77         - require the F77 interface and link the fortran library
-#  NETCDF_F90         - require the F90 interface and link the fortran library
-#
-# Or equivalently by calling FindNetCDF with a COMPONENTS argument containing one or
-# more of "CXX;F77;F90".
-#
-# When interfaces are requested the user has access to interface specific hints:
-#
-#  NETCDF_${LANG}_INCLUDE_DIR - where to search for interface header files
-#  NETCDF_${LANG}_LIBRARY     - where to search for interface libraries
-#
-# This module returns these variables for the rest of the project to use.
-#
-#  NETCDF_FOUND          - True if NetCDF found including required interfaces (see below)
-#  NETCDF_LIBRARIES      - All netcdf related libraries.
-#  NETCDF_INCLUDE_DIRS   - All directories to include.
-#  NETCDF_HAS_INTERFACES - Whether requested interfaces were found or not.
-#  NETCDF_${LANG}_INCLUDE_DIRS/NETCDF_${LANG}_LIBRARIES - C/C++/F70/F90 only interface
-#
-# Normal usage would be:
-#  set (NETCDF_F90 "YES")
-#  find_package (NetCDF REQUIRED)
-#  target_link_libraries (uses_everthing ${NETCDF_LIBRARIES})
-#  target_link_libraries (only_uses_f90 ${NETCDF_F90_LIBRARIES})
-
-#search starting from user editable cache var
-if (NETCDF_INCLUDE_DIR AND NETCDF_LIBRARY)
-  # Already in cache, be silent
-  set (NETCDF_FIND_QUIETLY TRUE)
-endif ()
-
-set(USE_DEFAULT_PATHS "NO_DEFAULT_PATH")
-if(NETCDF_USE_DEFAULT_PATHS)
-  set(USE_DEFAULT_PATHS "")
-endif()
-
-find_path (NETCDF_INCLUDE_DIR netcdf.h
-  HINTS "${NETCDF_DIR}/include")
-mark_as_advanced (NETCDF_INCLUDE_DIR)
-set (NETCDF_C_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR})
-
-find_library (NETCDF_LIBRARY NAMES netcdf
-  HINTS "${NETCDF_DIR}/lib")
-mark_as_advanced (NETCDF_LIBRARY)
-
-set (NETCDF_C_LIBRARIES ${NETCDF_LIBRARY})
-
-#start finding requested language components
-set (NetCDF_libs "")
-set (NetCDF_includes "${NETCDF_INCLUDE_DIR}")
-
-get_filename_component (NetCDF_lib_dirs "${NETCDF_LIBRARY}" PATH)
-set (NETCDF_HAS_INTERFACES "YES") # will be set to NO if we're missing any interfaces
-
-macro (NetCDF_check_interface lang header libs)
-  if (NETCDF_${lang})
-    #search starting from user modifiable cache var
-    find_path (NETCDF_${lang}_INCLUDE_DIR NAMES ${header}
-      HINTS "${NETCDF_INCLUDE_DIR}"
-      HINTS "${NETCDF_${lang}_ROOT}/include"
-      ${USE_DEFAULT_PATHS})
-
-    find_library (NETCDF_${lang}_LIBRARY NAMES ${libs}
-      HINTS "${NetCDF_lib_dirs}"
-      HINTS "${NETCDF_${lang}_ROOT}/lib"
-      ${USE_DEFAULT_PATHS})
-
-    mark_as_advanced (NETCDF_${lang}_INCLUDE_DIR NETCDF_${lang}_LIBRARY)
-
-    #export to internal varS that rest of project can use directly
-    set (NETCDF_${lang}_LIBRARIES ${NETCDF_${lang}_LIBRARY})
-    set (NETCDF_${lang}_INCLUDE_DIRS ${NETCDF_${lang}_INCLUDE_DIR})
-
-    if (NETCDF_${lang}_INCLUDE_DIR AND NETCDF_${lang}_LIBRARY)
-      list (APPEND NetCDF_libs ${NETCDF_${lang}_LIBRARY})
-      list (APPEND NetCDF_includes ${NETCDF_${lang}_INCLUDE_DIR})
-    else ()
-      set (NETCDF_HAS_INTERFACES "NO")
-      message (STATUS "Failed to find NetCDF interface for ${lang}")
-    endif ()
-  endif ()
-endmacro ()
-
-list (FIND NetCDF_FIND_COMPONENTS "CXX" _nextcomp)
-if (_nextcomp GREATER -1)
-  set (NETCDF_CXX 1)
-endif ()
-list (FIND NetCDF_FIND_COMPONENTS "F77" _nextcomp)
-if (_nextcomp GREATER -1)
-  set (NETCDF_F77 1)
-endif ()
-list (FIND NetCDF_FIND_COMPONENTS "F90" _nextcomp)
-if (_nextcomp GREATER -1)
-  set (NETCDF_F90 1)
-endif ()
-NetCDF_check_interface (CXX netcdfcpp.h netcdf_c++)
-NetCDF_check_interface (F77 netcdf.inc  netcdff)
-NetCDF_check_interface (F90 netcdf.mod  netcdff)
-
-#export accumulated results to internal varS that rest of project can depend on
-list (APPEND NetCDF_libs "${NETCDF_C_LIBRARIES}")
-set (NETCDF_LIBRARIES ${NetCDF_libs})
-set (NETCDF_INCLUDE_DIRS ${NetCDF_includes})
-
-# handle the QUIETLY and REQUIRED arguments and set NETCDF_FOUND to TRUE if
-# all listed variables are TRUE
-include (FindPackageHandleStandardArgs)
-find_package_handle_standard_args (NetCDF
-  DEFAULT_MSG NETCDF_LIBRARIES NETCDF_INCLUDE_DIRS NETCDF_HAS_INTERFACES)

cmake/Modules/FindQE.cmake

@@ -1,29 +0,0 @@
-# - Find quantum-espresso
-# Find the native QE headers and libraries.
-#
-#  QE_INCLUDE_DIRS - where to find quantum-espresso.h, etc.
-#  QE_LIBRARIES    - List of libraries when using quantum-espresso.
-#  QE_FOUND        - True if quantum-espresso found.
-#
-
-find_path(QE_INCLUDE_DIR libqecouple.h PATH_SUFFIXES COUPLE/include)
-
-find_library(QECOUPLE_LIBRARY NAMES qecouple)
-find_library(PW_LIBRARY NAMES pw)
-find_library(QEMOD_LIBRARY NAMES qemod)
-find_library(QEFFT_LIBRARY NAMES qefft)
-find_library(QELA_LIBRARY NAMES qela)
-find_library(CLIB_LIBRARY NAMES clib)
-find_library(IOTK_LIBRARY NAMES iotk)
-
-
-set(QE_LIBRARIES ${QECOUPLE_LIBRARY} ${PW_LIBRARY} ${QEMOD_LIBRARY} ${QEFFT_LIBRARY} ${QELA_LIBRARY} ${CLIB_LIBRARY} ${IOTK_LIBRARY})
-set(QE_INCLUDE_DIRS ${QE_INCLUDE_DIR})
-
-include(FindPackageHandleStandardArgs)
-# handle the QUIETLY and REQUIRED arguments and set QE_FOUND to TRUE
-# if all listed variables are TRUE
-
-find_package_handle_standard_args(QE DEFAULT_MSG QECOUPLE_LIBRARY PW_LIBRARY QEMOD_LIBRARY QEFFT_LIBRARY QELA_LIBRARY CLIB_LIBRARY IOTK_LIBRARY QE_INCLUDE_DIR)
-
-mark_as_advanced(QE_INCLUDE_DIR QECOUPLE_LIBRARY PW_LIBRARY QEMOD_LIBRARY QEFFT_LIBRARY QELA_LIBRARY CLIB_LIBRARY IOTK_LIBRARY)

cmake/Modules/FindQUIP.cmake

@@ -1,18 +0,0 @@
-# - Find quip
-# Find the native QUIP libraries.
-#
-#  QUIP_LIBRARIES    - List of libraries when using fftw3.
-#  QUIP_FOUND        - True if fftw3 found.
-#
-
-find_library(QUIP_LIBRARY NAMES quip)
-
-set(QUIP_LIBRARIES ${QUIP_LIBRARY})
-
-include(FindPackageHandleStandardArgs)
-# handle the QUIETLY and REQUIRED arguments and set QUIP_FOUND to TRUE
-# if all listed variables are TRUE
-
-find_package_handle_standard_args(QUIP DEFAULT_MSG QUIP_LIBRARY)
-
-mark_as_advanced(QUIP_LIBRARY)

cmake/Modules/FindVORO.cmake

@@ -1,22 +0,0 @@
-# - Find voro++
-# Find the native VORO headers and libraries.
-#
-#  VORO_INCLUDE_DIRS - where to find voro++.hh, etc.
-#  VORO_LIBRARIES    - List of libraries when using voro++.
-#  VORO_FOUND        - True if voro++ found.
-#
-
-find_path(VORO_INCLUDE_DIR voro++.hh PATH_SUFFIXES voro++)
-
-find_library(VORO_LIBRARY NAMES voro++)
-
-set(VORO_LIBRARIES ${VORO_LIBRARY})
-set(VORO_INCLUDE_DIRS ${VORO_INCLUDE_DIR})
-
-include(FindPackageHandleStandardArgs)
-# handle the QUIETLY and REQUIRED arguments and set VORO_FOUND to TRUE
-# if all listed variables are TRUE
-
-find_package_handle_standard_args(VORO DEFAULT_MSG VORO_LIBRARY VORO_INCLUDE_DIR)
-
-mark_as_advanced(VORO_INCLUDE_DIR VORO_LIBRARY )

cmake/Modules/OpenCLUtils.cmake

@@ -1,18 +0,0 @@
-function(GenerateOpenCLHeader varname outfile files)
-    message("Creating ${outfile}...")
-    file(WRITE ${outfile} "const char * ${varname} = \n")
-    math(EXPR ARG_END   "${ARGC}-1")
-
-    foreach(IDX RANGE 2 ${ARG_END})
-        list(GET ARGV ${IDX} filename)
-        file(READ ${filename} content)
-        string(REGEX REPLACE "\\s*//[^\n]*\n" "" content "${content}")
-        string(REGEX REPLACE "\\\\" "\\\\\\\\" content "${content}")
-        string(REGEX REPLACE "\"" "\\\\\"" content "${content}")
-        string(REGEX REPLACE "([^\n]+)\n" "\"\\1\\\\n\"\n" content "${content}")
-        string(REGEX REPLACE "\n+" "\n" content "${content}")
-        file(APPEND ${outfile} "${content}")
-    endforeach()
-
-    file(APPEND ${outfile} ";\n")
-endfunction(GenerateOpenCLHeader)

cmake/Modules/StyleHeaderUtils.cmake

@@ -1,161 +0,0 @@
-function(FindStyleHeaders path style_class file_pattern headers)
-    file(GLOB files "${path}/${file_pattern}*.h")
-    get_property(hlist GLOBAL PROPERTY ${headers})
-
-    foreach(file_name ${files})
-        file(STRINGS ${file_name} is_style LIMIT_COUNT 1 REGEX ${style_class})
-        if(is_style)
-            list(APPEND hlist ${file_name})
-        endif()
-    endforeach()
-    set_property(GLOBAL PROPERTY ${headers} "${hlist}")
-endfunction(FindStyleHeaders)
-
-function(FindStyleHeadersExt path style_class extension headers sources)
-    get_property(hlist GLOBAL PROPERTY ${headers})
-    get_property(slist GLOBAL PROPERTY ${sources})
-    set(ext_list)
-    get_filename_component(abs_path "${path}" ABSOLUTE)
-
-    foreach(file_name ${hlist})
-        get_filename_component(basename ${file_name} NAME_WE)
-        set(ext_file_name "${abs_path}/${basename}_${extension}.h")
-        if(EXISTS "${ext_file_name}")
-            file(STRINGS ${ext_file_name} is_style LIMIT_COUNT 1 REGEX ${style_class})
-            if(is_style)
-                list(APPEND ext_list ${ext_file_name})
-
-                set(source_file_name "${abs_path}/${basename}_${extension}.cpp")
-                if(EXISTS "${source_file_name}")
-                    list(APPEND slist ${source_file_name})
-                endif()
-            endif()
-        endif()
-    endforeach()
-
-    list(APPEND hlist ${ext_list})
-    set_property(GLOBAL PROPERTY ${headers} "${hlist}")
-    set_property(GLOBAL PROPERTY ${sources} "${slist}")
-endfunction(FindStyleHeadersExt)
-
-function(CreateStyleHeader path filename)
-    math(EXPR N "${ARGC}-2")
-
-    set(temp "")
-    if(N GREATER 0)
-        math(EXPR ARG_END   "${ARGC}-1")
- 
-        foreach(IDX RANGE 2 ${ARG_END})
-            list(GET ARGV ${IDX} FNAME)
-            get_filename_component(FNAME ${FNAME} NAME)
-            set(temp "${temp}#include \"${FNAME}\"\n")
-        endforeach()
-    endif()
-    message(STATUS "Generating ${filename}...")
-    file(WRITE "${path}/${filename}.tmp" "${temp}" )
-    execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${path}/${filename}.tmp" "${path}/${filename}")
-endfunction(CreateStyleHeader)
-
-function(GenerateStyleHeader path property style)
-    get_property(files GLOBAL PROPERTY ${property})
-    #message("${property} = ${files}")
-    CreateStyleHeader("${path}" "style_${style}.h" ${files})
-endfunction(GenerateStyleHeader)
-
-function(RegisterStyles search_path)
-    FindStyleHeaders(${search_path} ANGLE_CLASS     angle_     ANGLE     ) # angle     ) # force
-    FindStyleHeaders(${search_path} ATOM_CLASS      atom_vec_  ATOM_VEC  ) # atom      ) # atom      atom_vec_hybrid
-    FindStyleHeaders(${search_path} BODY_CLASS      body_      BODY      ) # body      ) # atom_vec_body
-    FindStyleHeaders(${search_path} BOND_CLASS      bond_      BOND      ) # bond      ) # force
-    FindStyleHeaders(${search_path} COMMAND_CLASS   ""         COMMAND   ) # command   ) # input
-    FindStyleHeaders(${search_path} COMPUTE_CLASS   compute_   COMPUTE   ) # compute   ) # modify
-    FindStyleHeaders(${search_path} DIHEDRAL_CLASS  dihedral_  DIHEDRAL  ) # dihedral  ) # force
-    FindStyleHeaders(${search_path} DUMP_CLASS      dump_      DUMP      ) # dump      ) # output    write_dump
-    FindStyleHeaders(${search_path} FIX_CLASS       fix_       FIX       ) # fix       ) # modify
-    FindStyleHeaders(${search_path} IMPROPER_CLASS  improper_  IMPROPER  ) # improper  ) # force
-    FindStyleHeaders(${search_path} INTEGRATE_CLASS ""         INTEGRATE ) # integrate ) # update
-    FindStyleHeaders(${search_path} KSPACE_CLASS    ""         KSPACE    ) # kspace    ) # force
-    FindStyleHeaders(${search_path} MINIMIZE_CLASS  min_       MINIMIZE  ) # minimize  ) # update
-    FindStyleHeaders(${search_path} NBIN_CLASS      nbin_      NBIN      ) # nbin      ) # neighbor
-    FindStyleHeaders(${search_path} NPAIR_CLASS     npair_     NPAIR     ) # npair     ) # neighbor
-    FindStyleHeaders(${search_path} NSTENCIL_CLASS  nstencil_  NSTENCIL  ) # nstencil  ) # neighbor
-    FindStyleHeaders(${search_path} NTOPO_CLASS     ntopo_     NTOPO     ) # ntopo     ) # neighbor
-    FindStyleHeaders(${search_path} PAIR_CLASS      pair_      PAIR      ) # pair      ) # force
-    FindStyleHeaders(${search_path} READER_CLASS    reader_    READER    ) # reader    ) # read_dump
-    FindStyleHeaders(${search_path} REGION_CLASS    region_    REGION    ) # region    ) # domain
-endfunction(RegisterStyles)
-
-function(RemovePackageHeader headers pkg_header)
-    get_property(hlist GLOBAL PROPERTY ${headers})
-    list(REMOVE_ITEM hlist ${pkg_header})
-    set_property(GLOBAL PROPERTY ${headers} "${hlist}")
-endfunction(RemovePackageHeader)
-
-function(DetectAndRemovePackageHeader fname)
-    RemovePackageHeader(ANGLE     ${fname})
-    RemovePackageHeader(ATOM_VEC  ${fname})
-    RemovePackageHeader(BODY      ${fname})
-    RemovePackageHeader(BOND      ${fname})
-    RemovePackageHeader(COMMAND   ${fname})
-    RemovePackageHeader(COMPUTE   ${fname})
-    RemovePackageHeader(DIHEDRAL  ${fname})
-    RemovePackageHeader(DUMP      ${fname})
-    RemovePackageHeader(FIX       ${fname})
-    RemovePackageHeader(IMPROPER  ${fname})
-    RemovePackageHeader(INTEGRATE ${fname})
-    RemovePackageHeader(KSPACE    ${fname})
-    RemovePackageHeader(MINIMIZE  ${fname})
-    RemovePackageHeader(NBIN      ${fname})
-    RemovePackageHeader(NPAIR     ${fname})
-    RemovePackageHeader(NSTENCIL  ${fname})
-    RemovePackageHeader(NTOPO     ${fname})
-    RemovePackageHeader(PAIR      ${fname})
-    RemovePackageHeader(READER    ${fname})
-    RemovePackageHeader(REGION    ${fname})
-endfunction(DetectAndRemovePackageHeader)
-
-function(RegisterStylesExt search_path extension sources)
-    FindStyleHeadersExt(${search_path} ANGLE_CLASS     ${extension}  ANGLE     ${sources})
-    FindStyleHeadersExt(${search_path} ATOM_CLASS      ${extension}  ATOM_VEC  ${sources})
-    FindStyleHeadersExt(${search_path} BODY_CLASS      ${extension}  BODY      ${sources})
-    FindStyleHeadersExt(${search_path} BOND_CLASS      ${extension}  BOND      ${sources})
-    FindStyleHeadersExt(${search_path} COMMAND_CLASS   ${extension}  COMMAND   ${sources})
-    FindStyleHeadersExt(${search_path} COMPUTE_CLASS   ${extension}  COMPUTE   ${sources})
-    FindStyleHeadersExt(${search_path} DIHEDRAL_CLASS  ${extension}  DIHEDRAL  ${sources})
-    FindStyleHeadersExt(${search_path} DUMP_CLASS      ${extension}  DUMP      ${sources})
-    FindStyleHeadersExt(${search_path} FIX_CLASS       ${extension}  FIX       ${sources})
-    FindStyleHeadersExt(${search_path} IMPROPER_CLASS  ${extension}  IMPROPER  ${sources})
-    FindStyleHeadersExt(${search_path} INTEGRATE_CLASS ${extension}  INTEGRATE ${sources})
-    FindStyleHeadersExt(${search_path} KSPACE_CLASS    ${extension}  KSPACE    ${sources})
-    FindStyleHeadersExt(${search_path} MINIMIZE_CLASS  ${extension}  MINIMIZE  ${sources})
-    FindStyleHeadersExt(${search_path} NBIN_CLASS      ${extension}  NBIN      ${sources})
-    FindStyleHeadersExt(${search_path} NPAIR_CLASS     ${extension}  NPAIR     ${sources})
-    FindStyleHeadersExt(${search_path} NSTENCIL_CLASS  ${extension}  NSTENCIL  ${sources})
-    FindStyleHeadersExt(${search_path} NTOPO_CLASS     ${extension}  NTOPO     ${sources})
-    FindStyleHeadersExt(${search_path} PAIR_CLASS      ${extension}  PAIR      ${sources})
-    FindStyleHeadersExt(${search_path} READER_CLASS    ${extension}  READER    ${sources})
-    FindStyleHeadersExt(${search_path} REGION_CLASS    ${extension}  REGION    ${sources})
-endfunction(RegisterStylesExt)
-
-function(GenerateStyleHeaders output_path)
-    GenerateStyleHeader(${output_path} ANGLE      angle     ) # force
-    GenerateStyleHeader(${output_path} ATOM_VEC   atom      ) # atom      atom_vec_hybrid
-    GenerateStyleHeader(${output_path} BODY       body      ) # atom_vec_body
-    GenerateStyleHeader(${output_path} BOND       bond      ) # force
-    GenerateStyleHeader(${output_path} COMMAND    command   ) # input
-    GenerateStyleHeader(${output_path} COMPUTE    compute   ) # modify
-    GenerateStyleHeader(${output_path} DIHEDRAL   dihedral  ) # force
-    GenerateStyleHeader(${output_path} DUMP       dump      ) # output    write_dump
-    GenerateStyleHeader(${output_path} FIX        fix       ) # modify
-    GenerateStyleHeader(${output_path} IMPROPER   improper  ) # force
-    GenerateStyleHeader(${output_path} INTEGRATE  integrate ) # update
-    GenerateStyleHeader(${output_path} KSPACE     kspace    ) # force
-    GenerateStyleHeader(${output_path} MINIMIZE   minimize  ) # update
-    GenerateStyleHeader(${output_path} NBIN       nbin      ) # neighbor
-    GenerateStyleHeader(${output_path} NPAIR      npair     ) # neighbor
-    GenerateStyleHeader(${output_path} NSTENCIL   nstencil  ) # neighbor
-    GenerateStyleHeader(${output_path} NTOPO      ntopo     ) # neighbor
-    GenerateStyleHeader(${output_path} PAIR       pair      ) # force
-    GenerateStyleHeader(${output_path} READER     reader    ) # read_dump
-    GenerateStyleHeader(${output_path} REGION     region    ) # domain
-endfunction(GenerateStyleHeaders)

cmake/README.md

@@ -1,19 +0,0 @@
-cmake-buildsystem
------------------
-
-To use the cmake build system instead of the make-driven one, do:
-```
-cmake /path/to/lammps/source/cmake
-```
-(please note the cmake directory as the very end)
-
-To enable package, e.g. GPU do
-```
-cmake /path/to/lammps/source/cmake -DENABLE_GPU=ON
-```
-
-cmake has many many options, do get an overview use the curses-based cmake interface, ccmake:
-```
-ccmake /path/to/lammps/source/cmake
-```
-(Don't forget to press "g" for generate once you are done with configuring)

cmake/gpu/lal_pppm_d.cu

@@ -1,4 +0,0 @@
-#define grdtyp double
-#define grdtyp4 double4
-
-#include "lal_pppm.cu"

cmake/gpu/lal_pppm_f.cu

@@ -1,4 +0,0 @@
-#define grdtyp float
-#define grdtyp4 float4
-
-#include "lal_pppm.cu"

cmake/pkgconfig/liblammps.pc.in

@@ -1,18 +0,0 @@
-# pkg-config file for lammps
-# https://people.freedesktop.org/~dbn/pkg-config-guide.html
-# Usage: cc `pkg-config --cflags --libs liblammps` -o myapp myapp.c
-# after you added @CMAKE_INSTALL_FULL_LIBDIR@/pkg-config to PKG_CONFIG_PATH,
-# e.g. export PKG_CONFIG_PATH=@CMAKE_INSTALL_FULL_LIBDIR@/pkgconfig
-
-prefix=@CMAKE_INSTALL_FULL_PREFIX@
-libdir=@CMAKE_INSTALL_FULL_LIBDIR@
-includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
-
-Name: liblammps@LAMMPS_MACHINE@
-Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library
-URL: http://lammps.sandia.gov
-Version:
-Requires:
-Libs: -L${libdir} -llammps@LAMMPS_MACHINE@
-Libs.private: -lm
-Cflags: -I${includedir} @LAMMPS_API_DEFINES@

doc/.gitignore

@@ -1,6 +0,0 @@
-/html
-/spelling
-/LAMMPS.epub
-/LAMMPS.mobi
-/Manual.pdf
-/Developer.pdf

doc/Makefile

@@ -6,7 +6,6 @@ BUILDDIR      = /tmp/lammps-docs-$(SHA1)
 RSTDIR        = $(BUILDDIR)/rst
 VENV          = $(BUILDDIR)/docenv
 TXT2RST       = $(VENV)/bin/txt2rst
-ANCHORCHECK   = $(VENV)/bin/doc_anchor_check
 
 PYTHON        = $(shell which python3)
 HAS_PYTHON3    = NO
@@ -23,7 +22,7 @@ endif
 SOURCES=$(wildcard src/*.txt)
 OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
 
-.PHONY: help clean-all clean epub html pdf old venv spelling anchor_check
+.PHONY: help clean-all clean epub html pdf old venv
 
 # ------------------------------------------
 
@@ -37,7 +36,6 @@ help:
 	@echo "  clean      remove all intermediate RST files"
 	@echo "  clean-all  reset the entire build environment"
 	@echo "  txt2html   build txt2html tool"
-	@echo "  anchor_check  scan for duplicate anchor labels"
 
 # ------------------------------------------
 
@@ -46,19 +44,12 @@ clean-all:
 
 clean:
 	rm -rf $(RSTDIR) html
-	rm -rf spelling
 
-clean-spelling:
-	rm -rf spelling
-
-html: $(OBJECTS) $(ANCHORCHECK)
+html: $(OBJECTS)
 	@(\
 		. $(VENV)/bin/activate ;\
 		cp -r src/* $(RSTDIR)/ ;\
 		sphinx-build -j 8 -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
-		echo "############################################" ;\
-		doc_anchor_check src/*.txt ;\
-		echo "############################################" ;\
 		deactivate ;\
 	)
 	-rm html/searchindex.js
@@ -73,17 +64,6 @@ html: $(OBJECTS) $(ANCHORCHECK)
 	@rm -rf html/USER/*/*.[sg]*
 	@echo "Build finished. The HTML pages are in doc/html."
 
-spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt
-	@(\
-		. $(VENV)/bin/activate ;\
-		pip install sphinxcontrib-spelling ;\
-		cp -r src/* $(RSTDIR)/ ;\
-        cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ;\
-		sphinx-build -b spelling -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) spelling ;\
-		deactivate ;\
-	)
-	@echo "Spell check finished."
-
 epub: $(OBJECTS)
 	@mkdir -p epub
 	@rm -f LAMMPS.epub
@@ -100,7 +80,6 @@ epub: $(OBJECTS)
 
 pdf: utils/txt2html/txt2html.exe
 	@(\
-		set -e; \
 		cd src; \
 		../utils/txt2html/txt2html.exe -b *.txt; \
 		htmldoc --batch lammps.book;          \
@@ -133,13 +112,6 @@ fetch:
 
 txt2html: utils/txt2html/txt2html.exe
 
-anchor_check : $(ANCHORCHECK)
-	@(\
-		. $(VENV)/bin/activate ;\
-		doc_anchor_check src/*.txt ;\
-		deactivate ;\
-	)
-
 # ------------------------------------------
 
 utils/txt2html/txt2html.exe: utils/txt2html/txt2html.cpp
@@ -159,12 +131,12 @@ $(VENV):
 	@( \
 		virtualenv -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
-		pip install Sphinx==1.5.6; \
+		pip install Sphinx; \
 		pip install sphinxcontrib-images; \
 		deactivate;\
 	)
 
-$(TXT2RST) $(ANCHORCHECK): $(VENV)
+$(TXT2RST): $(VENV)
 	@( \
 		. $(VENV)/bin/activate; \
 		(cd utils/converters;\

doc/src/2001/input_commands.html

@@ -464,7 +464,7 @@ the angletype option can only be assigned to a "fix style" of "shake",
   entirely rigid (e.g. water)
 the angletype option enables an additional check when SHAKE constraints
   are computed: if a cluster is of size 3 and both bonds in
-  the cluster are of a bondtype specified by the 2nd parameter of
+  the cluster are of a bondtype specified by the 2nd paramter of
   angletype, then the cluster is SHAKEn with an additional angle
   constraint that makes it rigid, using the equilibrium angle appropriate
   to the specified angletype
@@ -476,7 +476,7 @@ IMPORTANT NOTE: the angletype option has one additional affect, namely
   since they will not be SHAKEn but neither will the angle force by computed
 for style region, a coeff of INF means + or - infinity (all the way 
   to the boundary)
-an atom can be assigned to multiple constraints, the constraints will be
+an atom can be assigned to multiple constraints, the contraints will be
   applied in the reverse order they are assigned to that atom
   (e.g. each timestep, the last fix assigned to an atom will be applied 
   to it first, then the next-to-last applied second, etc)
@@ -689,7 +689,7 @@ coeffs:  types
          remainder
                no other parameters required
        
-used with "create temp" command to initialize velocities of atoms
+used with "create temp" commmand to initialize velocities of atoms
 by default, the "create temp" command initializes the velocities of all atoms,
   this command limits the initialization to a group of atoms
 this command is only in force for the next "create temp" command, any
@@ -1263,7 +1263,7 @@ when using constraints with the minimizer, fixes are
   applied when atoms move except for the following
 fixes associated with temperature control are not allowed
   (rescale, hoover/drag, langevin)
-the minimizer does not invoke the "fix style shake" constraints on
+the minimizer does not invoke the "fix style shake" contraints on
   bond lengths
 the minimizer does not invoke pressure control or volume control settings
 for good convergence, should specify use of smooth nonbond force fields 
@@ -1566,7 +1566,7 @@ mesh dimensions that are power-of-two are fastest for FFTs, but any sizes
   can be used that are supported by native machine libraries
 this command is optional - if not used, a default
   mesh size will be chosen to satisfy accuracy criterion - if used, the
-  specified mesh size will override the default
+  specifed mesh size will override the default
 </PRE>
 <HR>
 <H3>
@@ -1788,7 +1788,7 @@ if the style is 2, restart information will be written alternately to files
 when the minimizer is invoked this command means create a restart file
   at the end of the minimization with the filename filename.timestep.min
 a restart file stores atom and force-field information in binary form
-allows program to restart from where it left off (see &quot;read restart&quot; command)
+allows program to restart from where it left off (see &quot;read restart&quot; commmand)
 
 Default = 0
 </PRE>

doc/src/99/basics.html

@@ -167,7 +167,7 @@ tool on the small-system data file.</P>
 <P>
 (6) flow</P>
 <P>
-2-d flow of Lennard-Jones atoms in a channel using various constraint
+2-d flow of Lennard-Jones atoms in a channel using various contraint 
 options.</P>
 <P>
 (7) polymer</P>
@@ -201,7 +201,7 @@ The tools directory also has a F77 program called setup_chain.f
 (compile and link with print.c) which can be used to generate random 
 initial polymer configurations for bead-spring models like those used 
 in examples/polymer. It uses an input polymer definition file (see 
-examples/polymer for two sample def files) that specifies how many
+examples/polymer for two sample def files) that specfies how many 
 chains of what length, a random number seed, etc.</P>
 </BODY>
 </HTML>

doc/src/99/crib.html

@@ -40,7 +40,7 @@ Note: this file is somewhat out-of-date for LAMMPS 99.</P>
     <LI>
     maxtype = max # of atom types 
     <LI>
-    maxbond = max # of bonds to compute on one processor
+    maxbond = max # of bonds to compute on one procesor 
     <LI>
     maxangle = max # of angles to compute on one processor 
     <LI>

doc/src/99/input_commands.html

@@ -294,7 +294,7 @@ assign a group of atoms to a particular constraint
 use appropriate number of coeffs for a particular style
 the constraint itself is defined by the "fix style" command
 multiple groups of atoms can be assigned to the same constraint
-an atom can be assigned to multiple constraints, the constraints will be
+an atom can be assigned to multiple constraints, the contraints will be
   applied in the reverse order they are assigned to that atom
   (e.g. each timestep, the last fix assigned to an atom will be applied 
   to it first, then the next-to-last applied second, etc)
@@ -477,7 +477,7 @@ coeffs:  types
          remainder
                no other parameters required
        
-used with "create temp" command to initialize velocities of atoms
+used with "create temp" commmand to initialize velocities of atoms
 by default, the "create temp" command initializes the velocities of all atoms,
   this command limits the initialization to a group of atoms
 this command is only in force for the next "create temp" command, any
@@ -1124,7 +1124,7 @@ mesh dimensions that are power-of-two are fastest for FFTs, but any size
   can be used that are supported by native machine libraries
 this command is optional - if not used, a default
   mesh size will be chosen to satisfy accuracy criterion - if used, the
-  specified mesh size will override the default
+  specifed mesh size will override the default
 
 Default = none
 </PRE>
@@ -1343,7 +1343,7 @@ value of 0 means never create one
 program will toggle between 2 filenames as the run progresses
   so always have at least one good file even if the program dies in mid-write
 restart file stores atom positions and velocities in binary form
-allows program to restart from where it left off (see &quot;read restart&quot; command)
+allows program to restart from where it left off (see &quot;read restart&quot; commmand)
 
 Default = 0
 </PRE>

doc/src/Eqs/cnp_cutoff.tex

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

doc/src/Eqs/cnp_cutoff2.tex

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

doc/src/Eqs/cnp_eq.tex

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

doc/src/Eqs/fix_gcmc1.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-\mu &=&\mu^{id} + \mu^{ex}
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/fix_gcmc2.tex

@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-\mu^{id} &=& k T \ln{\rho \Lambda^3} \\
-&=& k T \ln{\frac{\phi P \Lambda^3}{k T}} 
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/fix_gcmc3.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-\Lambda &=& \sqrt{ \frac{h^2}{2 \pi m k T}}
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/fix_mvv_dpd.tex

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

doc/src/Eqs/fix_wall_ees.tex

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

doc/src/Eqs/pair_edpd_force.tex

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

doc/src/Eqs/pair_edpd_gov.tex

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

doc/src/Eqs/pair_edpd_heat.tex

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

doc/src/Eqs/pair_edpd_kappa.tex

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

doc/src/Eqs/pair_kolmogorov_crespi_z.tex

@@ -1,13 +0,0 @@
-\documentclass[12pt]{article}
-\thispagestyle{empty}
-
-\begin{document}
-
-\begin{eqnarray*}
-  E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
-  V_{ij} & = & e^{-\lambda(r_{ij} -z_0}) \left[ C + f(\rho_{ij}) + f(\rho_{ji}) \right] - A \left( \frac{r_{ij}}{z_0}\right)^{-6} + A \left( \frac{\textrm{cutoff}}{z_0}\right)^{-6} \\
-  \rho_{ij}^2 = \rho_{ji}^2 & = &  x_{ij}^2 + y_{ij}^2 ~\hspace{2cm} (\mathbf{n_i}\equiv\hat \mathbf{z})\\
-  f(\rho) & = &  e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} \left( \rho/\delta \right) ^{2n}
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/pair_lj_sf.tex

@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ F & = & F_{\mathrm{LJ}}(r) - F_{\mathrm{LJ}}(r_{\mathrm{c}}) \qquad r < r_{\mathrm{c}} \\
+ E & = & E_{\mathrm{LJ}}(r) - E_{\mathrm{LJ}}(r_{\mathrm{c}}) + (r - r_{\mathrm{c}}) F_{\mathrm{LJ}}(r_{\mathrm{c}}) \qquad r < r_{\mathrm{c}} \\
+ \mathrm{with} \qquad E_{\mathrm{LJ}}(r) & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \qquad \mathrm{and} \qquad F_{\mathrm{LJ}}(r) = - E^\prime_{\mathrm{LJ}}(r)
+\end{eqnarray*}                           
+
+\end{document}

doc/src/Eqs/pair_mdpd_force.tex

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

doc/src/Eqs/pair_meam_spline.tex

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

doc/src/Eqs/pair_meam_spline_multicomponent.tex

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

doc/src/Eqs/pair_momb.tex

@@ -1,13 +0,0 @@
-\documentclass[12pt,fleqn]{article}
-\usepackage{amsmath}
-\thispagestyle{empty}
-
-\begin{document}
-
-\setlength{\jot}{2ex}
-\begin{gather*}
-  E = D_0 [\exp^{-2 \alpha (r-r_0)} - 2\exp^{-\alpha (r-r_0)}] - s_6 \frac{C_6}{r^6} f_{damp}(r,R_r) \\
-  f_{damp}(r,R_r) = \frac{1}{1 + \exp^{-d(r/R_r - 1)}}
-\end{gather*}
-
-\end{document}

doc/src/Eqs/pair_tdpd_flux.tex

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

doc/src/Eqs/pair_tdpd_force.tex

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

doc/src/Eqs/pair_tdpd_gov.tex

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

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="22 Sep 2017 version">
+<META NAME="docnumber" CONTENT="26 Jan 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
-22 Sep 2017 version :c,h4
+26 Jan 2017 version :c,h4
 
 Version info: :h4
 
@@ -39,7 +39,7 @@ directory name created when you unpack a tarball, and at the top of
 the first page of the manual (this page).
 
 If you browse the HTML doc pages on the LAMMPS WWW site, they always
-describe the most current [development] version of LAMMPS. :ulb,l
+describe the most current version of LAMMPS. :ulb,l
 
 If you browse the HTML doc pages included in your tarball, they
 describe the version you have. :l
@@ -67,7 +67,7 @@ Labs and Temple University:
 
 "Steve Plimpton"_sjp, sjplimp at sandia.gov :ulb,l
 Aidan Thompson, athomps at sandia.gov :l
-Stan Moore, stamoor at sandia.gov :l
+Stan Moore, stamoore at sandia.gov :l
 "Axel Kohlmeyer"_ako, akohlmey at gmail.com :l
 :ule
 
@@ -79,7 +79,7 @@ bug reports and feature requests are mainly coordinated through the
 "LAMMPS project on GitHub."_https://github.com/lammps/lammps
 The lammps.org domain, currently hosting "public continuous integration
 testing"_https://ci.lammps.org/job/lammps/ and "precompiled Linux
-RPM and Windows installer packages"_http://packages.lammps.org is located
+RPM and Windows installer packages"_http://rpm.lammps.org is located
 at Temple University and managed by Richard Berger,
 richard.berger at temple.edu.
 
@@ -158,11 +158,12 @@ END_RST -->
   2.1 "What's in the LAMMPS distribution"_start_1 :ulb,b
   2.2 "Making LAMMPS"_start_2 :b
   2.3 "Making LAMMPS with optional packages"_start_3 :b
-  2.4 "Building LAMMPS as a library"_start_4 :b
-  2.5 "Running LAMMPS"_start_5 :b
-  2.6 "Command-line options"_start_6 :b
-  2.7 "Screen output"_start_7 :b
-  2.8 "Tips for users of previous versions"_start_8 :ule,b
+  2.4 "Building LAMMPS via the Make.py script"_start_4 :b
+  2.5 "Building LAMMPS as a library"_start_5 :b
+  2.6 "Running LAMMPS"_start_6 :b
+  2.7 "Command-line options"_start_7 :b
+  2.8 "Screen output"_start_8 :b
+  2.9 "Tips for users of previous versions"_start_9 :ule,b
 "Commands"_Section_commands.html :l
   3.1 "LAMMPS input script"_cmd_1 :ulb,b
   3.2 "Parsing rules"_cmd_2 :b
@@ -261,6 +262,7 @@ END_RST -->
 :link(start_6,Section_start.html#start_6)
 :link(start_7,Section_start.html#start_7)
 :link(start_8,Section_start.html#start_8)
+:link(start_9,Section_start.html#start_9)
 
 :link(cmd_1,Section_commands.html#cmd_1)
 :link(cmd_2,Section_commands.html#cmd_2)

doc/src/Section_accelerate.txt

@@ -56,7 +56,7 @@ timings; you can simply extrapolate from short runs.
 
 For the set of runs, look at the timing data printed to the screen and
 log file at the end of each LAMMPS run.  "This
-section"_Section_start.html#start_7 of the manual has an overview.
+section"_Section_start.html#start_8 of the manual has an overview.
 
 Running on one (or a few processors) should give a good estimate of
 the serial performance and what portions of the timestep are taking
@@ -226,16 +226,16 @@ re-build LAMMPS |
   make machine |
 prepare and test a regular LAMMPS simulation |
   lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script |
-enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_6, |
+enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_7, |
   only needed for KOKKOS package |
-set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_6 or "package"_package.html command, |
+set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_7 or "package"_package.html command, |
   only if defaults need to be changed |
-use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_6 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu
+use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_7 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu
 :tb(c=2,s=|)
 
-Note that the first 4 steps can be done as a single command with
-suitable make command invocations. This is discussed in "Section
-4"_Section_packages.html of the manual, and its use is
+Note that the first 4 steps can be done as a single command, using the
+src/Make.py tool.  This tool is discussed in "Section
+2.4"_Section_start.html#start_4 of the manual, and its use is
 illustrated in the individual accelerator sections.  Typically these
 steps only need to be done once, to create an executable that uses one
 or more accelerator packages.

doc/src/Section_commands.txt

@@ -281,12 +281,12 @@ the "minimize"_minimize.html command.  A parallel tempering
 
 3.4 Commands listed by category :link(cmd_4),h4
 
-This section lists core LAMMPS commands, grouped by category.
-The "next section"_#cmd_5 lists all commands alphabetically.  The
+This section lists all LAMMPS commands, grouped by category.  The
+"next section"_#cmd_5 lists the same commands alphabetically.  The
 next section also includes (long) lists of style options for entries
 that appear in the following categories as a single command (fix,
 compute, pair, etc).  Commands that are added by user packages are not
-included in the categories here, but they are in the next section.
+included in these categories, but they are in the next section.
 
 Initialization:
 
@@ -361,7 +361,7 @@ Settings:
 "timer"_timer.html,
 "timestep"_timestep.html
 
-Operations within timestepping (fixes) and diagnostics (computes):
+Operations within timestepping (fixes) and diagnositics (computes):
 
 "compute"_compute.html,
 "compute_modify"_compute_modify.html,
@@ -527,13 +527,12 @@ These are additional commands in USER packages, which can be used if
 "LAMMPS is built with the appropriate
 package"_Section_start.html#start_3.
 
-"dump netcdf"_dump_netcdf.html,
-"dump netcdf/mpiio"_dump_netcdf.html,
-"dump vtk"_dump_vtk.html,
+"dump custom/vtk"_dump_custom_vtk.html,
+"dump nc"_dump_nc.html,
+"dump nc/mpiio"_dump_nc.html,
 "group2ndx"_group2ndx.html,
 "ndx2group"_group2ndx.html,
-"temper/grem"_temper_grem.html,
-"temper/npt"_temper_npt.html :tb(c=3,ea=c)
+"temper/grem"_temper_grem.html :tb(c=3,ea=c)
 
 :line
 
@@ -580,7 +579,6 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "halt"_fix_halt.html,
 "heat"_fix_heat.html,
 "indent"_fix_indent.html,
-"latte"_fix_latte.html,
 "langevin (k)"_fix_langevin.html,
 "lineforce"_fix_lineforce.html,
 "momentum (k)"_fix_momentum.html,
@@ -620,7 +618,6 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "press/berendsen"_fix_press_berendsen.html,
 "print"_fix_print.html,
 "property/atom"_fix_property_atom.html,
-"python"_fix_python.html,
 "qeq/comb (o)"_fix_qeq_comb.html,
 "qeq/dynamic"_fix_qeq.html,
 "qeq/fire"_fix_qeq.html,
@@ -687,11 +684,9 @@ package"_Section_start.html#start_3.
 "drude"_fix_drude.html,
 "drude/transform/direct"_fix_drude_transform.html,
 "drude/transform/reverse"_fix_drude_transform.html,
-"edpd/source"_fix_dpd_source.html,
 "eos/cv"_fix_eos_cv.html,
 "eos/table"_fix_eos_table.html,
 "eos/table/rx"_fix_eos_table_rx.html,
-"filter/corotate"_fix_filter_corotate.html,
 "flow/gauss"_fix_flow_gauss.html,
 "gle"_fix_gle.html,
 "grem"_fix_grem.html,
@@ -707,9 +702,6 @@ package"_Section_start.html#start_3.
 "meso"_fix_meso.html,
 "manifoldforce"_fix_manifoldforce.html,
 "meso/stationary"_fix_meso_stationary.html,
-"mvv/dpd"_fix_mvv_dpd.html,
-"mvv/edpd"_fix_mvv_dpd.html,
-"mvv/tdpd"_fix_mvv_dpd.html,
 "nve/dot"_fix_nve_dot.html,
 "nve/dotc/langevin"_fix_nve_dotc_langevin.html,
 "nve/manifold/rattle"_fix_nve_manifold_rattle.html,
@@ -723,7 +715,7 @@ package"_Section_start.html#start_3.
 "phonon"_fix_phonon.html,
 "pimd"_fix_pimd.html,
 "qbmsst"_fix_qbmsst.html,
-"qeq/reax (ko)"_fix_qeq_reax.html,
+"qeq/reax"_fix_qeq_reax.html,
 "qmmm"_fix_qmmm.html,
 "qtb"_fix_qtb.html,
 "reax/c/bonds"_fix_reax_bonds.html,
@@ -738,12 +730,9 @@ package"_Section_start.html#start_3.
 "smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html,
 "smd/setvel"_fix_smd_setvel.html,
 "smd/wall/surface"_fix_smd_wall_surface.html,
-"tdpd/source"_fix_dpd_source.html,
 "temp/rescale/eff"_fix_temp_rescale_eff.html,
 "ti/spring"_fix_ti_spring.html,
-"ttm/mod"_fix_ttm.html,
-"wall/ees"_fix_wall_ees.html,
-"wall/region/ees"_fix_wall_ees.html :tb(c=6,ea=c)
+"ttm/mod"_fix_ttm.html :tb(c=6,ea=c)
 
 :line
 
@@ -757,7 +746,6 @@ package"_Section_accelerate.html.  This is indicated by additional
 letters in parenthesis: g = GPU, i = USER-INTEL, k =
 KOKKOS, o = USER-OMP, t = OPT.
 
-"aggregate/atom"_compute_cluster_atom.html,
 "angle"_compute_angle.html,
 "angle/local"_compute_angle_local.html,
 "angmom/chunk"_compute_angmom_chunk.html,
@@ -783,7 +771,6 @@ KOKKOS, o = USER-OMP, t = OPT.
 "erotate/sphere"_compute_erotate_sphere.html,
 "erotate/sphere/atom"_compute_erotate_sphere_atom.html,
 "event/displace"_compute_event_displace.html,
-"fragment/atom"_compute_cluster_atom.html,
 "global/atom"_compute_global_atom.html,
 "group/group"_compute_group_group.html,
 "gyration"_compute_gyration.html,
@@ -842,10 +829,8 @@ package"_Section_start.html#start_3.
 
 "ackland/atom"_compute_ackland_atom.html,
 "basal/atom"_compute_basal_atom.html,
-"cnp/atom"_compute_cnp_atom.html,
 "dpd"_compute_dpd.html,
 "dpd/atom"_compute_dpd_atom.html,
-"edpd/temp/atom"_compute_edpd_temp_atom.html,
 "fep"_compute_fep.html,
 "force/tally"_compute_tally.html,
 "heat/flux/tally"_compute_tally.html,
@@ -878,7 +863,6 @@ package"_Section_start.html#start_3.
 "smd/ulsph/stress"_compute_smd_ulsph_stress.html,
 "smd/vol"_compute_smd_vol.html,
 "stress/tally"_compute_tally.html,
-"tdpd/cc/atom"_compute_tdpd_cc_atom.html,
 "temp/drude"_compute_temp_drude.html,
 "temp/eff"_compute_temp_eff.html,
 "temp/deform/eff"_compute_temp_deform_eff.html,
@@ -903,8 +887,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 "hybrid"_pair_hybrid.html,
 "hybrid/overlay"_pair_hybrid.html,
 "adp (o)"_pair_adp.html,
-"airebo (oi)"_pair_airebo.html,
-"airebo/morse (oi)"_pair_airebo.html,
+"airebo (o)"_pair_airebo.html,
+"airebo/morse (o)"_pair_airebo.html,
 "beck (go)"_pair_beck.html,
 "body"_pair_body.html,
 "bop"_pair_bop.html,
@@ -938,27 +922,23 @@ KOKKOS, o = USER-OMP, t = OPT.
 "dpd/tstat (go)"_pair_dpd.html,
 "dsmc"_pair_dsmc.html,
 "eam (gkiot)"_pair_eam.html,
-"eam/alloy (gkiot)"_pair_eam.html,
-"eam/fs (gkiot)"_pair_eam.html,
+"eam/alloy (gkot)"_pair_eam.html,
+"eam/fs (gkot)"_pair_eam.html,
 "eim (o)"_pair_eim.html,
 "gauss (go)"_pair_gauss.html,
 "gayberne (gio)"_pair_gayberne.html,
 "gran/hertz/history (o)"_pair_gran.html,
 "gran/hooke (o)"_pair_gran.html,
 "gran/hooke/history (o)"_pair_gran.html,
-"gw"_pair_gw.html,
-"gw/zbl"_pair_gw.html,
 "hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,
 "hbond/dreiding/morse (o)"_pair_hbond_dreiding.html,
 "kim"_pair_kim.html,
 "lcbop"_pair_lcbop.html,
 "line/lj"_pair_line_lj.html,
-"lj/charmm/coul/charmm (kio)"_pair_charmm.html,
+"lj/charmm/coul/charmm (ko)"_pair_charmm.html,
 "lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
-"lj/charmm/coul/long (gkio)"_pair_charmm.html,
+"lj/charmm/coul/long (giko)"_pair_charmm.html,
 "lj/charmm/coul/msm"_pair_charmm.html,
-"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
-"lj/charmmfsw/coul/long"_pair_charmm.html,
 "lj/class2 (gko)"_pair_class2.html,
 "lj/class2/coul/cut (ko)"_pair_class2.html,
 "lj/class2/coul/long (gko)"_pair_class2.html,
@@ -977,7 +957,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "lj/expand (gko)"_pair_lj_expand.html,
 "lj/gromacs (gko)"_pair_gromacs.html,
 "lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html,
-"lj/long/coul/long (io)"_pair_lj_long.html,
+"lj/long/coul/long (o)"_pair_lj_long.html,
 "lj/long/dipole/long"_pair_dipole.html,
 "lj/long/tip4p/long"_pair_lj_long.html,
 "lj/smooth (o)"_pair_lj_smooth.html,
@@ -989,7 +969,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "lubricateU/poly"_pair_lubricateU.html,
 "meam"_pair_meam.html,
 "mie/cut (o)"_pair_mie.html,
-"morse (gkot)"_pair_morse.html,
+"morse (got)"_pair_morse.html,
 "nb3b/harmonic (o)"_pair_nb3b_harmonic.html,
 "nm/cut (o)"_pair_nm.html,
 "nm/cut/coul/cut (o)"_pair_nm.html,
@@ -999,9 +979,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 "peri/pmb (o)"_pair_peri.html,
 "peri/ves"_pair_peri.html,
 "polymorphic"_pair_polymorphic.html,
-"python"_pair_python.html,
 "reax"_pair_reax.html,
-"rebo (oi)"_pair_airebo.html,
+"rebo (o)"_pair_airebo.html,
 "resquared (go)"_pair_resquared.html,
 "snap"_pair_snap.html,
 "soft (go)"_pair_soft.html,
@@ -1034,12 +1013,9 @@ package"_Section_start.html#start_3.
 "dpd/fdt/energy"_pair_dpd_fdt.html,
 "eam/cd (o)"_pair_eam.html,
 "edip (o)"_pair_edip.html,
-"edip/multi"_pair_edip.html,
-"edpd"_pair_meso.html,
 "eff/cut"_pair_eff.html,
 "exp6/rx"_pair_exp6_rx.html,
 "gauss/cut"_pair_gauss.html,
-"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
 "lennard/mdf"_pair_mdf.html,
 "list"_pair_list.html,
 "lj/charmm/coul/long/soft (o)"_pair_charmm.html,
@@ -1053,13 +1029,10 @@ 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,
-"mdpd"_pair_meso.html,
-"mdpd/rhosum"_pair_meso.html,
-"meam/c"_pair_meam.html,
+"lj/sf (o)"_pair_lj_sf.html,
 "meam/spline (o)"_pair_meam_spline.html,
 "meam/sw/spline"_pair_meam_sw_spline.html,
 "mgpt"_pair_mgpt.html,
-"momb"_pair_momb.html,
 "morse/smooth/linear"_pair_morse.html,
 "morse/soft"_pair_morse.html,
 "multi/lucy"_pair_multi_lucy.html,
@@ -1069,12 +1042,8 @@ package"_Section_start.html#start_3.
 "oxdna/hbond"_pair_oxdna.html,
 "oxdna/stk"_pair_oxdna.html,
 "oxdna/xstk"_pair_oxdna.html,
-"oxdna2/coaxstk"_pair_oxdna2.html,
-"oxdna2/dh"_pair_oxdna2.html,
-"oxdna2/excv"_pair_oxdna2.html,
-"oxdna2/stk"_pair_oxdna2.html,
 "quip"_pair_quip.html,
-"reax/c (ko)"_pair_reaxc.html,
+"reax/c (k)"_pair_reax_c.html,
 "smd/hertz"_pair_smd_hertz.html,
 "smd/tlsph"_pair_smd_tlsph.html,
 "smd/triangulated/surface"_pair_smd_triangulated_surface.html,
@@ -1088,7 +1057,6 @@ package"_Section_start.html#start_3.
 "sph/taitwater/morris"_pair_sph_taitwater_morris.html,
 "srp"_pair_srp.html,
 "table/rx"_pair_table_rx.html,
-"tdpd"_pair_meso.html,
 "tersoff/table (o)"_pair_tersoff.html,
 "thole"_pair_thole.html,
 "tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)
@@ -1108,7 +1076,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "none"_bond_none.html,
 "zero"_bond_zero.html,
 "hybrid"_bond_hybrid.html,
-"class2 (ko)"_bond_class2.html,
+"class2 (o)"_bond_class2.html,
 "fene (iko)"_bond_fene.html,
 "fene/expand (o)"_bond_fene_expand.html,
 "harmonic (ko)"_bond_harmonic.html,
@@ -1123,8 +1091,7 @@ package"_Section_start.html#start_3.
 
 "harmonic/shift (o)"_bond_harmonic_shift.html,
 "harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
-"oxdna/fene"_bond_oxdna.html,
-"oxdna2/fene"_bond_oxdna.html :tb(c=4,ea=c)
+"oxdna/fene"_bond_oxdna_fene.html :tb(c=4,ea=c)
 
 :line
 
@@ -1142,7 +1109,7 @@ USER-OMP, t = OPT.
 "zero"_angle_zero.html,
 "hybrid"_angle_hybrid.html,
 "charmm (ko)"_angle_charmm.html,
-"class2 (ko)"_angle_class2.html,
+"class2 (o)"_angle_class2.html,
 "cosine (o)"_angle_cosine.html,
 "cosine/delta (o)"_angle_cosine_delta.html,
 "cosine/periodic (o)"_angle_cosine_periodic.html,
@@ -1178,8 +1145,7 @@ USER-OMP, t = OPT.
 "zero"_dihedral_zero.html,
 "hybrid"_dihedral_hybrid.html,
 "charmm (ko)"_dihedral_charmm.html,
-"charmmfsw"_dihedral_charmm.html,
-"class2 (ko)"_dihedral_class2.html,
+"class2 (o)"_dihedral_class2.html,
 "harmonic (io)"_dihedral_harmonic.html,
 "helix (o)"_dihedral_helix.html,
 "multi/harmonic (o)"_dihedral_multi_harmonic.html,
@@ -1211,7 +1177,7 @@ USER-OMP, t = OPT.
 "none"_improper_none.html,
 "zero"_improper_zero.html,
 "hybrid"_improper_hybrid.html,
-"class2 (ko)"_improper_class2.html,
+"class2 (o)"_improper_class2.html,
 "cvff (io)"_improper_cvff.html,
 "harmonic (ko)"_improper_harmonic.html,
 "umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)
@@ -1243,7 +1209,7 @@ USER-OMP, t = OPT.
 "msm/cg (o)"_kspace_style.html,
 "pppm (go)"_kspace_style.html,
 "pppm/cg (o)"_kspace_style.html,
-"pppm/disp (i)"_kspace_style.html,
+"pppm/disp"_kspace_style.html,
 "pppm/disp/tip4p"_kspace_style.html,
 "pppm/stagger"_kspace_style.html,
 "pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c)

doc/src/Section_errors.txt

@@ -22,7 +22,7 @@ either conceptually, or as printed out by the program.
 
 12.1 Common problems :link(err_1),h4
 
-If two LAMMPS runs do not produce the exact same answer on different
+If two LAMMPS runs do not produce the same answer on different
 machines or different numbers of processors, this is typically not a
 bug.  In theory you should get identical answers on any number of
 processors and on any machine.  In practice, numerical round-off can
@@ -71,7 +71,7 @@ style", with ... being fix, compute, pair, etc, it means that you
 mistyped the style name or that the command is part of an optional
 package which was not compiled into your executable.  The list of
 available styles in your executable can be listed by using "the -h
-command-line argument"_Section_start.html#start_6.  The installation
+command-line argument"_Section_start.html#start_7.  The installation
 and compilation of optional packages is explained in the "installation
 instructions"_Section_start.html#start_3.
 
@@ -80,24 +80,12 @@ order.  If you mess this up, LAMMPS will often flag the error, but it
 may also simply read a bogus argument and assign a value that is
 valid, but not what you wanted.  E.g. trying to read the string "abc"
 as an integer value of 0.  Careful reading of the associated doc page
-for the command should allow you to fix these problems. In most cases,
-where LAMMPS expects to read a number, either integer or floating point,
-it performs a stringent test on whether the provided input actually
-is an integer or floating-point number, respectively, and reject the
-input with an error message (for instance, when an integer is required,
-but a floating-point number 1.0 is provided):
-
-ERROR: Expected integer parameter in input script or data file :pre
-
-Some commands allow for using variable references in place of numeric
-constants so that the value can be evaluated and may change over the
-course of a run.  This is typically done with the syntax {v_name} for a
-parameter, where name is the name of the variable. On the other hand,
-immediate variable expansion with the syntax ${name} is performed while
-reading the input and before parsing commands,
-
-NOTE: Using a variable reference (i.e. {v_name}) is only allowed if
-the documentation of the corresponding command explicitly says it is.
+for the command should allow you to fix these problems.  Note that
+some commands allow for variables to be specified in place of numeric
+constants so that the value can be evaluated and change over the
+course of a run.  This is typically done with the syntax {v_name} for
+a parameter, where name is the name of the variable.  This is only
+allowed if the command documentation says it is.
 
 Generally, LAMMPS will print a message to the screen and logfile and
 exit gracefully when it encounters a fatal error.  Sometimes it will
@@ -574,11 +562,11 @@ group of atoms correctly. :dd
 
 {Bad quadratic solve for particle/line collision} :dt
 
-This is an internal error.  It should normally not occur. :dd
+This is an internal error.  It should nornally not occur. :dd
 
 {Bad quadratic solve for particle/tri collision} :dt
 
-This is an internal error.  It should normally not occur. :dd
+This is an internal error.  It should nornally not occur. :dd
 
 {Bad real space Coulomb cutoff in fix tune/kspace} :dt
 
@@ -912,7 +900,7 @@ Atoms can not be added afterwards to this fix option. :dd
 
 {Cannot append atoms to a triclinic box} :dt
 
-The simulation box must be defined with edges aligned with the
+The simulation box must be defined with edges alligned with the
 Cartesian axes. :dd
 
 {Cannot balance in z dimension for 2d simulation} :dt
@@ -992,7 +980,7 @@ file. :dd
 
 LAMMPS failed to compute an initial guess for the PPPM_disp g_ewald_6
 factor that partitions the computation between real space and k-space
-for Dispersion interactions. :dd
+for Disptersion interactions. :dd
 
 {Cannot create an atom map unless atoms have IDs} :dt
 
@@ -1327,7 +1315,7 @@ Self-explanatory. :dd
 
 This file is created when you use some LAMMPS features, to indicate
 what paper you should cite on behalf of those who implemented
-the feature.  Check that you have write privileges into the directory
+the feature.  Check that you have write priveleges into the directory
 you are running in. :dd
 
 {Cannot open log.lammps for writing} :dt
@@ -2005,7 +1993,7 @@ Self-explanatory. :dd
 
 {Cannot use fix reax/bonds without pair_style reax} :dt
 
-Self-explanatory. :dd
+Self-explantory. :dd
 
 {Cannot use fix rigid npt/nph and fix deform on same component of stress tensor} :dt
 
@@ -2088,7 +2076,7 @@ Self-explanatory. :dd
 
 {Cannot use lines with fix srd unless overlap is set} :dt
 
-This is because line segments are connected to each other. :dd
+This is because line segements are connected to each other. :dd
 
 {Cannot use multiple fix wall commands with pair brownian} :dt
 
@@ -2131,7 +2119,7 @@ Self-explanatory. :dd
 
 {Cannot use newton pair with born/gpu pair style} :dt
 
-Self-explanatory. :dd
+Self-explantory. :dd
 
 {Cannot use newton pair with buck/coul/cut/gpu pair style} :dt
 
@@ -2291,7 +2279,7 @@ Self-explanatory. :dd
 
 {Cannot use newton pair with zbl/gpu pair style} :dt
 
-Self-explanatory. :dd
+Self-explantory. :dd
 
 {Cannot use non-zero forces in an energy minimization} :dt
 
@@ -2641,11 +2629,11 @@ uses a pairwise neighbor list. :dd
 
 {Compute chunk/atom bin/cylinder radius is too large for periodic box} :dt
 
-Radius cannot be bigger than 1/2 of a non-axis  periodic dimension. :dd
+Radius cannot be bigger than 1/2 of a non-axis  periodic dimention. :dd
 
 {Compute chunk/atom bin/sphere radius is too large for periodic box} :dt
 
-Radius cannot be bigger than 1/2 of any periodic dimension. :dd
+Radius cannot be bigger than 1/2 of any periodic dimention. :dd
 
 {Compute chunk/atom compute array is accessed out-of-range} :dt
 
@@ -2706,15 +2694,15 @@ It will only store IDs if its compress option is enabled. :dd
 
 {Compute chunk/atom stores no coord1 for compute property/chunk} :dt
 
-Only certain binning options for compute chunk/atom store coordinates. :dd
+Only certain binning options for comptue chunk/atom store coordinates. :dd
 
 {Compute chunk/atom stores no coord2 for compute property/chunk} :dt
 
-Only certain binning options for compute chunk/atom store coordinates. :dd
+Only certain binning options for comptue chunk/atom store coordinates. :dd
 
 {Compute chunk/atom stores no coord3 for compute property/chunk} :dt
 
-Only certain binning options for compute chunk/atom store coordinates. :dd
+Only certain binning options for comptue chunk/atom store coordinates. :dd
 
 {Compute chunk/atom variable is not atom-style variable} :dt
 
@@ -2735,11 +2723,11 @@ is used to find clusters. :dd
 
 {Compute cna/atom cutoff is longer than pairwise cutoff} :dt
 
-Self-explanatory. :dd
+Self-explantory. :dd
 
 {Compute cna/atom requires a pair style be defined} :dt
 
-Self-explanatory. :dd
+Self-explantory. :dd
 
 {Compute com/chunk does not use chunk/atom compute} :dt
 
@@ -2747,7 +2735,7 @@ The style of the specified compute is not chunk/atom. :dd
 
 {Compute contact/atom requires a pair style be defined} :dt
 
-Self-explanatory. :dd
+Self-explantory. :dd
 
 {Compute contact/atom requires atom style sphere} :dt
 
@@ -2760,7 +2748,7 @@ since those atoms are not in the neighbor list. :dd
 
 {Compute coord/atom requires a pair style be defined} :dt
 
-Self-explanatory. :dd
+Self-explantory. :dd
 
 {Compute damage/atom requires peridynamic potential} :dt
 
@@ -2790,7 +2778,7 @@ Self-explanatory. :dd
 
 {Compute erotate/asphere requires extended particles} :dt
 
-This compute cannot be used with point particles. :dd
+This compute cannot be used with point paritlces. :dd
 
 {Compute erotate/rigid with non-rigid fix-ID} :dt
 
@@ -2835,7 +2823,7 @@ Cannot compute order parameter beyond cutoff. :dd
 
 {Compute hexorder/atom requires a pair style be defined} :dt
 
-Self-explanatory. :dd
+Self-explantory. :dd
 
 {Compute improper/local used when impropers are not allowed} :dt
 
@@ -2881,11 +2869,11 @@ Cannot compute order parameter beyond cutoff. :dd
 
 {Compute orientorder/atom requires a pair style be defined} :dt
 
-Self-explanatory. :dd
+Self-explantory. :dd
 
 {Compute pair must use group all} :dt
 
-Pair styles accumulate energy on all atoms. :dd
+Pair styles accumlate energy on all atoms. :dd
 
 {Compute pe must use group all} :dt
 
@@ -2935,7 +2923,7 @@ The style of the specified compute is not chunk/atom. :dd
 {Compute property/local cannot use these inputs together} :dt
 
 Only inputs that generate the same number of datums can be used
-together.  E.g. bond and angle quantities cannot be mixed. :dd
+togther.  E.g. bond and angle quantities cannot be mixed. :dd
 
 {Compute property/local does not (yet) work with atom_style template} :dt
 
@@ -3079,7 +3067,7 @@ Self-explanatory. :dd
 
 {Compute temp/asphere requires extended particles} :dt
 
-This compute cannot be used with point particles. :dd
+This compute cannot be used with point paritlces. :dd
 
 {Compute temp/body requires atom style body} :dt
 
@@ -3524,12 +3512,12 @@ path and name are correct. :dd
 
 {Could not process Python file} :dt
 
-The Python code in the specified file was not run successfully by
+The Python code in the specified file was not run sucessfully by
 Python, probably due to errors in the Python code. :dd
 
 {Could not process Python string} :dt
 
-The Python code in the here string was not run successfully by Python,
+The Python code in the here string was not run sucessfully by Python,
 probably due to errors in the Python code. :dd
 
 {Coulomb PPPMDisp order has been reduced below minorder} :dt
@@ -3638,7 +3626,7 @@ Self-explanatory. :dd
 
 {Cutoffs missing in pair_style buck/long/coul/long} :dt
 
-Self-explanatory. :dd
+Self-exlanatory. :dd
 
 {Cutoffs missing in pair_style lj/long/coul/long} :dt
 
@@ -4385,7 +4373,7 @@ Self-explanatory. :dd
 
 {Fix ave/chunk does not use chunk/atom compute} :dt
 
-The specified compute is not for a compute chunk/atom command. :dd
+The specified conpute is not for a compute chunk/atom command. :dd
 
 {Fix ave/chunk fix does not calculate a per-atom array} :dt
 
@@ -4617,11 +4605,11 @@ An index for the array is out of bounds. :dd
 
 {Fix ave/time compute does not calculate a scalar} :dt
 
-Self-explanatory. :dd
+Self-explantory. :dd
 
 {Fix ave/time compute does not calculate a vector} :dt
 
-Self-explanatory. :dd
+Self-explantory. :dd
 
 {Fix ave/time compute does not calculate an array} :dt
 
@@ -4696,9 +4684,9 @@ Self-explanatory. :dd
 
 {Fix bond/create induced too many angles/dihedrals/impropers per atom} :dt
 
-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
+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
 
 {Fix bond/create needs ghost atoms from further away} :dt
 
@@ -4970,7 +4958,7 @@ Self-explanatory. :dd
 
 {Fix langevin angmom requires extended particles} :dt
 
-This fix option cannot be used with point particles. :dd
+This fix option cannot be used with point paritlces. :dd
 
 {Fix langevin omega is not yet implemented with kokkos} :dt
 
@@ -6171,7 +6159,7 @@ map command will force an atom map to be created. :dd
 
 {Initial temperatures not all set in fix ttm} :dt
 
-Self-explanatory. :dd
+Self-explantory. :dd
 
 {Input line quote not followed by whitespace} :dt
 
@@ -6199,7 +6187,7 @@ Eigensolve for rigid body was not sufficiently accurate. :dd
 
 {Insufficient Jacobi rotations for triangle} :dt
 
-The calculation of the inertia tensor of the triangle failed.  This
+The calculation of the intertia tensor of the triangle failed.  This
 should not happen if it is a reasonably shaped triangle. :dd
 
 {Insufficient memory on accelerator} :dt
@@ -6463,15 +6451,15 @@ Self-explanatory. :dd
 
 {Invalid attribute in dump custom command} :dt
 
-Self-explanatory. :dd
+Self-explantory. :dd
 
 {Invalid attribute in dump local command} :dt
 
-Self-explanatory. :dd
+Self-explantory. :dd
 
 {Invalid attribute in dump modify command} :dt
 
-Self-explanatory. :dd
+Self-explantory. :dd
 
 {Invalid basis setting in create_atoms command} :dt
 
@@ -6737,7 +6725,7 @@ or cause multiple files to be written. :dd
 Filenames used with the dump xyz style cannot be binary or cause files
 to be written by each processor. :dd
 
-{Invalid dump_modify threshold operator} :dt
+{Invalid dump_modify threshhold operator} :dt
 
 Operator keyword used for threshold specification in not recognized. :dd
 
@@ -6751,7 +6739,7 @@ The fix is not recognized. :dd
 
 {Invalid fix ave/time off column} :dt
 
-Self-explanatory. :dd
+Self-explantory. :dd
 
 {Invalid fix box/relax command for a 2d simulation} :dt
 
@@ -7313,7 +7301,7 @@ Self-explanatory. Check the input script or data file. :dd
 
 {LJ6 off not supported in pair_style buck/long/coul/long} :dt
 
-Self-explanatory. :dd
+Self-exlanatory. :dd
 
 {Label wasn't found in input script} :dt
 
@@ -7361,7 +7349,7 @@ This should not occur.  Report the problem to the developers. :dd
 Lost atoms are checked for each time thermo output is done.  See the
 thermo_modify lost command for options.  Lost atoms usually indicate
 bad dynamics, e.g. atoms have been blown far out of the simulation
-box, or moved further than one processor's sub-domain away before
+box, or moved futher than one processor's sub-domain away before
 reneighboring. :dd
 
 {MEAM library error %d} :dt
@@ -7526,7 +7514,7 @@ Self-explanatory. :dd
 
 {Molecule template ID for create_atoms does not exist} :dt
 
-Self-explanatory. :dd
+Self-explantory. :dd
 
 {Molecule template ID for fix deposit does not exist} :dt
 
@@ -7552,7 +7540,7 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
-{Molecule topology/atom exceeds system topology/atom} :dt
+{Molecule toplogy/atom exceeds system topology/atom} :dt
 
 The number of bonds, angles, etc per-atom in the molecule exceeds the
 system setting.  See the create_box command for how to specify these
@@ -7792,7 +7780,7 @@ Self-explanatory. :dd
 
 {Must use variable energy with fix addforce} :dt
 
-Must define an energy variable when applying a dynamic
+Must define an energy vartiable when applyting a dynamic
 force during minimization. :dd
 
 {Must use variable energy with fix efield} :dt
@@ -7876,20 +7864,18 @@ 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 using the "extra/bond/per/atom"
-keyword to allow for additional bonds to be formed
+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
 
 {New bond exceeded bonds per atom in fix bond/create} :dt
 
-See the read_data command for info on using the "extra/bond/per/atom"
-keyword to allow for additional bonds to be formed :dd
+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
 
 {New bond exceeded special list size in fix bond/create} :dt
 
-See the "read_data extra/special/per/atom" command
-(or the "create_box extra/special/per/atom" command)
-for info on how to leave space in the special bonds
-list to allow for additional bonds to be formed. :dd
+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
 
 {Newton bond change after simulation box is defined} :dt
 
@@ -8044,7 +8030,7 @@ Self-explanatory. :dd
 
 {Non digit character between brackets in variable} :dt
 
-Self-explanatory. :dd
+Self-explantory. :dd
 
 {Non integer # of swaps in temper command} :dt
 
@@ -8665,7 +8651,7 @@ not be invoked by bond_style quartic. :dd
 {Pair style does not support compute group/group} :dt
 
 The pair_style does not have a single() function, so it cannot be
-invoked by the compute group/group command. :dd
+invokded by the compute group/group command. :dd
 
 {Pair style does not support compute pair/local} :dt
 
@@ -8892,14 +8878,6 @@ This is a requirement to use this potential. :dd
 
 See the newton command.  This is a restriction to use this potential. :dd
 
-{Pair style vashishta/gpu requires atom IDs} :dt
-
-This is a requirement to use this potential. :dd
-
-{Pair style vashishta/gpu requires newton pair off} :dt
-
-See the newton command.  This is a restriction to use this potential. :dd
-
 {Pair style tersoff/gpu requires atom IDs} :dt
 
 This is a requirement to use the tersoff/gpu potential. :dd
@@ -8958,11 +8936,11 @@ Self-explanatory. :dd
 
 {Pair yukawa/colloid requires atom style sphere} :dt
 
-Self-explanatory. :dd
+Self-explantory. :dd
 
 {Pair yukawa/colloid requires atoms with same type have same radius} :dt
 
-Self-explanatory. :dd
+Self-explantory. :dd
 
 {Pair yukawa/colloid/gpu requires atom style sphere} :dt
 
@@ -9176,7 +9154,7 @@ Self-explanatory. :dd
 
 {Python function evaluation failed} :dt
 
-The Python function did not run successfully and/or did not return a
+The Python function did not run succesfully and/or did not return a
 value (if it is supposed to return a value).  This is probably due to
 some error condition in the function. :dd
 
@@ -9666,10 +9644,9 @@ you are running. :dd
 
 {Special list size exceeded in fix bond/create} :dt
 
-See the "read_data extra/special/per/atom" command
-(or the "create_box extra/special/per/atom" command)
-for info on how to leave space in the special bonds
-list to allow for additional bonds to be formed. :dd
+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
 
 {Specified processors != physical processors} :dt
 
@@ -9686,23 +9663,23 @@ Self-explanatory. :dd
 
 {Subsequent read data induced too many angles per atom} :dt
 
-See the extra/angle/per/atom keyword for the create_box
-or the read_data command to set this limit larger :dd
+See the create_box extra/angle/per/atom or read_data "extra angle per
+atom" header value to set this limit larger. :dd
 
 {Subsequent read data induced too many bonds per atom} :dt
 
-See the extra/bond/per/atom keyword for the create_box
-or the read_data command to set this limit larger :dd
+See the create_box extra/bond/per/atom or read_data "extra bond per
+atom" header value to set this limit larger. :dd
 
 {Subsequent read data induced too many dihedrals per atom} :dt
 
-See the extra/dihedral/per/atom keyword for the create_box
-or the read_data command to set this limit larger :dd
+See the create_box extra/dihedral/per/atom or read_data "extra
+dihedral per atom" header value to set this limit larger. :dd
 
 {Subsequent read data induced too many impropers per atom} :dt
 
-See the extra/improper/per/atom keyword for the create_box
-or the read_data command to set this limit larger :dd
+See the create_box extra/improper/per/atom or read_data "extra
+improper per atom" header value to set this limit larger. :dd
 
 {Substitution for illegal variable} :dt
 
@@ -10036,7 +10013,7 @@ make sense in between runs. :dd
 
 {Threshhold for an atom property that isn't allocated} :dt
 
-A dump threshold has been requested on a quantity that is
+A dump threshhold has been requested on a quantity that is
 not defined by the atom style used in this simulation. :dd
 
 {Timestep must be >= 0} :dt
@@ -10098,7 +10075,7 @@ to a large size. :dd
 {Too many atom triplets for pair bop} :dt
 
 The number of three atom groups for angle determinations exceeds the
-expected number.  Check your atomic structure to ensure that it is
+expected number.  Check your atomic structrure to ensure that it is
 realistic. :dd
 
 {Too many atoms for dump dcd} :dt
@@ -10166,7 +10143,7 @@ to a large size. :dd
 
 {Too many timesteps} :dt
 
-The cumulative timesteps must fit in a 64-bit integer. :dd
+The cummulative timesteps must fit in a 64-bit integer. :dd
 
 {Too many timesteps for NEB} :dt
 
@@ -10665,7 +10642,7 @@ Only atom-style variables can be used. :dd
 
 {Variable for region cylinder is invalid style} :dt
 
-Only equal-style variables are allowed. :dd
+Only equal-style varaibles are allowed. :dd
 
 {Variable for region is invalid style} :dt
 
@@ -10677,7 +10654,7 @@ Self-explanatory. :dd
 
 {Variable for region sphere is invalid style} :dt
 
-Only equal-style variables are allowed. :dd
+Only equal-style varaibles are allowed. :dd
 
 {Variable for restart is invalid style} :dt
 
@@ -10718,7 +10695,7 @@ Self-explanatory. :dd
 {Variable has circular dependency} :dt
 
 A circular dependency is when variable "a" in used by variable "b" and
-variable "b" is also used by variable "a".  Circular dependencies with
+variable "b" is also used by varaible "a".  Circular dependencies with
 longer chains of dependence are also not allowed. :dd
 
 {Variable name between brackets must be alphanumeric or underscore characters} :dt
@@ -10807,7 +10784,7 @@ Self-explanatory. :dd
 
 {Variable name for fix deform does not exist} :dt
 
-Self-explanatory. :dd
+Self-explantory. :dd
 
 {Variable name for fix efield does not exist} :dt
 
@@ -11094,7 +11071,7 @@ for a dihedral) and adding a small amount of stretch. :dd
 
 {Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero} :dt
 
-Self-explanatory. :dd
+Self-explantory. :dd
 
 {Calling write_dump before a full system init.} :dt
 
@@ -11182,12 +11159,6 @@ Self-explanatory. :dd
 If the fix changes the timestep, the dump dcd file will not
 reflect the change. :dd
 
-{Energy due to X extra global DOFs will be included in minimizer energies} :dt
-
-When using fixes like box/relax, the potential energy used by the minimizer
-is augmented by an additional energy provided by the fix. Thus the printed
-converged energy may be different from the total potential energy. :dd
-
 {Energy tally does not account for 'zero yes'} :dt
 
 The energy removed by using the 'zero yes' flag is not accounted
@@ -11431,7 +11402,7 @@ The command options you have used caused atoms to be lost. :dd
 Lost atoms are checked for each time thermo output is done.  See the
 thermo_modify lost command for options.  Lost atoms usually indicate
 bad dynamics, e.g. atoms have been blown far out of the simulation
-box, or moved further than one processor's sub-domain away before
+box, or moved futher than one processor's sub-domain away before
 reneighboring. :dd
 
 {MSM mesh too small, increasing to 2 points in each direction} :dt
@@ -11469,7 +11440,7 @@ i.e. the first molecule in the template. :dd
 
 {Molecule template for fix shake has multiple molecules} :dt
 
-The fix shake command will only recognize molecules of a single
+The fix shake command will only recoginze molecules of a single
 type, i.e. the first molecule in the template. :dd
 
 {More than one compute centro/atom} :dt
@@ -11554,7 +11525,7 @@ neigh_modify exclude command. :dd
 
 If a thermo_style command is used after a thermo_modify command, the
 settings changed by the thermo_modify command will be reset to their
-default values.  This is because the thermo_modify command acts on
+default values.  This is because the thermo_modify commmand acts on
 the currently defined thermo style, and a thermo_style command creates
 a new style. :dd
 
@@ -11606,7 +11577,7 @@ This may not be what you intended. :dd
 
 {One or more dynamic groups may not be updated at correct point in timestep} :dt
 
-If there are other fixes that act immediately after the initial stage
+If there are other fixes that act immediately after the intitial stage
 of time integration within a timestep (i.e. after atoms move), then
 the command that sets up the dynamic group should appear after those
 fixes.  This will insure that dynamic group assignments are made
@@ -11903,7 +11874,7 @@ Self-explanatory. :dd
 
 {Using largest cutoff for buck/long/coul/long} :dt
 
-Self-explanatory. :dd
+Self-exlanatory. :dd
 
 {Using largest cutoff for lj/long/coul/long} :dt
 

doc/src/Section_example.txt

@@ -25,7 +25,9 @@ files and image files.
 
 If you uncomment the "dump"_dump.html command in the input script, a
 text dump file will be produced, which can be animated by various
-"visualization programs"_http://lammps.sandia.gov/viz.html.
+"visualization programs"_http://lammps.sandia.gov/viz.html.  It can
+also be animated using the xmovie tool described in the "Additional
+Tools"_Section_tools.html section of the LAMMPS documentation.
 
 If you uncomment the "dump image"_dump.html command in the input
 script, and assuming you have built LAMMPS with a JPG library, JPG
@@ -49,14 +51,11 @@ Lists of both kinds of directories are given below.
 Lowercase directories :h4
 
 accelerate: run with various acceleration options (OpenMP, GPU, Phi)
-airebo:   polyethylene with AIREBO potential
 balance:  dynamic load balancing, 2d system
 body:     body particles, 2d system
-cmap:     CMAP 5-body contributions to CHARMM force field
 colloid:  big colloid particles in a small particle solvent, 2d system
 comb:     models using the COMB potential
 coreshell: core/shell model using CORESHELL package
-controller: use of fix controller as a thermostat
 crack:    crack propagation in a 2d solid
 deposit:  deposit atoms and molecules on a surface
 dipole:   point dipolar particles, 2d system
@@ -65,8 +64,6 @@ eim:      NaCl using the EIM potential
 ellipse:  ellipsoidal particles in spherical solvent, 2d system
 flow:     Couette and Poiseuille flow in a 2d channel
 friction: frictional contact of spherical asperities between 2d surfaces
-gcmc:     Grand Canonical Monte Carlo (GCMC) via the fix gcmc command
-granregion: use of fix wall/region/gran as boundary on granular particles
 hugoniostat: Hugoniostat shock dynamics
 indent:   spherical indenter into a 2d solid
 kim:      use of potentials in Knowledge Base for Interatomic Models (KIM)
@@ -74,7 +71,6 @@ meam:     MEAM test for SiC and shear (same as shear examples)
 melt:     rapid melt of 3d LJ system
 micelle:  self-assembly of small lipid-like molecules into 2d bilayers
 min:      energy minimization of 2d LJ melt
-mscg:     parameterize a multi-scale coarse-graining (MSCG) model
 msst:     MSST shock dynamics
 nb3b:     use of nonbonded 3-body harmonic pair style
 neb:      nudged elastic band (NEB) calculation for barrier finding
@@ -93,8 +89,7 @@ snap:     NVE dynamics for BCC tantalum crystal using SNAP potential
 srd:      stochastic rotation dynamics (SRD) particles as solvent
 streitz:  use of Streitz/Mintmire potential with charge equilibration
 tad:      temperature-accelerated dynamics of vacancy diffusion in bulk Si
-vashishta: use of the Vashishta potential
-voronoi:  Voronoi tesselation via compute voronoi/atom command :tb(s=:)
+vashishta: use of the Vashishta potential :tb(s=:)
 
 Here is how you can run and visualize one of the sample problems: