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Merge branch 'master' into cauchystat and resolve conflicts 

# Conflicts:
#	cmake/CMakeLists.txt
#	doc/src/Commands_fix.txt
#	doc/src/Packages_details.txt
#	doc/src/Packages_user.txt
#	doc/src/fix_nh.txt
#	doc/src/fixes.txt
#	doc/src/lammps.book
#	src/Makefile
This commit is contained in:
Axel Kohlmeyer 2020-01-12 13:58:41 -05:00
parent 2231feaf9b 587fc9d962
commit 107c5bbced
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GPG Key ID: D9B44E93BF0C375A
6945 changed files with 741191 additions and 464815 deletions
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@ -29,6 +29,7 @@ src/USER-MEAMC/* @martok
src/USER-MOFFF/* @hheenen
src/USER-MOLFILE/* @akohlmey
src/USER-NETCDF/* @pastewka
src/USER-PLUMED/* @gtribello
src/USER-PHONON/* @lingtikong
src/USER-PTM/* @pmla
src/USER-OMP/* @akohlmey
@ -110,6 +111,7 @@ src/exceptions.h @rbberger
src/fix_nh.* @athomps
src/info.* @akohlmey @rbberger
src/timer.* @akohlmey
src/min* @sjplimp @stanmoore1
# tools
tools/msi2lmp/* @akohlmey
@ -125,3 +127,6 @@ python/* @rbberger
doc/utils/*/* @rbberger
doc/Makefile @rbberger
doc/README @rbberger
# for releases
src/version.h @sjplimp

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# Code of Conduct for the LAMMPS Project on GitHub
## Our Pledge
In the interest of fostering an open and welcoming environment, we as LAMMPS
developers, contributors, and maintainers pledge to making participation in
our project a harassment-free experience for everyone.
## Our Standards
Examples of behavior that contributes to creating a positive environment
include:
* Using welcoming and inclusive language
* Being respectful of differing viewpoints and experiences
* Gracefully accepting constructive criticism
* Focusing on what is best for the community
* Showing empathy towards other community members
Examples of unacceptable behavior by participants include:
* The use of explicit language or imagery
* Trolling, insulting/derogatory comments, and personal or political attacks
* Public or private harassment
* Publishing others' private information, such as a physical or electronic
address, without explicit permission
## Our Responsibilities
Project maintainers are responsible for clarifying the standards of acceptable
behavior and are expected to take appropriate and fair corrective action in
response to any instances of unacceptable behavior.
Project maintainers have the right and responsibility to remove, edit, or
reject comments, commits, code, issues, and other contributions that are not
aligned to this Code of Conduct, or to ban temporarily or permanently any
developer, maintainer, or contributor for this or other behaviors that they
deem inappropriate, threatening, offensive, or harmful.
## Scope
This Code of Conduct applies to all public exchanges in the LAMMPS project
on GitHub and in submitted code.
## Enforcement
Instances of abusive, harassing, or otherwise unacceptable behavior may be
reported by contacting the project team at developer@lammps.org. All
complaints will be reviewed and investigated and will result in a response
that is deemed necessary and appropriate to the circumstances. The project
team is obligated to maintain confidentiality with regard to the reporter
of an incident.
Project maintainers who do not follow or enforce the Code of Conduct in good
faith may face temporary or permanent repercussions as determined by other
members of the project's leadership.
## Attribution
This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
[homepage]: https://www.contributor-covenant.org
For answers to common questions about this code of conduct, see
https://www.contributor-covenant.org/faq

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@ -2,11 +2,11 @@
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.
The following is a set of guidelines as well as explanations of policies and work flows 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)
* [The Section on submitting new features for inclusion in LAMMPS of the Manual](https://lammps.sandia.gov/doc/Modify_contribute.html)
* [The LAMMPS GitHub Tutorial in the Manual](http://lammps.sandia.gov/doc/Howto_github.html)
## Table of Contents
@ -18,7 +18,7 @@ Thus please also have a look at:
* [Suggesting Enhancements](#suggesting-enhancements)
* [Contributing Code](#contributing-code)
[GitHub Workflows](#github-workflows)
[GitHub Work flows](#github-workflows)
* [Issues](#issues)
* [Pull Requests](#pull-requests)
@ -26,17 +26,17 @@ __
## 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.
> **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](https://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](https://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.
to one of the [LAMMPS core developers](https://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.
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](https://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.
@ -44,7 +44,7 @@ If you post a message and you are a subscriber, your message will appear immedia
### 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.
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](https://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).
@ -62,13 +62,14 @@ To be able to submit an issue on GitHub, you have to register for an account (fo
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)
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](https://lammps.sandia.gov/doc/Howto_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.
* 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, style class header files should not import any system headers, 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. There MUST NOT be any "using namespace XXX;" statements in headers. In the implementation file (<name>.cpp) system includes should be placed in angular brackets (<>) and for c-library functions the C++ style header files should be included (<cstdio> instead of <stdio.h>, or <cstring> instead of <string.h>). 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.
* Source, style name, and documentation file should follow the following naming convention: style names should be lowercase and words separated by a forward slash; for a new fix style 'foo/bar', the class should be named FixFooBar, the name of the source files should be 'fix_foo_bar.h' and 'fix_foo_bar.cpp' and the corresponding documentation should be in a file 'fix_foo_bar.txt'.
* 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.
@ -102,11 +103,11 @@ For bug reports, the next step is that one of the core LAMMPS developers will se
### 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.
For submitting pull requests, there is a [detailed tutorial](https://lammps.sandia.gov/doc/Howto_github.html) in the LAMMPS manual. Thus only a brief breakdown of the steps is presented here. Please note, that the LAMMPS developers are still reviewing and trying to improve the process. If you are unsure about something, do not hesitate to post a question on the lammps-users mailing list or contact one fo the core LAMMPS developers.
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.
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. As part of the assesment, the pull request will be categorized with labels. There are two special labels: `needs_work` (indicates that work from the submitter of the pull request is needed) and `work_in_progress` (indicates, that the assigned LAMMPS developer will make changes, if not done by the contributor who made the submit).
You may also receive comments and suggestions on the overall submission or specific details and on occasion specific requests for changes as part of the review. If permitted, also 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.
If the assigned developer is satisfied and considers the submission ready for inclusion into LAMMPS, the pull request will receive approvals and be merged into the master branch by one of the core LAMMPS developers. After the pull request is merged, you may delete the feature branch used for the pull request 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 nothing set in stone. So depending on the nature of the contribution, the workflow may be adjusted.

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## 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_

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---
name: Bug report
about: Create a bug report to help us eliminate issues and improve LAMMPS
title: "[BUG] _Replace With Suitable Title_"
labels: bug
assignees: ''
---
**Summary**
_Please provide a clear and concise description of what the bug is._
**LAMMPS Version and Platform**
_Please specify precisely which LAMMPS version this issue was detected with (the first line of the output) and what platform (operating system and its version, hardware) you are running on. If possible, test with the most recent LAMMPS patch version_
**Expected Behavior**
_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**
_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 area of research._
**Steps to Reproduce**
_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 an input set that is as minimal and small as possible and reproduces the bug as quickly as possible. **NOTE:** the less effort and time it takes to reproduce your reported bug, the more likely it becomes, that somebody will look into it and fix the problem._
**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_

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---
name: Feature request
about: Make a suggestion for a new feature or a change to LAMMPS
title: "[Feature Request] _Replace with Title_"
labels: enhancement
assignees: ''
---
**Summary**
_Please provide a brief and concise description of the suggested feature or change_
**Detailed Description**
_Please explain how you would like to see LAMMPS enhanced, what feature(s) you are looking for, what specific problems this will solve. If possible, provide references to relevant background information like publications or web pages, and whether you are planning to implement the enhancement yourself or would like to participate in the implementation. If applicable add a reference to an existing bug report or issue that this will address._
**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_

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---
name: Generic Issue
about: For issues that do not fit any of the other categories
title: "_Replace With a Descriptive Title_"
labels:
assignees: ''
---
**Summary**
_Please provide a clear and concise description of what this issue report is about._
**LAMMPS Version and Platform**
_Please specify precisely which LAMMPS version this issue was detected with (the first line of the output) and what platform (operating system and its version, hardware) you are running on. If possible, test with the most recent LAMMPS patch version_
**Details**
_Please explain the issue in detail here_

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---
name: Request for Help
about: "Don't post help requests here, email the lammps-users mailing list"
title: ""
labels: invalid
assignees: ''
---
Please **do not** post requests for help (e.g. with installing or using LAMMPS) here.
Instead send an e-mail to the lammps-users mailing list.
This issue tracker is for tracking LAMMPS development related issues only.
Thanks for your cooperation.

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## Purpose
**Summary**
_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_
_Briefly describe the new feature(s), enhancement(s), or bugfix(es) included in this pull request._
## Author(s)
**Related Issues**
_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request_
_If this addresses an open GitHub issue for this project, please mention the issue number here, and describe the relation. Use the phrases `fixes #221` or `closes #135`, when you want an issue to be automatically closed when the pull request is merged_
## Backward Compatibility
**Author(s)**
_Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why_
_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request. If this pull request adds new files to the distribution, please also provide a suitable "long-lived" e-mail address (ideally something that can outlive your institution's e-mail, in case you change jobs) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this contributed code._
## Implementation Notes
**Licensing**
By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).
**Backward Compatibility**
_Please state whether any changes in the pull request will 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
**Post Submission Checklist**
_Please check the fields below as they are completed **after** the pull request has been submitted. Delete lines that don't apply_
_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
- [ ] Licensing information is complete
- [ ] Corresponding author information is complete
- [ ] The source code follows the LAMMPS formatting guidelines
- [ ] Suitable new documentation files and/or updates to the existing docs are included
- [ ] The added/updated documentation is integrated and tested with the documentation build system
- [ ] The feature has been verified to work with the conventional build system
- [ ] The feature has been verified to work with the CMake based build system
- [ ] A package specific README file has been included or updated
- [ ] One or more example input decks are included
## Further Information, Files, and Links
**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)_

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---
name: Bug fix
about: Submit a pull request that fixes one or more bugs
title: "[BUGFIX] _Replace With Suitable Title_"
labels: bugfix
assignees: ''
---
**Summary**
_Briefly describe the bug or bugs, that are eliminated by this pull request._
**Related Issue(s)**
_If this request addresses or is related to an existing (open) GitHub issue, e.g. a bug report, mention the issue number number here following a pound sign (aka hashmark), e.g.`#222`._
**Author(s)**
_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request_
**Licensing**
By submitting this pull request I implicitly accept, that my submission is subject to the same licensing terms as the files that are modified.
**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_
**Detailed Description**
_Provide any relevant details about how the fixed bug can be reproduced, 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 *after* the pull request is submitted_
- [ ] The code in this pull request is complete
- [ ] 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. to download input decks for testing)_

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---
name: Maintenance or Refactoring
about: Submit a pull request that does code refactoring or other maintenance changes
title: "[MAINTENANCE] _Replace With Suitable Title_"
labels: maintenance
assignees: ''
---
**Summary**
_Briefly describe the included changes._
**Related Issue(s)**
_If this request addresses or is related to an existing (open) GitHub issue, e.g. a bug report, mention the issue number number here following a pound sign (aka hashmark), e.g.`#222`.
**Author(s)**
_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request_
**Licensing**
By submitting this pull request I implicitly accept, that my submission is subject to the same licensing terms as the files that are modified.
**Detailed Description**
_Provide any relevant details about the included changes._
## Post Submission Checklist
_Please check the fields below as they are completed *after* the pull request is submitted_
- [ ] The pull request is complete
- [ ] The source code follows the LAMMPS formatting guidelines

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---
name: New Feature
about: Submit a pull request that adds new Features (complete files) to LAMMPS
title: "[New Feature] _Replace With Suitable Title_"
labels: enhancement
assignees: ''
---
**Summary**
_Briefly describe the new feature(s) included in this pull request._
**Related Issues**
_If this addresses an existing (open) GitHub issue, e.g. a feature request, mention the issue number here following a pound sign (aka hashmark), e.g. `#331`._
**Author(s)**
_Please state name and affiliation of the author or authors that should be credited with the features added in this pull request. Please provide a suitable "long-lived" e-mail address (e.g. from gmail, yahoo, outlook, etc.) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this code. now and in the future_
**Licensing**
_Please add *yes* or *no* to the following two statements (please contact @lammps/core if you have questions about this)_
My contribution may be licensed as GPL v2 (default LAMMPS license):
My contribution may be licensed as LGPL (for use as a library with proprietary software):
**Backward Compatibility**
_Please state if any of the changes in this pull request will affect backward compatibility for inputs, and - if yes - explain what has been changed and why_
**Implementation Notes**
_Provide any relevant details about how the new features are implemented, how correctness was verified, what platforms (OS, compiler, MPI, hardware, number of processors, accelerator(s)) it was tested on_
## Post Submission Checklist
_Please check the fields below as they are completed *after* the pull request has been submitted_
- [ ] The feature or features in this pull request is complete
- [ ] Licensing information is complete
- [ ] Corresponding author information is complete
- [ ] The source code follows the LAMMPS formatting guidelines
- [ ] Suitable new documentation files and/or updates to the existing docs are included
- [ ] The added/updated documentation is integrated and tested with the documentation build system
- [ ] The feature has been verified to work with the conventional build system
- [ ] The feature has been verified to work with the CMake based build system
- [ ] A package specific README file has been included or updated
- [ ] One or more example input decks are included
## 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)_

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---
name: Update or Enhancement
about: Submit a pull request that provides update or enhancements for a package or feature in LAMMPS
title: "[UPDATE] _Replace With Suitable Title_"
labels: enhancement
assignees: ''
---
**Summary**
_Briefly describe what kind of updates or enhancements for a package or feature are included. If you are not the original author of the package or feature, please mention, whether your contribution was created independently or in collaboration/cooperation with the original author._
**Author(s)**
_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request_
**Licensing**
By submitting this pull request I implicitly accept, that my submission is subject to the same licensing terms as the original package or feature(s) that are updated or amended by 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 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)_

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.*.swp
*.orig
*.rej
vgcore.*
.vagrant
\#*#
.#*

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Cu functions (universal 3), SM Foiles et al, PRB, 33, 7983 (1986)
29 63.550 3.6150 FCC
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4.2812043923464138e-01 4.0511048870905242e-01 3.8326339142174781e-01 3.6253379771729577e-01 3.4287677583286325e-01
3.2424796479760154e-01 3.0660370758054967e-01 2.8990116598452254e-01 2.7409841872609064e-01 2.5915454407883409e-01
2.4502968839369110e-01 2.3168512174254197e-01 2.1908328186436687e-01 2.0718780752542632e-01 1.9596356233750800e-01
1.8537665001230508e-01 1.7539442196444632e-01 1.6598547811304609e-01 1.5711966166996927e-01 1.4876804864444715e-01
1.4090293273673637e-01 1.3349780623990259e-01 1.2652733751724909e-01 1.1996734557434463e-01 1.1379477219856060e-01
1.0798765209582406e-01 1.0252508141368288e-01 9.7387185001678311e-02 9.2555082724584015e-02 8.8010855111109620e-02
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3.0236983660070216e-02 2.9300620393215571e-02 2.8411323597772320e-02 2.7566082075896281e-02 2.6762082737777249e-02
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2.0000139967999431e-02 1.9528853594166895e-02 1.9075514584991349e-02 1.8639062787818239e-02 1.8218510416650235e-02
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9.8462227798860602e-03 9.6665086187306404e-03 9.4903361536790021e-03 9.3176005668363371e-03 9.1482025960089031e-03
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8.1969532666261724e-03 8.0485306492223962e-03 7.9028101885199598e-03 7.7597280899136256e-03 7.6192232834934315e-03
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1.9669847428123305e-03 1.9275503327108034e-03 1.8888330325659355e-03 1.8508211032951805e-03 1.8135029833145980e-03
1.7768672855772646e-03 1.7409027946878666e-03 1.7055984640891586e-03 1.6709434133182904e-03 1.6369269253308227e-03
1.6035384438881917e-03 1.5707675710093030e-03 1.5386040644797400e-03 1.5070378354209296e-03 1.4760589459142243e-03
1.4456576066784674e-03 1.4158241748004133e-03 1.3865491515145517e-03 1.3578231800324136e-03 1.3296370434173130e-03
1.3019816625059188e-03 1.2748480938728074e-03 1.2482275278369870e-03 1.2221112865106742e-03 1.1964908218862064e-03
1.1713577139624703e-03 1.1467036689077198e-03 1.1225205172586891e-03 1.0988002121543120e-03 1.0755348276031765e-03
1.0527165567835728e-03 1.0303377103750150e-03 1.0083907149206553e-03 9.8686811121878604e-04 9.6576255274356815e-04
9.4506680409354657e-04 9.2477373946662708e-04 9.0487634116191706e-04 8.8536769810608137e-04 8.6624100440530968e-04
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4.8302261220136561e-04 4.7198413328763435e-04 4.6117450548847222e-04 4.5058943143359842e-04 4.4022468403297037e-04
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3.8243496100300207e-04 3.7349984881274514e-04 3.6475366510662147e-04 3.5619277391102898e-04 3.4781360051482253e-04
3.3961263062063513e-04 3.3158640950565685e-04 3.2373154119109092e-04 3.1604468762060252e-04 3.0852256784754707e-04
3.0116195723081836e-04 2.9395968663908575e-04 2.8691264166377101e-04 2.8001776184017647e-04 2.7327203987681688e-04
2.6667252089326854e-04 2.6021630166557681e-04 2.5390052988028163e-04 2.4772240339593181e-04 2.4167916951265550e-04
2.3576812424967210e-04 2.2998661163024531e-04 2.2433202297460642e-04 2.1880179620031078e-04 2.1339341513026532e-04
2.0810440880823181e-04 2.0293235082175821e-04 1.9787485863260665e-04 1.9292959291436311e-04 1.8809425689761319e-04
1.8336659572205580e-04 1.7874439579616125e-04 1.7422548416372047e-04 1.6980772787763936e-04 1.6548903338088530e-04
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1.4154473513841234e-04 1.3786403554466153e-04 1.3426699533172857e-04 1.3075184873951283e-04 1.2731686358694039e-04
1.2396034072819674e-04 1.2068061351527565e-04 1.1747604726729168e-04 1.1434503874632306e-04 1.1128601563955686e-04
1.0829743604811193e-04 1.0537778798212988e-04 1.0252558886227753e-04 9.9739385027582898e-05 9.7017751249615057e-05
9.4359290252773662e-05 9.1762632240957511e-05 8.9226434430383569e-05 8.6749380588361721e-05 8.4330180578390864e-05
8.1967569911181246e-05 7.9660309301724484e-05 7.7407184232279429e-05 7.5207004521348451e-05 7.3058603898526649e-05
7.0960839585107720e-05 6.8912591880629977e-05 6.6912763755002085e-05 6.4960280446513426e-05 6.3054089065330086e-05
6.1193158202771814e-05 5.9376477546041213e-05 5.7603057498502742e-05 5.5871928805544500e-05 5.4182142185708361e-05
5.2532767967318744e-05 5.0922895730446966e-05 4.9351633954125953e-05 4.7818109668823321e-05 4.6321468114150300e-05
4.4860872401664663e-05 4.3435503182825573e-05 4.2044558321957873e-05 4.0687252574273750e-05 3.9362817268785450e-05
3.8070499996214428e-05 3.6809564301621984e-05 3.5579289382025496e-05 3.4378969788611451e-05 3.3207915133769052e-05
3.2065449802711312e-05 3.0950912669766876e-05 2.9863656819185611e-05 2.8803049270468119e-05 2.7768470708167169e-05
2.6759315216115260e-05 2.5774990015931323e-05 2.4814915209964844e-05 2.3878523528387922e-05 2.2965260080560611e-05
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1.7941797449145505e-05 1.7175884233475961e-05 1.6429077288930018e-05 1.5700922618341645e-05 1.4990976337865471e-05
1.4298804471386687e-05 1.3623982748522034e-05 1.2966096406226424e-05 1.2324739993882115e-05 1.1699517181902770e-05
1.1090040573734860e-05 1.0495931521266495e-05 9.9168199435395021e-06 9.3523441487842465e-06 8.8021506596591475e-06
8.2658940417265321e-06 7.7432367350197678e-06 7.2338488887770244e-06 6.7374081991923703e-06 6.2535997501888662e-06
5.7821158571569505e-06 5.3226559136389283e-06 4.8749262408651290e-06 4.4386399401326240e-06 4.0135167480073166e-06
3.5992828942305738e-06 3.1956709623667747e-06 2.8024197531120341e-06 2.4192741502208947e-06 2.0459849890155880e-06
1.6823089274468580e-06 1.3280083196495871e-06 9.8285109196557868e-07 6.4661062138351467e-07 3.1906561636122974e-07
0. 0. 0. 0. 0.

1
bench/POTENTIALS/Cu_u3.eam Symbolic link
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../../potentials/Cu_u3.eam

43007
bench/POTENTIALS/Ni.adp
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1
bench/POTENTIALS/Ni.adp Symbolic link
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../../potentials/Ni.adp

1207
cmake/CMakeLists.txt
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28
cmake/Modules/CodeCoverage.cmake Normal file
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@ -0,0 +1,28 @@
###############################################################################
# Coverage
#
# Requires latest gcovr (for GCC 8.1 support):#
# pip install git+https://github.com/gcovr/gcovr.git
###############################################################################
if(ENABLE_COVERAGE)
find_program(GCOVR_BINARY gcovr)
find_package_handle_standard_args(GCOVR DEFAULT_MSG GCOVR_BINARY)
if(GCOVR_FOUND)
get_filename_component(ABSOLUTE_LAMMPS_SOURCE_DIR ${LAMMPS_SOURCE_DIR} ABSOLUTE)
add_custom_target(
gen_coverage_xml
COMMAND ${GCOVR_BINARY} -s -x -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.xml
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
COMMENT "Generating XML Coverage Report..."
)
add_custom_target(
gen_coverage_html
COMMAND ${GCOVR_BINARY} -s --html --html-details -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.html
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
COMMENT "Generating HTML Coverage Report..."
)
endif()
endif()

42
cmake/Modules/Documentation.cmake Normal file
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@ -0,0 +1,42 @@
###############################################################################
# Build documentation
###############################################################################
option(BUILD_DOC "Build LAMMPS documentation" OFF)
if(BUILD_DOC)
include(ProcessorCount)
ProcessorCount(NPROCS)
find_package(PythonInterp 3 REQUIRED)
set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)
file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
add_custom_command(
OUTPUT docenv
COMMAND ${VIRTUALENV} docenv
)
set(DOCENV_BINARY_DIR ${CMAKE_BINARY_DIR}/docenv/bin)
add_custom_command(
OUTPUT requirements.txt
DEPENDS docenv
COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/utils/requirements.txt requirements.txt
COMMAND ${DOCENV_BINARY_DIR}/pip install -r requirements.txt --upgrade
COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
)
add_custom_command(
OUTPUT html
DEPENDS ${DOC_SOURCES} docenv requirements.txt
COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${LAMMPS_DOC_DIR}/src html
)
add_custom_target(
doc ALL
DEPENDS html
SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES}
)
install(DIRECTORY ${CMAKE_BINARY_DIR}/html DESTINATION ${CMAKE_INSTALL_DOCDIR})
endif()

85
cmake/Modules/FindKIM-API.cmake Normal file
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@ -0,0 +1,85 @@
#
# CDDL HEADER START
#
# The contents of this file are subject to the terms of the Common Development
# and Distribution License Version 1.0 (the "License").
#
# You can obtain a copy of the license at
# http://www.opensource.org/licenses/CDDL-1.0. See the License for the
# specific language governing permissions and limitations under the License.
#
# When distributing Covered Code, include this CDDL HEADER in each file and
# include the License file in a prominent location with the name LICENSE.CDDL.
# If applicable, add the following below this CDDL HEADER, with the fields
# enclosed by brackets "[]" replaced with your own identifying information:
#
# Portions Copyright (c) [yyyy] [name of copyright owner]. All rights reserved.
#
# CDDL HEADER END
#
#
# Copyright (c) 2013--2019, Regents of the University of Minnesota.
# All rights reserved.
#
# Contributors:
# Richard Berger
# Christoph Junghans
# Ryan S. Elliott
#
# - Find KIM-API
#
# sets standard pkg_check_modules variables plus:
#
# KIM-API-CMAKE_C_COMPILER
# KIM-API-CMAKE_CXX_COMPILER
# KIM-API-CMAKE_Fortran_COMPILER
#
function(_KIMAPI_GET_VERSION _OUT_ver _version_hdr)
if(NOT EXISTS ${_version_hdr})
message(FATAL_ERROR "Header file ${_version_hdr} not found (check value of KIM-API_INCLUDE_DIR)")
endif()
foreach(_var KIM_VERSION_MAJOR KIM_VERSION_MINOR KIM_VERSION_PATCH)
file(STRINGS ${_version_hdr} _contents REGEX "#define ${_var}[ \t]+")
if(_contents)
string(REGEX REPLACE ".*#define ${_var}[ \t]+([0-9]+).*" "\\1" _${_var} "${_contents}")
if(${_${_var}} STREQUAL "")
message(FATAL_ERROR "Version parsing failed for ${_var} in ${_version_hdr}, got empty return!")
elseif(NOT ${_${_var}} MATCHES "^[0-9]+$")
message(FATAL_ERROR "Version parsing failed for ${_var} in ${_version_hdr}, excepted a number but got ${_${_var}}!")
endif()
else()
message(FATAL_ERROR "No ${_var} line found in include file ${_version_hdr}")
endif()
endforeach()
set(${_OUT_ver} ${_KIM_VERSION_MAJOR}.${_KIM_VERSION_MINOR}.${_KIM_VERSION_PATCH} PARENT_SCOPE)
endfunction()
if(KIM-API_FIND_QUIETLY)
set(REQ_OR_QUI "QUIET")
else()
set(REQ_OR_QUI "REQUIRED")
endif()
find_package(PkgConfig ${REQ_OR_QUI})
include(FindPackageHandleStandardArgs)
pkg_check_modules(KIM-API ${REQ_OR_QUI} libkim-api>=2.0)
if(KIM-API_FOUND)
pkg_get_variable(KIM-API-CMAKE_C_COMPILER libkim-api CMAKE_C_COMPILER)
pkg_get_variable(KIM-API-CMAKE_CXX_COMPILER libkim-api CMAKE_CXX_COMPILER)
pkg_get_variable(KIM-API_CMAKE_Fortran_COMPILER libkim-api CMAKE_Fortran_COMPILER)
endif()
if(KIM-API_INCLUDEDIR)
_KIMAPI_GET_VERSION(KIM-API_VERSION ${KIM-API_INCLUDEDIR}/KIM_Version.h)
else()
set(KIM-API_VERSION 0)
endif()
# handle the QUIETLY and REQUIRED arguments and set KIM-API_FOUND to TRUE
# if all listed variables are TRUE
find_package_handle_standard_args(KIM-API REQUIRED_VARS KIM-API_LIBRARIES VERSION_VAR KIM-API_VERSION)

22
cmake/Modules/FindKIM.cmake
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@ -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 )

6
cmake/Modules/FindNetCDF.cmake
View File

@ -46,10 +46,14 @@ endif()
find_path (NETCDF_INCLUDE_DIR netcdf.h
HINTS "${NETCDF_DIR}/include")
mark_as_advanced (NETCDF_INCLUDE_DIR)
set (NETCDF_C_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR})
string(REGEX REPLACE "/include/?$" ""
NETCDF_LIB_HINT ${NETCDF_INCLUDE_DIR})
find_library (NETCDF_LIBRARY NAMES netcdf
HINTS "${NETCDF_DIR}/lib")
HINTS "${NETCDF_DIR}" "${NETCDF_LIB_HINT}" PATH_SUFFIXES lib lib64)
mark_as_advanced (NETCDF_LIBRARY)
set (NETCDF_C_LIBRARIES ${NETCDF_LIBRARY})

55
cmake/Modules/FindPNetCDF.cmake Normal file
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@ -0,0 +1,55 @@
# source: https://ftp.space.dtu.dk/pub/Ioana/pism0.6.1-10/CMake/FindPNetCDF.cmake
# license: GPL v3 (https://ftp.space.dtu.dk/pub/Ioana/pism0.6.1-10/COPYING)
#
# - Find PNetCDF
# Find the native PNetCDF includes and library
#
# PNETCDF_INCLUDES - where to find netcdf.h, etc
# PNETCDF_LIBRARIES - Link these libraries when using NetCDF
# PNETCDF_FOUND - True if PNetCDF was found
#
# Normal usage would be:
# find_package (PNetCDF REQUIRED)
# target_link_libraries (uses_pnetcdf ${PNETCDF_LIBRARIES})
if (PNETCDF_INCLUDES AND PNETCDF_LIBRARIES)
# Already in cache, be silent
set (PNETCDF_FIND_QUIETLY TRUE)
endif (PNETCDF_INCLUDES AND PNETCDF_LIBRARIES)
find_path (PNETCDF_INCLUDES pnetcdf.h
HINTS "${PNETCDF_ROOT}/include" "$ENV{PNETCDF_ROOT}/include")
string(REGEX REPLACE "/include/?$" ""
PNETCDF_LIB_HINT ${PNETCDF_INCLUDES})
find_library (PNETCDF_LIBRARIES
NAMES pnetcdf
HINTS ${PNETCDF_LIB_HINT} PATH_SUFFIXES lib lib64)
if ((NOT PNETCDF_LIBRARIES) OR (NOT PNETCDF_INCLUDES))
message(STATUS "Trying to find PNetCDF using LD_LIBRARY_PATH (we're desperate)...")
file(TO_CMAKE_PATH "$ENV{LD_LIBRARY_PATH}" LD_LIBRARY_PATH)
find_library(PNETCDF_LIBRARIES
NAMES pnetcdf
HINTS ${LD_LIBRARY_PATH})
if (PNETCDF_LIBRARIES)
get_filename_component(PNETCDF_LIB_DIR ${PNETCDF_LIBRARIES} PATH)
string(REGEX REPLACE "/(lib|lib64)/?$" "/include"
PNETCDF_H_HINT ${PNETCDF_LIB_DIR})
find_path (PNETCDF_INCLUDES pnetcdf.h
HINTS ${PNETCDF_H_HINT}
DOC "Path to pnetcdf.h")
endif()
endif()
# handle the QUIETLY and REQUIRED arguments and set PNETCDF_FOUND to TRUE if
# all listed variables are TRUE
include (FindPackageHandleStandardArgs)
find_package_handle_standard_args (PNetCDF DEFAULT_MSG PNETCDF_LIBRARIES PNETCDF_INCLUDES)
mark_as_advanced (PNETCDF_LIBRARIES PNETCDF_INCLUDES)

71
cmake/Modules/LAMMPSUtils.cmake Normal file
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@ -0,0 +1,71 @@
# Utility functions
function(list_to_bulletpoints result)
list(REMOVE_AT ARGV 0)
set(temp "")
foreach(item ${ARGV})
set(temp "${temp}* ${item}\n")
endforeach()
set(${result} "${temp}" PARENT_SCOPE)
endfunction(list_to_bulletpoints)
function(validate_option name values)
string(TOLOWER ${${name}} needle_lower)
string(TOUPPER ${${name}} needle_upper)
list(FIND ${values} ${needle_lower} IDX_LOWER)
list(FIND ${values} ${needle_upper} IDX_UPPER)
if(${IDX_LOWER} LESS 0 AND ${IDX_UPPER} LESS 0)
list_to_bulletpoints(POSSIBLE_VALUE_LIST ${${values}})
message(FATAL_ERROR "\n########################################################################\n"
"Invalid value '${${name}}' for option ${name}\n"
"\n"
"Possible values are:\n"
"${POSSIBLE_VALUE_LIST}"
"########################################################################")
endif()
endfunction(validate_option)
function(get_lammps_version version_header variable)
file(READ ${version_header} line)
set(MONTHS x Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec)
string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\1" day "${line}")
string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\2" month "${line}")
string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\3" year "${line}")
string(STRIP ${day} day)
string(STRIP ${month} month)
string(STRIP ${year} year)
list(FIND MONTHS "${month}" month)
string(LENGTH ${day} day_length)
string(LENGTH ${month} month_length)
if(day_length EQUAL 1)
set(day "0${day}")
endif()
if(month_length EQUAL 1)
set(month "0${month}")
endif()
set(${variable} "${year}${month}${day}" PARENT_SCOPE)
endfunction()
function(check_for_autogen_files source_dir)
message(STATUS "Running check for auto-generated files from make-based build system")
file(GLOB SRC_AUTOGEN_FILES ${source_dir}/style_*.h)
file(GLOB SRC_AUTOGEN_PACKAGES ${source_dir}/packages_*.h)
list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/lmpinstalledpkgs.h ${source_dir}/lmpgitversion.h)
foreach(_SRC ${SRC_AUTOGEN_FILES})
get_filename_component(FILENAME "${_SRC}" NAME)
if(EXISTS ${source_dir}/${FILENAME})
message(FATAL_ERROR "\n########################################################################\n"
"Found header file(s) generated by the make-based build system\n"
"\n"
"Please run\n"
"make -C ${source_dir} purge\n"
"to remove\n"
"########################################################################")
endif()
endforeach()
endfunction()
macro(pkg_depends PKG1 PKG2)
if(PKG_${PKG1} AND NOT (PKG_${PKG2} OR BUILD_${PKG2}))
message(FATAL_ERROR "${PKG1} package needs LAMMPS to be build with ${PKG2}")
endif()
endmacro()

2
cmake/Modules/OpenCLUtils.cmake
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@ -6,7 +6,7 @@ function(GenerateOpenCLHeader varname outfile files)
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 "\\s*//[^\n]*\n" "\n" content "${content}")
string(REGEX REPLACE "\\\\" "\\\\\\\\" content "${content}")
string(REGEX REPLACE "\"" "\\\\\"" content "${content}")
string(REGEX REPLACE "([^\n]+)\n" "\"\\1\\\\n\"\n" content "${content}")

5
cmake/Modules/Packages/COMPRESS.cmake Normal file
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if(PKG_COMPRESS)
find_package(ZLIB REQUIRED)
include_directories(${ZLIB_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${ZLIB_LIBRARIES})
endif()

13
cmake/Modules/Packages/CORESHELL.cmake Normal file
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if(PKG_CORESHELL)
set(CORESHELL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/CORESHELL)
set(CORESHELL_SOURCES)
set_property(GLOBAL PROPERTY "CORESHELL_SOURCES" "${CORESHELL_SOURCES}")
# detects styles which have a CORESHELL version
RegisterStylesExt(${CORESHELL_SOURCES_DIR} cs CORESHELL_SOURCES)
get_property(CORESHELL_SOURCES GLOBAL PROPERTY CORESHELL_SOURCES)
list(APPEND LIB_SOURCES ${CORESHELL_SOURCES})
include_directories(${CORESHELL_SOURCES_DIR})
endif()

194
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if(PKG_GPU)
if (CMAKE_VERSION VERSION_LESS "3.1")
message(FATAL_ERROR "For the GPU package you need at least cmake-3.1")
endif()
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(GPU_API_VALUES opencl cuda)
set_property(CACHE GPU_API PROPERTY STRINGS ${GPU_API_VALUES})
validate_option(GPU_API GPU_API_VALUES)
string(TOUPPER ${GPU_API} GPU_API)
set(GPU_PREC "mixed" CACHE STRING "LAMMPS GPU precision")
set(GPU_PREC_VALUES double mixed single)
set_property(CACHE GPU_PREC PROPERTY STRINGS ${GPU_PREC_VALUES})
validate_option(GPU_PREC GPU_PREC_VALUES)
string(TOUPPER ${GPU_PREC} GPU_PREC)
if(GPU_PREC STREQUAL "DOUBLE")
set(GPU_PREC_SETTING "DOUBLE_DOUBLE")
elseif(GPU_PREC STREQUAL "MIXED")
set(GPU_PREC_SETTING "SINGLE_DOUBLE")
elseif(GPU_PREC STREQUAL "SINGLE")
set(GPU_PREC_SETTING "SINGLE_SINGLE")
endif()
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 "Could not find bin2c, use -DBIN2C=/path/to/bin2c to help cmake finding it.")
endif()
option(CUDPP_OPT "Enable CUDPP_OPT" ON)
option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF)
if(CUDA_MPS_SUPPORT)
set(GPU_CUDA_MPS_FLAGS "-DCUDA_PROXY")
endif()
set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. 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 ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
endif()
# build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH} ")
# Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
if((CUDA_VERSION VERSION_GREATER "3.1") AND (CUDA_VERSION VERSION_LESS "9.0"))
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_20,code=[sm_20,compute_20] ")
endif()
# Kepler (GPU Arch 3.x) is supported by CUDA 5 and later
if(CUDA_VERSION VERSION_GREATER "4.9")
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35] ")
endif()
# Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
if(CUDA_VERSION VERSION_GREATER "5.9")
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] ")
endif()
# Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
if(CUDA_VERSION VERSION_GREATER "7.9")
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] ")
endif()
# Volta (GPU Arch 7.0) is supported by CUDA 9 and later
if(CUDA_VERSION VERSION_GREATER "8.9")
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_70,code=[sm_70,compute_70] ")
endif()
# Turing (GPU Arch 7.5) is supported by CUDA 10 and later
if(CUDA_VERSION VERSION_GREATER "9.9")
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ")
endif()
cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
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_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS})
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(OCL_TUNE_VALUES intel fermi kepler cypress generic)
set_property(CACHE OCL_TUNE PROPERTY STRINGS ${OCL_TUNE_VALUES})
validate_option(OCL_TUNE OCL_TUNE_VALUES)
string(TOUPPER ${OCL_TUNE} OCL_TUNE)
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
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.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)
GenerateOpenCLHeader(re_squared ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu)
GenerateOpenCLHeader(re_squared_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu)
GenerateOpenCLHeader(tersoff ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu)
GenerateOpenCLHeader(tersoff_zbl ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu)
GenerateOpenCLHeader(tersoff_mod ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu)
list(APPEND GPU_LIB_SOURCES
${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h
${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h
${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h
${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h
${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h
${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h
${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_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_SETTING} -D${OCL_TUNE}_OCL -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()

67
cmake/Modules/Packages/KIM.cmake Normal file
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@ -0,0 +1,67 @@
if(PKG_KIM)
set(KIM-API_MIN_VERSION 2.1)
find_package(CURL)
if(CURL_FOUND)
include_directories(${CURL_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES})
add_definitions(-DLMP_KIM_CURL)
set(LMP_DEBUG_CURL OFF CACHE STRING "Set libcurl verbose mode on/off. If on, it displays a lot of verbose information about its operations.")
mark_as_advanced(LMP_DEBUG_CURL)
if(LMP_DEBUG_CURL)
add_definitions(-DLMP_DEBUG_CURL)
endif()
set(LMP_NO_SSL_CHECK OFF CACHE STRING "Tell libcurl to not verify the peer. If on, the connection succeeds regardless of the names in the certificate. Insecure - Use with caution!")
mark_as_advanced(LMP_NO_SSL_CHECK)
if(LMP_NO_SSL_CHECK)
add_definitions(-DLMP_NO_SSL_CHECK)
endif()
endif()
find_package(KIM-API QUIET)
if(KIM-API_FOUND)
if (KIM-API_VERSION VERSION_LESS ${KIM-API_MIN_VERSION})
if ("${DOWNLOAD_KIM}" STREQUAL "")
message(WARNING "Unsuitable KIM-API version \"${KIM-API_VERSION}\" found, but required is at least \"${KIM-API_MIN_VERSION}\". Default behavior set to download and build our own.")
endif()
set(DOWNLOAD_KIM_DEFAULT ON)
else()
set(DOWNLOAD_KIM_DEFAULT OFF)
endif()
else()
if ("${DOWNLOAD_KIM}" STREQUAL "")
message(WARNING "KIM-API package not found. Default behavior set to download and build our own")
endif()
set(DOWNLOAD_KIM_DEFAULT ON)
endif()
option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT})
if(DOWNLOAD_KIM)
if(CMAKE_GENERATOR STREQUAL "Ninja")
message(FATAL_ERROR "Cannot build downloaded KIM-API library with Ninja build tool")
endif()
message(STATUS "KIM-API download requested - we will build our own")
include(CheckLanguage)
include(ExternalProject)
enable_language(C)
check_language(Fortran)
if(NOT CMAKE_Fortran_COMPILER)
message(FATAL_ERROR "Compiling the KIM-API library requires a Fortran compiler")
endif()
ExternalProject_Add(kim_build
URL https://s3.openkim.org/kim-api/kim-api-2.1.3.txz
URL_MD5 6ee829a1bbba5f8b9874c88c4c4ebff8
BINARY_DIR build
CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
-DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
)
ExternalProject_get_property(kim_build INSTALL_DIR)
set(KIM-API_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api)
set(KIM-API_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX})
list(APPEND LAMMPS_DEPS kim_build)
else()
find_package(KIM-API ${KIM-API_MIN_VERSION} REQUIRED)
endif()
list(APPEND LAMMPS_LINK_LIBS "${KIM-API_LDFLAGS}")
include_directories(${KIM-API_INCLUDE_DIRS})
endif()

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cmake/Modules/Packages/KOKKOS.cmake Normal file
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@ -0,0 +1,66 @@
if(PKG_KOKKOS)
# TODO: this option needs to be documented when this works with a
# regular release version of KOKKOS, and a version compatibility check
# of external KOKKOS lib versus what the KOKKOS package needs is required.
option(EXTERNAL_KOKKOS "Build against external kokkos library")
if(EXTERNAL_KOKKOS)
find_package(Kokkos REQUIRED)
list(APPEND LAMMPS_LINK_LIBS Kokkos::kokkos)
else()
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
add_subdirectory(${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)
endif()
add_definitions(-DLMP_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}/min_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/min_linesearch_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}/nbin_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/npair_halffull_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
if(PKG_KSPACE)
list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp)
endif()
set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
# detects styles which have KOKKOS version
RegisterStylesExt(${KOKKOS_PKG_SOURCES_DIR} kokkos KOKKOS_PKG_SOURCES)
# register kokkos-only styles
RegisterNBinStyle(${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.h)
RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.h)
RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_halffull_kokkos.h)
if(PKG_USER-DPD)
get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.cpp)
RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.h)
set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
endif()
get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
list(APPEND LIB_SOURCES ${KOKKOS_PKG_SOURCES})
include_directories(${KOKKOS_PKG_SOURCES_DIR})
endif()

42
cmake/Modules/Packages/KSPACE.cmake Normal file
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if(PKG_KSPACE)
option(FFT_SINGLE "Use single precision FFTs instead of double precision FFTs" OFF)
set(FFTW "FFTW3")
if(FFT_SINGLE)
set(FFTW "FFTW3F")
add_definitions(-DFFT_SINGLE)
endif()
find_package(${FFTW} QUIET)
if(${FFTW}_FOUND)
set(FFT "FFTW3" CACHE STRING "FFT library for KSPACE package")
else()
set(FFT "KISS" CACHE STRING "FFT library for KSPACE package")
endif()
set(FFT_VALUES KISS FFTW3 MKL)
set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES})
validate_option(FFT FFT_VALUES)
string(TOUPPER ${FFT} FFT)
if(FFT STREQUAL "FFTW3")
find_package(${FFTW} REQUIRED)
add_definitions(-DFFT_FFTW3)
include_directories(${${FFTW}_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${${FFTW}_LIBRARIES})
elseif(FFT STREQUAL "MKL")
find_package(MKL REQUIRED)
add_definitions(-DFFT_MKL)
include_directories(${MKL_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES})
else()
# last option is KISSFFT
add_definitions(-DFFT_KISS)
endif()
set(FFT_PACK "array" CACHE STRING "Optimization for FFT")
set(FFT_PACK_VALUES array pointer memcpy)
set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES})
validate_option(FFT_PACK FFT_PACK_VALUES)
if(NOT FFT_PACK STREQUAL "array")
string(TOUPPER ${FFT_PACK} FFT_PACK)
add_definitions(-DFFT_PACK_${FFT_PACK})
endif()
endif()

38
cmake/Modules/Packages/LATTE.cmake Normal file
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if(PKG_LATTE)
enable_language(Fortran)
find_package(LATTE)
if(LATTE_FOUND)
set(DOWNLOAD_LATTE_DEFAULT OFF)
else()
set(DOWNLOAD_LATTE_DEFAULT ON)
endif()
option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
if(DOWNLOAD_LATTE)
if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
endif()
if(CMAKE_GENERATOR STREQUAL "Ninja")
message(FATAL_ERROR "Cannot build downloaded LATTE library with Ninja build tool")
endif()
message(STATUS "LATTE download requested - we will build our own")
include(ExternalProject)
ExternalProject_Add(latte_build
URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz
URL_MD5 85ac414fdada2d04619c8f936344df14
SOURCE_SUBDIR cmake
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC}
-DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
-DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=${CMAKE_Fortran_FLAGS}
-DCMAKE_Fortran_FLAGS_${BTYPE}=${CMAKE_Fortran_FLAGS_${BTYPE}} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
)
ExternalProject_get_property(latte_build INSTALL_DIR)
set(LATTE_LIBRARIES ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/liblatte.a)
list(APPEND LAMMPS_DEPS latte_build)
else()
find_package(LATTE)
if(NOT LATTE_FOUND)
message(FATAL_ERROR "LATTE library not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
endif()
endif()
list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES})
endif()

32
cmake/Modules/Packages/MESSAGE.cmake Normal file
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if(PKG_MESSAGE)
if(LAMMPS_SIZES STREQUAL BIGBIG)
message(FATAL_ERROR "The MESSAGE Package is not compatible with -DLAMMPS_BIGBIG")
endif()
option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F
${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c
${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
add_library(cslib STATIC ${cslib_SOURCES})
if(BUILD_MPI)
target_compile_definitions(cslib PRIVATE -DMPI_YES)
set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi")
else()
target_compile_definitions(cslib PRIVATE -DMPI_NO)
target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_MPI)
set_target_properties(cslib PROPERTIES OUTPUT_NAME "csnompi")
endif()
if(MESSAGE_ZMQ)
target_compile_definitions(cslib PRIVATE -DZMQ_YES)
find_package(ZMQ REQUIRED)
target_include_directories(cslib PRIVATE ${ZMQ_INCLUDE_DIRS})
target_link_libraries(cslib PUBLIC ${ZMQ_LIBRARIES})
else()
target_compile_definitions(cslib PRIVATE -DZMQ_NO)
target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_ZMQ)
endif()
list(APPEND LAMMPS_LINK_LIBS cslib)
include_directories(${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src)
endif()

45
cmake/Modules/Packages/MSCG.cmake Normal file
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if(PKG_MSCG)
find_package(GSL REQUIRED)
find_package(MSCG QUIET)
if(MSGC_FOUND)
set(DOWNLOAD_MSCG_DEFAULT OFF)
else()
set(DOWNLOAD_MSCG_DEFAULT ON)
endif()
option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
if(DOWNLOAD_MSCG)
if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
message(FATAL_ERROR "For downlading MSCG you need at least cmake-3.7")
endif()
if(CMAKE_GENERATOR STREQUAL "Ninja")
message(FATAL_ERROR "Cannot build downloaded MSCG library with Ninja build tool")
endif()
include(ExternalProject)
if(NOT LAPACK_FOUND)
set(EXTRA_MSCG_OPTS "-DLAPACK_LIBRARIES=${CMAKE_CURRENT_BINARY_DIR}/liblinalg.a")
endif()
ExternalProject_Add(mscg_build
URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz
URL_MD5 8c45e269ee13f60b303edd7823866a91
SOURCE_SUBDIR src/CMake
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} ${EXTRA_MSCG_OPTS}
BUILD_COMMAND make mscg INSTALL_COMMAND ""
)
ExternalProject_get_property(mscg_build BINARY_DIR)
set(MSCG_LIBRARIES ${BINARY_DIR}/libmscg.a)
ExternalProject_get_property(mscg_build SOURCE_DIR)
set(MSCG_INCLUDE_DIRS ${SOURCE_DIR}/src)
list(APPEND LAMMPS_DEPS mscg_build)
if(NOT LAPACK_FOUND)
file(MAKE_DIRECTORY ${MSCG_INCLUDE_DIRS})
add_dependencies(mscg_build linalg)
endif()
else()
find_package(MSCG)
if(NOT MSCG_FOUND)
message(FATAL_ERROR "MSCG not found, help CMake to find it by setting MSCG_LIBRARY and MSCG_INCLUDE_DIRS, or set DOWNLOAD_MSCG=ON to download it")
endif()
endif()
list(APPEND LAMMPS_LINK_LIBS ${MSCG_LIBRARIES} ${GSL_LIBRARIES} ${LAPACK_LIBRARIES})
include_directories(${MSCG_INCLUDE_DIRS})
endif()

13
cmake/Modules/Packages/OPT.cmake Normal file
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if(PKG_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()

6
cmake/Modules/Packages/PYTHON.cmake Normal file
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if(PKG_PYTHON)
find_package(PythonLibs REQUIRED)
add_definitions(-DLMP_PYTHON)
include_directories(${PYTHON_INCLUDE_DIR})
list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY})
endif()

20
cmake/Modules/Packages/QEQ.cmake Normal file
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# Fix qeq/fire requires MANYBODY (i.e. COMB and COMB3) to be installed
if(PKG_QEQ)
set(QEQ_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/QEQ)
file(GLOB QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix*.h)
file(GLOB QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix*.cpp)
if(NOT PKG_MANYBODY)
list(REMOVE_ITEM QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix_qeq_fire.h)
list(REMOVE_ITEM QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix_qeq_fire.cpp)
endif()
set_property(GLOBAL PROPERTY "QEQ_SOURCES" "${QEQ_SOURCES}")
foreach(MY_HEADER ${QEQ_HEADERS})
AddStyleHeader(${MY_HEADER} FIX)
endforeach()
get_property(QEQ_SOURCES GLOBAL PROPERTY QEQ_SOURCES)
list(APPEND LIB_SOURCES ${QEQ_SOURCES})
include_directories(${QEQ_SOURCES_DIR})
endif()

42
cmake/Modules/Packages/USER-COLVARS.cmake Normal file
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if(PKG_USER-COLVARS)
set(COLVARS_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars)
file(GLOB COLVARS_SOURCES ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
# Build Lepton by default
set(COLVARS_LEPTON_DEFAULT ON)
# but not if C++11 is disabled per user request
if(DEFINED DISABLE_CXX11_REQUIREMENT)
if(DISABLE_CXX11_REQUIREMENT)
set(COLVARS_LEPTON_DEFAULT OFF)
endif()
endif()
option(COLVARS_LEPTON "Build and link the Lepton library" ${COLVARS_LEPTON_DEFAULT})
# Verify that the user's choice is consistent
if(DEFINED DISABLE_CXX11_REQUIREMENT)
if((DISABLE_CXX11_REQUIREMENT) AND (COLVARS_LEPTON))
message(FATAL_ERROR "Building the Lepton library requires C++11 or later.")
endif()
endif()
if(COLVARS_LEPTON)
set(LEPTON_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton)
file(GLOB LEPTON_SOURCES ${LEPTON_DIR}/src/[^.]*.cpp)
add_library(lepton STATIC ${LEPTON_SOURCES})
target_include_directories(lepton PRIVATE ${LEPTON_DIR}/include)
endif()
add_library(colvars STATIC ${COLVARS_SOURCES})
target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
list(APPEND LAMMPS_LINK_LIBS colvars)
if(COLVARS_LEPTON)
list(APPEND LAMMPS_LINK_LIBS lepton)
target_compile_options(colvars PRIVATE -DLEPTON)
target_include_directories(colvars PUBLIC ${LEPTON_DIR}/include)
endif()
endif()

8
cmake/Modules/Packages/USER-H5MD.cmake Normal file
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if(PKG_USER-H5MD)
enable_language(C)
find_package(HDF5 REQUIRED)
target_link_libraries(h5md ${HDF5_LIBRARIES})
target_include_directories(h5md PRIVATE ${HDF5_INCLUDE_DIRS})
include_directories(${HDF5_INCLUDE_DIRS})
endif()

118
cmake/Modules/Packages/USER-INTEL.cmake Normal file
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if(PKG_USER-INTEL)
check_include_file_cxx(immintrin.h FOUND_IMMINTRIN)
if(NOT FOUND_IMMINTRIN)
message(FATAL_ERROR "immintrin.h header not found, Intel package won't work without it")
endif()
add_definitions(-DLMP_USER_INTEL)
set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)")
set(INTEL_ARCH_VALUES cpu knl)
set_property(CACHE INTEL_ARCH PROPERTY STRINGS ${INTEL_ARCH_VALUES})
validate_option(INTEL_ARCH INTEL_ARCH_VALUES)
string(TOUPPER ${INTEL_ARCH} INTEL_ARCH)
find_package(Threads QUIET)
if(Threads_FOUND)
set(INTEL_LRT_MODE "threads" CACHE STRING "Long-range threads mode (none, threads, or c++11)")
else()
set(INTEL_LRT_MODE "none" CACHE STRING "Long-range threads mode (none, threads, or c++11)")
endif()
set(INTEL_LRT_VALUES none threads c++11)
set_property(CACHE INTEL_LRT_MODE PROPERTY STRINGS ${INTEL_LRT_VALUES})
validate_option(INTEL_LRT_MODE INTEL_LRT_VALUES)
string(TOUPPER ${INTEL_LRT_MODE} INTEL_LRT_MODE)
if(INTEL_LRT_MODE STREQUAL "THREADS")
if(Threads_FOUND)
add_definitions(-DLMP_INTEL_USELRT)
list(APPEND LAMMPS_LINK_LIBS ${CMAKE_THREAD_LIBS_INIT})
else()
message(FATAL_ERROR "Must have working threads library for Long-range thread support")
endif()
endif()
if(INTEL_LRT_MODE STREQUAL "C++11")
add_definitions(-DLMP_INTEL_USERLRT -DLMP_INTEL_LRT11)
endif()
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
message(FATAL_ERROR "USER-INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
endif()
else()
message(WARNING "USER-INTEL gives best performance with Intel compilers")
endif()
find_package(TBB QUIET)
if(TBB_FOUND)
list(APPEND LAMMPS_LINK_LIBS ${TBB_MALLOC_LIBRARIES})
else()
add_definitions(-DLMP_INTEL_NO_TBB)
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
message(WARNING "USER-INTEL with Intel compilers should use TBB malloc libraries")
endif()
endif()
find_package(MKL QUIET)
if(MKL_FOUND)
add_definitions(-DLMP_USE_MKL_RNG)
list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES})
else()
message(STATUS "Pair style dpd/intel will be faster with MKL libraries")
endif()
if((NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "64") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "128") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "256"))
message(FATAL_ERROR "USER-INTEL only supports memory alignment of 64, 128 or 256 on this platform")
endif()
if(INTEL_ARCH STREQUAL "KNL")
if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
message(FATAL_ERROR "Must use Intel compiler with USER-INTEL for KNL architecture")
endif()
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload")
set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"")
add_compile_options(-xMIC-AVX512 -qoffload -fno-alias -ansi-alias -restrict -qoverride-limits ${MIC_OPTIONS})
add_definitions(-DLMP_INTEL_OFFLOAD)
else()
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xCOMMON-AVX512")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xHost")
endif()
include(CheckCXXCompilerFlag)
foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
check_cxx_compiler_flag("${__FLAG}" COMPILER_SUPPORTS${_FLAG})
if(COMPILER_SUPPORTS${_FLAG})
add_compile_options(${_FLAG})
endif()
endforeach()
else()
add_compile_options(-O3 -ffast-math)
endif()
endif()
# collect sources
set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/fix_intel.cpp
${USER-INTEL_SOURCES_DIR}/fix_nh_intel.cpp
${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp
${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp
${USER-INTEL_SOURCES_DIR}/npair_intel.cpp)
set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")
# detect styles which have a USER-INTEL version
RegisterStylesExt(${USER-INTEL_SOURCES_DIR} intel USER-INTEL_SOURCES)
RegisterNBinStyle(${USER-INTEL_SOURCES_DIR}/nbin_intel.h)
RegisterNPairStyle(${USER-INTEL_SOURCES_DIR}/npair_intel.h)
RegisterFixStyle(${USER-INTEL_SOURCES_DIR}/fix_intel.h)
get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES)
if(PKG_KSPACE)
list(APPEND USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
RegisterIntegrateStyle(${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
endif()
list(APPEND LIB_SOURCES ${USER-INTEL_SOURCES})
include_directories(${USER-INTEL_SOURCES_DIR})
endif()

14
cmake/Modules/Packages/USER-MOLFILE.cmake Normal file
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if(PKG_USER-MOLFILE)
if (CMAKE_VERSION VERSION_LESS "3.10") # due to INTERFACE without a library
message(FATAL_ERROR "For configuring USER-MOLFILE you need CMake 3.10 or later")
endif()
set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
add_library(molfile INTERFACE)
target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
# no need to link with -ldl on windows
if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
endif()
list(APPEND LAMMPS_LINK_LIBS molfile)
endif()

24
cmake/Modules/Packages/USER-NETCDF.cmake Normal file
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if(PKG_USER-NETCDF)
# USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
# NetCDF library enables dump sytle "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
find_package(NetCDF)
if(NETCDF_FOUND)
find_package(PNetCDF)
else(NETCDF_FOUND)
find_package(PNetCDF REQUIRED)
endif(NETCDF_FOUND)
if(NETCDF_FOUND)
include_directories(${NETCDF_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES})
add_definitions(-DLMP_HAS_NETCDF)
endif(NETCDF_FOUND)
if(PNETCDF_FOUND)
include_directories(${PNETCDF_INCLUDES})
list(APPEND LAMMPS_LINK_LIBS ${PNETCDF_LIBRARIES})
add_definitions(-DLMP_HAS_PNETCDF)
endif(PNETCDF_FOUND)
add_definitions(-DNC_64BIT_DATA=0x0020)
endif()

42
cmake/Modules/Packages/USER-OMP.cmake Normal file
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if(PKG_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_omp.cpp
${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp
${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp
${USER-OMP_SOURCES_DIR}/domain_omp.cpp)
add_definitions(-DLMP_USER_OMP)
set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}")
# detects styles which have USER-OMP version
RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
RegisterFixStyle(${USER-OMP_SOURCES_DIR}/fix_omp.h)
get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
# manually add package dependent source files from USER-OMP that do not provide styles
if(PKG_ASPHERE)
list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_nh_asphere_omp.cpp)
endif()
if(PKG_RIGID)
list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp)
endif()
if(PKG_USER-REAXC)
list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/reaxc_bond_orders_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_hydrogen_bonds_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_bonds_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_init_md_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_torsion_angles_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_forces_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp)
endif()
list(APPEND LIB_SOURCES ${USER-OMP_SOURCES})
include_directories(${USER-OMP_SOURCES_DIR})
endif()

91
cmake/Modules/Packages/USER-PLUMED.cmake Normal file
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if(PKG_USER-PLUMED)
set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")
set(PLUMED_MODE_VALUES static shared runtime)
set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})
validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
set(PLUMED_LINK_LIBS "")
if(PLUMED_MODE STREQUAL "STATIC")
find_package(LAPACK REQUIRED)
find_package(BLAS REQUIRED)
find_package(GSL REQUIRED)
list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
list(APPEND PLUMED_LINK_LIBS ${LAPACK_LIBRARIES} ${GSL_LIBRARIES})
find_package(ZLIB QUIET)
if(ZLIB_FOUND)
list(APPEND PLUMED_LINK_LIBS ${ZLIB_LIBRARIES})
endif()
endif()
find_package(PkgConfig QUIET)
set(DOWNLOAD_PLUMED_DEFAULT ON)
if(PKG_CONFIG_FOUND)
pkg_check_modules(PLUMED QUIET plumed)
if(PLUMED_FOUND)
set(DOWNLOAD_PLUMED_DEFAULT OFF)
endif()
endif()
option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT})
if(DOWNLOAD_PLUMED)
if(CMAKE_GENERATOR STREQUAL "Ninja")
message(FATAL_ERROR "Cannot build downloaded Plumed library with Ninja build tool")
endif()
if(BUILD_MPI)
set(PLUMED_CONFIG_MPI "--enable-mpi")
set(PLUMED_CONFIG_CC ${CMAKE_MPI_C_COMPILER})
set(PLUMED_CONFIG_CXX ${CMAKE_MPI_CXX_COMPILER})
else()
set(PLUMED_CONFIG_MPI "--disable-mpi")
set(PLUMED_CONFIG_CC ${CMAKE_C_COMPILER})
set(PLUMED_CONFIG_CXX ${CMAKE_CXX_COMPILER})
endif()
if(BUILD_OMP)
set(PLUMED_CONFIG_OMP "--enable-openmp")
else()
set(PLUMED_CONFIG_OMP "--disable-openmp")
endif()
message(STATUS "PLUMED download requested - we will build our own")
include(ExternalProject)
ExternalProject_Add(plumed_build
URL https://github.com/plumed/plumed2/releases/download/v2.5.3/plumed-src-2.5.3.tgz
URL_MD5 de30d6e7c2dcc0973298e24a6da24286
BUILD_IN_SOURCE 1
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
${CONFIGURE_REQUEST_PIC}
--enable-modules=all
${PLUMED_CONFIG_MPI}
${PLUMED_CONFIG_OMP}
CXX=${PLUMED_CONFIG_CXX}
CC=${PLUMED_CONFIG_CC}
)
ExternalProject_get_property(plumed_build INSTALL_DIR)
set(PLUMED_INSTALL_DIR ${INSTALL_DIR})
list(APPEND LAMMPS_DEPS plumed_build)
if(PLUMED_MODE STREQUAL "STATIC")
add_definitions(-D__PLUMED_WRAPPER_CXX=1)
list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.a ${PLUMED_LINK_LIBS} ${CMAKE_DL_LIBS})
elseif(PLUMED_MODE STREQUAL "SHARED")
list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX} ${PLUMED_INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX} ${CMAKE_DL_LIBS})
elseif(PLUMED_MODE STREQUAL "RUNTIME")
add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX})
list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumedWrapper.a -rdynamic ${CMAKE_DL_LIBS})
endif()
set(PLUMED_INCLUDE_DIRS "${PLUMED_INSTALL_DIR}/include")
else()
find_package(PkgConfig REQUIRED)
pkg_check_modules(PLUMED REQUIRED plumed)
if(PLUMED_MODE STREQUAL "STATIC")
add_definitions(-D__PLUMED_WRAPPER_CXX=1)
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
elseif(PLUMED_MODE STREQUAL "SHARED")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
elseif(PLUMED_MODE STREQUAL "RUNTIME")
add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX})
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
endif()
list(APPEND LAMMPS_LINK_LIBS ${PLUMED_LOAD})
endif()
include_directories(${PLUMED_INCLUDE_DIRS})
endif()

9
cmake/Modules/Packages/USER-QMMM.cmake Normal file
View File

@ -0,0 +1,9 @@
if(PKG_USER-QMMM)
enable_language(Fortran)
enable_language(C)
message(WARNING "Building QMMM with CMake is still experimental")
find_package(QE REQUIRED)
include_directories(${QE_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES})
endif()

5
cmake/Modules/Packages/USER-QUIP.cmake Normal file
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@ -0,0 +1,5 @@
if(PKG_USER-QUIP)
enable_language(Fortran)
find_package(QUIP REQUIRED)
list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES})
endif()

62
cmake/Modules/Packages/USER-SCAFACOS.cmake Normal file
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@ -0,0 +1,62 @@
if(PKG_USER-SCAFACOS)
enable_language(Fortran)
enable_language(C)
find_package(GSL REQUIRED)
find_package(PkgConfig QUIET)
set(DOWNLOAD_SCAFACOS_DEFAULT ON)
if(PKG_CONFIG_FOUND)
pkg_check_modules(SCAFACOS QUIET scafacos)
if(SCAFACOS_FOUND)
set(DOWNLOAD_SCAFACOS_DEFAULT OFF)
endif()
endif()
option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
if(DOWNLOAD_SCAFACOS)
if(CMAKE_GENERATOR STREQUAL "Ninja")
message(FATAL_ERROR "Cannot build downloaded ScaFaCoS library with Ninja build tool")
endif()
message(STATUS "ScaFaCoS download requested - we will build our own")
include(ExternalProject)
ExternalProject_Add(scafacos_build
URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
URL_MD5 bd46d74e3296bd8a444d731bb10c1738
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc
--enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
--with-internal-fftw --with-internal-pfft
--with-internal-pnfft ${CONFIGURE_REQUEST_PIC}
FC=${CMAKE_MPI_Fortran_COMPILER}
CXX=${CMAKE_MPI_CXX_COMPILER}
CC=${CMAKE_MPI_C_COMPILER}
F77=
)
ExternalProject_get_property(scafacos_build INSTALL_DIR)
set(SCAFACOS_BUILD_DIR ${INSTALL_DIR})
set(SCAFACOS_INCLUDE_DIRS ${SCAFACOS_BUILD_DIR}/include)
list(APPEND LAMMPS_DEPS scafacos_build)
# list and order from pkg_config file of ScaFaCoS build
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_direct.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_ewald.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fmm.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p2nfft.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p3m.a)
list(APPEND LAMMPS_LINK_LIBS ${GSL_LIBRARIES})
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_near.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_gridsort.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_resort.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_redist.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_common.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pnfft.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pfft.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3_mpi.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3.a)
list(APPEND LAMMPS_LINK_LIBS ${MPI_Fortran_LIBRARIES})
list(APPEND LAMMPS_LINK_LIBS ${MPI_C_LIBRARIES})
else()
find_package(PkgConfig REQUIRED)
pkg_check_modules(SCAFACOS REQUIRED scafacos)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_LDFLAGS})
endif()
include_directories(${SCAFACOS_INCLUDE_DIRS})
endif()

13
cmake/Modules/Packages/USER-SDPD.cmake Normal file
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@ -0,0 +1,13 @@
# Fix rigid/meso requires RIGID to be installed
if(PKG_USER-SDPD)
set(USER-SDPD_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-SDPD)
get_property(hlist GLOBAL PROPERTY FIX)
if(NOT PKG_RIGID)
list(REMOVE_ITEM hlist ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.h)
list(REMOVE_ITEM LIB_SOURCES ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.cpp)
endif()
set_property(GLOBAL PROPERTY FIX "${hlist}")
include_directories(${USER-SDPD_SOURCES_DIR})
endif()

28
cmake/Modules/Packages/USER-SMD.cmake Normal file
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@ -0,0 +1,28 @@
if(PKG_USER-SMD)
find_package(Eigen3 NO_MODULE)
if(EIGEN3_FOUND)
set(DOWNLOAD_EIGEN3_DEFAULT OFF)
else()
set(DOWNLOAD_EIGEN3_DEFAULT ON)
endif()
option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT})
if(DOWNLOAD_EIGEN3)
message(STATUS "Eigen3 download requested - we will build our own")
include(ExternalProject)
ExternalProject_Add(Eigen3_build
URL http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz
URL_MD5 f2a417d083fe8ca4b8ed2bc613d20f07
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
)
ExternalProject_get_property(Eigen3_build SOURCE_DIR)
set(EIGEN3_INCLUDE_DIR ${SOURCE_DIR})
list(APPEND LAMMPS_DEPS Eigen3_build)
else()
find_package(Eigen3 NO_MODULE)
mark_as_advanced(Eigen3_DIR)
if(NOT EIGEN3_FOUND)
message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_EIGEN3=ON to download it")
endif()
endif()
include_directories(${EIGEN3_INCLUDE_DIR})
endif()

6
cmake/Modules/Packages/USER-VTK.cmake Normal file
View File

@ -0,0 +1,6 @@
if(PKG_USER-VTK)
find_package(VTK REQUIRED NO_MODULE)
include(${VTK_USE_FILE})
add_definitions(-DLAMMPS_VTK)
list(APPEND LAMMPS_LINK_LIBS ${VTK_LIBRARIES})
endif()

45
cmake/Modules/Packages/VORONOI.cmake Normal file
View File

@ -0,0 +1,45 @@
if(PKG_VORONOI)
find_package(VORO)
if(VORO_FOUND)
set(DOWNLOAD_VORO_DEFAULT OFF)
else()
set(DOWNLOAD_VORO_DEFAULT ON)
endif()
option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT})
if(DOWNLOAD_VORO)
if(CMAKE_GENERATOR STREQUAL "Ninja")
message(FATAL_ERROR "Cannot build downloaded Voro++ library with Ninja build tool")
endif()
message(STATUS "Voro++ download requested - we will build our own")
include(ExternalProject)
if(BUILD_SHARED_LIBS)
set(VORO_BUILD_CFLAGS "${CMAKE_SHARED_LIBRARY_CXX_FLAGS} ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
else()
set(VORO_BUILD_CFLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
endif()
if(APPLE)
get_filename_component(VORO_CXX ${CMAKE_CXX_COMPILER} NAME_WE)
set(VORO_BUILD_OPTIONS CXX=${VORO_CXX} CFLAGS=${VORO_BUILD_CFLAGS})
else()
set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
endif()
ExternalProject_Add(voro_build
URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
URL_MD5 2338b824c3b7b25590e18e8df5d68af9
CONFIGURE_COMMAND "" BUILD_COMMAND make ${VORO_BUILD_OPTIONS} BUILD_IN_SOURCE 1 INSTALL_COMMAND ""
)
ExternalProject_get_property(voro_build SOURCE_DIR)
set(VORO_LIBRARIES ${SOURCE_DIR}/src/libvoro++.a)
set(VORO_INCLUDE_DIRS ${SOURCE_DIR}/src)
list(APPEND LAMMPS_DEPS voro_build)
else()
find_package(VORO)
if(NOT VORO_FOUND)
message(FATAL_ERROR "Voro++ library not found. Help CMake to find it by setting VORO_LIBRARY and VORO_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
endif()
endif()
include_directories(${VORO_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${VORO_LIBRARIES})
endif()

91
cmake/Modules/StyleHeaderUtils.cmake
View File

@ -50,6 +50,7 @@ function(CreateStyleHeader path filename)
list(REMOVE_AT ARGV 0 1)
set(header_list)
foreach(FNAME ${ARGV})
set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS "${FNAME}")
get_filename_component(FNAME ${FNAME} NAME)
list(APPEND header_list ${FNAME})
endforeach()
@ -61,6 +62,7 @@ function(CreateStyleHeader path filename)
message(STATUS "Generating ${filename}...")
file(WRITE "${path}/${filename}.tmp" "${temp}" )
execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${path}/${filename}.tmp" "${path}/${filename}")
set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS "${path}/${filename}")
endfunction(CreateStyleHeader)
function(GenerateStyleHeader path property style)
@ -89,6 +91,10 @@ function(RegisterFixStyle path)
AddStyleHeader(${path} FIX)
endfunction(RegisterFixStyle)
function(RegisterIntegrateStyle path)
AddStyleHeader(${path} INTEGRATE)
endfunction(RegisterIntegrateStyle)
function(RegisterStyles search_path)
FindStyleHeaders(${search_path} ANGLE_CLASS angle_ ANGLE ) # angle ) # force
FindStyleHeaders(${search_path} ATOM_CLASS atom_vec_ ATOM_VEC ) # atom ) # atom atom_vec_hybrid
@ -175,3 +181,88 @@ function(DetectBuildSystemConflict lammps_src_dir)
endforeach()
endif()
endfunction(DetectBuildSystemConflict)
function(FindPackagesHeaders path style_class file_pattern headers)
file(GLOB files "${path}/${file_pattern}*.h")
get_property(plist GLOBAL PROPERTY ${headers})
foreach(file_name ${files})
file(STRINGS ${file_name} is_style LIMIT_COUNT 1 REGEX ${style_class})
if(is_style)
list(APPEND plist ${file_name})
endif()
endforeach()
set_property(GLOBAL PROPERTY ${headers} "${plist}")
endfunction(FindPackagesHeaders)
function(RegisterPackages search_path)
FindPackagesHeaders(${search_path} ANGLE_CLASS angle_ PKGANGLE ) # angle ) # force
FindPackagesHeaders(${search_path} ATOM_CLASS atom_vec_ PKGATOM_VEC ) # atom ) # atom atom_vec_hybrid
FindPackagesHeaders(${search_path} BODY_CLASS body_ PKGBODY ) # body ) # atom_vec_body
FindPackagesHeaders(${search_path} BOND_CLASS bond_ PKGBOND ) # bond ) # force
FindPackagesHeaders(${search_path} COMMAND_CLASS "[^.]" PKGCOMMAND ) # command ) # input
FindPackagesHeaders(${search_path} COMPUTE_CLASS compute_ PKGCOMPUTE ) # compute ) # modify
FindPackagesHeaders(${search_path} DIHEDRAL_CLASS dihedral_ PKGDIHEDRAL ) # dihedral ) # force
FindPackagesHeaders(${search_path} DUMP_CLASS dump_ PKGDUMP ) # dump ) # output write_dump
FindPackagesHeaders(${search_path} FIX_CLASS fix_ PKGFIX ) # fix ) # modify
FindPackagesHeaders(${search_path} IMPROPER_CLASS improper_ PKGIMPROPER ) # improper ) # force
FindPackagesHeaders(${search_path} INTEGRATE_CLASS "[^.]" PKGINTEGRATE ) # integrate ) # update
FindPackagesHeaders(${search_path} KSPACE_CLASS "[^.]" PKGKSPACE ) # kspace ) # force
FindPackagesHeaders(${search_path} MINIMIZE_CLASS min_ PKGMINIMIZE ) # minimize ) # update
FindPackagesHeaders(${search_path} NBIN_CLASS nbin_ PKGNBIN ) # nbin ) # neighbor
FindPackagesHeaders(${search_path} NPAIR_CLASS npair_ PKGNPAIR ) # npair ) # neighbor
FindPackagesHeaders(${search_path} NSTENCIL_CLASS nstencil_ PKGNSTENCIL ) # nstencil ) # neighbor
FindPackagesHeaders(${search_path} NTOPO_CLASS ntopo_ PKGNTOPO ) # ntopo ) # neighbor
FindPackagesHeaders(${search_path} PAIR_CLASS pair_ PKGPAIR ) # pair ) # force
FindPackagesHeaders(${search_path} READER_CLASS reader_ PKGREADER ) # reader ) # read_dump
FindPackagesHeaders(${search_path} REGION_CLASS region_ PKGREGION ) # region ) # domain
endfunction(RegisterPackages)
function(CreatePackagesHeader path filename)
set(temp "")
if(ARGC GREATER 2)
list(REMOVE_AT ARGV 0 1)
foreach(FNAME ${ARGV})
set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS "${FNAME}")
get_filename_component(DNAME ${FNAME} DIRECTORY)
get_filename_component(DNAME ${DNAME} NAME)
get_filename_component(FNAME ${FNAME} NAME)
set(temp "${temp}#undef PACKAGE\n#define PACKAGE \"${DNAME}\"\n")
set(temp "${temp}#include \"${DNAME}/${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}/${filename}")
set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS "${path}/${filename}")
endfunction(CreatePackagesHeader)
function(GeneratePackagesHeader path property style)
get_property(files GLOBAL PROPERTY ${property})
CreatePackagesHeader("${path}" "packages_${style}.h" ${files})
endfunction(GeneratePackagesHeader)
function(GeneratePackagesHeaders output_path)
GeneratePackagesHeader(${output_path} PKGANGLE angle ) # force
GeneratePackagesHeader(${output_path} PKGATOM_VEC atom ) # atom atom_vec_hybrid
GeneratePackagesHeader(${output_path} PKGBODY body ) # atom_vec_body
GeneratePackagesHeader(${output_path} PKGBOND bond ) # force
GeneratePackagesHeader(${output_path} PKGCOMMAND command ) # input
GeneratePackagesHeader(${output_path} PKGCOMPUTE compute ) # modify
GeneratePackagesHeader(${output_path} PKGDIHEDRAL dihedral ) # force
GeneratePackagesHeader(${output_path} PKGDUMP dump ) # output write_dump
GeneratePackagesHeader(${output_path} PKGFIX fix ) # modify
GeneratePackagesHeader(${output_path} PKGIMPROPER improper ) # force
GeneratePackagesHeader(${output_path} PKGINTEGRATE integrate ) # update
GeneratePackagesHeader(${output_path} PKGKSPACE kspace ) # force
GeneratePackagesHeader(${output_path} PKGMINIMIZE minimize ) # update
GeneratePackagesHeader(${output_path} PKGNBIN nbin ) # neighbor
GeneratePackagesHeader(${output_path} PKGNPAIR npair ) # neighbor
GeneratePackagesHeader(${output_path} PKGNSTENCIL nstencil ) # neighbor
GeneratePackagesHeader(${output_path} PKGNTOPO ntopo ) # neighbor
GeneratePackagesHeader(${output_path} PKGPAIR pair ) # force
GeneratePackagesHeader(${output_path} PKGREADER reader ) # read_dump
GeneratePackagesHeader(${output_path} PKGREGION region ) # domain
endfunction(GeneratePackagesHeaders)

52
cmake/Modules/Testing.cmake Normal file
View File

@ -0,0 +1,52 @@
###############################################################################
# Testing
###############################################################################
option(ENABLE_TESTING "Enable testing" OFF)
if(ENABLE_TESTING AND BUILD_EXE)
enable_testing()
option(LAMMPS_TESTING_SOURCE_DIR "Location of lammps-testing source directory" "")
option(LAMMPS_TESTING_GIT_TAG "Git tag of lammps-testing" "master")
mark_as_advanced(LAMMPS_TESTING_SOURCE_DIR LAMMPS_TESTING_GIT_TAG)
if (CMAKE_VERSION VERSION_GREATER "3.10.3" AND NOT LAMMPS_TESTING_SOURCE_DIR)
include(FetchContent)
FetchContent_Declare(lammps-testing
GIT_REPOSITORY https://github.com/lammps/lammps-testing.git
GIT_TAG ${LAMMPS_TESTING_GIT_TAG}
)
FetchContent_GetProperties(lammps-testing)
if(NOT lammps-testing_POPULATED)
message(STATUS "Downloading tests...")
FetchContent_Populate(lammps-testing)
endif()
set(LAMMPS_TESTING_SOURCE_DIR ${lammps-testing_SOURCE_DIR})
elseif(NOT LAMMPS_TESTING_SOURCE_DIR)
message(WARNING "Full test-suite requires CMake >= 3.11 or copy of\n"
"https://github.com/lammps/lammps-testing in LAMMPS_TESTING_SOURCE_DIR")
endif()
add_test(ShowHelp ${CMAKE_BINARY_DIR}/${LAMMPS_BINARY} -help)
if(EXISTS ${LAMMPS_TESTING_SOURCE_DIR})
message(STATUS "Running test discovery...")
file(GLOB_RECURSE TEST_SCRIPTS ${LAMMPS_TESTING_SOURCE_DIR}/tests/core/*/in.*)
foreach(script_path ${TEST_SCRIPTS})
get_filename_component(TEST_NAME ${script_path} EXT)
get_filename_component(SCRIPT_NAME ${script_path} NAME)
get_filename_component(PARENT_DIR ${script_path} DIRECTORY)
string(SUBSTRING ${TEST_NAME} 1 -1 TEST_NAME)
string(REPLACE "-" "_" TEST_NAME ${TEST_NAME})
string(REPLACE "+" "_" TEST_NAME ${TEST_NAME})
set(TEST_NAME "test_core_${TEST_NAME}_serial")
add_test(${TEST_NAME} ${CMAKE_BINARY_DIR}/${LAMMPS_BINARY} -in ${SCRIPT_NAME})
set_tests_properties(${TEST_NAME} PROPERTIES WORKING_DIRECTORY ${PARENT_DIR})
endforeach()
list(LENGTH TEST_SCRIPTS NUM_TESTS)
message(STATUS "Found ${NUM_TESTS} tests.")
endif()
endif()

30
cmake/Modules/generate_lmpgitversion.cmake Normal file
View File

@ -0,0 +1,30 @@
set(temp "#ifndef LMP_GIT_VERSION_H\n#define LMP_GIT_VERSION_H\n")
set(temp_git_commit "(unknown)")
set(temp_git_branch "(unknown)")
set(temp_git_describe "(unknown)")
set(temp_git_info "false")
if(GIT_FOUND AND EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/../.git)
set(temp_git_info "true")
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse HEAD
OUTPUT_VARIABLE temp_git_commit
ERROR_QUIET
OUTPUT_STRIP_TRAILING_WHITESPACE)
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse --abbrev-ref HEAD
OUTPUT_VARIABLE temp_git_branch
ERROR_QUIET
OUTPUT_STRIP_TRAILING_WHITESPACE)
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. describe --dirty=-modified
OUTPUT_VARIABLE temp_git_describe
ERROR_QUIET
OUTPUT_STRIP_TRAILING_WHITESPACE)
endif()
set(temp "${temp}const bool LAMMPS_NS::LAMMPS::has_git_info = ${temp_git_info};\n")
set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_commit[] = \"${temp_git_commit}\";\n")
set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_branch[] = \"${temp_git_branch}\";\n")
set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_descriptor[] = \"${temp_git_describe}\";\n")
set(temp "${temp}#endif\n\n")
message(STATUS "Generating lmpgitversion.h...")
file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${temp}" )
execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h")

805
cmake/README.md
View File

File diff suppressed because it is too large Load Diff

6
cmake/etc/profile.d/lammps.csh.in
View File

@ -1,2 +1,4 @@
# set environment for LAMMPS executables to find potential files
if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_POTENTIALS_DIR@
# set environment for LAMMPS and msi2lmp executables
# to find potential and force field files
if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_INSTALL_DATADIR@/potentials
if ( "$?MSI2LMP_LIBRARY" == 0 ) setenv MSI2LMP_LIBRARY @LAMMPS_INSTALL_DATADIR@/frc_files

7
cmake/etc/profile.d/lammps.sh.in
View File

@ -1,2 +1,5 @@
# set environment for LAMMPS executables to find potential files
export LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@}
# set environment for LAMMPS and msi2lmp executables
# to find potential and force field files
LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_INSTALL_DATADIR@/potentials}
MSI2LMP_LIBRARY=${MSI2LMP_LIBRARY-@LAMMPS_INSTALL_DATADIR@/frc_files}
export LAMMPS_POTENTIALS MSI2LMP_LIBRARY

24
cmake/pkgconfig/liblammps.pc.in
View File

@ -1,9 +1,29 @@
# 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,
# Add the directory where lammps.pc got installed to your PKG_CONFIG_PATH
# e.g. export PKG_CONFIG_PATH=@CMAKE_INSTALL_FULL_LIBDIR@/pkgconfig
# Use this on commandline with:
# c++ `pkg-config --cflags --libs lammps` -o myapp myapp.cpp
# Use this in a Makefile:
# myapp: myapp.cpp
# $(CC) `pkg-config --cflags --libs lammps` -o $@ $<
# Use this in autotools:
# configure.ac:
# PKG_CHECK_MODULES([LAMMPS], [lammps])
# Makefile.am:
# myapp_CFLAGS = $(LAMMPS_CFLAGS)
# myapp_LDADD = $(LAMMPS_LIBS)
# Use this in CMake:
# CMakeLists.txt:
# find_package(PkgConfig)
# pkg_check_modules(LAMMPS IMPORTED_TARGET lammps)
# target_link_libraries(<lib> PkgConfig::LAMMPS)
prefix=@CMAKE_INSTALL_PREFIX@
libdir=@CMAKE_INSTALL_FULL_LIBDIR@
includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@

30
cmake/presets/all_off.cmake
View File

@ -1,21 +1,17 @@
set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
MOLECULE MPIIO MSCG OPT PERI POEMS
PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
# preset that turns on all existing packages off. can be used to reset
# an existing package selection without losing any other settings
set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
USER-UEF USER-VTK)
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MOLECULE
MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-YAFF)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

32
cmake/presets/all_on.cmake
View File

@ -1,21 +1,19 @@
set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
MOLECULE MPIIO MSCG OPT PERI POEMS
PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
# preset that turns on all existing packages. using the combination
# this preset followed by the nolib.cmake preset should configure a
# LAMMPS binary, with as many packages included, that can be compiled
# with just a working C++ compiler and an MPI library.
set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
USER-UEF USER-VTK)
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MOLECULE
MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-YAFF)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)

17
cmake/presets/clang.cmake Normal file
View File

@ -0,0 +1,17 @@
# preset that will enable clang/clang++ with support for MPI and OpenMP (on Linux boxes)
set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS "-Wall -Wextra -g -O2 -DNDEBG" CACHE STRING "" FORCE)
set(MPI_CXX "clang++" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "clang" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_CXX "clang++" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_omp_LIBRARY "/usr/lib64/libomp.so" CACHE PATH "" FORCE)

69
cmake/presets/manual_selection.cmake
View File

@ -1,69 +0,0 @@
set(PKG_ASPHERE OFF CACHE BOOL "" FORCE)
set(PKG_BODY OFF CACHE BOOL "" FORCE)
set(PKG_CLASS2 OFF CACHE BOOL "" FORCE)
set(PKG_COLLOID OFF CACHE BOOL "" FORCE)
set(PKG_COMPRESS OFF CACHE BOOL "" FORCE)
set(PKG_CORESHELL OFF CACHE BOOL "" FORCE)
set(PKG_DIPOLE OFF CACHE BOOL "" FORCE)
set(PKG_GPU OFF CACHE BOOL "" FORCE)
set(PKG_GRANULAR OFF CACHE BOOL "" FORCE)
set(PKG_KIM OFF CACHE BOOL "" FORCE)
set(PKG_KOKKOS OFF CACHE BOOL "" FORCE)
set(PKG_KSPACE OFF CACHE BOOL "" FORCE)
set(PKG_LATTE OFF CACHE BOOL "" FORCE)
set(PKG_LIB OFF CACHE BOOL "" FORCE)
set(PKG_MANYBODY OFF CACHE BOOL "" FORCE)
set(PKG_MC OFF CACHE BOOL "" FORCE)
set(PKG_MEAM OFF CACHE BOOL "" FORCE)
set(PKG_MISC OFF CACHE BOOL "" FORCE)
set(PKG_MOLECULE OFF CACHE BOOL "" FORCE)
set(PKG_MPIIO OFF CACHE BOOL "" FORCE)
set(PKG_MSCG OFF CACHE BOOL "" FORCE)
set(PKG_OPT OFF CACHE BOOL "" FORCE)
set(PKG_PERI OFF CACHE BOOL "" FORCE)
set(PKG_POEMS OFF CACHE BOOL "" FORCE)
set(PKG_PYTHOFF OFF CACHE BOOL "" FORCE)
set(PKG_QEQ OFF CACHE BOOL "" FORCE)
set(PKG_REAX OFF CACHE BOOL "" FORCE)
set(PKG_REPLICA OFF CACHE BOOL "" FORCE)
set(PKG_RIGID OFF CACHE BOOL "" FORCE)
set(PKG_SHOCK OFF CACHE BOOL "" FORCE)
set(PKG_SNAP OFF CACHE BOOL "" FORCE)
set(PKG_SRD OFF CACHE BOOL "" FORCE)
set(PKG_VOROFFOI OFF CACHE BOOL "" FORCE)
set(PKG_USER OFF CACHE BOOL "" FORCE)
set(PKG_USER-ATC OFF CACHE BOOL "" FORCE)
set(PKG_USER-AWPMD OFF CACHE BOOL "" FORCE)
set(PKG_USER-BOCS OFF CACHE BOOL "" FORCE)
set(PKG_USER-CGDNA OFF CACHE BOOL "" FORCE)
set(PKG_USER-CGSDK OFF CACHE BOOL "" FORCE)
set(PKG_USER-COLVARS OFF CACHE BOOL "" FORCE)
set(PKG_USER-DIFFRACTIOFF OFF CACHE BOOL "" FORCE)
set(PKG_USER-DPD OFF CACHE BOOL "" FORCE)
set(PKG_USER-DRUDE OFF CACHE BOOL "" FORCE)
set(PKG_USER-EFF OFF CACHE BOOL "" FORCE)
set(PKG_USER-FEP OFF CACHE BOOL "" FORCE)
set(PKG_USER-H5MD OFF CACHE BOOL "" FORCE)
set(PKG_USER-INTEL OFF CACHE BOOL "" FORCE)
set(PKG_USER-LB OFF CACHE BOOL "" FORCE)
set(PKG_USER-MANIFOLD OFF CACHE BOOL "" FORCE)
set(PKG_USER-MEAMC OFF CACHE BOOL "" FORCE)
set(PKG_USER-MESO OFF CACHE BOOL "" FORCE)
set(PKG_USER-MGPT OFF CACHE BOOL "" FORCE)
set(PKG_USER-MISC OFF CACHE BOOL "" FORCE)
set(PKG_USER-MOFFF OFF CACHE BOOL "" FORCE)
set(PKG_USER-MOLFILE OFF CACHE BOOL "" FORCE)
set(PKG_USER-NETCDF OFF CACHE BOOL "" FORCE)
set(PKG_USER-OMP OFF CACHE BOOL "" FORCE)
set(PKG_USER-PHOFFOFF OFF CACHE BOOL "" FORCE)
set(PKG_USER-QMMM OFF CACHE BOOL "" FORCE)
set(PKG_USER-QTB OFF CACHE BOOL "" FORCE)
set(PKG_USER-QUIP OFF CACHE BOOL "" FORCE)
set(PKG_USER-REAXC OFF CACHE BOOL "" FORCE)
set(PKG_USER-SMD OFF CACHE BOOL "" FORCE)
set(PKG_USER-SMTBQ OFF CACHE BOOL "" FORCE)
set(PKG_USER-SPH OFF CACHE BOOL "" FORCE)
set(PKG_USER-TALLY OFF CACHE BOOL "" FORCE)
set(PKG_USER-UEF OFF CACHE BOOL "" FORCE)
set(PKG_USER-VTK OFF CACHE BOOL "" FORCE)

17
cmake/presets/mingw-cross.cmake Normal file
View File

@ -0,0 +1,17 @@
set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI POEMS QEQ
REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI USER-ATC USER-AWPMD
USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
USER-DPD USER-DRUDE USER-EFF USER-FEP USER-INTEL USER-MANIFOLD
USER-MEAMC USER-MESO USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE
USER-OMP USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SDPD
USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-YAFF)
foreach(PKG ${WIN_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)
endforeach()
set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
set(LAMMPS_MEMALIGN "0" CACHE STRING "" FORCE)
set(CMAKE_INSTALL_PREFIX "${CMAKE_CURRENT_BINARY_DIR}/lammps-installer")

8
cmake/presets/minimal.cmake Normal file
View File

@ -0,0 +1,8 @@
# preset that turns on just a few, frequently used packages
# this will be compiled quickly and handle a lot of common inputs.
set(ALL_PACKAGES KSPACE MANYBODY MOLECULE RIGID)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)
endforeach()

15
cmake/presets/most.cmake Normal file
View File

@ -0,0 +1,15 @@
# preset that turns on a wide range of packages, some of which require
# external libraries. Compared to all_on.cmake some more unusual packages
# are removed. The resulting binary should be able to run most inputs.
set(ALL_PACKAGES ASPHERE CLASS2 COLLOID CORESHELL DIPOLE
GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI
PYTHON QEQ REPLICA RIGID SHOCK SNAP SRD VORONOI
USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD
USER-DRUDE USER-FEP USER-MEAMC USER-MESO
USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REAXC
USER-SPH USER-SMD USER-UEF USER-YAFF)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)
endforeach()

23
cmake/presets/nolib.cmake
View File

@ -1,21 +1,10 @@
set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
MOLECULE MPIIO MSCG OPT PERI POEMS
PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
# preset that turns off all packages that require some form of external
# library or special compiler (fortran or cuda) or equivalent.
set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
USER-UEF USER-VTK)
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MPIIO MSCG PYTHON
VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB
USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP
USER-SCAFACOS USER-SMD USER-VTK)
foreach(PKG ${PACKAGES_WITH_LIB})
set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

22
cmake/presets/std.cmake
View File

@ -1,22 +0,0 @@
set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
MOLECULE MPIIO MSCG OPT PERI POEMS
PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
USER-UEF USER-VTK)
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
foreach(PKG ${STANDARD_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)
endforeach()

26
cmake/presets/std_nolib.cmake
View File

@ -1,26 +0,0 @@
set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
MOLECULE MPIIO MSCG OPT PERI POEMS
PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
USER-UEF USER-VTK)
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
foreach(PKG ${STANDARD_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)
endforeach()
foreach(PKG ${PACKAGES_WITH_LIB})
set(PKG_${PKG} OFF CACHE BOOL "" FORCE)
endforeach()

22
cmake/presets/user.cmake
View File

@ -1,22 +0,0 @@
set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
MOLECULE MPIIO MSCG OPT PERI POEMS
PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
USER-UEF USER-VTK)
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
foreach(PKG ${USER_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)
endforeach()

4
doc/.gitignore vendored
View File

@ -1,6 +1,10 @@
/old
/html
/latex
/spelling
/LAMMPS.epub
/LAMMPS.mobi
/Manual.pdf
/Developer.pdf
/doctrees
/docenv

95
doc/Makefile
View File

@ -1,12 +1,12 @@
# Makefile for LAMMPS documentation
SHELL = /bin/bash
SHA1 = $(shell echo $USER-$PWD | python utils/sha1sum.py)
BUILDDIR = /tmp/lammps-docs-$(SHA1)
RSTDIR = $(BUILDDIR)/rst
SHELL = /bin/bash
BUILDDIR = ${CURDIR}
RSTDIR = $(BUILDDIR)/src
TXTDIR = $(BUILDDIR)/txt
VENV = $(BUILDDIR)/docenv
TXT2RST = $(VENV)/bin/txt2rst
ANCHORCHECK = $(VENV)/bin/doc_anchor_check
ANCHORCHECK = $(VENV)/bin/rst_anchor_check
PYTHON = $(shell which python3)
VIRTUALENV = virtualenv
@ -28,10 +28,10 @@ HAS_VIRTUALENV = YES
endif
SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
SOURCES=$(filter-out $(wildcard src/lammps_commands*.txt) src/lammps_support.txt src/lammps_tutorials.txt,$(wildcard src/*.txt))
OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
SOURCES=$(filter-out $(wildcard $(TXTDIR)/lammps_commands*.txt) $(TXTDIR)/lammps_support.txt $(TXTDIR)/lammps_tutorials.txt,$(wildcard $(TXTDIR)/*.txt))
OBJECTS=$(SOURCES:$(TXTDIR)/%.txt=$(RSTDIR)/%.rst)
.PHONY: help clean-all clean epub mobi html pdf old venv spelling anchor_check
.PHONY: help clean-all clean epub mobi rst html pdf venv spelling anchor_check
# ------------------------------------------
@ -39,35 +39,36 @@ help:
@echo "Please use \`make <target>' where <target> is one of"
@echo " html create HTML doc pages in html dir"
@echo " pdf create Developer.pdf and Manual.pdf in this dir"
@echo " old create old-style HTML doc pages in old dir"
@echo " fetch fetch HTML and PDF files from LAMMPS web site"
@echo " epub create ePUB format manual for e-book readers"
@echo " mobi convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
@echo " (requires ebook-convert tool from calibre)"
@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"
@echo " spelling spell-check the manual"
# ------------------------------------------
clean-all: clean
rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe
rm -rf $(BUILDDIR)/docenv $(BUILDDIR)/doctrees
clean:
rm -rf $(RSTDIR) html old epub
rm -rf html epub latex
rm -rf spelling
clean-spelling:
rm -rf spelling
rst: clean $(OBJECTS) $(ANCHORCHECK)
html: $(OBJECTS) $(ANCHORCHECK)
@(\
. $(VENV)/bin/activate ;\
cp -r src/* $(RSTDIR)/ ;\
sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
echo "############################################" ;\
doc_anchor_check src/*.txt ;\
rst_anchor_check src/*.rst ;\
env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
echo "############################################" ;\
deactivate ;\
)
@ -87,20 +88,19 @@ 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)/ ;\
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
@mkdir -p epub/JPG
@rm -f LAMMPS.epub
@cp src/JPG/lammps-logo.png epub/
@cp src/JPG/*.* epub/JPG
@(\
. $(VENV)/bin/activate ;\
cp -r src/* $(RSTDIR)/ ;\
sphinx-build $(SPHINXEXTRA) -b epub -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
deactivate ;\
)
@ -113,30 +113,43 @@ mobi: epub
@ebook-convert LAMMPS.epub LAMMPS.mobi
@echo "Conversion finished. The MOBI manual file is created."
pdf: utils/txt2html/txt2html.exe
pdf: $(OBJECTS) $(ANCHORCHECK)
@(\
set -e; \
cd src/Developer; \
pdflatex developer; \
pdflatex developer; \
mv developer.pdf ../../Developer.pdf; \
cd ..; \
../utils/txt2html/txt2html.exe -b *.txt; \
htmldoc --batch lammps.book; \
for s in `echo *.txt | sed -e 's,\.txt,\.html,g'` ; \
do grep -q $$s lammps.book || \
echo doc file $$s missing in src/lammps.book; done; \
rm *.html; \
cd ../../; \
)
old: utils/txt2html/txt2html.exe
@rm -rf old
@mkdir old; mkdir old/Eqs; mkdir old/JPG; mkdir old/PDF
@cd src; ../utils/txt2html/txt2html.exe -b *.txt; \
mv *.html ../old; \
cp Eqs/*.jpg ../old/Eqs; \
cp JPG/* ../old/JPG; \
cp PDF/* ../old/PDF;
@(\
. $(VENV)/bin/activate ;\
sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
echo "############################################" ;\
rst_anchor_check src/*.rst ;\
echo "############################################" ;\
deactivate ;\
)
@cd latex && \
sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \
mv temp Makefile && \
sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \
mv tmp.tex LAMMPS.tex && \
sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
mv tmp.tex LAMMPS.tex && \
make && \
make && \
mv LAMMPS.pdf ../Manual.pdf && \
cd ../;
@rm -rf latex/_sources
@rm -rf latex/PDF
@rm -rf latex/USER
@cp -r src/PDF latex/PDF
@cp -r src/USER latex/USER
@rm -rf latex/PDF/.[sg]*
@rm -rf latex/USER/.[sg]*
@rm -rf latex/USER/*/.[sg]*
@rm -rf latex/USER/*/*.[sg]*
@echo "Build finished. Manual.pdf and Developer.pdf are in this directory."
fetch:
@rm -rf html_www Manual_www.pdf Developer_www.pdf
@ -146,21 +159,16 @@ fetch:
@tar xzf lammps-doc.tar.gz
@rm -f lammps-doc.tar.gz
txt2html: utils/txt2html/txt2html.exe
anchor_check : $(ANCHORCHECK)
@(\
. $(VENV)/bin/activate ;\
doc_anchor_check src/*.txt ;\
rst_anchor_check src/*.txt ;\
deactivate ;\
)
# ------------------------------------------
utils/txt2html/txt2html.exe: utils/txt2html/txt2html.cpp
g++ -O -Wall -o $@ $<
$(RSTDIR)/%.rst : src/%.txt $(TXT2RST)
$(RSTDIR)/%.rst : $(TXTDIR)/%.txt $(TXT2RST)
@(\
mkdir -p $(RSTDIR) ; \
. $(VENV)/bin/activate ;\
@ -175,7 +183,6 @@ $(VENV):
$(VIRTUALENV) -p $(PYTHON) $(VENV); \
. $(VENV)/bin/activate; \
pip install Sphinx; \
pip install sphinxcontrib-images; \
deactivate;\
)

43
doc/README
View File

@ -5,7 +5,7 @@ sub-directories and optionally 2 PDF files and an ePUB file:
src content files for LAMMPS documentation
html HTML version of the LAMMPS manual (see html/Manual.html)
tools tools and settings for building the documentation
utils utilities and settings for building the documentation
Manual.pdf large PDF version of entire manual
Developer.pdf small PDF with info about how LAMMPS is structured
LAMMPS.epub Manual in ePUB format
@ -25,17 +25,12 @@ the fetched documentation will include those changes (but your source
code will not, unless you update your local repository).
(b) You can build the HTML and PDF files yourself, by typing "make
html" followed by "make pdf". Note that the PDF make requires the
HTML files already exist. This requires various tools including
Sphinx, which the build process will attempt to download and install
on your system, if not already available. See more details below.
(c) You can genererate an older, simpler, less-fancy style of HTML
documentation by typing "make old". This will create an "old"
directory. This can be useful if (b) does not work on your box for
some reason, or you want to quickly view the HTML version of a doc
page you have created or edited yourself within the src directory.
E.g. if you are planning to submit a new feature to LAMMPS.
html" or by "make pdf", respectively. This requires various tools
including the Python documentation processing tool Sphinx, which the
build process will attempt to download and install on your system into
a python virtual environment, if not already available. The PDF file
will require a working LaTeX installation with several add-on packages
in addition to the Python/Sphinx setup. See more details below.
----------------
@ -46,11 +41,10 @@ Options:
make html # generate HTML in html dir using Sphinx
make pdf # generate 2 PDF files (Manual.pdf,Developer.pdf)
# in this dir via htmldoc and pdflatex
make old # generate old-style HTML pages in old dir via txt2html
# in this dir via Sphinx and PDFLaTeX
make fetch # fetch HTML doc pages and 2 PDF files from web site
# as a tarball and unpack into html dir and 2 PDFs
make epub # generate LAMMPS.epub in ePUB format using Sphinx
make epub # generate LAMMPS.epub in ePUB format using Sphinx
make clean # remove intermediate RST files created by HTML build
make clean-all # remove entire build folder and any cached data
@ -94,8 +88,17 @@ This will install virtualenv from the Python Package Index.
Installing prerequisites for PDF build
[TBA]
Same as for HTML plus a compatible LaTeX installation with
support for PDFLaTeX. Also the following LaTeX packages need
to be installed (e.g. from texlive):
- amsmath
- babel
- cmap
- fncychap
- geometry
- hyperref
- hypcap
- times
----------------
Installing prerequisites for epub build
@ -103,7 +106,11 @@ Installing prerequisites for epub build
## ePUB
Same as for HTML. This uses the same tools and configuration
files as the HTML tree.
files as the HTML tree. The ePUB format conversion currently
does not support processing mathematical expressions via MathJAX,
so there will be limitations on some pages. For the time being
until this is resolved, building and using the PDF format file
is recommended instead.
For converting the generated ePUB file to a mobi format file
(for e-book readers like Kindle, that cannot read ePUB), you

196
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@ -0,0 +1,196 @@
# Outline of the GitHub Development Workflow
This purpose of this document is to provide a point of reference for the
core LAMMPS developers and other LAMMPS contributors to understand the
choices the LAMMPS developers have agreed on. Git and GitHub provide the
tools, but do not set policies, so it is up to the developers to come to
an agreement as to how to define and interpret policies. This document
is likely to change as our experiences and needs change and we try to
adapt accordingly. Last change 2018-12-19.
## Table of Contents
* [GitHub Merge Management](#github-merge-management)
* [Pull Requests](#pull-requests)
* [Pull Request Assignments](#pull-request-assignments)
* [Pull Request Reviews](#pull-request-reviews)
* [Pull Request Discussions](#pull-request-discussions)
* [Checklist for Pull Requests](#checklist-for-pull-requests)
* [GitHub Issues](#github-issues)
* [Milestones and Release Planning](#milestones-and-release-planning)
## GitHub Merge Management
In the interest of consistency, ONLY ONE of the core LAMMPS developers
should doing the merging itself. This is currently
[@akohlmey](https://github.com/akohlmey) (Axel Kohlmeyer).
If this assignment needs to be changed, it shall be done right after a
stable release. If the currently assigned developer cannot merge outstanding pull
requests in a timely manner, or in other extenuating circumstances,
other core LAMMPS developers with merge rights can merge pull requests,
when necessary.
## Pull Requests
ALL changes to the LAMMPS code and documentation, however trivial, MUST
be submitted as a pull request to GitHub. All changes to the "master"
branch must be made exclusively through merging pull requests. The
"unstable" and "stable" branches, respectively are only to be updated
upon patch or stable releases with fast-forward merges based on the
associated tags. Pull requests may also be submitted to (long-running)
feature branches created by LAMMPS developers inside the LAMMPS project,
if needed. Those are not subject to the merge and review restrictions
discussed in this document, though, but get managed as needed on a
case-by-case basis.
### Pull Request Assignments
Pull requests can be "chaperoned" by one of the LAMMPS core developers.
This is indicated by who the pull request is assigned to. LAMMPS core
developers can self-assign or they can decide to assign a pull request
to a different LAMMPS developer. Being assigned to a pull request means,
that this pull request may need some work and the assignee is tasked to
determine whether this might be needed or not, and may either implement
the required changes or ask the submitter of the pull request to implement
them. Even though, all LAMMPS developers may have write access to pull
requests (if enabled by the submitter, which is the default), only the
submitter or the assignee of a pull request may do so. During this
period the `work_in_progress` label shall be applied to the pull
request. The assignee gets to decide what happens to the pull request
next, e.g. whether it should be assigned to a different developer for
additional checks and changes, or is recommended to be merged. Removing
the `work_in_progress` label and assigning the pull request to the
developer tasked with merging signals that a pull request is ready to be
merged.
### Pull Request Reviews
People can be assigned to review a pull request in two ways:
* They can be assigned manually to review a pull request
by the submitter or a LAMMPS developer
* They can be automatically assigned, because a developers matches
a file pattern in the `.github/CODEOWNERS` file, which associates
developers with the code they contributed and maintain.
Reviewers are requested to state their appraisal of the proposed changes
and either approve or request changes. People may unassign themselves
from review, if they feel not competent about the changes proposed. At
least two approvals from LAMMPS developers with write access are required
before merging in addition to the automated compilation tests.
Merging counts as implicit approval, so does submission of a pull request
(by a LAMMPS developer). So the person doing the merge may not also submit
an approving review. The feature, that reviews from code owners are "hard"
reviews (i.e. they must all be approved before merging is allowed), is
currently disabled and it is in the discretion of the merge maintainer to
assess when a sufficient degree of approval, especially from external
contributors, has been reached in these cases. Reviews may be
(automatically) dismissed, when the reviewed code has been changed,
and then approval is required a second time.
### Pull Request Discussions
All discussions about a pull request should be kept as much as possible
on the pull request discussion page on GitHub, so that other developers
can later review the entire discussion after the fact and understand the
rationale behind choices made. Exceptions to this policy are technical
discussions, that are centered on tools or policies themselves
(git, github, c++) rather than on the content of the pull request.
### Checklist for Pull Requests
Here are some items to check:
* source and text files should not have CR/LF line endings (use dos2unix to remove)
* every new command or style should have documentation. The names of
source files (c++ and manual) should follow the name of the style.
(example: `src/fix_nve.cpp`, `src/fix_nve.h` for `fix nve` command,
implementing the class `FixNVE`, documented in `doc/src/fix_nve.txt`)
* all new style names should be lower case, the must be no dashes,
blanks, or underscores separating words, only forward slashes.
* new style docs should be added to the "overview" files in
`doc/src/Commands_*.txt`, `doc/src/{fixes,computes,pairs,bonds,...}.txt`
and `doc/src/lammps.book`
* check whether manual cleanly translates with `make html` and `make pdf`
* check spelling of manual with `make spelling` in doc folder
* new source files in packages should be added to `src/.gitignore`
* removed or renamed files in packages should be added to `src/Purge.list`
* C++ source files should use C++ style include files for accessing
C-library APIs, e.g. `#include <cstdlib>` instead of `#include <stdlib.h>`.
And they should use angular brackets instead of double quotes. Full list:
* assert.h -> cassert
* ctype.h -> cctype
* errno.h -> cerrno
* float.h -> cfloat
* limits.h -> climits
* math.h -> cmath
* complex.h -> complex
* setjmp.h -> csetjmp
* signal.h -> csignal
* stddef.h -> cstddef
* stdint.h -> cstdint
* stdio.h -> cstdio
* stdlib.h -> cstdlib
* string.h -> cstring
* time.h -> ctime
* Do NOT replace (as they are C++-11): `inttypes.h` and `stdint.h`.
* Code should follow the C++-98 standard. C++-11 is only accepted
in individual special purpose packages
* indentation is 2 spaces per level
* there should be NO tabs and no trailing whitespace
* header files, especially of new styles, should not include any
other headers, except the header with the base class or cstdio.
Forward declarations should be used instead when possible.
* iostreams should be avoided. LAMMPS uses stdio from the C-library.
* use of STL in headers and class definitions should be avoided.
* there MUST NOT be any "using namespace XXX;" statements in headers.
* static class members should be avoided at all cost.
* anything storing atom IDs should be using `tagint` and not `int`.
This can be flagged by the compiler only for pointers and only when
compiling LAMMPS with `-DLAMMPS_BIGBIG`.
* when including both `lmptype.h` (and using defines or macros from it)
and `mpi.h`, `lmptype.h` must be included first.
* when pair styles are added, check if settings for flags like
`single_enable`, `writedata`, `reinitflag`, `manybody_flag`
and others are correctly set and supported.
## GitHub Issues
The GitHub issue tracker is the location where the LAMMPS developers
and other contributors or LAMMPS users can report issues or bugs with
the LAMMPS code or request new features to be added. Feature requests
are usually indicated by a `[Feature Request]` marker in the subject.
Issues are assigned to a person, if this person is working on this
feature or working to resolve an issue. Issues that have nobody working
on them at the moment, have the label `volunteer needed` attached.
When an issue, say `#125` is resolved by a specific pull request,
the comment for the pull request shall contain the text `closes #125`
or `fixes #125`, so that the issue is automatically deleted when
the pull request is merged.
## Milestones and Release Planning
LAMMPS uses a continuous release development model with incremental
changes, i.e. significant effort is made - including automated pre-merge
testing - that the code in the branch "master" does not get broken.
More extensive testing (including regression testing) is performed after
code is merged to the "master" branch. There are patch releases of
LAMMPS every 1-3 weeks at a point, when the LAMMPS developers feel, that
a sufficient amount of changes have happened, and the post-merge testing
has been successful. These patch releases are marked with a
`patch_<version date>` tag and the "unstable" branch follows only these
versions (and thus is always supposed to be of production quality,
unlike "master", which may be temporary broken, in the case of larger
change sets or unexpected incompatibilities or side effects.
About 3-4 times each year, there are going to be "stable" releases
of LAMMPS. These have seen additional, manual testing and review of
results from testing with instrumented code and static code analysis.
Also, in the last 2-3 patch releases before a stable release are
"release candidate" versions which only contain bugfixes and
documentation updates. For release planning and the information of
code contributors, issues and pull requests being actively worked on
are assigned a "milestone", which corresponds to the next stable
release or the stable release after that, with a tentative release
date.

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@ -0,0 +1,133 @@
# Outline of include file conventions in LAMMPS
This purpose of this document is to provide a point of reference
for LAMMPS developers and contributors as to what include files
and definitions to put where into LAMMPS source.
Last change 2019-07-05
## Table of Contents
* [Motivation](#motivation)
* [Rules](#rules)
* [Tools](#tools)
* [Legacy Code](#legacy-code)
## Motivation
The conventions outlined in this document are supposed to help make
maintenance of the LAMMPS software easier. By trying to achieve
consistency across files contributed by different developers, it will
become easier for the code maintainers to modify and adjust files and,
overall, the chance for errors or portability issues will be reduced.
The rules employed are supposed to minimize naming conflicts and
simplify dependencies between files and thus speed up compilation. They
may, as well, make otherwise hidden dependencies visible.
## Rules
Below are the various rules that are applied. Not all are enforced
strictly and automatically. If there are no significant side effects,
exceptions may be possible for cases where a full compliance to the
rules may require a large effort compared to the benefit.
### Core Files Versus Package Files
All rules listed below are most strictly observed for core LAMMPS files,
which are the files that are not part of a package, and the files of the
packages MOLECULE, MANYBODY, KSPACE, and RIGID. On the other end of
the spectrum are USER packages and legacy packages that predate these
rules and thus may not be fully compliant. Also, new contributions
will be checked more closely, while existing code will be incrementally
adapted to the rules as time and required effort permits.
### System Versus Local Header Files
All system- or library-provided include files are included with angular
brackets (examples: `#include <cstring>` or `#include <mpi.h>`) while
include files provided with LAMMPS are included with double quotes
(examples: `#include "pointers.h"` or `#include "compute_temp.h"`).
For headers declaring functions of the C-library, the corresponding
C++ versions should be included (examples: `#include <cstdlib>` or
`#include <cctypes>`). However, these includes are limited to those defined
in the C++98 standard. Some files thus must use the older style until
the minimum C++ standard requirement of LAMMPS is lifted to C++11 or
even beyond (examples: `#include <stdint.h>` versus `#include <cstdint>`
or `#include <inttypes.h>` versus `#include <cinttypes>`).
### C++ Standard Compliance
LAMMPS core files currently correspond to the C++98 standard. Files
requiring C++11 or later are only permitted in (optional) packages
and particularly packages that are not part of the list of commonly
used packages such as MOLECULE, KSPACE, MANYBODY, or RIGID.
Also, LAMMPS uses the C-style stdio library for I/O instead of iostreams.
Since using both at the same time can cause problems, iostreams should
be avoided where possible.
### Lean Header Files
Header files will typically contain the definition of a (single) class.
These header files should have as few include statements as possible.
This is particularly important for classes that implement a "style" and
thus use a macro of the kind `SomeStyle(some/name,SomeName)`. These will
all be included in the auto-generated `"some_style.h"` files which
results in a high potential for direct or indirect symbol name clashes.
In the ideal case, the header would only include one file defining the
parent class. That would typically be either `#include "pointers.h"` for
the `Pointers` class, or a header of a class derived from it like
`#include "pair.h"` for the `Pair` class and so on. References to other
classes inside the class should be make through pointers, for which forward
declarations (inside the `LAMMPS_NS` or the new class' namespace) can
be employed. The full definition will then be included into the corresponding
implementation file. In the given example from above, the header file
would be called `some_name.h` and the implementation `some_name.cpp` (all
lower case with underscores, while the class itself would be in camel case
and no underscores `SomeName`, and the style name with lower case names separated by
a forward slash).
### Implementation Files
In the implementation files (typically, those would have the same base name
as the corresponding header with a .cpp extension instead of .h) include
statements should follow the "include what you use" principle.
### Order of Include Statements
Include files should be included in this order:
* the header matching the implementation (`some_class.h` for file `some_class.cpp`)
* mpi.h
* system and library headers (anything that is using angular brackets; C-library headers first, then C++)
* LAMMPS local headers (preferably in alphabetical order)
### Special Cases and Exceptions
#### pointers.h
The `pointer.h` header file also includes `cstdio` and `lmptype.h`
(and through it `stdint.h`, `intttypes.h`, cstdlib, and `climits`).
This means any header including `pointers.h` can assume that `FILE`,
`NULL`, `INT_MAX` are defined.
## Tools
The [Include What You Use tool](https://include-what-you-use.org/)
can be used to provide supporting information about compliance with
the rules listed here. There are some limitations and the IWYU tool
may give incorrect advice. The tools is activated by setting the
CMake variable `CMAKE_CXX_INCLUDE_WHAT_YOU_USE` variable to the
path of the `include-what-you-use` command. When activated, the
tool will be run after each compilation and provide suggestions for
which include files should be added or removed.
## Legacy Code
A lot of code predates the application of the rules in this document
and the rules themselves are a moving target. So there are going to be
significant chunks of code that do not fully comply. This applies
for example to the USER-REAXC, or the USER-ATC package. The LAMMPS
developers are dedicated to make an effort to improve the compliance
and welcome volunteers wanting to help with the process.

259
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@ -1,40 +1,259 @@
.TH LAMMPS "2018-08-22"
.TH LAMMPS "9 January 2020" "2020-01-09"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator.
.SH SYNOPSIS
.B lmp
-in in.file
.B lmp
\-in <input file> [OPTIONS] ...
or
mpirun \-np 2
.B lmp
-in in.file
mpirun \-np 2
.B lmp
<input file> [OPTIONS] ...
or
.B lmp
\-r2data file.restart file.data
.SH DESCRIPTION
.B LAMMPS
LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale
Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft
materials (biomolecules, polymers) and solid-state materials (metals,
semiconductors) and coarse-grained or mesoscopic systems. It can be used to
model atoms or, more generically, as a parallel particle simulator at the
.B LAMMPS
is a classical molecular dynamics code, and an acronym for \fBL\fRarge-scale
\fBA\fRtomic/\fBM\fRolecular \fBM\fRassively \fBP\fRarallel \fBS\fRimulator.
.B LAMMPS
has potentials for soft
materials (bio-molecules, polymers) and solid-state materials (metals,
semiconductors) and coarse-grained or mesoscopic systems. It can be used to
model atoms or, more generically, as a parallel particle simulator at the
atomic, meso, or continuum scale.
See http://lammps.sandia.gov/ for documentation.
See https://lammps.sandia.gov/ for more information and documentation.
.SH EXECUTABLE NAME
The
.B LAMMPS
executable can have different names depending on how it was configured,
compiled and installed. It will be either
.B lmp
or
.B lmp_<machine name>.
The <machine name> suffix corresponds to the (machine specific) makefile
used to compile
.B LAMMPS
when using the conventional build process. When building
.B LAMMPS
using
.B CMake
this <machine name> parameter can be chosen arbitrarily at configuration
time, but more common is to just use
.B lmp
without a suffix. In this manpage we will use
.B lmp
to represent any of those names.
.SH OPTIONS
See https://lammps.sandia.gov/doc/Run_options.html for details on
command-line options.
.SH COPYRIGHT
© 2003--2018 Sandia Corporation
.TP
\fB\-h\fR or \fB\-help\fR
Print a brief help summary and a list of settings and options compiled
into this executable. It also explicitly lists all LAMMPS styles
(atom_style, fix, compute, pair_style, bond_style, etc) available in
the specific executable. This can tell you if the command you want to
use was included via the appropriate package at compile time.
LAMMPS will print the info and immediately exit if this switch is used.
.TP
\fB\-e\fR or \fB\-echo\fR
Set the style of command echoing. The style can be
.B none
or
.B screen
or
.B log
or
.B both.
Depending on the style, each command read from the input script will
be echoed to the screen and/or logfile. This can be useful to figure
out which line of your script is causing an input error.
The default value is
.B log.
.TP
\fB\-i <input file>\fR or \fB\-in <input file>\fR
Specify a file to use as an input script. If it is not specified,
LAMMPS reads its script from standard input. This is a required
switch when running LAMMPS in multi-partition mode.
.TP
\fB\-k on/off [keyword value]\fR or \fB\-kokkos on/off [keyword value]\fR
Enable or disable general KOKKOS support, as provided by the KOKKOS
package. Even if LAMMPS is built with this package, this switch must
be set to \fBon\fR to enable running with KOKKOS-enabled styles. More
details on this switch and its optional keyword value pairs are discussed
at: https://lammps.sandia.gov/doc/Run_options.html
.TP
\fB\-l <log file>\fR or \fB\-log <log file>\fR
Specify a log file for LAMMPS to write status information to.
The default value is "log.lammps". If the file name "none" is used,
\fBLAMMPS\fR will not write a log file. In multi-partition mode only
some high-level all-partition information is written to the "<log file>"
file, the remainder is written in a per-partition file "<log file>.N"
with "N" being the respective partition number, unless overridden
by the \-plog flag (see below).
.TP
\fB\-m <number>\fR or \fB\-mpicolor <number>\fR
If used, this must be the first command-line argument after the
.B LAMMPS
executable name. It is only used when
.B LAMMPS
is launched by an mpirun command which also launches one or more
other executable(s) at the same time.
.B LAMMPS
and the other executable(s) perform an MPI_Comm_split(), each with
their own different colors, to split the MPI_COMM_WORLD communicator
for each executable to the subset of processors they are supposed to
be actually running on. Currently, this is only used in
.B LAMMPS
to perform client/server messaging with another application.
.B LAMMPS
can act as either a client or server (or both).
.TP
\fB\-nc\fR or \fB\-nocite\fR
Disable writing the "log.cite" file which is normally written to
list references for specific cite-able features used during a
.B LAMMPS
run.
.TP
\fB\-pk <style> [options]\fR or \fB\-package <style> [options]\fR
Invoke the \fBpackage\R command with <style> and optional arguments.
The syntax is the same as if the command appeared in an input script.
For example "-pk gpu 2" is the same as "package gpu 2" in the input
script. The possible styles and options are discussed in the
.B LAMMPS
manual for the "package" command. This switch can be used multiple
times, e.g. to set options for the USER-INTEL and USER-OMP packages
when used together. Along with the "-sf" or "-suffix" switch, this
is a convenient mechanism for invoking accelerator packages and their
options without having to edit an input script.
.TP
\fB\-p\fR or \fB\-partition\fR
Invoke
.B LAMMPS
in multi-partition mode. Without this,
.B LAMMPS
uses all P processors allocated via MPI to run a single simulation.
If this switch is used, the P processors are split into separate
partitions and each partition runs its own simulation. The arguments
to the switch specify the number of processors in each partition.
Arguments of the form "MxN" mean M partitions, each with N processors.
Arguments of the form "N" mean a single partition with N processors.
The sum of processors in all partitions must be equal P. Thus the
command “-partition 8x2 4 5” has 10 partitions and runs on a total
of 25 processors. Running with multiple partitions is required for
multi-replica simulations, where each replica runs on on one or more
few processors.
.TP
\fB\-pl <basename>\fR or \fB\-plog <basename>\fR
Specify the base name for the per-partition log files in multi-partition
runs, where partition N writes log information to <basename>.N.
If basename is set to "none", then no per-partition log files are created.
This overrides the name specified in the \-log command-line option.
.TP
\fB\-ps <basename>\fR or \fB\-pscreen <basename>\fR
Specify the base name for the per-partition screen files in multi-partition
runs, where partition N writes screen output to <basename>.N.
If basename is set to "none", then no per-partition screen files are created.
The default value is "screen" or whatever is set by the \-screen flag.
.TP
\fB\-r2data <restart file> [remap] <data file>\fR or
\fB\-restart2data <restart file> [remap] <data file>\fR
Convert <restart file> previously written by
.B LAMMPS
into a data file and immediately exit. This option has replaced the
external restart2data executable. Following <restart file>
argument, the optional word "remap" may be used. This has the
same effect like adding it to a "read_restart" command.
The syntax following the <data file> name is identical to the
arguments of the "write_data" command. See the
.B LAMMPS
manual for details on either of the two commands.
.TP
\fB\-r2dump <restart file> [remap] <dump file>\fR or
\fB\-restart2dump <restart file> [remap] <dump file>\fR
Convert <restart file> previously written by
.B LAMMPS
into a dump file and immediately exit. Following <restart file>
argument, the optional word "remap" may be used. This has the
same effect like adding it to a "read_restart" command.
The syntax following the <dump file> name is identical to the
arguments of the "dump" command. See the
.B LAMMPS
manual for details on either of the two commands.
.TP
\fB\-sc <file name>\fR or \fB\-screen <file name>\fR
Specify a file for
.B LAMMPS
to write its screen information to. By default, this will be
the standard output. If <file name> is "none", (most) screen
output will be suppressed. In multi-partition mode only
some high-level all-partition information is written to the
screen or "<file name>" file, the remainder is written in a
per-partition file "screen.N" or "<file name>.N"
with "N" being the respective partition number, and unless
overridden by the \-pscreen flag (see above).
.TP
\fB\-sf <suffix>\fR or \fB\-suffix <suffix>\fR
Use variants of various styles in the input, if they exist. This is
achieved by transparently trying to convert a style named <my/style>
into <my/style/suffix> if that latter style exists, but otherwise
fall back to the former. The most useful suffixes are "gpu",
"intel", "kk", "omp", "opt", or "hybrid". These refer to styles from
optional packages that LAMMPS can be built with. The hybrid suffix is
special, as it enables, having two suffixes tried (e.g. first "intel"
and then "omp") and thus requires two arguments. Along with the
"-package" command-line switch, this is a convenient mechanism for
invoking styles from accelerator packages and setting their options
without having to edit an input script.
See https://lammps.sandia.gov/doc/Run_options.html for additional
details and discussions on command-line options.
.SH LAMMPS BASICS
LAMMPS executes by reading commands from a input script (text file),
one line at a time. When the input script ends, LAMMPS exits. Each
command causes LAMMPS to take some action. It may set or change an
internal, read and parse a file, or run a simulation. Most commands
have default settings, which means you only need to use the command
if you wish to change the default.
The ordering of commands in an input script is usually not very important
unless a command like "run" is encountered, which starts some calculation
using the current internal state. Also, if a "pair_style" or "bond_style"
other similar style command is issued that has a different name from what
was previously active, it will replace the previous style and wipe out
all corresponding "pair_coeff" or "bond_coeff" or equivalent settings.
Some commands are only valid when they follow other commands. For
example you cannot set the temperature of a group of atoms until atoms
have been defined and a group command is used to define which atoms
belong to the group of a given name. Sometimes command B will use values
that can be set by command A. This means command A must precede command
B in the input to have the desired effect. Some commands must be issued
.B before
the simulation box is defined and others can only be issued
.B after.
Many input script errors are detected by
.B LAMMPS
and an ERROR or WARNING message is printed. The documentation for
each command lists restrictions on how the command can be used, and
the chapter on errors in the
.B LAMMPS
manual gives some additional information about error messages, if possible.
.SH COPYRIGHT
© 2003--2019 Sandia Corporation
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
it under the terms of the GNU General Public License version 2 as
published by the Free Software Foundation.
This package is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of

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.TH MSI2LMP "v3.9.9" "2018-11-05"
.SH NAME
.B MSI2LMP
\- Converter for Materials Studio files to LAMMPS
.SH SYNOPSIS
.B msi2lmp
<ROOTNAME> [-class <I|1|II|2|O|0>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift <x> <y> <z>]
.SH DESCRIPTION
.PP
.B MSI2LMP
is a tool bundled with LAMMPS to aide in the conversion of simulation
inputs from Biovia's Materials Studio software for use with LAMMPS.
It is a standalone program that generates a LAMMPS data file based on
the information in an MS .car file (atom coordinates), an .mdf file
(molecular topology and atom types) and an .frc (forcefield parameters)
file. The .car and .mdf files are specific to a molecular system while
the .frc file is specific to a forcefield (variant). The only coherency
needed between .frc and .car/.mdf files are the atom types.
.PP
.SH OPTIONS
.TP
\fB\<ROOTNAME>\fR
This has to be the first argument and is a
.B mandatory
argument. It defines the root of the file names; i.e. for a
.B <ROOTNAME>
of benzene, you have to provide the files 'benzene.car' and 'benzene.mdf'
in the current working directory.
.B msi2lmp
will then read and process those files according to its remaining settings.
All other settins are optional and have defaults as listed.
.TP
\fB\-c <I,1,II,2,O,0>\fR, \fB\-class <I,1,II,2,O,0>\fR
The \-c or \-class option selects the force field class, i.e which pair
styles and bond styles and so on are required in the LAMMPS input file.
Class I or class 1 uses similar combination of functional forms as Amber
and Charmm force field and support the force fields
.B cvff
and
.B clayff.
Class II or class 2 corresponds to the more complex force fields
.B COMPASS
and
.B pcff.
Class O or class 0 finally is an experimental and incomplete extension
and supports generating output for
.B OPLS-AA
.TP
\fB\-f <ffname>\fR, \fB\-frc <ffname>\fR
The \-c or \-frc option allows the selection of the force field parameter
file
.B<ffname>.frc.
Valid names for <ffname> with this distribution are: cvff, clayff, cvff_aug,
pcff, compass_published, cff91, and oplsaa. If the argument is a pathname,
i.e. it starts with a '.' or a '/', then this absolute path is used to read
the force field, otherwise
.B msi2lmp
will look in the folder pointed to by the environment variable
$MSI2LMP_LIBRARY. If the variable is not set, then it will look in the current
directory. The extension '.frc' is appended, if missing.
Default is to look for the cvff.frc force field file.
.TP
\fB\-p <loglevel>\fR, \fB\-print <loglevel>\fR,
Selects the amount of information messages about the progress of the
conversion printed to the screen.
.B <loglevel>
can be a number from 0 (silent except for errors) to 3 (very detailed).
.TP
\fB\-i\fR, \fB\-ignore\fR,
Ignore errors about missing parameters and use 0.0 for the respective
force constants making these no-ops. Is correct to be used for a few
molecules and settings, but often an indication, that either the atom
type assignment have errors, or the force field file is missing entries.
.TP
\fB\-n\fR, \fB\-nocenter\fR,
Do not center the box around the (geometrical) center of the atoms,
but around the origin. Default is to recenter.
.TP
\fB\-o\fR, \fB\-oldstyle\fR,
Write out a data file without style hint comments to be compatible
with old LAMMPS versions. Default is to write out those comments.
.TP
\fB-s <x> <y> <z>\fR, \fB-shift <x> <y> <z>\fR,
Shift the entire system (box and coordinates) by a vector
(default: 0.0 0.0 0.0).
.TP
.SH EXAMPLES
msi2lmp benzene -c 2 -p 1 -f ../frc_files/pcff.frc
msi2lmp benzene-class1 -c I
msi2lmp decane -c 0 -f oplsaa
.SH COPYRIGHT
© 2003--2019 Sandia Corporation
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License version 2 as
published by the Free Software Foundation.
This package is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.

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/Eqs
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Build LAMMPS
************
LAMMPS can be built as an executable or library from source code via
either traditional makefiles (which may require manual editing)
for use with GNU make or gmake, or a build environment generated by CMake
(Unix Makefiles, Xcode, Visual Studio, KDevelop or more). As an
alternative you can download a package with pre-built executables
as described on the :doc:`Install <Install>` doc page.
.. toctree::
:maxdepth: 1
Build_cmake
Build_make
Build_link
Build_basics
Build_settings
Build_package
Build_extras
Build_windows
Build_development
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

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Basic build options
===================
The following topics are covered on this page, for building both with
CMake and make:
* :ref:`Serial vs parallel build <serial>`
* :ref:`Choice of compiler and compile/link options <compile>`
* :ref:`Build LAMMPS as an executable or a library <exe>`
* :ref:`Build the LAMMPS documentation <doc>`
* :ref:`Install LAMMPS after a build <install>`
----------
.. _serial:
Serial vs parallel build
-------------------------------------
LAMMPS can be built to run in parallel using the ubiquitous `MPI (message-passing interface) <https://en.wikipedia.org/wiki/Message_Passing_Interface>`_
library. Or it can built to run on a single processor (serial)
without MPI. It can also be built with support for OpenMP threading
(see more discussion below).
**CMake variables**\ :
.. parsed-literal::
-D BUILD_MPI=value # yes or no, default is yes if CMake finds MPI, else no
-D BUILD_OMP=value # yes or no (default)
-D LAMMPS_MACHINE=name # name = mpi, serial, mybox, titan, laptop, etc
# no default value
The executable created by CMake (after running make) is lmp\_name. If
the LAMMPS\_MACHINE variable is not specified, the executable is just
lmp. Using BUILD\_MPI=no will produce a serial executable.
**Traditional make**\ :
.. parsed-literal::
cd lammps/src
make mpi # parallel build, produces lmp_mpi using Makefile.mpi
make serial # serial build, produces lmp_serial using Makefile/serial
make mybox # uses Makefile.mybox to produce lmp_mybox
Serial build (see src/MAKE/Makefile.serial):
.. parsed-literal::
MPI_INC = -I../STUBS
MPI_PATH = -L../STUBS
MPI_LIB = -lmpi_stubs
For a parallel build, if MPI is installed on your system in the usual
place (e.g. under /usr/local), you do not need to specify the 3
variables MPI\_INC, MPI\_PATH, MPI\_LIB. The MPI wrapper on the compiler
(e.g. mpicxx, mpiCC) knows where to find the needed include and
library files. Failing this, these 3 variables can be used to specify
where the mpi.h file (MPI\_INC), and the MPI library files (MPI\_PATH)
are found, and the name of the library files (MPI\_LIB).
For a serial build, you need to specify the 3 variables, as shown
above.
For a serial LAMMPS build, use the dummy MPI library provided in
src/STUBS. You also need to build the STUBS library for your platform
before making LAMMPS itself. A "make serial" build does this for.
Otherwise, type "make mpi-stubs" from the src directory, or "make"
from the src/STUBS dir. If the build fails, you will need to edit the
STUBS/Makefile for your platform.
The file STUBS/mpi.c provides a CPU timer function called MPI\_Wtime()
that calls gettimeofday() . If your system doesn't support
gettimeofday() , you'll need to insert code to call another timer.
Note that the ANSI-standard function clock() rolls over after an hour
or so, and is therefore insufficient for timing long LAMMPS
simulations.
**CMake and make info**\ :
If you are installing MPI yourself, we recommend MPICH2 from Argonne
National Laboratory or OpenMPI. MPICH can be downloaded from the
`Argonne MPI site <http://www.mcs.anl.gov/research/projects/mpich2/>`_.
OpenMPI can be downloaded from the `OpenMPI site <http://www.open-mpi.org>`_. Other MPI packages should also work.
If you are running on a large parallel machine, your system admins or
the vendor should have already installed a version of MPI, which is
likely to be faster than a self-installed MPICH or OpenMPI, so find
out how to build and link with it.
The majority of OpenMP (threading) support in LAMMPS is provided by
the USER-OMP package; see the :doc:`Speed omp <Speed_omp>` doc page for
details. The USER-INTEL package also provides OpenMP support (it is
compatible with USER-OMP) and adds vectorization support when compiled
with the Intel compilers on top of that. Also, the KOKKOS package can
be compiled for using OpenMP threading.
However, there are a few commands in LAMMPS that have native OpenMP
support. These are commands in the MPIIO, SNAP, USER-DIFFRACTION, and
USER-DPD packages. In addition some packages support OpenMP threading
indirectly through the libraries they interface to: e.g. LATTE and
USER-COLVARS. See the :doc:`Packages details <Packages_details>` doc
page for more info on these packages and the doc pages for their
respective commands for OpenMP threading info.
For CMake, if you use BUILD\_OMP=yes, you can use these packages and
turn on their native OpenMP support and turn on their native OpenMP
support at run time, by setting the OMP\_NUM\_THREADS environment
variable before you launch LAMMPS.
For building via conventional make, the CCFLAGS and LINKFLAGS
variables in Makefile.machine need to include the compiler flag that
enables OpenMP. For GNU compilers it is -fopenmp. For (recent) Intel
compilers it is -qopenmp. If you are using a different compiler,
please refer to its documentation.
.. _default-none-issues:
**OpenMP Compiler compatibility info**\ :
Some compilers do not fully support the 'default(none)' directive
and others (e.g. GCC version 9 and beyond) may implement OpenMP 4.0
semantics, which are incompatible with the OpenMP 3.1 directives used
in LAMMPS (for maximal compatibility with compiler versions in use).
In those case, all 'default(none)' directives (which aid in detecting
incorrect and unwanted sharing) can be replaced with 'default(shared)'
while dropping all 'shared()' directives. The script
'src/USER-OMP/hack\_openmp\_for\_pgi\_gcc9.sh' can be used to automate
this conversion.
----------
.. _compile:
Choice of compiler and compile/link options
---------------------------------------------------------
The choice of compiler and compiler flags can be important for
performance. Vendor compilers can produce faster code than
open-source compilers like GNU. On boxes with Intel CPUs, we suggest
trying the `Intel C++ compiler <intel_>`_.
.. _intel: https://software.intel.com/en-us/intel-compilers
On parallel clusters or supercomputers which use "modules" for their
compile/link environments, you can often access different compilers by
simply loading the appropriate module before building LAMMPS.
**CMake variables**\ :
.. parsed-literal::
-D CMAKE_CXX_COMPILER=name # name of C++ compiler
-D CMAKE_C_COMPILER=name # name of C compiler
-D CMAKE_Fortran_COMPILER=name # name of Fortran compiler
-D CMAKE_CXX_FLAGS=string # flags to use with C++ compiler
-D CMAKE_C_FLAGS=string # flags to use with C compiler
-D CMAKE_Fortran_FLAGS=string # flags to use with Fortran compiler
By default CMake will use a compiler it finds and it will add
optimization flags appropriate to that compiler and any :doc:`accelerator packages <Speed_packages>` you have included in the build.
You can tell CMake to look for a specific compiler with these variable
settings. Likewise you can specify the FLAGS variables if you want to
experiment with alternate optimization flags. You should specify all
3 compilers, so that the small number of LAMMPS source files written
in C or Fortran are built with a compiler consistent with the one used
for all the C++ files:
.. parsed-literal::
Building with GNU Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
Building with Intel Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
Building with LLVM/Clang Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
.. note::
When the cmake command completes, it prints info to the screen
as to which compilers it is using, and what flags will be used in the
compilation. Note that if the top-level compiler is mpicxx, it is
simply a wrapper on a real compiler. The underlying compiler info is
what will be listed in the CMake output. You should check to insure
you are using the compiler and optimization flags are the ones you
want.
**Makefile.machine settings**\ :
Parallel build (see src/MAKE/Makefile.mpi):
.. parsed-literal::
CC = mpicxx
CCFLAGS = -g -O3
LINK = mpicxx
LINKFLAGS = -g -O
Serial build (see src/MAKE/Makefile.serial):
.. parsed-literal::
CC = g++
CCFLAGS = -g -O3
LINK = g++
LINKFLAGS = -g -O
The "compiler/linker settings" section of a Makefile.machine lists
compiler and linker settings for your C++ compiler, including
optimization flags. You should always use mpicxx or mpiCC for
a parallel build, since these compiler wrappers will include
a variety of settings appropriate for your MPI installation.
.. note::
If you build LAMMPS with any :doc:`accelerator packages <Speed_packages>` included, they have specific
optimization flags that are either required or recommended for optimal
performance. You need to include these in the CCFLAGS and LINKFLAGS
settings above. For details, see the individual package doc pages
listed on the :doc:`Speed packages <Speed_packages>` doc page. Or
examine these files in the src/MAKE/OPTIONS directory. They
correspond to each of the 5 accelerator packages and their hardware
variants:
.. parsed-literal::
Makefile.opt # OPT package
Makefile.omp # USER-OMP package
Makefile.intel_cpu # USER-INTEL package for CPUs
Makefile.intel_coprocessor # USER-INTEL package for KNLs
Makefile.gpu # GPU package
Makefile.kokkos_cuda_mpi # KOKKOS package for GPUs
Makefile.kokkos_omp # KOKKOS package for CPUs (OpenMP)
Makefile.kokkos_phi # KOKKOS package for KNLs (OpenMP)
----------
.. _exe:
Build LAMMPS as an executable or a library
----------------------------------------------------
LAMMPS can be built as either an executable or as a static or shared
library. The LAMMPS library can be called from another application or
a scripting language. See the :doc:`Howto couple <Howto_couple>` doc
page for more info on coupling LAMMPS to other codes. See the
:doc:`Python <Python_head>` doc page for more info on wrapping and
running LAMMPS from Python via its library interface.
**CMake variables**\ :
.. parsed-literal::
-D BUILD_EXE=value # yes (default) or no
-D BUILD_LIB=value # yes or no (default)
-D BUILD_SHARED_LIBS=value # yes or no (default)
-D LAMMPS_LIB_SUFFIX=name # name = mpi, serial, mybox, titan, laptop, etc
# no default value
Setting BUILD\_EXE=no will not produce an executable. Setting
BUILD\_LIB=yes will produce a static library named liblammps.a.
Setting both BUILD\_LIB=yes and BUILD\_SHARED\_LIBS=yes will produce a
shared library named liblammps.so. If LAMMPS\_LIB\_SUFFIX is set the generated
libraries will be named liblammps\_name.a or liblammps\_name.so instead.
**Traditional make**\ :
.. parsed-literal::
cd lammps/src
make machine # build LAMMPS executable lmp_machine
make mode=lib machine # build LAMMPS static lib liblammps_machine.a
make mode=shlib machine # build LAMMPS shared lib liblammps_machine.so
The two library builds also create generic soft links, named
liblammps.a and liblammps.so, which point to the liblammps\_machine
files.
**CMake and make info**\ :
Note that for a shared library to be usable by a calling program, all
the auxiliary libraries it depends on must also exist as shared
libraries. This will be the case for libraries included with LAMMPS,
such as the dummy MPI library in src/STUBS or any package libraries in
the lib/packages directory, since they are always built as shared
libraries using the -fPIC switch. However, if a library like MPI or
FFTW does not exist as a shared library, the shared library build will
generate an error. This means you will need to install a shared
library version of the auxiliary library. The build instructions for
the library should tell you how to do this.
As an example, here is how to build and install the `MPICH library <mpich_>`_, a popular open-source version of MPI, distributed by
Argonne National Lab, as a shared library in the default
/usr/local/lib location:
.. _mpich: http://www-unix.mcs.anl.gov/mpi
.. parsed-literal::
./configure --enable-shared
make
make install
You may need to use "sudo make install" in place of the last line if
you do not have write privileges for /usr/local/lib. The end result
should be the file /usr/local/lib/libmpich.so.
----------
.. _doc:
Build the LAMMPS documentation
----------------------------------------
**CMake variable**\ :
.. parsed-literal::
-D BUILD_DOC=value # yes or no (default)
This will create the HTML doc pages within the CMake build directory.
The reason to do this is if you want to "install" LAMMPS on a system
after the CMake build via "make install", and include the doc pages in
the install.
**Traditional make**\ :
.. parsed-literal::
cd lammps/doc
make html # html doc pages
make pdf # single Manual.pdf file
This will create a lammps/doc/html dir with the HTML doc pages so that
you can browse them locally on your system. Type "make" from the
lammps/doc dir to see other options.
.. note::
You can also download a tarball of the documentation for the
current LAMMPS version (HTML and PDF files), from the website
`download page <http://lammps.sandia.gov/download.html>`_.
----------
.. _tools:
Build LAMMPS tools
------------------------------
Some tools described in :doc:`Auxiliary tools <Tools>` can be built directly
using CMake or Make.
**CMake variable**\ :
.. parsed-literal::
-D BUILD_TOOLS=value # yes or no (default)
The generated binaries will also become part of the LAMMPS installation (see below)
**Traditional make**\ :
.. parsed-literal::
cd lammps/tools
make all # build all binaries of tools
make binary2txt # build only binary2txt tool
make chain # build only chain tool
make micelle2d # build only micelle2d tool
make thermo_extract # build only thermo_extract tool
----------
.. _install:
Install LAMMPS after a build
------------------------------------------
After building LAMMPS, you may wish to copy the LAMMPS executable of
library, along with other LAMMPS files (library header, doc files) to
a globally visible place on your system, for others to access. Note
that you may need super-user privileges (e.g. sudo) if the directory
you want to copy files to is protected.
**CMake variable**\ :
.. parsed-literal::
cmake -D CMAKE_INSTALL_PREFIX=path [options ...] ../cmake
make # perform make after CMake command
make install # perform the installation into prefix
**Traditional make**\ :
There is no "install" option in the src/Makefile for LAMMPS. If you
wish to do this you will need to first build LAMMPS, then manually
copy the desired LAMMPS files to the appropriate system directories.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

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Build LAMMPS with CMake
=======================
This page is a short summary of how to use CMake to build LAMMPS.
Details on CMake variables that enable specific LAMMPS build options
are given on the pages linked to from the :doc:`Build <Build>` doc page.
Richard Berger (Temple U) has also written a `more comprehensive guide <https://github.com/lammps/lammps/blob/master/cmake/README.md>`_
for how to use CMake to build LAMMPS. If you are new to CMake it is a
good place to start.
----------
Building LAMMPS with CMake is a two-step process. First you use CMake
to create a build environment in a new directory. On Linux systems,
this will be based on makefiles for use with make. Then you use the
make command to build LAMMPS, which uses the created
Makefile(s). Example:
.. parsed-literal::
cd lammps # change to the LAMMPS distribution directory
mkdir build; cd build # create a new directory (folder) for build
cmake [options ...] ../cmake # configuration with (command-line) cmake
make # compilation
The cmake command will detect available features, enable selected
packages and options, and will generate the build environment. By default
this build environment will be created for "Unix Makefiles" on most
platforms and particularly on Linux. However, alternate build tools
(e.g. Ninja) and support files for Integrated Development Environments
(IDE) like Eclipse, CodeBlocks, or Kate can be generated, too. This is
selected via the "-G" command line flag. For the rest of the documentation
we will assume that the build environment is generated for makefiles
and thus the make command will be used to compile and link LAMMPS as
indicated above, producing (by default) an executable called "lmp" and
a library called "liblammps.a" in the "build" folder. When generating
a build environment for the "Ninja" build tool, the build command would
be "ninja" instead of "make".
If your machine has multiple CPU cores (most do these days), using a
command like "make -jN" (with N being the number of available local
CPU cores) can be much faster. If you plan to do development on
LAMMPS or need to re-compile LAMMPS repeatedly, installation of the
ccache (= Compiler Cache) software may speed up repeated compilation
even more.
After compilation, you may optionally install the LAMMPS executable into
your system with:
.. parsed-literal::
make install # optional, copy LAMMPS executable & library elsewhere
This will install the lammps executable and library (if requested), some
tools (if configured) and additional files like library API headers,
manpages, potential and force field files. The location of the installation
tree is set by the CMake variable "CMAKE\_INSTALL\_PREFIX" which defaults
to ${HOME}/.local
----------
There are 3 variants of CMake: a command-line version (cmake), a text mode
UI version (ccmake), and a graphical GUI version (cmake-GUI). You can use
any of them interchangeably to configure and create the LAMMPS build
environment. On Linux all the versions produce a Makefile as their
output. See more details on each below.
You can specify a variety of options with any of the 3 versions, which
affect how the build is performed and what is included in the LAMMPS
executable. Links to pages explaining all the options are listed on
the :doc:`Build <Build>` doc page.
You must perform the CMake build system generation and compilation in
a new directory you create. It can be anywhere on your local machine.
In these Build pages we assume that you are building in a directory
called "lammps/build". You can perform separate builds independently
with different options, so long as you perform each of them in a
separate directory you create. All the auxiliary files created by one
build process (executable, object files, log files, etc) are stored in
this directory or sub-directories within it that CMake creates.
.. note::
To perform a CMake build, no packages can be installed or a
build been previously attempted in the LAMMPS src directory by using
"make" commands to :doc:`perform a conventional LAMMPS build <Build_make>`. CMake detects if this is the case and
generates an error, telling you to type "make no-all purge" in the src
directory to un-install all packages. The purge removes all the \*.h
files auto-generated by make.
You must have CMake version 2.8 or later on your system to build
LAMMPS. A handful of LAMMPS packages (KOKKOS, LATTE, MSCG) require a
later version. CMake will print a message telling you if a later
version is required. Installation instructions for CMake are below.
After the initial build, if you edit LAMMPS source files, or add your
own new files to the source directory, you can just re-type make from
your build directory and it will re-compile only the files that have
changed. If you want to change CMake options you can run cmake (or
ccmake or cmake-gui) again from the same build directory and alter
various options; see details below. Or you can remove the entire build
folder, recreate the directory and start over.
----------
**Command-line version of CMake**\ :
.. parsed-literal::
cmake [options ...] /path/to/lammps/cmake # build from any dir
cmake [options ...] ../cmake # build from lammps/build
The cmake command takes one required argument, which is the LAMMPS
cmake directory which contains the CMakeLists.txt file.
The argument can be preceeded or followed by various CMake
command-line options. Several useful ones are:
.. parsed-literal::
-D CMAKE_INSTALL_PREFIX=path # where to install LAMMPS executable/lib if desired
-D CMAKE_BUILD_TYPE=type # type = RelWithDebInfo (default), Release, MinSizeRel, or Debug
-G output # style of output CMake generates
-DVARIABLE=value # setting for a LAMMPS feature to enable
-D VARIABLE=value # ditto, but cannot come after CMakeLists.txt dir
-C path/to/preset/file # load some CMake settings before configuring
All the LAMMPS-specific -D variables that a LAMMPS build supports are
described on the pages linked to from the :doc:`Build <Build>` doc page.
All of these variable names are upper-case and their values are
lower-case, e.g. -D LAMMPS\_SIZES=smallbig. For boolean values, any of
these forms can be used: yes/no, on/off, 1/0.
On Unix/Linux machines, CMake generates a Makefile by default to
perform the LAMMPS build. Alternate forms of build info can be
generated via the -G switch, e.g. Visual Studio on a Windows machine,
Xcode on MacOS, or KDevelop on Linux. Type "cmake --help" to see the
"Generator" styles of output your system supports.
.. note::
When CMake runs, it prints configuration info to the screen.
You should review this to verify all the features you requested were
enabled, including packages. You can also see what compilers and
compile options will be used for the build. Any errors in CMake
variable syntax will also be flagged, e.g. mis-typed variable names or
variable values.
CMake creates a CMakeCache.txt file when it runs. This stores all the
settings, so that when running CMake again you can use the current
folder '.' instead of the path to the LAMMPS cmake folder as the
required argument to the CMake command. Either way the existing
settings will be inherited unless the CMakeCache.txt file is removed.
If you later want to change a setting you can rerun cmake in the build
directory with different setting. Please note that some automatically
detected variables will not change their value when you rerun cmake.
In these cases it is usually better to first remove all the
files/directories in the build directory, or start with a fresh build
directory.
----------
**Curses version (terminal-style menu) of CMake**\ :
.. parsed-literal::
ccmake ../cmake
You initiate the configuration and build environment generation steps
separately. For the first you have to type **c**\ , for the second you
have to type **g**\ . You may need to type **c** multiple times, and may be
required to edit some of the entries of CMake configuration variables
in between. Please see the `ccmake manual <https://cmake.org/cmake/help/latest/manual/ccmake.1.html>`_ for
more information.
----------
**GUI version of CMake**\ :
.. parsed-literal::
cmake-gui ../cmake
You initiate the configuration and build environment generation steps
separately. For the first you have to click on the **Configure** button,
for the second you have to click on the **Generate** button. You may
need to click on **Configure** multiple times, and may be required to
edit some of the entries of CMake configuration variables in between.
Please see the `cmake-gui manual <https://cmake.org/cmake/help/latest/manual/cmake-gui.1.html>`_
for more information.
----------
**Installing CMake**
Check if your machine already has CMake installed:
.. parsed-literal::
which cmake # do you have it?
which cmake3 # version 3 may have this name
cmake --version # what specific version you have
On clusters or supercomputers which use environment modules to manage
software packages, do this:
.. parsed-literal::
module list # is a cmake module already loaded?
module avail # is a cmake module available?
module load cmake3 # load cmake module with appropriate name
Most Linux distributions offer pre-compiled cmake packages through
their package management system. If you do not have CMake or a new
enough version, you can download the latest version at
`https://cmake.org/download/ <https://cmake.org/download/>`_.
Instructions on how to install it on various platforms can be found
`on this page <https://cmake.org/install/>`_.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

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Development build options (CMake only)
======================================
The CMake build of LAMMPS has a few extra options which are useful during
development, testing or debugging.
----------
.. _compilation:
Verify compilation flags
------------------------------------------
Sometimes it is necessary to verify the complete sequence of compilation flags
generated by the CMake build. To enable a more verbose output during
compilation you can use the following option.
.. parsed-literal::
-D CMAKE_VERBOSE_MAKEFILE=value # value = no (default) or yes
Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1:
.. parsed-literal::
make VERBOSE=1
----------
.. _sanitizer:
Address, Undefined Behavior, and Thread Sanitizer Support
-------------------------------------------------------------------------
Compilers such as GCC and Clang support generating binaries which use different
sanitizers to detect problems in code during run-time. They can detect `memory leaks <https://clang.llvm.org/docs/AddressSanitizer.html>`_,
code that runs into `undefined behavior <https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html>`_ of the
language and `data races <https://clang.llvm.org/docs/ThreadSanitizer.html>`_ in threaded code.
The following settings allow you enable these features if your compiler supports
it. Please note that they come with a performance hit. However, they are
usually faster than using tools like Valgrind.
.. parsed-literal::
-D ENABLE_SANITIZE_ADDRESS=value # enable Address Sanitizer, value = no (default) or yes
-D ENABLE_SANITIZE_UNDEFINED=value # enable Undefined Behaviour Sanitizer, value = no (default) or yes
-D ENABLE_SANITIZE_THREAD=value # enable Thread Sanitizer, value = no (default) or yes
----------
.. _testing:
Code Coverage and Testing
---------------------------------------
We do extensive regression testing of the LAMMPS code base on a continuous
basis. Some of the logic to do this has been added to the CMake build so
developers can run the tests directly on their workstation.
.. note::
this is incomplete and only represents a small subset of tests that we run
.. parsed-literal::
-D ENABLE_TESTING=value # enable simple run tests of LAMMPS, value = no (default) or yes
-D LAMMPS_TESTING_SOURCE_DIR=path # path to lammps-testing repository (option if in custom location)
-D LAMMPS_TESTING_GIT_TAG=value # version of lammps-testing repository that should be used, value = master (default) or custom git commit or tag
If you enable testing in the CMake build it will create an additional target called "test". You can run them with:
.. parsed-literal::
make test
The test cases used come from the lammps-testing repository. They are
derivatives of the examples folder with some modifications to make the run
faster.
You can also collect code coverage metrics while running the tests by enabling
coverage support during building.
.. parsed-literal::
-D ENABLE_COVERAGE=value # enable coverage measurements, value = no (default) or yes
This will also add the following targets to generate coverage reports after running the LAMMPS executable:
.. parsed-literal::
make test # run tests first!
make gen_coverage_html # generate coverage report in HTML format
make gen_coverage_xml # generate coverage report in XML format
These reports require GCOVR to be installed. The easiest way to do this to install it via pip:
.. parsed-literal::
pip install git+https://github.com/gcovr/gcovr.git
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

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Link LAMMPS as a library to another code
========================================
LAMMPS can be used as a library by another application, including
Python scripts. The files src/library.cpp and library.h define the
C-style API for using LAMMPS as a library. See the :doc:`Howto library <Howto_library>` doc page for a description of the
interface and how to extend it for your needs.
The :doc:`Build basics <Build_basics>` doc page explains how to build
LAMMPS as either a shared or static library. This results in one of
these 2 files:
liblammps.so # shared library
liblammps.a # static library
----------
**Link with LAMMPS as a static library**\ :
The calling application can link to LAMMPS as a static library with a
link command like this:
g++ caller.o -L/home/sjplimp/lammps/src -llammps -o caller
The -L argument is the path to where the liblammps.a file is. The
-llammps argument is shorthand for the file liblammps.a.
----------
**Link with LAMMPS as a shared library**\ :
If you wish to link to liblammps.so, the operating system finds shared
libraries to load at run-time using the environment variable
LD\_LIBRARY\_PATH. To enable this you can do one of two things:
(1) Copy the liblammps.so file to a location the system can find it,
such as /usr/local/lib. I.e. a directory already listed in your
LD\_LIBRARY\_PATH variable. You can type
.. parsed-literal::
printenv LD_LIBRARY_PATH
to see what directories are in that list.
(2) Add the LAMMPS src directory (or the directory you perform CMake
build in) to your LD\_LIBRARY\_PATH, so that the current version of the
shared library is always available to programs that use it.
For the csh or tcsh shells, you would add something like this to your
~/.cshrc file:
.. parsed-literal::
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
----------
**Calling the LAMMPS library**\ :
Either flavor of library (static or shared) allows one or more LAMMPS
objects to be instantiated from the calling program.
When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS\_NS
namespace; you can safely use any of its classes and methods from
within the calling code, as needed.
When used from a C or Fortran program, the library has a simple
C-style interface, provided in src/library.cpp and src/library.h.
See the :doc:`Python library <Python_library>` doc page for a
description of the Python interface to LAMMPS, which wraps the C-style
interface.
See the sample codes in examples/COUPLE/simple for examples of C++ and
C and Fortran codes that invoke LAMMPS through its library interface.
Other examples in the COUPLE directory use coupling ideas discussed on
the :doc:`Howto couple <Howto_couple>` doc page.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

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Build LAMMPS with make
======================
Building LAMMPS with traditional makefiles requires that you have a
Makefile."machine" file appropriate for your system in the src/MAKE,
src/MAKE/MACHINES, src/MAKE/OPTIONS, or src/MAKE/MINE directory (see
below). It can include various options for customizing your LAMMPS
build with a number of global compilation options and features.
To include LAMMPS packages (i.e. optional commands and styles) you
must install them first, as discussed on the :doc:`Build package <Build_package>` doc page. If the packages require
provided or external libraries, you must build those libraries before
building LAMMPS. Building :doc:`LAMMPS with CMake <Build_cmake>` can
automate all of this for many types of machines, especially
workstations, desktops and laptops, so we suggest you try it first.
These commands perform a default LAMMPS build, producing the LAMMPS
executable lmp\_serial or lmp\_mpi in lammps/src:
.. parsed-literal::
cd lammps/src
make serial # build a serial LAMMPS executable
make mpi # build a parallel LAMMPS executable with MPI
make # see a variety of make options
This initial compilation can take a long time, since LAMMPS is a large
project with many features. If your machine has multiple CPU cores
(most do these days), using a command like "make -jN mpi" (with N =
the number of available CPU cores) can be much faster. If you plan to
do development on LAMMPS or need to re-compile LAMMPS repeatedly, the
installation of the ccache (= Compiler Cache) software may speed up
compilation even more.
After the initial build, whenever you edit LAMMPS source files, or add
or remove new files to the source directory (e.g. by installing or
uninstalling packages), you must re-compile and relink the LAMMPS
executable with the same "make" command. This makefiles dependencies
should insure that only the subset of files that need to be are
re-compiled.
.. note::
When you build LAMMPS for the first time, a long list of \*.d
files will be printed out rapidly. This is not an error; it is the
Makefile doing its normal creation of dependencies.
----------
The lammps/src/MAKE tree contains all the Makefile.machine files
included in the LAMMPS distribution. Typing "make machine" uses
Makefile.machine. Thus the "make serial" or "make mpi" lines above
use Makefile.serial and Makefile.mpi. Others are in these dirs:
.. parsed-literal::
OPTIONS # Makefiles which enable specific options
MACHINES # Makefiles for specific machines
MINE # customized Makefiles you create (you may need to create this folder)
Typing "make" lists all the available Makefile.machine files. A file
with the same name can appear in multiple folders (not a good idea).
The order the dirs are searched is as follows: src/MAKE/MINE,
src/MAKE, src/MAKE/OPTIONS, src/MAKE/MACHINES. This gives preference
to a customized file you put in src/MAKE/MINE.
Makefiles you may wish to try include these (some require a package
first be installed). Many of these include specific compiler flags
for optimized performance. Please note, however, that some of these
customized machine Makefile are contributed by users. Since both
compilers, OS configurations, and LAMMPS itself keep changing, their
settings may become outdated:
.. parsed-literal::
make mac # build serial LAMMPS on a Mac
make mac_mpi # build parallel LAMMPS on a Mac
make intel_cpu # build with the USER-INTEL package optimized for CPUs
make knl # build with the USER-INTEL package optimized for KNLs
make opt # build with the OPT package optimized for CPUs
make omp # build with the USER-OMP package optimized for OpenMP
make kokkos_omp # build with the KOKKOS package for OpenMP
make kokkos_cuda_mpi # build with the KOKKOS package for GPUs
make kokkos_phi # build with the KOKKOS package for KNLs
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

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Include packages in build
=========================
In LAMMPS, a package is a group of files that enable a specific set of
features. For example, force fields for molecular systems or
rigid-body constraints are in packages. In the src directory, each
package is a sub-directory with the package name in capital letters.
An overview of packages is given on the :doc:`Packages <Packages>` doc
page. Brief overviews of each package are on the :doc:`Packages details <Packages_details>` doc page.
When building LAMMPS, you can choose to include or exclude each
package. In general there is no need to include a package if you
never plan to use its features.
If you get a run-time error that a LAMMPS command or style is
"Unknown", it is often because the command is contained in a package,
and your build did not include that package. Running LAMMPS with the
:doc:`-h command-line switch <Run_options>` will print all the included
packages and commands for that executable.
For the majority of packages, if you follow the single step below to
include it, you can then build LAMMPS exactly the same as you would
without any packages installed. A few packages may require additional
steps, as explained on the :doc:`Build extras <Build_extras>` doc page.
These links take you to the extra instructions for those select
packages:
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`COMPRESS <compress>` | :ref:`GPU <gpu>` | :ref:`KIM <kim>` | :ref:`KOKKOS <kokkos>` | :ref:`LATTE <latte>` | :ref:`MESSAGE <message>` |
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`MSCG <mscg>` | :ref:`OPT <opt>` | :ref:`POEMS <poems>` | :ref:`PYTHON <python>` | :ref:`VORONOI <voronoi>` | :ref:`USER-ADIOS <user-adios>` |
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`USER-ATC <user-atc>` | :ref:`USER-AWPMD <user-awpmd>` | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>` | :ref:`USER-INTEL <user-intel>` | :ref:`USER-MOLFILE <user-molfile>` |
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`USER-NETCDF <user-netcdf>` | :ref:`USER-PLUMED <user-plumed>` | :ref:`USER-OMP <user-omp>` | :ref:`USER-QMMM <user-qmmm>` | :ref:`USER-QUIP <user-quip>` | :ref:`USER-SCAFACOS <user-scafacos>` |
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`USER-SMD <user-smd>` | :ref:`USER-VTK <user-vtk>` | | | | |
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
The mechanism for including packages is simple but different for CMake
versus make.
**CMake variables**\ :
.. parsed-literal::
-D PKG_NAME=value # yes or no (default)
Examples:
.. parsed-literal::
-D PKG_MANYBODY=yes
-D PKG_USER-INTEL=yes
All standard and user packages are included the same way. Note that
USER packages have a hyphen between USER and the rest of the package
name, not an underscore.
See the shortcut section below for how to install many packages at
once with CMake.
.. note::
If you toggle back and forth between building with CMake vs
make, no packages in the src directory can be installed when you
invoke cmake. CMake will give an error if that is not the case,
indicating how you can un-install all packages in the src dir.
**Traditional make**\ :
.. parsed-literal::
cd lammps/src
make ps # check which packages are currently installed
make yes-name # install a package with name
make no-name # un-install a package with name
make mpi # build LAMMPS with whatever packages are now installed
Examples:
.. parsed-literal::
make no-rigid
make yes-user-intel
All standard and user packages are included the same way.
See the shortcut section below for how to install many packages at
once with make.
.. note::
You must always re-build LAMMPS (via make) after installing or
un-installing a package, for the action to take effect.
.. note::
You cannot install or un-install packages and build LAMMPS in a
single make command with multiple targets, e.g. make yes-colloid mpi.
This is because the make procedure creates a list of source files that
will be out-of-date for the build if the package configuration changes
within the same command. You can include or exclude multiple packages
in a single make command, e.g. make yes-colloid no-manybody.
**CMake and make info**\ :
Any package can be included or excluded in a LAMMPS build, independent
of all other packages. However, some packages include files derived
from files in other packages. LAMMPS checks for this and does the
right thing. Individual files are only included if their dependencies
are already included. Likewise, if a package is excluded, other files
dependent on that package are also excluded.
When you download a LAMMPS tarball or download LAMMPS source files
from the Git or SVN repositories, no packages are pre-installed in the
src directory.
.. note::
Prior to Aug 2018, if you downloaded a tarball, 3 packages
(KSPACE, MANYBODY, MOLECULE) were pre-installed in the src directory.
That is no longer the case, so that CMake will build as-is without the
need to un-install those packages.
----------
**CMake shortcuts for installing many packages**\ :
Instead of specifying all the CMake options via the command-line,
CMake allows initializing the variable cache using script files. These
are regular CMake files which can manipulate and set variables, and
can also contain control flow constructs.
LAMMPS includes several of these files to define configuration
"presets", similar to the options that exist for the Make based
system. Using these files you can enable/disable portions of the
available packages in LAMMPS. If you need a custom preset you can take
one of them as a starting point and customize it to your needs.
+-------------------------------------------------------------+-----------------------------------------------------------+
| cmake -C ../cmake/presets/all\_on.cmake [OPTIONS] ../cmake | enable all packages |
+-------------------------------------------------------------+-----------------------------------------------------------+
| cmake -C ../cmake/presets/all\_off.cmake [OPTIONS] ../cmake | disable all packages |
+-------------------------------------------------------------+-----------------------------------------------------------+
| cmake -C ../cmake/presets/minimal.cmake [OPTIONS] ../cmake | enable just a few core packages |
+-------------------------------------------------------------+-----------------------------------------------------------+
| cmake -C ../cmake/presets/most.cmake [OPTIONS] ../cmake | enable most common packages |
+-------------------------------------------------------------+-----------------------------------------------------------+
| cmake -C ../cmake/presets/nolib.cmake [OPTIONS] ../cmake | disable packages that do require extra libraries or tools |
+-------------------------------------------------------------+-----------------------------------------------------------+
| cmake -C ../cmake/presets/clang.cmake [OPTIONS] ../cmake | change settings to use the Clang compilers by default |
+-------------------------------------------------------------+-----------------------------------------------------------+
| cmake -C ../cmake/presets/mingw.cmake [OPTIONS] ../cmake | enable all packages compatible with MinGW compilers |
+-------------------------------------------------------------+-----------------------------------------------------------+
.. note::
Running cmake this way manipulates the variable cache in your
current build directory. You can combine multiple presets and options
in a single cmake run, or change settings incrementally by running
cmake with new flags.
**Example:**
.. parsed-literal::
# build LAMMPS with most commonly used packages, but then remove
# those requiring additional library or tools, but still enable
# GPU package and configure it for using CUDA. You can run.
mkdir build
cd build
cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake -D PKG_GPU=on -D GPU_API=cuda ../cmake
# to add another package, say BODY to the previous configuration you can run:
cmake -D PKG_BODY=on .
# to reset the package selection from above to the default of no packages
# but leaving all other settings untouched. You can run:
cmake -C ../cmake/presets/no_all.cmake .
----------
**Make shortcuts for installing many packages**\ :
The following commands are useful for managing package source files
and their installation when building LAMMPS via traditional make.
Just type "make" in lammps/src to see a one-line summary.
These commands install/un-install sets of packages:
+-----------------------------------+-----------------------------------------------------+
| make yes-all | install all packages |
+-----------------------------------+-----------------------------------------------------+
| make no-all | un-install all packages |
+-----------------------------------+-----------------------------------------------------+
| make yes-standard or make yes-std | install standard packages |
+-----------------------------------+-----------------------------------------------------+
| make no-standard or make no-std | un-install standard packages |
+-----------------------------------+-----------------------------------------------------+
| make yes-user | install user packages |
+-----------------------------------+-----------------------------------------------------+
| make no-user | un-install user packages |
+-----------------------------------+-----------------------------------------------------+
| make yes-lib | install packages that require extra libraries |
+-----------------------------------+-----------------------------------------------------+
| make no-lib | un-install packages that require extra libraries |
+-----------------------------------+-----------------------------------------------------+
| make yes-ext | install packages that require external libraries |
+-----------------------------------+-----------------------------------------------------+
| make no-ext | un-install packages that require external libraries |
+-----------------------------------+-----------------------------------------------------+
which install/un-install various sets of packages. Typing "make
package" will list all the these commands.
.. note::
Installing or un-installing a package works by simply copying
files back and forth between the main src directory and
sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC),
so that the files are included or excluded when LAMMPS is built.
The following make commands help manage files that exist in both the
src directory and in package sub-directories. You do not normally
need to use these commands unless you are editing LAMMPS files or are
:doc:`installing a patch <Install_patch>` downloaded from the LAMMPS web
site.
Type "make package-status" or "make ps" to show which packages are
currently installed. For those that are installed, it will list any
files that are different in the src directory and package
sub-directory.
Type "make package-installed" or "make pi" to show which packages are
currently installed, without listing the status of packages that are
not installed.
Type "make package-update" or "make pu" to overwrite src files with
files from the package sub-directories if the package is installed.
It should be used after a :doc:`patch has been applied <Install_patch>`,
since patches only update the files in the package sub-directory, but
not the src files.
Type "make package-overwrite" to overwrite files in the package
sub-directories with src files.
Type "make package-diff" to list all differences between pairs of
files in both the src dir and a package dir.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

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Optional build settings
=======================
LAMMPS can be built with several optional settings. Each sub-section
explain how to do this for building both with CMake and make.
| :ref:`C++11 standard compliance test <cxx11>` when building all of LAMMPS
| :ref:`FFT library <fft>` for use with the :doc:`kspace\_style pppm <kspace_style>` command
| :ref:`Size of LAMMPS data types <size>`
| :ref:`Read or write compressed files <gzip>`
| :ref:`Output of JPG and PNG files <graphics>` via the :doc:`dump image <dump_image>` command
| :ref:`Output of movie files <graphics>` via the :doc:`dump\_movie <dump_image>` command
| :ref:`Memory allocation alignment <align>`
| :ref:`Workaround for long long integers <longlong>`
| :ref:`Error handling exceptions <exceptions>` when using LAMMPS as a library
|
----------
.. _cxx11:
C++11 standard compliance test
------------------------------------------
The LAMMPS developers plan to transition to make the C++11 standard the
minimum requirement for compiling LAMMPS. Currently this only applies to
some packages like KOKKOS while the rest aims to be compatible with the C++98
standard. Most currently used compilers are compatible with C++11; some need
to set extra flags to switch. To determine the impact of requiring C++11,
we have added a simple compliance test to the source code, that will cause
the compilation to abort, if C++11 compliance is not available or enabled.
To bypass this check, you need to change a setting in the makefile or
when calling CMake.
**CMake variable**\ :
.. parsed-literal::
-D DISABLE_CXX11_REQUIREMENT=yes
You can set additional C++ compiler flags (beyond those selected by CMake)
through the CMAKE\_CXX\_FLAGS variable. Example for CentOS 7:
.. parsed-literal::
-D CMAKE_CXX_FLAGS="-O3 -g -fopenmp -DNDEBUG -std=c++11"
**Makefile.machine setting**\ :
.. parsed-literal::
LMP_INC = -DLAMMPS_CXX98
----------
.. _fft:
FFT library
---------------------
When the KSPACE package is included in a LAMMPS build, the
:doc:`kspace\_style pppm <kspace_style>` command performs 3d FFTs which
require use of an FFT library to compute 1d FFTs. The KISS FFT
library is included with LAMMPS but other libraries can be faster.
LAMMPS can use them if they are available on your system.
**CMake variables**\ :
.. parsed-literal::
-D FFT=value # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
-D FFT_SINGLE=value # yes or no (default), no = double precision
-D FFT_PACK=value # array (default) or pointer or memcpy
.. note::
The values for the FFT variable must be in upper-case. This is
an exception to the rule that all CMake variables can be specified
with lower-case values.
Usually these settings are all that is needed. If CMake cannot find
the FFT library, you can set these variables:
.. parsed-literal::
-D FFTW3_INCLUDE_DIRS=path # path to FFTW3 include files
-D FFTW3_LIBRARIES=path # path to FFTW3 libraries
-D MKL_INCLUDE_DIRS=path # ditto for Intel MKL library
-D MKL_LIBRARIES=path
**Makefile.machine settings**\ :
.. parsed-literal::
FFT_INC = -DFFT_FFTW3 # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
# default is KISS if not specified
FFT_INC = -DFFT_SINGLE # do not specify for double precision
FFT_INC = -DFFT_PACK_ARRAY # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
# default is FFT\_PACK\_ARRAY if not specified
.. parsed-literal::
FFT_INC = -I/usr/local/include
FFT_PATH = -L/usr/local/lib
FFT_LIB = -lfftw3 # FFTW3 double precision
FFT_LIB = -lfftw3 -lfftw3f # FFTW3 single precision
FFT_LIB = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core # MKL with Intel compiler
FFT_LIB = -lmkl_gf_lp64 -lmkl_sequential -lmkl_core # MKL with GNU compier
As with CMake, you do not need to set paths in FFT\_INC or FFT\_PATH, if
make can find the FFT header and library files. You must specify
FFT\_LIB with the appropriate FFT libraries to include in the link.
**CMake and make info**\ :
The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS
distribution. It is portable across all platforms. Depending on the
size of the FFTs and the number of processors used, the other
libraries listed here can be faster.
However, note that long-range Coulombics are only a portion of the
per-timestep CPU cost, FFTs are only a portion of long-range
Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
communication can be costly). A breakdown of these timings is printed
to the screen at the end of a run using the :doc:`kspace\_style pppm <kspace_style>` command. The :doc:`Run output <Run_output>`
doc page gives more details.
FFTW is a fast, portable FFT library that should also work on any
platform and can be faster than the KISS FFT library. You can
download it from `www.fftw.org <http://www.fftw.org>`_. LAMMPS requires
version 3.X; the legacy version 2.1.X is no longer supported.
Building FFTW for your box should be as simple as ./configure; make;
make install. The install command typically requires root privileges
(e.g. invoke it via sudo), unless you specify a local directory with
the "--prefix" option of configure. Type "./configure --help" to see
various options.
The Intel MKL math library is part of the Intel compiler suite. It
can be used with the Intel or GNU compiler (see FFT\_LIB setting above).
Performing 3d FFTs in parallel can be time consuming due to data
access and required communication. This cost can be reduced by
performing single-precision FFTs instead of double precision. Single
precision means the real and imaginary parts of a complex datum are
4-byte floats. Double precision means they are 8-byte doubles. Note
that Fourier transform and related PPPM operations are somewhat less
sensitive to floating point truncation errors and thus the resulting
error is less than the difference in precision. Using the -DFFT\_SINGLE
setting trades off a little accuracy for reduced memory use and
parallel communication costs for transposing 3d FFT data.
When using -DFFT\_SINGLE with FFTW3 you may need to build the FFTW
library a second time with support for single-precision.
For FFTW3, do the following, which should produce the additional
library libfftw3f.a
.. parsed-literal::
make clean
./configure --enable-single; make; make install
Performing 3d FFTs requires communication to transpose the 3d FFT
grid. The data packing/unpacking for this can be done in one of 3
modes (ARRAY, POINTER, MEMCPY) as set by the FFT\_PACK syntax above.
Depending on the machine, the size of the FFT grid, the number of
processors used, one option may be slightly faster. The default is
ARRAY mode.
----------
.. _size:
Size of LAMMPS data types
------------------------------------
LAMMPS has a few integer data types which can be defined as 4-byte or
8-byte integers. The default setting of "smallbig" is almost always
adequate.
**CMake variable**\ :
.. parsed-literal::
-D LAMMPS_SIZES=value # smallbig (default) or bigbig or smallsmall
**Makefile.machine setting**\ :
.. parsed-literal::
LMP_INC = -DLAMMPS_SMALLBIG # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL
# default is LAMMPS\_SMALLBIG if not specified
**CMake and make info**\ :
The default "smallbig" setting allows for simulations with:
* total atom count = 2\^63 atoms (about 9e18)
* total timesteps = 2\^63 (about 9e18)
* atom IDs = 2\^31 (about 2 billion)
* image flags = roll over at 512
The "bigbig" setting increases the latter two limits. It allows for:
* total atom count = 2\^63 atoms (about 9e18)
* total timesteps = 2\^63 (about 9e18)
* atom IDs = 2\^63 (about 9e18)
* image flags = roll over at about 1 million (2\^20)
The "smallsmall" setting is only needed if your machine does not
support 8-byte integers. It allows for:
* total atom count = 2\^31 atoms (about 2 billion)
* total timesteps = 2\^31 (about 2 billion)
* atom IDs = 2\^31 (about 2 billion)
* image flags = roll over at 512 (2\^9)
Atom IDs are not required for atomic systems which do not store bond
topology information, though IDs are enabled by default. The
:doc:`atom\_modify id no <atom_modify>` command will turn them off. Atom
IDs are required for molecular systems with bond topology (bonds,
angles, dihedrals, etc). Thus if you model a molecular system with
more than 2 billion atoms, you need the "bigbig" setting.
Image flags store 3 values per atom which count the number of times an
atom has moved through the periodic box in each dimension. See the
:doc:`dump <dump>` doc page for a discussion. If an atom moves through
the periodic box more than this limit, the value will "roll over",
e.g. from 511 to -512, which can cause diagnostics like the
mean-squared displacement, as calculated by the :doc:`compute msd <compute_msd>` command, to be faulty.
Note that the USER-ATC package and the USER-INTEL package are currently
not compatible with the "bigbig" setting. Also, there are limitations
when using the library interface. Some functions with known issues
have been replaced by dummy calls printing a corresponding error rather
than crashing randomly or corrupting data.
Also note that the GPU package requires its lib/gpu library to be
compiled with the same size setting, or the link will fail. A CMake
build does this automatically. When building with make, the setting
in whichever lib/gpu/Makefile is used must be the same as above.
----------
.. _graphics:
Output of JPG, PNG, and movie files
--------------------------------------------------
The :doc:`dump image <dump_image>` command has options to output JPEG or
PNG image files. Likewise the :doc:`dump movie <dump_image>` command
outputs movie files in MPEG format. Using these options requires the
following settings:
**CMake variables**\ :
.. parsed-literal::
-D WITH_JPEG=value # yes or no
# default = yes if CMake finds JPEG files, else no
-D WITH_PNG=value # yes or no
# default = yes if CMake finds PNG and ZLIB files, else no
-D WITH_FFMPEG=value # yes or no
# default = yes if CMake can find ffmpeg, else no
Usually these settings are all that is needed. If CMake cannot find
the graphics header, library, executable files, you can set these
variables:
.. parsed-literal::
-D JPEG_INCLUDE_DIR=path # path to jpeglib.h header file
-D JPEG_LIBRARIES=path # path to libjpeg.a (.so) file
-D PNG_INCLUDE_DIR=path # path to png.h header file
-D PNG_LIBRARIES=path # path to libpng.a (.so) file
-D ZLIB_INCLUDE_DIR=path # path to zlib.h header file
-D ZLIB_LIBRARIES=path # path to libz.a (.so) file
-D FFMPEG_EXECUTABLE=path # path to ffmpeg executable
**Makefile.machine settings**\ :
.. parsed-literal::
LMP_INC = -DLAMMPS_JPEG
LMP_INC = -DLAMMPS_PNG
LMP_INC = -DLAMMPS_FFMPEG
JPG_INC = -I/usr/local/include # path to jpeglib.h, png.h, zlib.h header files if make cannot find them
JPG_PATH = -L/usr/lib # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them
JPG_LIB = -ljpeg -lpng -lz # library names
As with CMake, you do not need to set JPG\_INC or JPG\_PATH, if make can
find the graphics header and library files. You must specify JPG\_LIB
with a list of graphics libraries to include in the link. You must
insure ffmpeg is in a directory where LAMMPS can find it at runtime,
i.e. a dir in your PATH environment variable.
**CMake and make info**\ :
Using ffmpeg to output movie files requires that your machine
supports the "popen" function in the standard runtime library.
.. note::
On some clusters with high-speed networks, using the fork()
library calls (required by popen()) can interfere with the fast
communication library and lead to simulations using ffmpeg to hang or
crash.
----------
.. _gzip:
Read or write compressed files
-----------------------------------------
If this option is enabled, large files can be read or written with
gzip compression by several LAMMPS commands, including
:doc:`read\_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
**CMake variables**\ :
.. parsed-literal::
-D WITH_GZIP=value # yes or no
# default is yes if CMake can find gzip, else no
-D GZIP_EXECUTABLE=path # path to gzip executable if CMake cannot find it
**Makefile.machine setting**\ :
.. parsed-literal::
LMP_INC = -DLAMMPS_GZIP
**CMake and make info**\ :
This option requires that your machine supports the "popen()" function
in the standard runtime library and that a gzip executable can be
found by LAMMPS during a run.
.. note::
On some clusters with high-speed networks, using the fork()
library calls (required by popen()) can interfere with the fast
communication library and lead to simulations using compressed output
or input to hang or crash. For selected operations, compressed file
I/O is also available using a compression library instead, which is
what the :ref:`COMPRESS package <PKG-COMPRESS>` enables.
----------
.. _align:
Memory allocation alignment
---------------------------------------
This setting enables the use of the posix\_memalign() call instead of
malloc() when LAMMPS allocates large chunks or memory. This can make
vector instructions on CPUs more efficient, if dynamically allocated
memory is aligned on larger-than-default byte boundaries.
On most current systems, the malloc() implementation returns
pointers that are aligned to 16-byte boundaries. Using SSE vector
instructions efficiently, however, requires memory blocks being
aligned on 64-byte boundaries.
**CMake variable**\ :
.. parsed-literal::
-D LAMMPS_MEMALIGN=value # 0, 8, 16, 32, 64 (default)
Use a LAMMPS\_MEMALIGN value of 0 to disable using posix\_memalign()
and revert to using the malloc() C-library function instead. When
compiling LAMMPS for Windows systems, malloc() will always be used
and this setting ignored.
**Makefile.machine setting**\ :
.. parsed-literal::
LMP_INC = -DLAMMPS_MEMALIGN=value # 8, 16, 32, 64
Do not set -DLAMMPS\_MEMALIGN, if you want to have memory allocated
with the malloc() function call instead. -DLAMMPS\_MEMALIGN **cannot**
be used on Windows, as it does use different function calls for
allocating aligned memory, that are not compatible with how LAMMPS
manages its dynamical memory.
----------
.. _longlong:
Workaround for long long integers
------------------------------------------------
If your system or MPI version does not recognize "long long" data
types, the following setting will be needed. It converts "long long"
to a "long" data type, which should be the desired 8-byte integer on
those systems:
**CMake variable**\ :
.. parsed-literal::
-D LAMMPS_LONGLONG_TO_LONG=value # yes or no (default)
**Makefile.machine setting**\ :
.. parsed-literal::
LMP_INC = -DLAMMPS_LONGLONG_TO_LONG
----------
.. _exceptions:
Exception handling when using LAMMPS as a library
------------------------------------------------------------------
This setting is useful when external codes drive LAMMPS as a library.
With this option enabled LAMMPS errors do not kill the caller.
Instead, the call stack is unwound and control returns to the caller,
e.g. to Python.
**CMake variable**\ :
.. parsed-literal::
-D LAMMPS_EXCEPTIONS=value # yes or no (default)
**Makefile.machine setting**\ :
.. parsed-literal::
LMP_INC = -DLAMMPS_EXCEPTIONS
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

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Notes for building LAMMPS on Windows
====================================
* :ref:`General remarks <generic>`
* :ref:`Running Linux on Windows <linux>`
* :ref:`Using GNU GCC ported to Windows <gnu>`
* :ref:`Using a cross-compiler <cross>`
----------
.. _generic:
General remarks
-----------------------------
LAMMPS is developed and tested primarily on Linux machines. The vast
majority of HPC clusters and supercomputers today runs on Linux as well.
Thus portability to other platforms is desired, but not always achieved.
The LAMMPS developers strongly rely on LAMMPS users giving feedback and
providing assistance in resolving portability issues. This particularly
true for compiling LAMMPS on Windows, since this platform has significant
differences with some low-level functionality.
.. _linux:
Running Linux on Windows
------------------------------------
So before trying to build LAMMPS on Windows, please consider if using
the pre-compiled Windows binary packages are sufficient for your needs
(as an aside, those packages themselves are build on a Linux machine
using cross-compilers). If it is necessary for your to compile LAMMPS
on a Windows machine (e.g. because it is your main desktop), please also
consider using a virtual machine software and run a Linux virtual machine,
or - if have a recently updated Windows 10 installation - consider using
the Windows subsystem for Linux, which allows to run a bash shell from
Ubuntu and from there on, you can pretty much use that shell like you
are running on an Ubuntu Linux machine (e.g. installing software via
apt-get). For more details on that, please see :doc:`this tutorial <Howto_bash>`
.. _gnu:
Using GNU GCC ported to Windows
-----------------------------------------
One option for compiling LAMMPS on Windows natively, that has been known
to work in the past is to install a bash shell, unix shell utilities,
perl, GNU make, and a GNU compiler ported to Windows. The Cygwin package
provides a unix/linux interface to low-level Windows functions, so LAMMPS
can be compiled on Windows. The necessary (minor) modifications to LAMMPS
are included, but may not always up-to-date for recently added functionality
and the corresponding new code. A machine makefile for using cygwin for
the old build system is provided. Using CMake for this mode of compilation
is untested and not likely to work.
When compiling for Windows do **not** set the -DLAMMPS\_MEMALIGN define
in the LMP\_INC makefile variable and add -lwsock32 -lpsapi to the linker
flags in LIB makefile variable. Try adding -static-libgcc or -static or
both to the linker flags when your resulting LAMMPS Windows executable
complains about missing .dll files. The CMake configuration should set
this up automatically, but is untested.
In case of problems, you are recommended to contact somebody with
experience in using cygwin. If you do come across portability problems
requiring changes to the LAMMPS source code, or figure out corrections
yourself, please report them on the lammps-users mailing list, or file
them as an issue or pull request on the LAMMPS GitHub project.
.. _cross:
Using a cross-compiler
----------------------------------
If you need to provide custom LAMMPS binaries for Windows, but do not
need to do the compilation on Windows, please consider using a Linux
to Windows cross-compiler. This is how currently the Windows binary
packages are created by the LAMMPS developers. Because of that, this is
probably the currently best tested and supported way to build LAMMPS
executables for Windows. There are makefiles provided for the
traditional build system, but CMake has also been successfully tested
using the mingw32-cmake and mingw64-cmake wrappers that are bundled
with the cross-compiler environment on Fedora machines. A CMake preset
selecting all packages compatible with this cross-compilation build
is provided. You likely need to disable the GPU package unless you
download and install the contents of the pre-compiled `OpenCL ICD loader library <https://download.lammps.org/thirdparty/opencl-win-devel.tar.gz>`_
into your MinGW64 cross-compiler environment. The cross-compilation
currently will only produce non-MPI serial binaries.
Please keep in mind, though, that this only applies to compiling LAMMPS.
Whether the resulting binaries do work correctly is no tested by the
LAMMPS developers. We instead rely on the feedback of the users
of these pre-compiled LAMMPS packages for Windows. We will try to resolve
issues to the best of our abilities if we become aware of them. However
this is subject to time constraints and focus on HPC platforms.
.. _native:
Native Visual C++ support
--------------------------------------
Support for the Visual C++ compilers is currently not available. The
CMake build system is capable of creating suitable a Visual Studio
style build environment, but the LAMMPS code itself is not fully ported
to support Visual C++. Volunteers to take on this task are welcome.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

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Commands
********
These pages describe how a LAMMPS input script is formatted and the
commands in it are used to define a LAMMPS simulation.
.. toctree::
:maxdepth: 1
Commands_input
Commands_parse
Commands_structure
Commands_category
.. toctree::
:maxdepth: 1
Commands_all
Commands_fix
Commands_compute
Commands_pair
Commands_bond
Commands_kspace
.. toctree::
:maxdepth: 1
Commands_removed

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"Previous Section"_Run_head.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Packages.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html#comm)
:line
Commands :h2
These pages describe how a LAMMPS input script is formatted and the
commands in it are used to define a LAMMPS simulation.
<!-- RST
.. toctree::
:maxdepth: 1
Commands_input
Commands_parse
Commands_structure
Commands_category
.. toctree::
:maxdepth: 1
Commands_all
Commands_fix
Commands_compute
Commands_pair
Commands_bond
Commands_kspace
END_RST -->
<!-- HTML_ONLY -->
"LAMMPS input scripts"_Commands_input.html
"Parsing rules for input scripts"_Commands_parse.html
"Input script structure"_Commands_structure.html
"Commands by category"_Commands_category.html :all(b)
"All commands"_Commands_all.html
"Fix commands"_Commands_fix.html
"Compute commands"_Commands_compute.html
"Pair commands"_Commands_pair.html
"Bond, angle, dihedral, improper commands"_Commands_bond.html
"KSpace solvers"_Commands_kspace.html :all(b)
<!-- END_HTML_ONLY -->

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.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
General commands
================
An alphabetic list of all general LAMMPS commands.
.. table_from_list::
:columns: 6
* :doc:`angle_coeff <angle_coeff>`
* :doc:`angle_style <angle_style>`
* :doc:`atom_modify <atom_modify>`
* :doc:`atom_style <atom_style>`
* :doc:`balance <balance>`
* :doc:`bond_coeff <bond_coeff>`
* :doc:`bond_style <bond_style>`
* :doc:`bond_write <bond_write>`
* :doc:`boundary <boundary>`
* :doc:`box <box>`
* :doc:`change_box <change_box>`
* :doc:`clear <clear>`
* :doc:`comm_modify <comm_modify>`
* :doc:`comm_style <comm_style>`
* :doc:`compute <compute>`
* :doc:`compute_modify <compute_modify>`
* :doc:`create_atoms <create_atoms>`
* :doc:`create_bonds <create_bonds>`
* :doc:`create_box <create_box>`
* :doc:`delete_atoms <delete_atoms>`
* :doc:`delete_bonds <delete_bonds>`
* :doc:`dielectric <dielectric>`
* :doc:`dihedral_coeff <dihedral_coeff>`
* :doc:`dihedral_style <dihedral_style>`
* :doc:`dimension <dimension>`
* :doc:`displace_atoms <displace_atoms>`
* :doc:`dump <dump>`
* :doc:`dump adios <dump_adios>`
* :doc:`dump image <dump_image>`
* :doc:`dump movie <dump_image>`
* :doc:`dump netcdf <dump_netcdf>`
* :doc:`dump netcdf/mpiio <dump_netcdf>`
* :doc:`dump vtk <dump_vtk>`
* :doc:`dump_modify <dump_modify>`
* :doc:`dynamical_matrix <dynamical_matrix>`
* :doc:`echo <echo>`
* :doc:`fix <fix>`
* :doc:`fix_modify <fix_modify>`
* :doc:`group <group>`
* :doc:`group2ndx <group2ndx>`
* :doc:`hyper <hyper>`
* :doc:`if <if>`
* :doc:`improper_coeff <improper_coeff>`
* :doc:`improper_style <improper_style>`
* :doc:`include <include>`
* :doc:`info <info>`
* :doc:`jump <jump>`
* :doc:`kim_init <kim_commands>`
* :doc:`kim_interactions <kim_commands>`
* :doc:`kim_param <kim_commands>`
* :doc:`kim_query <kim_commands>`
* :doc:`kspace_modify <kspace_modify>`
* :doc:`kspace_style <kspace_style>`
* :doc:`label <label>`
* :doc:`lattice <lattice>`
* :doc:`log <log>`
* :doc:`mass <mass>`
* :doc:`message <message>`
* :doc:`minimize <minimize>`
* :doc:`min_modify <min_modify>`
* :doc:`min_style <min_style>`
* :doc:`min_style spin <min_spin>`
* :doc:`molecule <molecule>`
* :doc:`ndx2group <group2ndx>`
* :doc:`neb <neb>`
* :doc:`neb/spin <neb_spin>`
* :doc:`neigh_modify <neigh_modify>`
* :doc:`neighbor <neighbor>`
* :doc:`newton <newton>`
* :doc:`next <next>`
* :doc:`package <package>`
* :doc:`pair_coeff <pair_coeff>`
* :doc:`pair_modify <pair_modify>`
* :doc:`pair_write <pair_write>`
* :doc:`partition <partition>`
* :doc:`prd <prd>`
* :doc:`print <print>`
* :doc:`processors <processors>`
* :doc:`python <python>`
* :doc:`quit <quit>`
* :doc:`read_data <read_data>`
* :doc:`read_dump <read_dump>`
* :doc:`read_restart <read_restart>`
* :doc:`region <region>`
* :doc:`replicate <replicate>`
* :doc:`rerun <rerun>`
* :doc:`reset_ids <reset_ids>`
* :doc:`reset_timestep <reset_timestep>`
* :doc:`restart <restart>`
* :doc:`run <run>`
* :doc:`run_style <run_style>`
* :doc:`server <server>`
* :doc:`set <set>`
* :doc:`shell <shell>`
* :doc:`special_bonds <special_bonds>`
* :doc:`suffix <suffix>`
* :doc:`tad <tad>`
* :doc:`temper <temper>`
* :doc:`temper/grem <temper_grem>`
* :doc:`temper/npt <temper_npt>`
* :doc:`thermo <thermo>`
* :doc:`thermo_modify <thermo_modify>`
* :doc:`thermo_style <thermo_style>`
* :doc:`third_order <third_order>`
* :doc:`timer <timer>`
* :doc:`timestep <timestep>`
* :doc:`uncompute <uncompute>`
* :doc:`undump <undump>`
* :doc:`unfix <unfix>`
* :doc:`units <units>`
* :doc:`variable <variable>`
* :doc:`velocity <velocity>`
* :doc:`write_coeff <write_coeff>`
* :doc:`write_data <write_data>`
* :doc:`write_dump <write_dump>`
* :doc:`write_restart <write_restart>`
*
*
*
*

130
doc/src/Commands_all.txt
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@ -1,130 +0,0 @@
"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
"All commands"_Commands_all.html,
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,
"Bond styles"_Commands_bond.html,
"Angle styles"_Commands_bond.html#angle,
"Dihedral styles"_Commands_bond.html#dihedral,
"Improper styles"_Commands_bond.html#improper,
"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
All commands :h3
An alphabetic list of all LAMMPS commands.
"angle_coeff"_angle_coeff.html,
"angle_style"_angle_style.html,
"atom_modify"_atom_modify.html,
"atom_style"_atom_style.html,
"balance"_balance.html,
"bond_coeff"_bond_coeff.html,
"bond_style"_bond_style.html,
"bond_write"_bond_write.html,
"boundary"_boundary.html,
"box"_box.html,
"change_box"_change_box.html,
"clear"_clear.html,
"comm_modify"_comm_modify.html,
"comm_style"_comm_style.html,
"compute"_compute.html,
"compute_modify"_compute_modify.html,
"create_atoms"_create_atoms.html,
"create_bonds"_create_bonds.html,
"create_box"_create_box.html,
"delete_atoms"_delete_atoms.html,
"delete_bonds"_delete_bonds.html,
"dielectric"_dielectric.html,
"dihedral_coeff"_dihedral_coeff.html,
"dihedral_style"_dihedral_style.html,
"dimension"_dimension.html,
"displace_atoms"_displace_atoms.html,
"dump"_dump.html,
"dump image"_dump_image.html,
"dump_modify"_dump_modify.html,
"dump movie"_dump_image.html,
"dump netcdf"_dump_netcdf.html,
"dump netcdf/mpiio"_dump_netcdf.html,
"dump vtk"_dump_vtk.html,
"echo"_echo.html,
"fix"_fix.html,
"fix_modify"_fix_modify.html,
"group"_group.html,
"group2ndx"_group2ndx.html,
"if"_if.html,
"info"_info.html,
"improper_coeff"_improper_coeff.html,
"improper_style"_improper_style.html,
"include"_include.html,
"jump"_jump.html,
"kspace_modify"_kspace_modify.html,
"kspace_style"_kspace_style.html,
"label"_label.html,
"lattice"_lattice.html,
"log"_log.html,
"mass"_mass.html,
"message"_message.html,
"minimize"_minimize.html,
"min_modify"_min_modify.html,
"min_style"_min_style.html,
"molecule"_molecule.html,
"ndx2group"_group2ndx.html,
"neb"_neb.html,
"neigh_modify"_neigh_modify.html,
"neighbor"_neighbor.html,
"newton"_newton.html,
"next"_next.html,
"package"_package.html,
"pair_coeff"_pair_coeff.html,
"pair_modify"_pair_modify.html,
"pair_style"_pair_style.html,
"pair_write"_pair_write.html,
"partition"_partition.html,
"prd"_prd.html,
"print"_print.html,
"processors"_processors.html,
"python"_python.html,
"quit"_quit.html,
"read_data"_read_data.html,
"read_dump"_read_dump.html,
"read_restart"_read_restart.html,
"region"_region.html,
"replicate"_replicate.html,
"rerun"_rerun.html,
"reset_ids"_reset_ids.html,
"reset_timestep"_reset_timestep.html,
"restart"_restart.html,
"run"_run.html,
"run_style"_run_style.html,
"server"_server.html,
"set"_set.html,
"shell"_shell.html,
"special_bonds"_special_bonds.html,
"suffix"_suffix.html,
"tad"_tad.html,
"temper"_temper.html,
"temper/grem"_temper_grem.html,
"temper/npt"_temper_npt.html,
"thermo"_thermo.html,
"thermo_modify"_thermo_modify.html,
"thermo_style"_thermo_style.html,
"timer"_timer.html,
"timestep"_timestep.html,
"uncompute"_uncompute.html,
"undump"_undump.html,
"unfix"_unfix.html,
"units"_units.html,
"variable"_variable.html,
"velocity"_velocity.html,
"write_coeff"_write_coeff.html,
"write_data"_write_data.html,
"write_dump"_write_dump.html,
"write_restart"_write_restart.html :tb(c=6,ea=c)

165
doc/src/Commands_bond.rst Normal file
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.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
.. _bond:
Bond_style potentials
=====================
All LAMMPS :doc:`bond_style <bond_style>` commands. Some styles have
accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
.. table_from_list::
:columns: 4
* :doc:`none <bond_none>`
* :doc:`zero <bond_zero>`
* :doc:`hybrid <bond_hybrid>`
*
*
*
*
*
* :doc:`class2 (ko) <bond_class2>`
* :doc:`fene (iko) <bond_fene>`
* :doc:`fene/expand (o) <bond_fene_expand>`
* :doc:`gromos (o) <bond_gromos>`
* :doc:`harmonic (iko) <bond_harmonic>`
* :doc:`harmonic/shift (o) <bond_harmonic_shift>`
* :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>`
* :doc:`mm3 <bond_mm3>`
* :doc:`morse (o) <bond_morse>`
* :doc:`nonlinear (o) <bond_nonlinear>`
* :doc:`oxdna/fene <bond_oxdna>`
* :doc:`oxdna2/fene <bond_oxdna>`
* :doc:`oxrna2/fene <bond_oxdna>`
* :doc:`quartic (o) <bond_quartic>`
* :doc:`table (o) <bond_table>`
*
.. _angle:
Angle_style potentials
======================
All LAMMPS :doc:`angle_style <angle_style>` commands. Some styles have
accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
.. table_from_list::
:columns: 4
* :doc:`none <angle_none>`
* :doc:`zero <angle_zero>`
* :doc:`hybrid <angle_hybrid>`
*
*
*
*
*
* :doc:`charmm (iko) <angle_charmm>`
* :doc:`class2 (ko) <angle_class2>`
* :doc:`class2/p6 <angle_class2>`
* :doc:`cosine (ko) <angle_cosine>`
* :doc:`cosine/buck6d <angle_cosine_buck6d>`
* :doc:`cosine/delta (o) <angle_cosine_delta>`
* :doc:`cosine/periodic (o) <angle_cosine_periodic>`
* :doc:`cosine/shift (o) <angle_cosine_shift>`
* :doc:`cosine/shift/exp (o) <angle_cosine_shift_exp>`
* :doc:`cosine/squared (o) <angle_cosine_squared>`
* :doc:`cross <angle_cross>`
* :doc:`dipole (o) <angle_dipole>`
* :doc:`fourier (o) <angle_fourier>`
* :doc:`fourier/simple (o) <angle_fourier_simple>`
* :doc:`harmonic (iko) <angle_harmonic>`
* :doc:`mm3 <angle_mm3>`
* :doc:`quartic (o) <angle_quartic>`
* :doc:`sdk (o) <angle_sdk>`
* :doc:`table (o) <angle_table>`
*
.. _dihedral:
Dihedral_style potentials
=========================
All LAMMPS :doc:`dihedral_style <dihedral_style>` commands. Some styles
have accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
.. table_from_list::
:columns: 4
* :doc:`none <dihedral_none>`
* :doc:`zero <dihedral_zero>`
* :doc:`hybrid <dihedral_hybrid>`
*
*
*
*
*
* :doc:`charmm (iko) <dihedral_charmm>`
* :doc:`charmmfsw <dihedral_charmm>`
* :doc:`class2 (ko) <dihedral_class2>`
* :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>`
* :doc:`fourier (io) <dihedral_fourier>`
* :doc:`harmonic (iko) <dihedral_harmonic>`
* :doc:`helix (o) <dihedral_helix>`
* :doc:`multi/harmonic (o) <dihedral_multi_harmonic>`
* :doc:`nharmonic (o) <dihedral_nharmonic>`
* :doc:`opls (iko) <dihedral_opls>`
* :doc:`quadratic (o) <dihedral_quadratic>`
* :doc:`spherical <dihedral_spherical>`
* :doc:`table (o) <dihedral_table>`
* :doc:`table/cut <dihedral_table_cut>`
*
*
.. _improper:
Improper_style potentials
=========================
All LAMMPS :doc:`improper\_style <improper_style>` commands. Some styles
have accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
.. table_from_list::
:columns: 4
* :doc:`none <improper_none>`
* :doc:`zero <improper_zero>`
* :doc:`hybrid <improper_hybrid>`
*
*
*
*
*
* :doc:`class2 (ko) <improper_class2>`
* :doc:`cossq (o) <improper_cossq>`
* :doc:`cvff (io) <improper_cvff>`
* :doc:`distance <improper_distance>`
* :doc:`distharm <improper_distharm>`
* :doc:`fourier (o) <improper_fourier>`
* :doc:`harmonic (iko) <improper_harmonic>`
* :doc:`inversion/harmonic <improper_inversion_harmonic>`
* :doc:`ring (o) <improper_ring>`
* :doc:`sqdistharm <improper_sqdistharm>`
* :doc:`umbrella (o) <improper_umbrella>`
*

124
doc/src/Commands_bond.txt
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@ -1,124 +0,0 @@
"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
"All commands"_Commands_all.html,
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,
"Bond styles"_Commands_bond.html#bond,
"Angle styles"_Commands_bond.html#angle,
"Dihedral styles"_Commands_bond.html#dihedral,
"Improper styles"_Commands_bond.html#improper,
"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
Bond, angle, dihedral, and improper commands :h3
:line
Bond_style potentials :h3,link(bond)
All LAMMPS "bond_style"_bond_style.html commands. Some styles have
accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
"none"_bond_none.html,
"zero"_bond_zero.html,
"hybrid"_bond_hybrid.html :tb(c=3,ea=c)
"class2 (ko)"_bond_class2.html,
"fene (iko)"_bond_fene.html,
"fene/expand (o)"_bond_fene_expand.html,
"gromos (o)"_bond_gromos.html,
"harmonic (ko)"_bond_harmonic.html,
"harmonic/shift (o)"_bond_harmonic_shift.html,
"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
"morse (o)"_bond_morse.html,
"nonlinear (o)"_bond_nonlinear.html,
"oxdna/fene"_bond_oxdna.html,
"oxdna2/fene"_bond_oxdna.html,
"quartic (o)"_bond_quartic.html,
"table (o)"_bond_table.html :tb(c=4,ea=c)
:line
Angle_style potentials :h3,link(angle)
All LAMMPS "angle_style"_angle_style.html commands. Some styles have
accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
"none"_angle_none.html,
"zero"_angle_zero.html,
"hybrid"_angle_hybrid.html :tb(c=3,ea=c)
"charmm (ko)"_angle_charmm.html,
"class2 (ko)"_angle_class2.html,
"cosine (o)"_angle_cosine.html,
"cosine/delta (o)"_angle_cosine_delta.html,
"cosine/periodic (o)"_angle_cosine_periodic.html,
"cosine/shift (o)"_angle_cosine_shift.html,
"cosine/shift/exp (o)"_angle_cosine_shift_exp.html,
"cosine/squared (o)"_angle_cosine_squared.html,
"dipole (o)"_angle_dipole.html,
"fourier (o)"_angle_fourier.html,
"fourier/simple (o)"_angle_fourier_simple.html,
"harmonic (iko)"_angle_harmonic.html,
"quartic (o)"_angle_quartic.html,
"sdk (o)"_angle_sdk.html,
"table (o)"_angle_table.html :tb(c=4,ea=c)
:line
Dihedral_style potentials :h3,link(dihedral)
All LAMMPS "dihedral_style"_dihedral_style.html commands. Some styles
have accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
"none"_dihedral_none.html,
"zero"_dihedral_zero.html,
"hybrid"_dihedral_hybrid.html :tb(c=3,ea=c)
"charmm (iko)"_dihedral_charmm.html,
"charmmfsw"_dihedral_charmm.html,
"class2 (ko)"_dihedral_class2.html,
"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
"fourier (io)"_dihedral_fourier.html,
"harmonic (io)"_dihedral_harmonic.html,
"helix (o)"_dihedral_helix.html,
"multi/harmonic (o)"_dihedral_multi_harmonic.html,
"nharmonic (o)"_dihedral_nharmonic.html,
"opls (iko)"_dihedral_opls.html,
"quadratic (o)"_dihedral_quadratic.html,
"spherical (o)"_dihedral_spherical.html,
"table (o)"_dihedral_table.html,
"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)
:line
Improper_style potentials :h3,link(improper)
All LAMMPS "improper_style"_improper_style.html commands. Some styles
have accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
"none"_improper_none.html,
"zero"_improper_zero.html,
"hybrid"_improper_hybrid.html :tb(c=3,ea=c)
"class2 (ko)"_improper_class2.html,
"cossq (o)"_improper_cossq.html,
"cvff (io)"_improper_cvff.html,
"distance"_improper_distance.html,
"fourier (o)"_improper_fourier.html,
"harmonic (iko)"_improper_harmonic.html,
"ring (o)"_improper_ring.html,
"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)

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