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Merge branch 'master' into gran_mods

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Axel Kohlmeyer 2019-03-15 14:30:36 -04:00
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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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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 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 +62,13 @@ 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/Howto_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 outside of <cstdio>, 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.
* 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.
@ -102,10 +102,10 @@ 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/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.
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 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

56
.github/PULL_REQUEST_TEMPLATE/new_feature.md vendored Normal file
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@ -0,0 +1,56 @@
---
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)_

42
.github/PULL_REQUEST_TEMPLATE/update_enhancement.md vendored Normal file
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@ -0,0 +1,42 @@
---
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)_

114
cmake/CMakeLists.txt
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@ -11,6 +11,8 @@ get_filename_component(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib
get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUTE)
find_package(Git)
# by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed
if (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "default install path" FORCE )
@ -85,7 +87,7 @@ string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
# this is fast, so check for it all the time
message(STATUS "Running check for auto-generated files from make-based build system")
file(GLOB SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/style_*.h)
list(APPEND SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/lmpinstalledpkgs.h)
list(APPEND SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/lmpinstalledpkgs.h ${LAMMPS_SOURCE_DIR}/lmpgitversion.h)
foreach(_SRC ${SRC_AUTOGEN_FILES})
get_filename_component(FILENAME "${_SRC}" NAME)
if(EXISTS ${LAMMPS_SOURCE_DIR}/${FILENAME})
@ -171,14 +173,14 @@ set(LAMMPS_DEPS)
set(LAMMPS_API_DEFINES)
set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK
KSPACE MANYBODY MC MESSAGE MISC MOLECULE PERI REPLICA RIGID SHOCK
SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD
USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION
USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD
USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF
USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC USER-SCAFACOS
USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK
USER-QUIP USER-QMMM)
USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
set(OTHER_PACKAGES CORESHELL QEQ)
foreach(PKG ${DEFAULT_PACKAGES})
@ -191,16 +193,27 @@ endforeach()
######################################################
# packages with special compiler needs or external libs
######################################################
if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS)
if(PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS)
enable_language(Fortran)
endif()
if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS)
if(PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS)
enable_language(C)
endif()
include_directories(${LAMMPS_SOURCE_DIR})
if(PKG_USER-ADIOS)
# The search for ADIOS2 must come before MPI because
# it includes its own MPI search with the latest FindMPI.cmake
# script that defines the MPI::MPI_C target
enable_language(C)
find_package(ADIOS2 REQUIRED)
list(APPEND LAMMPS_LINK_LIBS adios2::adios2)
endif()
# do MPI detection after language activation, if MPI for these language is required
find_package(MPI QUIET)
option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
@ -453,7 +466,7 @@ if(PKG_VORONOI)
set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
ExternalProject_Add(voro_build
URL http://math.lbl.gov/voro++/download/dir/voro++-0.4.6.tar.gz
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 ""
)
@ -559,10 +572,15 @@ if(PKG_USER-PLUMED)
message(STATUS "PLUMED download requested - we will build our own")
include(ExternalProject)
ExternalProject_Add(plumed_build
URL https://github.com/plumed/plumed2/releases/download/v2.4.3/plumed-src-2.4.3.tgz
URL_MD5 b1be7c48971627febc11c61b70767fc5
URL https://github.com/plumed/plumed2/releases/download/v2.4.4/plumed-src-2.4.4.tgz
URL_MD5 71ed465bdc7c2059e282dbda8d564e71
BUILD_IN_SOURCE 1
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> ${CONFIGURE_REQUEST_PIC})
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
${CONFIGURE_REQUEST_PIC}
--enable-modules=all
CXX=${CMAKE_MPI_CXX_COMPILER}
CC=${CMAKE_MPI_C_COMPILER}
)
ExternalProject_get_property(plumed_build INSTALL_DIR)
set(PLUMED_INSTALL_DIR ${INSTALL_DIR})
list(APPEND LAMMPS_DEPS plumed_build)
@ -608,14 +626,15 @@ if(PKG_USER-NETCDF)
add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
endif()
if(PKG_USER-SMD)
option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" OFF)
if(DOWNLOAD_EIGEN3)
message(STATUS "Eigen3 download requested - we will build our own")
include(ExternalProject)
ExternalProject_Add(Eigen3_build
URL http://bitbucket.org/eigen/eigen/get/3.3.4.tar.gz
URL_MD5 1a47e78efe365a97de0c022d127607c3
URL http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz
URL_MD5 f2a417d083fe8ca4b8ed2bc613d20f07
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
)
ExternalProject_get_property(Eigen3_build SOURCE_DIR)
@ -651,28 +670,34 @@ if(PKG_USER-VTK)
endif()
if(PKG_KIM)
option(DOWNLOAD_KIM "Download KIM-API v1 from OpenKIM instead of using an already installed one)" OFF)
option(DOWNLOAD_KIM "Download KIM-API v2 from OpenKIM instead of using an already installed one" OFF)
if(DOWNLOAD_KIM)
message(STATUS "KIM-API v1 download requested - we will build our own")
message(STATUS "KIM-API v2 download requested - we will build our own")
enable_language(C)
enable_language(Fortran)
include(ExternalProject)
ExternalProject_Add(kim_build
URL https://github.com/openkim/kim-api/archive/v1.9.5.tar.gz
URL_MD5 9f66efc128da33039e30659f36fc6d00
BUILD_IN_SOURCE 1
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
URL https://s3.openkim.org/kim-api/kim-api-v2-2.0.1.txz
URL_MD5 289c57f0c3bc2a549662283cac1c4ef1
BINARY_DIR build
CMAKE_ARGS -DCMAKE_C_COMPILER=${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_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v1)
set(KIM_LIBRARIES ${INSTALL_DIR}/lib/libkim-api-v1.so)
set(KIM-API-V2_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v2)
set(KIM-API-V2_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api-v2${CMAKE_SHARED_LIBRARY_SUFFIX})
list(APPEND LAMMPS_DEPS kim_build)
else()
find_package(KIM)
if(NOT KIM_FOUND)
message(FATAL_ERROR "KIM-API v1 not found, help CMake to find it by setting KIM_LIBRARY and KIM_INCLUDE_DIR, or set DOWNLOAD_KIM=ON to download it")
find_package(KIM-API-V2)
if(NOT KIM-API-V2_FOUND)
message(FATAL_ERROR "KIM-API v2 not found, help CMake to find it by setting PKG_CONFIG_PATH, or set DOWNLOAD_KIM=ON to download it")
endif()
endif()
list(APPEND LAMMPS_LINK_LIBS ${KIM_LIBRARIES})
include_directories(${KIM_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS "${KIM-API-V2_LDFLAGS}")
include_directories(${KIM-API-V2_INCLUDE_DIRS})
endif()
if(PKG_MESSAGE)
@ -756,7 +781,7 @@ endif()
# Basic system tests (standard libraries, headers, functions, types) #
########################################################################
include(CheckIncludeFileCXX)
foreach(HEADER math.h)
foreach(HEADER cmath)
check_include_file_cxx(${HEADER} FOUND_${HEADER})
if(NOT FOUND_${HEADER})
message(FATAL_ERROR "Could not find needed header - ${HEADER}")
@ -826,7 +851,7 @@ endforeach()
##############################################
# add lib sources of (simple) enabled packages
############################################
foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
USER-QMMM)
if(PKG_${SIMPLE_LIB})
string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
@ -1303,6 +1328,40 @@ message(STATUS "Generating lmpinstalledpkgs.h...")
file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${temp}" )
execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h")
######################################
# Generate lmpgitversion.h
######################################
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}/../.git rev-parse HEAD
OUTPUT_VARIABLE temp_git_commit
ERROR_QUIET
OUTPUT_STRIP_TRAILING_WHITESPACE)
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git rev-parse --abbrev-ref HEAD
OUTPUT_VARIABLE temp_git_branch
ERROR_QUIET
OUTPUT_STRIP_TRAILING_WHITESPACE)
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git describe --dirty=-modified
OUTPUT_VARIABLE temp_git_describe
ERROR_QUIET
OUTPUT_STRIP_TRAILING_WHITESPACE)
endif()
set(temp "${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")
###########################################
# Actually add executable and lib to build
############################################
@ -1325,7 +1384,7 @@ if(BUILD_LIB)
configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Module)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Modules)
else()
list(APPEND LMP_SOURCES ${LIB_SOURCES})
endif()
@ -1349,6 +1408,7 @@ if(BUILD_EXE)
endif()
endif()
###############################################################################
# Build documentation
###############################################################################

50
cmake/Modules/FindKIM-API-V2.cmake Normal file
View File

@ -0,0 +1,50 @@
#
# 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--2018, Regents of the University of Minnesota.
# All rights reserved.
#
# Contributors:
# Richard Berger
# Christoph Junghans
# Ryan S. Elliott
#
# - Find KIM-API-V2
#
# sets standard pkg_check_modules variables plus:
#
# KIM-API-V2-CMAKE_C_COMPILER
# KIM-API-V2-CMAKE_CXX_COMPILER
# KIM-API-V2-CMAKE_Fortran_COMPILER
#
find_package(PkgConfig REQUIRED)
include(FindPackageHandleStandardArgs)
pkg_check_modules(KIM-API-V2 REQUIRED libkim-api-v2>=2.0)
pkg_get_variable(KIM-API-V2-CMAKE_C_COMPILER libkim-api-v2 CMAKE_C_COMPILER)
pkg_get_variable(KIM-API-V2-CMAKE_CXX_COMPILER libkim-api-v2 CMAKE_CXX_COMPILER)
pkg_get_variable(KIM-API-V2_CMAKE_Fortran_COMPILER libkim-api-v2 CMAKE_Fortran_COMPILER)
# handle the QUIETLY and REQUIRED arguments and set KIM-API-V2_FOUND to TRUE
# if all listed variables are TRUE
find_package_handle_standard_args(KIM-API-V2 REQUIRED_VARS KIM-API-V2_LIBRARIES)

22
cmake/Modules/FindKIM.cmake
View File

@ -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 )

2
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)

21
cmake/README.md
View File

@ -24,7 +24,7 @@ tasks, act as a reference and provide examples of typical use cases.
* [Build directory vs. Source Directory](#build-directory-vs-source-directory)
* [Defining and using presets](#defining-and-using-presets)
* [Reference](#reference)
* [Common CMAKE Configuration Options](#common-cmake-configuration-options)
* [Common CMake Configuration Options](#common-cmake-configuration-options)
* [LAMMPS Configuration Options](#lammps-configuration-options)
* [Parallelization and Accelerator Packages](#parallelization-and-accelerator-packages)
* [Default Packages](#default-packages)
@ -179,7 +179,7 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
# Reference
## Common CMAKE Configuration Options
## Common CMake Configuration Options
<table>
@ -208,6 +208,16 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
</dl>
</td>
</tr>
<tr>
<td><code><CMAKE_VERBOSE_MAKEFILE/code></td>
<td>Enable verbose output from Makefile builds (useful for debugging), the same can be achived by adding `VERBOSE=1` to the `make` call.</td>
<td>
<dl>
<dt><code>off</code> (default)</dt>
<dt><code>on</code></dt>
</dl>
</td>
</tr>
</tbody>
</table>
@ -1729,6 +1739,13 @@ cache by setting the `CMAKE_C_COMPILER`, `CMAKE_CXX_COMPILER`,
value of `FC` environment variable at first `cmake` run
</td>
</tr>
<tr>
<td><code>CXX_COMPILER_LAUNCHER</code></td>
<td>CMake will run this tool and pass the compiler and its arguments to the tool. Some example tools are distcc and ccache.</td>
<td>
(empty)
</td>
</tr>
</tbody>
</table>

2
doc/.gitignore vendored
View File

@ -1,4 +1,6 @@
/old
/html
/latex
/spelling
/LAMMPS.epub
/LAMMPS.mobi

58
doc/Makefile
View File

@ -39,7 +39,7 @@ 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 " old create old-style HTML doc pages and Manual.pdf 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)"
@ -48,6 +48,7 @@ help:
@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"
# ------------------------------------------
@ -55,7 +56,7 @@ clean-all: clean
rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe
clean:
rm -rf $(RSTDIR) html old epub
rm -rf $(RSTDIR) html old epub latex
rm -rf spelling
clean-spelling:
@ -114,21 +115,44 @@ 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)
@(\
. $(VENV)/bin/activate ;\
cp -r src/* $(RSTDIR)/ ;\
sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
echo "############################################" ;\
doc_anchor_check src/*.txt ;\
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 ../;
@(\
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/ \(pairs\|bonds\|angles\|dihedrals\|impropers\|commands_list\|fixes\|computes\).txt/ /g' | sed -e 's,\.txt,\.html,g'` ; \
do grep -q ^$$s lammps.book || \
echo WARNING: doc file $$s missing in src/lammps.book; done; \
rm *.html; \
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."
old: utils/txt2html/txt2html.exe
@rm -rf old
@ -138,6 +162,18 @@ old: utils/txt2html/txt2html.exe
cp Eqs/*.jpg ../old/Eqs; \
cp JPG/* ../old/JPG; \
cp PDF/* ../old/PDF;
@( set -e;\
cd src/Developer; \
pdflatex developer; \
pdflatex developer; \
mv developer.pdf ../../old/Developer.pdf; \
cd ../../old; \
for s in `echo ../src/*.txt | sed -e 's,\.\./src/,,g' -e 's/ \(pairs\|bonds\|angles\|dihedrals\|impropers\|commands_list\|fixes\|computes\).txt/ /g' | sed -e 's,\.txt,\.html,g'` ; \
do grep -q ^$$s ../src/lammps.book || \
echo WARNING: doc file $$s missing in src/lammps.book; done; \
htmldoc --batch ../src/lammps.book; \
)
fetch:
@rm -rf html_www Manual_www.pdf Developer_www.pdf

30
doc/github-development-workflow.md
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@ -6,7 +6,7 @@ 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 2018-11-15.
adapt accordingly. Last change 2018-12-19.
## Table of Contents
@ -50,8 +50,8 @@ 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 what this might be needed or not, and may either implement the
required changes or ask the submitter of the pull request to implement
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
@ -76,12 +76,15 @@ People can be assigned to review a pull request in two ways:
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 one review from a LAMMPS developer with write access is required
before merging in addition to the automated compilation tests. 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 has been reached. Reviews may be
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.
@ -120,7 +123,7 @@ Here are some items to check:
* float.h -> cfloat
* limits.h -> climits
* math.h -> cmath
* omplex.h -> complex
* complex.h -> complex
* setjmp.h -> csetjmp
* signal.h -> csignal
* stddef.h -> cstddef
@ -129,16 +132,17 @@ Here are some items to check:
* stdlib.h -> cstdlib
* string.h -> cstring
* time.h -> ctime
Do not replace (as they are C++-11): `inttypes.h` and `stdint.h`.
* 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 two spaces per level
* there should be no tabs and no trailing whitespace
* 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

12
doc/src/Build_basics.txt
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@ -116,6 +116,18 @@ 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.
[OpenMP Compiler compatibility info]: :link(default-none-issues)
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.
:line
Choice of compiler and compile/link options :h4,link(compile)

96
doc/src/Build_extras.txt
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@ -36,8 +36,8 @@ This is the list of packages that may require additional steps.
"OPT"_#opt,
"POEMS"_#poems,
"PYTHON"_#python,
"REAX"_#reax,
"VORONOI"_#voronoi,
"USER-ADIOS"_#user-adios,
"USER-ATC"_#user-atc,
"USER-AWPMD"_#user-awpmd,
"USER-COLVARS"_#user-colvars,
@ -96,6 +96,7 @@ which GPU hardware to build for.
GPU_ARCH settings for different GPU hardware is as follows:
sm_12 or sm_13 for GT200 (supported by CUDA 3.2 until CUDA 6.5)
sm_20 or sm_21 for Fermi (supported by CUDA 3.2 until CUDA 7.5)
sm_30 or sm_35 or sm_37 for Kepler (supported since CUDA 5)
sm_50 or sm_52 for Maxwell (supported since CUDA 6)
@ -136,7 +137,7 @@ specified by the "-m" switch. For your convenience, machine makefiles
for "mpi" and "serial" are provided, which have the same settings as
the corresponding machine makefiles in the main LAMMPS source
folder. In addition you can alter 4 important settings in the
Makefile.machine you start from via the corresponding -h, -a, -p, -e
Makefile.machine you start from via the corresponding -c, -a, -p, -e
switches (as in the examples above), and also save a copy of the new
Makefile if desired:
@ -180,27 +181,19 @@ library with all its models, may take around 30 min to build. Of
course you only need to do that once.
See the list of KIM model drivers here:
https://openkim.org/kim-items/model-drivers/alphabetical
https://openkim.org/browse/model-drivers/alphabetical
See the list of all KIM models here:
https://openkim.org/kim-items/models/by-model-drivers
See the list of example KIM models included by default here:
https://openkim.org/kim-api on the "What is in the KIM API source
package?" page.
https://openkim.org/browse/models/by-model-drivers
[CMake build]:
-D DOWNLOAD_KIM=value # download OpenKIM API v1 for build, value = no (default) or yes
-D KIM_LIBRARY=path # KIM library file (only needed if a custom location)
-D KIM_INCLUDE_DIR=path # KIM include directory (only needed if a custom location) :pre
-D DOWNLOAD_KIM=value # download OpenKIM API v2 for build, value = no (default) or yes :pre
If DOWNLOAD_KIM is set, the KIM library will be downloaded and built
inside the CMake build directory. If the KIM library is already on
your system (in a location CMake cannot find it), KIM_LIBRARY is the
filename (plus path) of the KIM library file, not the directory the
library file is in. KIM_INCLUDE_DIR is the directory the KIM include
file is in.
your system (in a location CMake cannot find it), set the PKG_CONFIG_PATH
environment variable so that libkim-api-v2 can be found.
[Traditional make]:
@ -214,8 +207,8 @@ make lib-kim args="-b " # (re-)install KIM API lib with only example models
make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model
make lib-kim args="-b -a everything" # install KIM API lib with all models
make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver
make lib-kim args="-p /usr/local/kim-api" # use an existing KIM API installation at the provided location
make lib-kim args="-p /usr/local/kim-api -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre
make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location
make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre
:line
@ -536,45 +529,6 @@ build fails.
:line
REAX package :h4,link(reax)
NOTE: the use of the REAX package and its "pair_style
reax"_pair_reax.html command is discouraged, as it is no longer
maintained. Please use the USER-REAXC package and its "pair_style
reax/c"_pair_reaxc.html command instead, and possibly its KOKKOS
enabled variant (pair_style reax/c/kk), which has a more robust memory
management. See the "pair_style reax/c"_pair_reaxc.html doc page for
details.
[CMake build]:
No additional settings are needed besides "-D PKG_REAX=yes".
[Traditional make]:
Before building LAMMPS, you must build the REAX library in lib/reax.
You can do this manually if you prefer; follow the instructions in
lib/reax/README. You can also do it in one step from the lammps/src
dir, using a command like these, which simply invoke the
lib/reax/Install.py script with the specified args:
make lib-reax # print help message
make lib-reax args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
make lib-reax args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
make lib-reax args="-m ifort" # build with Intel ifort compiler :pre
The build should produce two files: lib/reax/libreax.a and
lib/reax/Makefile.lammps. The latter is copied from an existing
Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
Fortran (REAX library). Typically the two compilers used for LAMMPS
and the REAX library need to be consistent (e.g. both Intel or both
GNU compilers). If necessary, you can edit/create a new
lib/reax/Makefile.machine file for your system, which should define an
EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
file.
:line
VORONOI package :h4,link(voronoi)
To build with this package, you must download and build the "Voro++
@ -615,6 +569,32 @@ the lib/voronoi/Makefile.lammps file.
:line
USER-ADIOS package :h4,link(user-adios)
The USER-ADIOS package requires the "ADIOS I/O library"_https://github.com/ornladios/ADIOS2,
version 2.3.1 or newer. Make sure that you have ADIOS built either with or
without MPI to match if you build LAMMPS with or without MPI.
ADIOS compilation settings for LAMMPS are automatically detected, if the PATH
and LD_LIBRARY_PATH environment variables have been updated for the local ADIOS
installation and the instructions below are followed for the respective build systems.
[CMake build]:
-D ADIOS2_DIR=path # path is where ADIOS 2.x is installed
-D PKG_USER-ADIOS=yes :pre
[Traditional make]:
Turn on the USER-ADIOS package before building LAMMPS. If the ADIOS 2.x software is installed in PATH, there is nothing else to do:
make yes-user-adios :pre
otherwise, set ADIOS2_DIR environment variable when turning on the package:
ADIOS2_DIR=path make yes-user-adios # path is where ADIOS 2.x is installed :pre
:line
USER-ATC package :h4,link(user-atc)
The USER-ATC package requires the MANYBODY package also be installed.
@ -971,7 +951,9 @@ LINKFLAGS: -fopenmp # for GNU Compilers
LINKFLAGS: -qopenmp # for Intel compilers on Linux :pre
For other platforms and compilers, please consult the documentation
about OpenMP support for your compiler.
about OpenMP support for your compiler. Please see the note about
how to address compatibility "issues with the 'default(none)'
directive"_Build_basics.html#default-none-issues of some compilers.
:line

2
doc/src/Build_link.txt
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@ -78,7 +78,7 @@ 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 thru its library interface.
C and Fortran codes that invoke LAMMPS through its library interface.
Other examples in the COUPLE directory use coupling ideas discussed on
the "Howto couple"_Howto_couple.html doc page.

2
doc/src/Build_package.txt
View File

@ -47,8 +47,8 @@ packages:
"OPT"_Build_extras.html#opt,
"POEMS"_Build_extras.html#poems,
"PYTHON"_Build_extras.html#python,
"REAX"_Build_extras.html#reax,
"VORONOI"_Build_extras.html#voronoi,
"USER-ADIOS"_Build_extras.html#user-adios,
"USER-ATC"_Build_extras.html#user-atc,
"USER-AWPMD"_Build_extras.html#user-awpmd,
"USER-COLVARS"_Build_extras.html#user-colvars,

2
doc/src/Commands_all.txt
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@ -48,12 +48,14 @@ An alphabetic list of all general LAMMPS commands.
"dimension"_dimension.html,
"displace_atoms"_displace_atoms.html,
"dump"_dump.html,
"dump adios"_dump_adios.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,
"dynamical_matrix"_dynamical_matrix.html,
"echo"_echo.html,
"fix"_fix.html,
"fix_modify"_fix_modify.html,

7
doc/src/Commands_bond.txt
View File

@ -37,6 +37,7 @@ OPT.
"harmonic (iko)"_bond_harmonic.html,
"harmonic/shift (o)"_bond_harmonic_shift.html,
"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
"mm3"_bond_mm3.html,
"morse (o)"_bond_morse.html,
"nonlinear (o)"_bond_nonlinear.html,
"oxdna/fene"_bond_oxdna.html,
@ -60,17 +61,19 @@ OPT.
"charmm (iko)"_angle_charmm.html,
"class2 (ko)"_angle_class2.html,
"class2/p6"_angle_class2.html,
"cosine (o)"_angle_cosine.html,
"cosine (ko)"_angle_cosine.html,
"cosine/buck6d"_angle_cosine_buck6d.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,
"cross"_angle_cross.html,
"dipole (o)"_angle_dipole.html,
"fourier (o)"_angle_fourier.html,
"fourier/simple (o)"_angle_fourier_simple.html,
"harmonic (iko)"_angle_harmonic.html,
"mm3"_angle_mm3.html,
"quartic (o)"_angle_quartic.html,
"sdk (o)"_angle_sdk.html,
"table (o)"_angle_table.html :tb(c=4,ea=c)
@ -120,8 +123,10 @@ OPT.
"cossq (o)"_improper_cossq.html,
"cvff (io)"_improper_cvff.html,
"distance"_improper_distance.html,
"distharm"_improper_distharm.html,
"fourier (o)"_improper_fourier.html,
"harmonic (iko)"_improper_harmonic.html,
"inversion/harmonic"_improper_inversion_harmonic.html,
"ring (o)"_improper_ring.html,
"sqdistharm"_improper_sqdistharm.html,
"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)

3
doc/src/Commands_fix.txt
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@ -169,8 +169,7 @@ OPT.
"qmmm"_fix_qmmm.html,
"qtb"_fix_qtb.html,
"rattle"_fix_shake.html,
"reax/bonds"_fix_reax_bonds.html,
"reax/c/bonds (k)"_fix_reax_bonds.html,
"reax/c/bonds (k)"_fix_reaxc_bonds.html,
"reax/c/species (k)"_fix_reaxc_species.html,
"recenter"_fix_recenter.html,
"restrain"_fix_restrain.html,

27
doc/src/Commands_pair.txt
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@ -63,13 +63,13 @@ OPT.
"comb (o)"_pair_comb.html,
"comb3"_pair_comb.html,
"coul/cut (gko)"_pair_coul.html,
"coul/cut/soft (o)"_pair_lj_soft.html,
"coul/cut/soft (o)"_pair_fep_soft.html,
"coul/debye (gko)"_pair_coul.html,
"coul/diel (o)"_pair_coul_diel.html,
"coul/dsf (gko)"_pair_coul.html,
"coul/long (gko)"_pair_coul.html,
"coul/long/cs (g)"_pair_cs.html,
"coul/long/soft (o)"_pair_lj_soft.html,
"coul/long/soft (o)"_pair_fep_soft.html,
"coul/msm (o)"_pair_coul.html,
"coul/shield"_pair_coul_shield.html,
"coul/streitz"_pair_coul.html,
@ -107,38 +107,42 @@ OPT.
"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
"lcbop"_pair_lcbop.html,
"lebedeva/z"_pair_lebedeva_z.html,
"lennard/mdf"_pair_mdf.html,
"line/lj"_pair_line_lj.html,
"list"_pair_list.html,
"lj/charmm/coul/charmm (iko)"_pair_charmm.html,
"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
"lj/charmm/coul/long (gikot)"_pair_charmm.html,
"lj/charmm/coul/long/soft (o)"_pair_lj_soft.html,
"lj/charmm/coul/long/soft (o)"_pair_fep_soft.html,
"lj/charmm/coul/msm (o)"_pair_charmm.html,
"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
"lj/charmmfsw/coul/long"_pair_charmm.html,
"lj/class2 (gko)"_pair_class2.html,
"lj/class2/coul/cut (ko)"_pair_class2.html,
"lj/class2/coul/cut/soft"_pair_fep_soft.html,
"lj/class2/coul/long (gko)"_pair_class2.html,
"lj/class2/coul/long/soft"_pair_fep_soft.html,
"lj/class2/soft"_pair_fep_soft.html,
"lj/cubic (go)"_pair_lj_cubic.html,
"lj/cut (gikot)"_pair_lj.html,
"lj/cut/coul/cut (gko)"_pair_lj.html,
"lj/cut/coul/cut/soft (o)"_pair_lj_soft.html,
"lj/cut/coul/cut/soft (o)"_pair_fep_soft.html,
"lj/cut/coul/debye (gko)"_pair_lj.html,
"lj/cut/coul/dsf (gko)"_pair_lj.html,
"lj/cut/coul/long (gikot)"_pair_lj.html,
"lj/cut/coul/long/cs"_pair_cs.html,
"lj/cut/coul/long/soft (o)"_pair_lj_soft.html,
"lj/cut/coul/long/soft (o)"_pair_fep_soft.html,
"lj/cut/coul/msm (go)"_pair_lj.html,
"lj/cut/coul/wolf (o)"_pair_lj.html,
"lj/cut/dipole/cut (go)"_pair_dipole.html,
"lj/cut/dipole/long (g)"_pair_dipole.html,
"lj/cut/dipole/sf (go)"_pair_dipole.html,
"lj/cut/soft (o)"_pair_lj_soft.html,
"lj/cut/soft (o)"_pair_fep_soft.html,
"lj/cut/thole/long (o)"_pair_thole.html,
"lj/cut/tip4p/cut (o)"_pair_lj.html,
"lj/cut/tip4p/long (ot)"_pair_lj.html,
"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html,
"lj/cut/tip4p/long/soft (o)"_pair_fep_soft.html,
"lj/expand (gko)"_pair_lj_expand.html,
"lj/expand/coul/long (g)"_pair_lj_expand.html,
"lj/gromacs (gko)"_pair_gromacs.html,
@ -153,6 +157,7 @@ OPT.
"lj/sf/dipole/sf (go)"_pair_dipole.html,
"lj/smooth (o)"_pair_lj_smooth.html,
"lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
"lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html,
"lj96/cut (go)"_pair_lj96.html,
"lubricate (o)"_pair_lubricate.html,
"lubricate/poly (o)"_pair_lubricate.html,
@ -160,8 +165,7 @@ OPT.
"lubricateU/poly"_pair_lubricateU.html,
"mdpd"_pair_meso.html,
"mdpd/rhosum"_pair_meso.html,
"meam"_pair_meam.html,
"meam/c"_pair_meam.html,
"meam/c"_pair_meamc.html,
"meam/spline (o)"_pair_meam_spline.html,
"meam/sw/spline"_pair_meam_sw_spline.html,
"mgpt"_pair_mgpt.html,
@ -169,7 +173,7 @@ OPT.
"momb"_pair_momb.html,
"morse (gkot)"_pair_morse.html,
"morse/smooth/linear (o)"_pair_morse.html,
"morse/soft"_pair_morse.html,
"morse/soft"_pair_fep_soft.html,
"multi/lucy"_pair_multi_lucy.html,
"multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
"nb3b/harmonic"_pair_nb3b_harmonic.html,
@ -194,7 +198,6 @@ OPT.
"polymorphic"_pair_polymorphic.html,
"python"_pair_python.html,
"quip"_pair_quip.html,
"reax"_pair_reax.html,
"reax/c (ko)"_pair_reaxc.html,
"rebo (io)"_pair_airebo.html,
"resquared (go)"_pair_resquared.html,
@ -230,7 +233,7 @@ OPT.
"thole"_pair_thole.html,
"tip4p/cut (o)"_pair_coul.html,
"tip4p/long (o)"_pair_coul.html,
"tip4p/long/soft (o)"_pair_lj_soft.html,
"tip4p/long/soft (o)"_pair_fep_soft.html,
"tri/lj"_pair_tri_lj.html,
"ufm (got)"_pair_ufm.html,
"vashishta (gko)"_pair_vashishta.html,

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@ -0,0 +1,9 @@
\documentclass[12pt]{article}
\begin{document}
\thispagestyle{empty}
$$
E = K_{SS} \left(r_{12}-r_{12,0}\right)\left(r_{32}-r_{32,0}\right) + K_{BS0}\left(r_{12}-r_{12,0}\right)\left(\theta-\theta_0\right) + K_{BS1}\left(r_{32}-r_{32,0}\right)\left(\theta-\theta_0\right)
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
\thispagestyle{empty}
$$
E = K (\theta - \theta_0)^2 \left[ 1 - 0.014(\theta - \theta_0) + 5.6(10)^{-5} (\theta - \theta_0)^2 - 7.0(10)^{-7} (\theta - \theta_0)^3 + 9(10)^{-10} (\theta - \theta_0)^4 \right]
$$
\end{document}

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@ -0,0 +1,9 @@
\documentclass[12pt]{article}
\begin{document}
\thispagestyle{empty}
$$
E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right]
$$
\end{document}

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@ -0,0 +1,9 @@
\documentclass[12pt]{article}
\begin{document}
\thispagestyle{empty}
$$
E = K (d - d_0)^2
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
\thispagestyle{empty}
$$
E = K (d^2 - d_0^2)^2
$$
\end{document}

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@ -0,0 +1,9 @@
\documentclass[12pt]{article}
\begin{document}
\thispagestyle{empty}
\begin{eqnarray*}
E &=& \frac{q_i q_j \mathrm{erf}\left( r/\sqrt{\gamma_1^2+\gamma_2^2} \right) }{\epsilon r_{ij}}
\end{eqnarray*}
\end{document}

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@ -0,0 +1,11 @@
\documentclass[12pt]{article}
\begin{document}
\thispagestyle{empty}
\begin{eqnarray*}
E = 4\epsilon \left[ \left(\frac{\sigma}{r}\right)^{12}-\left(\frac{\sigma}{r}\right)^{6} \right]
% \qquad r < r_c \\
\end{eqnarray*}
\end{document}

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\documentclass[12pt]{article}
\begin{document}
\thispagestyle{empty}
\begin{eqnarray*}
E &=& \epsilon_{ij} \left[ -2.25 \left(\frac{r_{v,ij}}{r_{ij}}\right)^6 + 1.84(10)^5 \exp\left[-12.0 r_{ij}/r_{v,ij}\right] \right] S_3(r_{ij}) \\
r_{v,ij} &=& r_{v,i} + r_{v,j} \\
\epsilon_{ij} &=& \sqrt{\epsilon_i \epsilon_j}
\end{eqnarray*}
\end{document}

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@ -0,0 +1,14 @@
\documentclass[12pt]{article}
\begin{document}
\thispagestyle{empty}
\begin{eqnarray*}
S_3(r) = \left\lbrace \begin{array}{ll}
1 & \quad\mathrm{if}\quad r < r_\mathrm{c} - w \\
3x^2 - 2x^3 & \quad\mathrm{if}\quad r < r_\mathrm{c} \quad\mathrm{with\quad} x=\frac{r_\mathrm{c} - r}{w} \\
0 & \quad\mathrm{if}\quad r >= r_\mathrm{c}
\end{array} \right.
\end{eqnarray*}
\end{document}

5
doc/src/Errors_common.txt
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@ -74,7 +74,7 @@ is an integer or floating-point number, respectively, and reject the
input with an error message (for instance, when an integer is required,
but a floating-point number 1.0 is provided):
ERROR: Expected integer parameter in input script or data file :pre
ERROR: Expected integer parameter instead of '1.0' in input script or data file :pre
Some commands allow for using variable references in place of numeric
constants so that the value can be evaluated and may change over the
@ -85,6 +85,9 @@ reading the input and before parsing commands,
NOTE: Using a variable reference (i.e. {v_name}) is only allowed if
the documentation of the corresponding command explicitly says it is.
Otherwise, you will receive an error message of this kind:
ERROR: Expected floating point parameter instead of 'v_name' in input script or data file :pre
Generally, LAMMPS will print a message to the screen and logfile and
exit gracefully when it encounters a fatal error. Sometimes it will

12
doc/src/Errors_messages.txt
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@ -6917,7 +6917,7 @@ types. :dd
{Invalid use of library file() function} :dt
This function is called thru the library interface. This
This function is called through the library interface. This
error should not occur. Contact the developers if it does. :dd
{Invalid value in set command} :dt
@ -6988,12 +6988,6 @@ The atom style defined does not have this attribute. :dd
The atom style defined does not have these attributes. :dd
{KIM neighbor iterator exceeded range} :dt
This should not happen. It likely indicates a bug
in the KIM implementation of the interatomic potential
where it is requesting neighbors incorrectly. :dd
{KOKKOS package does not yet support comm_style tiled} :dt
Self-explanatory. :dd
@ -10185,10 +10179,6 @@ valid. :dd
Self-explanatory. :dd
{Unrecognized virial argument in pair_style command} :dt
Only two options are supported: LAMMPSvirial and KIMvirial :dd
{Unsupported mixing rule in kspace_style ewald/disp} :dt
Only geometric mixing is supported. :dd

6
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@ -178,12 +178,6 @@ When using fixes like box/relax, the potential energy used by the minimizer
is augmented by an additional energy provided by the fix. Thus the printed
converged energy may be different from the total potential energy. :dd
{Energy tally does not account for 'zero yes'} :dt
The energy removed by using the 'zero yes' flag is not accounted
for in the energy tally and thus energy conservation cannot be
monitored in this case. :dd
{Estimated error in splitting of dispersion coeffs is %g} :dt
Error is greater than 0.0001 percent. :dd

0
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2
doc/src/Howto_client_server.txt
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@ -82,7 +82,7 @@ Monte Carlo client code as the driver.
The lammps_vasp dir shows how to couple LAMMPS as a client code
running MD timestepping to VASP acting as a server providing quantum
DFT forces, thru a Python wrapper script on VASP.
DFT forces, through a Python wrapper script on VASP.
Here is how to launch a client and server code together for any of the
4 modes of message exchange that the "message"_message.html command

2
doc/src/Howto_couple.txt
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@ -50,7 +50,7 @@ In this scenario, the other code can be called as a library, as in
(1), or it could be a stand-alone code, invoked by a system() call
made by the command (assuming your parallel machine allows one or more
processors to start up another program). In the latter case the
stand-alone code could communicate with LAMMPS thru files that the
stand-alone code could communicate with LAMMPS through files that the
command writes and reads.
See the "Modify command"_Modify_command.html doc page for info on how

2
doc/src/Howto_library.txt
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@ -87,7 +87,7 @@ commands to LAMMPS to execute, the same as if they were coming from an
input script.
Via these functions, the calling code can read or generate a series of
LAMMPS commands one or multiple at a time and pass it thru the library
LAMMPS commands one or multiple at a time and pass it through the library
interface to setup a problem and then run it in stages. The caller
can interleave the command function calls with operations it performs,
calls to extract information from or set information within LAMMPS, or

11
doc/src/Install_git.txt
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@ -48,15 +48,8 @@ your machine and "unstable" is one of the 3 branches listed above.
between them at any time using "git checkout <branch name>".)
Once the command completes, your directory will contain the same files
as if you unpacked a current LAMMPS tarball, with two exceptions:
1) No LAMMPS packages are initially installed in the src dir (a few
packages are installed by default in the tarball src dir). You can
install whichever packages you wish before building LAMMPS; type "make
package" from the src dir to see the options, and the
"Packages"_Packages.html doc page for a discussion of packages.
2) The HTML documentation files are not included. They can be fetched
as if you unpacked a current LAMMPS tarball, with the exception, that
the HTML documentation files are not included. They can be fetched
from the LAMMPS website by typing "make fetch" in the doc directory.
Or they can be generated from the content provided in doc/src by
typing "make html" from the the doc directory.

12
doc/src/Install_linux.txt
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@ -15,7 +15,7 @@ Binaries are available for different versions of Linux:
"Pre-built Fedora Linux executables"_#fedora
"Pre-built EPEL Linux executables (RHEL, CentOS)"_#epel
"Pre-built OpenSuse Linux executables"_#opensuse
"Pre-built Gentoo Linux executable"_#gentoo :all(b)
"Gentoo Linux executable"_#gentoo :all(b)
:line
@ -87,11 +87,11 @@ linking to the C library interface (lammps-devel, lammps-mpich-devel,
lammps-openmpi-devel), the header for compiling programs using
the C library interface (lammps-headers), and the LAMMPS python
module for Python 3. All packages can be installed at the same
time and the name of the LAMMPS executable is {lmp} in all 3 cases.
By default, {lmp} will refer to the serial executable, unless
one of the MPI environment modules is loaded
time and the name of the LAMMPS executable is {lmp} and {lmp_openmpi}
or {lmp_mpich} respectively. By default, {lmp} will refer to the
serial executable, unless one of the MPI environment modules is loaded
("module load mpi/mpich-x86_64" or "module load mpi/openmpi-x86_64").
Then the corresponding parallel LAMMPS executable is used.
Then the corresponding parallel LAMMPS executable can be used.
The same mechanism applies when loading the LAMMPS python module.
To install LAMMPS with OpenMPI and run an input in.lj with 2 CPUs do:
@ -150,7 +150,7 @@ Thanks to Christoph Junghans (LANL) for making LAMMPS available in OpenSuse.
:line
Pre-built Gentoo Linux executable :h4,link(gentoo)
Gentoo Linux executable :h4,link(gentoo)
LAMMPS is part of Gentoo's main package tree and can be installed by
typing:

11
doc/src/Install_svn.txt
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@ -36,15 +36,8 @@ where "mylammps" is the name of the directory you wish to create on
your machine.
Once the command completes, your directory will contain the same files
as if you unpacked a current LAMMPS tarball, with two exceptions:
1) No LAMMPS packages are initially installed in the src dir (a few
packages are installed by default in the tarball src dir). You can
install whichever packages you wish before building LAMMPS; type "make
package" from the src dir to see the options, and the
"Packages"_Packages.html doc page for a discussion of packages.
2) The HTML documentation files are not included. They can be fetched
as if you unpacked a current LAMMPS tarball, with the exception, that
the HTML documentation files are not included. They can be fetched
from the LAMMPS website by typing "make fetch" in the doc directory.
Or they can be generated from the content provided in doc/src by
typing "make html" from the the doc directory.

8
doc/src/Install_windows.txt
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@ -12,7 +12,7 @@ Download an executable for Windows :h3
Pre-compiled Windows installers which install LAMMPS executables on a
Windows system can be downloaded from this site:
"http://rpm.lammps.org/windows.html"_http://rpm.lammps.org/windows.html
"http://packages.lammps.org/windows.html"_http://packages.lammps.org/windows.html
Note that each installer package has a date in its name, which
corresponds to the LAMMPS version of the same date. Installers for
@ -23,8 +23,8 @@ install the Windows MPI package (MPICH2 from Argonne National Labs),
needed to run in parallel.
The LAMMPS binaries contain all optional packages included in the
source distribution except: KIM, REAX, KOKKOS, USER-INTEL,
and USER-QMMM. The serial version also does not include the MPIIO and
source distribution except: KIM, KOKKOS, USER-INTEL, and USER-QMMM.
The serial version also does not include the MPIIO and
USER-LB packages. GPU support is provided for OpenCL.
The installer site also has instructions on how to run LAMMPS under
@ -42,7 +42,7 @@ environment manipulations.
Note that to update to a newer version of LAMMPS, you should typically
uninstall the version you currently have, download a new installer,
and go thru the install procedure described above. I.e. the same
and go through the install procedure described above. I.e. the same
procedure for installing/updating most Windows programs. You can
install multiple versions of LAMMPS (in different directories), but
only the executable for the last-installed package will be found

2
doc/src/Intro_features.txt
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@ -40,7 +40,7 @@ General features :h4,link(general)
syntax for defining and using variables and formulas
syntax for looping over runs and breaking out of loops
run one or multiple simulations simultaneously (in parallel) from one script
build as library, invoke LAMMPS thru library interface or provided Python wrapper
build as library, invoke LAMMPS through library interface or provided Python wrapper
couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both :ul
Particle and model types :h4,link(particle)

39
doc/src/Intro_nonfeatures.txt
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@ -15,8 +15,8 @@ functionality for setting up simulations and analyzing their output.
Specifically, LAMMPS was not conceived and designed for:
being run thru a GUI
build molecular systems, or building molecular topologies
being run through a GUI
building molecular systems, or building molecular topologies
assign force-field coefficients automagically
perform sophisticated analysis of your MD simulation
visualize your MD simulation interactively
@ -24,18 +24,18 @@ plot your output data :ul
Although over the years these limitations have been somewhat
reduced through features added to LAMMPS or external tools
that either interface with LAMMPS or extend LAMMPS.
that either closely interface with LAMMPS or extend LAMMPS.
Here are suggestions on how to perform these tasks:
GUI: LAMMPS can be built as a library and a Python wrapper that wraps
[GUI:] LAMMPS can be built as a library and a Python wrapper that wraps
the library interface is provided. Thus, GUI interfaces can be
written in Python (or C or C++ if desired) that run LAMMPS and
visualize or plot its output. Examples of this are provided in the
python directory and described on the "Python"_Python_head.html doc
page. Also, there are several external wrappers or GUI front ends.:ulb,l
page. Also, there are several external wrappers or GUI front ends. :ulb,l
Builder: Several pre-processing tools are packaged with LAMMPS. Some
[Builder:] Several pre-processing tools are packaged with LAMMPS. Some
of them convert input files in formats produced by other MD codes such
as CHARMM, AMBER, or Insight into LAMMPS input formats. Some of them
are simple programs that will build simple molecular systems, such as
@ -45,15 +45,20 @@ the "Tools"_Tools.html doc page for details on tools packaged with
LAMMPS. The "Pre/post processing
page"_http:/lammps.sandia.gov/prepost.html of the LAMMPS website
describes a variety of 3rd party tools for this task. Furthermore,
some LAMMPS internal commands to reconstruct topology, as well as
the option to insert molecule templates instead of atoms.:l
some LAMMPS internal commands allow to reconstruct, or selectively add
topology information, as well as provide the option to insert molecule
templates instead of atoms for building bulk molecular systems. :l
Force-field assignment: The conversion tools described in the previous
[Force-field assignment:] The conversion tools described in the previous
bullet for CHARMM, AMBER, and Insight will also assign force field
coefficients in the LAMMPS format, assuming you provide CHARMM, AMBER,
or BIOVIA (formerly Accelrys) force field files. :l
or BIOVIA (formerly Accelrys) force field files. The tools
"ParmEd"_https://parmed.github.io/ParmEd/html/index.html and
"InterMol"_https://github.com/shirtsgroup/InterMol are particularly
powerful and flexible in converting force field and topology data
between various MD simulation programs. :l
Simulation analysis: If you want to perform analysis on-the-fly as
[Simulation analysis:] If you want to perform analysis on-the-fly as
your simulation runs, see the "compute"_compute.html and
"fix"_fix.html doc pages, which list commands that can be used in a
LAMMPS input script. Also see the "Modify"_Modify.html doc page for
@ -71,22 +76,22 @@ tools/python directory can extract and massage data in dump files to
make it easier to import into other programs. See the
"Tools"_Tools.html doc page for details on these various options. :l
Visualization: LAMMPS can produce JPG or PNG snapshot images
[Visualization:] LAMMPS can produce NETPBM, JPG or PNG snapshot images
on-the-fly via its "dump image"_dump_image.html command and pass
them to an external program FFmpeg to generate movies from them. For
high-quality, interactive visualization there are many excellent and
free tools available. See the "Other Codes
them to an external program, "FFmpeg"_https://www.ffmpeg.org to generate
movies from them. For high-quality, interactive visualization there are
many excellent and free tools available. See the "Other Codes
page"_http://lammps.sandia.gov/viz.html page of the LAMMPS website for
visualization packages that can use LAMMPS output data. :l
Plotting: See the next bullet about Pizza.py as well as the
[Plotting:] See the next bullet about Pizza.py as well as the
"Python"_Python_head.html doc page for examples of plotting LAMMPS
output. Scripts provided with the {python} tool in the tools
directory will extract and massage data in log and dump files to make
it easier to analyze and plot. See the "Tools"_Tools.html doc page
for more discussion of the various tools. :l
Pizza.py: Our group has also written a separate toolkit called
[Pizza.py:] Our group has also written a separate toolkit called
"Pizza.py"_http://pizza.sandia.gov which can do certain kinds of
setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS
simulations. It thus provides some functionality for several of the

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14
doc/src/Manual.txt
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@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="12 Dec 2018 version">
<META NAME="docnumber" CONTENT="28 Feb 2019 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
:line
LAMMPS Documentation :c,h1
12 Dec 2018 version :c,h2
28 Feb 2019 version :c,h2
"What is a LAMMPS version?"_Manual_version.html
@ -37,27 +37,21 @@ LAMMPS is an open-source code, distributed freely under the terms of
the GNU Public License (GPL).
The "LAMMPS website"_lws has a variety of information about the code.
It includes links to an on-line version of this manual, a "mail
It includes links to an on-line version of this manual, a "mailing
list"_http://lammps.sandia.gov/mail.html where users can post
questions, and a "GitHub site"https://github.com/lammps/lammps where
questions, and a "GitHub site"_https://github.com/lammps/lammps where
all LAMMPS development is coordinated.
:line
"PDF file"_Manual.pdf of the entire manual, generated by
"htmldoc"_http://freecode.com/projects/htmldoc
The content for this manual is part of the LAMMPS distribution. You
can build a local copy of the Manual as HTML pages or a PDF file, by
following the steps on the "Manual build"_Manual_build.html doc page.
There is also a "Developer.pdf"_Developer.pdf document which gives
a brief description of the basic code structure of LAMMPS.
:line
This manual is organized into the following sections.
Once you are familiar with LAMMPS, you may want to bookmark "this
page"_Commands.html since it gives quick access to a doc page for
every LAMMPS command.

11
doc/src/Manual_build.txt
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@ -65,6 +65,8 @@ make epub # generate LAMMPS.epub in ePUB format using Sphinx
make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert
make clean # remove intermediate RST files created by HTML build
make clean-all # remove entire build folder and any cached data :pre
make anchor_check # check for duplicate anchor labels
make spelling # spell-check the manual
:line
@ -106,7 +108,14 @@ This will install virtualenv from the Python Package Index.
Installing prerequisites for PDF build
[TBA]
Building the PDF manual requires a working C++ compiler (to
compile the txt2html tool and a working installation of
"HTMLDOC"_https://www.msweet.org/htmldoc/
HTMLDOC has its own list of prerequisites, but in most cases
you can install a binary package of it either through your
Linux package manager or MacOS (dmg) and Windows installer
(msi) packages from its
"GitHub releases page at"_https://github.com/michaelrsweet/htmldoc/releases
:line

10
doc/src/Modify_contribute.txt
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@ -108,9 +108,13 @@ 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.
the C-style stdio library (mixing of stdio and iostreams is generally
discouraged), class header files should not import any system headers
outside of <cstdio>, STL containers should be avoided in headers,
system header from the C library should use the C++-style names
(<cstdlib>, <cstdio>, or <cstring>) instead of the C-style names
<stdlib.h>, <stdio.h>, or <string.h>), and forward declarations
used where possible or needed to avoid including headers.
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.

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@ -45,7 +45,6 @@ as contained in the file name.
"LATTE"_#PKG-LATTE,
"MANYBODY"_#PKG-MANYBODY,
"MC"_#PKG-MC,
"MEAM"_#PKG-MEAM,
"MESSAGE"_#PKG-MESSAGE,
"MISC"_#PKG-MISC,
"MOLECULE"_#PKG-MOLECULE,
@ -56,7 +55,6 @@ as contained in the file name.
"POEMS"_#PKG-POEMS,
"PYTHON"_#PKG-PYTHON,
"QEQ"_#PKG-QEQ,
"REAX"_#PKG-REAX,
"REPLICA"_#PKG-REPLICA2,
"RIGID"_#PKG-RIGID,
"SHOCK"_#PKG-SHOCK,
@ -65,6 +63,7 @@ as contained in the file name.
"SRD"_#PKG-SRD,
"VORONOI"_#PKG-VORONOI :tb(c=6,ea=c)
"USER-ADIOS"_#PKG-USER-ADIOS,
"USER-ATC"_#PKG-USER-ATC,
"USER-AWPMD"_#PKG-USER-AWPMD,
"USER-BOCS"_#PKG-USER-BOCS,
@ -102,7 +101,8 @@ as contained in the file name.
"USER-SPH"_#PKG-USER-SPH,
"USER-TALLY"_#PKG-USER-TALLY,
"USER-UEF"_#PKG-USER-UEF,
"USER-VTK"_#PKG-USER-VTK :tb(c=6,ea=c)
"USER-VTK"_#PKG-USER-VTK,
"USER-YAFF"_#PKG-USER-YAFF, :tb(c=6,ea=c)
:line
@ -347,12 +347,11 @@ system.
Information about the KIM project can be found at its website:
https://openkim.org. The KIM project is led by Ellad Tadmor and Ryan
Elliott (U Minnesota) and James Sethna (Cornell U).
Elliott (U Minnesota).
[Authors:] Ryan Elliott (U Minnesota) is the main developer for the KIM
API which the "pair_style kim"_pair_kim.html command uses. He
developed the pair style in collaboration with Valeriu Smirichinski (U
Minnesota).
developed the pair style.
[Install:]
@ -533,37 +532,6 @@ http://lammps.sandia.gov/movies.html#gcmc :ul
:line
MEAM package :link(PKG-MEAM),h4
[Contents:]
A pair style for the modified embedded atom (MEAM) potential.
Please note that the use of the MEAM package is discouraged as
it has been superseded by the "USER-MEAMC"_#PKG-USER-MEAMC package,
which is a direct translation of the MEAM package to C++.
USER-MEAMC contains additional optimizations making it run faster
than MEAM on most machines, while providing the identical features
and user interface.
[Author:] Greg Wagner (Northwestern U) while at Sandia.
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
extras"_Build_extras.html doc page.
[Supporting info:]
src/MEAM: filenames -> commands
src/meam/README
lib/meam/README
"pair_style meam"_pair_meam.html
examples/meam :ul
:line
MESSAGE package :link(PKG-MESSAGE),h4
[Contents:]
@ -834,38 +802,6 @@ examples/streitz :ul
:line
REAX package :link(PKG-REAX),h4
[Contents:]
NOTE: the use of the REAX package is discouraged, as it is no longer
maintained. Please use the "USER-REAXC"_#PKG-USER-REAXC package instead,
and possibly the KOKKOS enabled variant of that, which has a more robust
memory management.
A pair style which wraps a Fortran library which implements the ReaxFF
potential, which is a universal reactive force field. Also included is
a "fix reax/bonds"_fix_reax_bonds.html command for monitoring molecules
as bonds are created and destroyed.
[Author:] Aidan Thompson (Sandia).
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
extras"_Build_extras.html doc page.
[Supporting info:]
src/REAX: filenames -> commands
lib/reax/README
"pair_style reax"_pair_reax.html
"fix reax/bonds"_fix_reax_bonds.html
examples/reax :ul
:line
REPLICA package :link(PKG-REPLICA2),h4
[Contents:]
@ -1039,6 +975,31 @@ examples/voronoi :ul
:line
USER-ADIOS package :link(PKG-USER-ADIOS),h4
[Contents:]
ADIOS is a high-performance I/O library. This package implements the
dump "atom/adios" and dump "custom/adios" commands to write data using
the ADIOS library.
[Authors:] Norbert Podhorszki (ORNL) from the ADIOS developer team.
[Install:]
This package has "specific installation
instructions"_Build_extras.html#user-adios on the "Build
extras"_Build_extras.html doc page.
[Supporting info:]
src/USER-ADIOS: filenames -> commands
src/USER-ADIOS/README
examples/USER/adios
https://github.com/ornladios/ADIOS2 :ul
:line
USER-ATC package :link(PKG-USER-ATC),h4
[Contents:]
@ -1370,7 +1331,7 @@ src/USER-FEP: filenames -> commands
src/USER-FEP/README
"fix adapt/fep"_fix_adapt_fep.html
"compute fep"_compute_fep.html
"pair_style */soft"_pair_lj_soft.html
"pair_style */soft"_pair_fep_soft.html
examples/USER/fep
tools/fep/README
tools/fep :ul
@ -1552,10 +1513,9 @@ USER-MEAMC package :link(PKG-USER-MEAMC),h4
[Contents:]
A pair style for the modified embedded atom (MEAM) potential
translated from the Fortran version in the "MEAM"_#PKG-MEAM package
to plain C++. In contrast to the MEAM package, no library
needs to be compiled and the pair style can be instantiated
multiple times.
translated from the Fortran version in the (obsolete) "MEAM" package
to plain C++. The USER-MEAMC fully replaces the MEAM package, which
has been removed from LAMMPS after the 12 December 2018 version.
[Author:] Sebastian Huetter, (Otto-von-Guericke University Magdeburg)
based on the Fortran version of Greg Wagner (Northwestern U) while at
@ -1565,8 +1525,8 @@ Sandia.
src/USER-MEAMC: filenames -> commands
src/USER-MEAMC/README
"pair_style meam/c"_pair_meam.html
examples/meam :ul
"pair_style meam/c"_pair_meamc.html
examples/meamc :ul
:line
@ -1765,14 +1725,19 @@ USER-PHONON package :link(PKG-USER-PHONON),h4
A "fix phonon"_fix_phonon.html command that calculates dynamical
matrices, which can then be used to compute phonon dispersion
relations, directly from molecular dynamics simulations.
And a "dynamical_matrix" command to compute the dynamical matrix
from finite differences.
[Authors:] Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon"
and Charlie Sievers (UC Davis) for "dynamical_matrix"
[Author:] Ling-Ti Kong (Shanghai Jiao Tong University).
[Supporting info:]
src/USER-PHONON: filenames -> commands
src/USER-PHONON/README
"fix phonon"_fix_phonon.html
"dynamical_matrix"_dynamical_matrix.html
examples/USER/phonon :ul
:line
@ -1894,9 +1859,8 @@ USER-REAXC package :link(PKG-USER-REAXC),h4
[Contents:]
A pair style which implements the ReaxFF potential in C/C++ (in
contrast to the "REAX package"_#PKG-REAX and its Fortran library). ReaxFF
is universal reactive force field. See the src/USER-REAXC/README file
A pair style which implements the ReaxFF potential in C/C++. ReaxFF
is a universal reactive force field. See the src/USER-REAXC/README file
for more info on differences between the two packages. Also two fixes
for monitoring molecules as bonds are created and destroyed.
@ -1907,7 +1871,7 @@ for monitoring molecules as bonds are created and destroyed.
src/USER-REAXC: filenames -> commands
src/USER-REAXC/README
"pair_style reax/c"_pair_reaxc.html
"fix reax/c/bonds"_fix_reax_bonds.html
"fix reax/c/bonds"_fix_reaxc_bonds.html
"fix reax/c/species"_fix_reaxc_species.html
examples/reax :ul
@ -2134,3 +2098,37 @@ lib/vtk/README
"dump vtk"_dump_vtk.html :ul
:line
USER-YAFF package :link(PKG-USER-YAFF),h4
[Contents:]
Some potentials that are also implemented in the Yet Another Force Field ("YAFF"_yaff) code.
The expressions and their use are discussed in the following papers
Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015) "link"_vanduyfhuys2015
Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018) "link"_vanduyfhuys2018 :ul
which discuss the "QuickFF"_quickff methodology.
:link(vanduyfhuys2015,http://dx.doi.org/10.1002/jcc.23877)
:link(vanduyfhuys2018,http://dx.doi.org/10.1002/jcc.25173)
:link(quickff,http://molmod.github.io/QuickFF)
:link(yaff,https://github.com/molmod/yaff)
[Author:] Steven Vandenbrande.
[Supporting info:]
src/USER-YAFF/README
"angle_style cross"_angle_cross.html
"angle_style mm3"_angle_mm3.html
"bond_style mm3"_bond_mm3.html
"improper_style distharm"_improper_distharm.html
"improper_style sqdistharm"_improper_sqdistharm.html
"pair_style mm3/switch3/coulgauss/long"_pair_mm3_switch3_coulgauss.html
"pair_style lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html
examples/USER/yaff :ul

2
doc/src/Packages_standard.txt
View File

@ -46,7 +46,6 @@ Package, Description, Doc page, Example, Library
"LATTE"_Packages_details.html#PKG-LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
"MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, no
"MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, n/a, no
"MEAM"_Packages_details.html#PKG-MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
"MESSAGE"_Packages_details.html#PKG-MESSAGE, client/server messaging, "message"_message.html, message, int
"MISC"_Packages_details.html#PKG-MISC, miscellaneous single-file commands, n/a, no, no
"MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, no
@ -57,7 +56,6 @@ Package, Description, Doc page, Example, Library
"POEMS"_Packages_details.html#PKG-POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
"PYTHON"_Packages_details.html#PKG-PYTHON, embed Python code in an input script, "python"_python.html, python, sys
"QEQ"_Packages_details.html#PKG-QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, no
"REAX"_Packages_details.html#PKG-REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
"REPLICA"_Packages_details.html#PKG-REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, no
"RIGID"_Packages_details.html#PKG-RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, no
"SHOCK"_Packages_details.html#PKG-SHOCK, shock loading methods, "fix msst"_fix_msst.html, n/a, no

6
doc/src/Packages_user.txt
View File

@ -38,6 +38,7 @@ int = internal library: provided with LAMMPS, but you may need to build it
ext = external library: you will need to download and install it on your machine :ul
Package, Description, Doc page, Example, Library
"USER-ADIOS"_Packages_details.html#PKG-USER-ADIOS, dump output via ADIOS, "dump adios"_dump_adios.html, USER/adios, ext
"USER-ATC"_Packages_details.html#PKG-USER-ATC, Atom-to-Continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
"USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
"USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, no
@ -53,7 +54,7 @@ Package, Description, Doc page, Example, Library
"USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
"USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, no
"USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, no
"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, no
"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meamc.html, meamc, no
"USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no
"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no
"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no
@ -75,7 +76,8 @@ Package, Description, Doc page, Example, Library
"USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, no
"USER-TALLY"_Packages_details.html#PKG-USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, no
"USER-UEF"_Packages_details.html#PKG-USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, no
"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, n/a, ext :tb(ea=c,ca1=l)
"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, n/a, ext
"USER-YAFF"_Packages_details.html#PKG-USER-YAFF, additional styles implemented in YAFF, "angle_style cross"_angle_cross.html, USER/yaff, no :tb(ea=c,ca1=l)
:link(MOFplus,https://www.mofplus.org/content/show/MOF-FF)
:link(PLUMED,http://www.plumed.org)

2
doc/src/Python_examples.txt
View File

@ -15,7 +15,7 @@ things that are possible when Python wraps LAMMPS. If you create your
own scripts, send them to us and we can include them in the LAMMPS
distribution.
trivial.py, read/run a LAMMPS input script thru Python,
trivial.py, read/run a LAMMPS input script through Python,
demo.py, invoke various LAMMPS library interface routines,
simple.py, run in parallel, similar to examples/COUPLE/simple/simple.cpp,
split.py, same as simple.py but running in parallel on a subset of procs,

2
doc/src/Python_run.txt
View File

@ -31,7 +31,7 @@ language is, and that it can be run interactively, enabling rapid
development and debugging. If you use it to mostly invoke costly
operations within LAMMPS, such as running a simulation for a
reasonable number of timesteps, then the overhead cost of invoking
LAMMPS thru Python will be negligible.
LAMMPS through Python will be negligible.
The Python wrapper for LAMMPS uses the "ctypes" package in Python,
which auto-generates the interface code needed between Python and a

2
doc/src/Python_test.txt
View File

@ -32,7 +32,7 @@ first importing from the lammps.py file:
>>> from ctypes import CDLL
>>> CDLL("liblammps.so") :pre
If an error occurs, carefully go thru the steps on the
If an error occurs, carefully go through the steps on the
"Build_basics"_Build_basics.html doc page about building a shared
library and the "Python_install"_Python_install.html doc page about
insuring Python can find the necessary two files it needs.

15
doc/src/Tools.txt
View File

@ -391,15 +391,16 @@ definition file. This tool was used to create the system for the
moltemplate tool :h4,link(moltemplate)
The moltemplate sub-directory contains a Python-based tool for
building molecular systems based on a text-file description, and
creating LAMMPS data files that encode their molecular topology as
lists of bonds, angles, dihedrals, etc. See the README.TXT file for
more information.
The moltemplate sub-directory contains instructions for installing
moltemplate, a Python-based tool for building molecular systems based
on a text-file description, and creating LAMMPS data files that encode
their molecular topology as lists of bonds, angles, dihedrals, etc.
See the README.txt file for more information.
This tool was written by Andrew Jewett (jewett.aij at gmail.com), who
supports it. It has its own WWW page at
"http://moltemplate.org"_http://moltemplate.org.
The latest sources can be found "on its GitHub page"_https://github.com/jewettaij/moltemplate/releases
:line
@ -486,8 +487,8 @@ README for more info on Pizza.py and how to use these scripts.
reax tool :h4,link(reax_tool)
The reax sub-directory contains stand-alone codes that can
post-process the output of the "fix reax/bonds"_fix_reax_bonds.html
command from a LAMMPS simulation using "ReaxFF"_pair_reax.html. See
post-process the output of the "fix reax/c/bonds"_fix_reaxc_bonds.html
command from a LAMMPS simulation using "ReaxFF"_pair_reaxc.html. See
the README.txt file for more info.
These tools were written by Aidan Thompson at Sandia.

1
doc/src/angle_cosine.txt
View File

@ -8,6 +8,7 @@
angle_style cosine command :h3
angle_style cosine/omp command :h3
angle_style cosine/kk command :h3
[Syntax:]

62
doc/src/angle_cross.txt Normal file
View File

@ -0,0 +1,62 @@
"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
angle_style cross command :h3
[Syntax:]
angle_style cross :pre
[Examples:]
angle_style cross
angle_coeff 1 200.0 100.0 100.0 1.25 1.25 107.0 :pre
[Description:]
The {cross} angle style uses a potential that couples the bond stretches of
a bend with the angle stretch of that bend:
:c,image(Eqs/angle_cross.jpg)
where r12,0 is the rest value of the bond length between atom 1 and 2,
r32,0 is the rest value of the bond length between atom 2 and 2,
and theta0 is the rest value of the angle. KSS is the force constant of
the bond stretch-bond stretch term and KBS0 and KBS1 are the force constants
of the bond stretch-angle stretch terms.
The following coefficients must be defined for each angle type via the
"angle_coeff"_angle_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
KSS (energy/distance^2)
KBS0 (energy/distance/rad)
KBS1 (energy/distance/rad)
r12,0 (distance)
r32,0 (distance)
theta0 (degrees) :ul
Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of KBS0 and KBS1 are in energy/distance/radian.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
USER_YAFF package. See the "Build package"_Build_package.html doc
page for more info.
[Related commands:]
"angle_coeff"_angle_coeff.html
[Default:] none
:line

55
doc/src/angle_mm3.txt Normal file
View File

@ -0,0 +1,55 @@
"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
angle_style mm3 command :h3
[Syntax:]
angle_style mm3 :pre
[Examples:]
angle_style mm3
angle_coeff 1 100.0 107.0 :pre
[Description:]
The {mm3} angle style uses the potential that is anharmonic in the angle
as defined in "(Allinger)"_#mm3-allinger1989
:c,image(Eqs/angle_mm3.jpg)
where theta0 is the equilibrium value of the angle, and K is a
prefactor. The anharmonic prefactors have units deg^(-n), for example
-0.014 deg^(-1), 5.6(10)^(-5) deg^(-2), ...
The following coefficients must be defined for each angle type via the
"angle_coeff"_angle_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy/radian^2)
theta0 (degrees) :ul
Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
USER_YAFF package. See the "Build package"_Build_package.html doc
page for more info.
[Related commands:]
"angle_coeff"_angle_coeff.html
[Default:] none
:line

2
doc/src/angle_style.txt
View File

@ -81,10 +81,12 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
"cosine/shift"_angle_cosine_shift.html - angle cosine with a shift
"cosine/shift/exp"_angle_cosine_shift_exp.html - cosine with shift and exponential term in spring constant
"cosine/squared"_angle_cosine_squared.html - angle with cosine squared term
"cross"_angle_cross.html - cross term coupling angle and bond lengths
"dipole"_angle_dipole.html - angle that controls orientation of a point dipole
"fourier"_angle_fourier.html - angle with multiple cosine terms
"fourier/simple"_angle_fourier_simple.html - angle with a single cosine term
"harmonic"_angle_harmonic.html - harmonic angle
"mm3"_angle_mm3.html - anharmonic angle
"quartic"_angle_quartic.html - angle with cubic and quartic terms
"sdk"_angle_sdk.html - harmonic angle with repulsive SDK pair style between 1-3 atoms
"table"_angle_table.html - tabulated by angle :ul

2
doc/src/angles.txt
View File

@ -14,11 +14,13 @@ Angle Styles :h1
angle_cosine_shift
angle_cosine_shift_exp
angle_cosine_squared
angle_cross
angle_dipole
angle_fourier
angle_fourier_simple
angle_harmonic
angle_hybrid
angle_mm3
angle_none
angle_quartic
angle_sdk

58
doc/src/bond_mm3.txt Normal file
View File

@ -0,0 +1,58 @@
"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
bond_style mm3 command :h3
[Syntax:]
bond_style mm3 :pre
[Examples:]
bond_style mm3
bond_coeff 1 100.0 107.0 :pre
[Description:]
The {mm3} bond style uses the potential that is anharmonic in the bond
as defined in "(Allinger)"_#mm3-allinger1989
:c,image(Eqs/bond_mm3.jpg)
where r0 is the equilibrium value of the bond, and K is a
prefactor. The anharmonic prefactors have units angstrom^(-n):
-2.55 angstrom^(-1) and (7/12)2.55^2 angstrom^(-2). The code takes
care of the necessary unit conversion for these factors internally.
Note that the MM3 papers contains an error in Eq (1):
(7/12)2.55 should be replaced with (7/12)2.55^2
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy/distance^2)
r0 (distance) :ul
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
USER_YAFF package. See the "Build package"_Build_package.html doc
page for more info.
[Related commands:]
"bond_coeff"_bond_coeff.html
[Default:] none
:line
:link(mm3-allinger1989)
[(Allinger)] Allinger, Yuh, Lii, JACS, 111(23), 8551-8566
(1989),

1
doc/src/bond_style.txt
View File

@ -86,6 +86,7 @@ accelerated styles exist.
"harmonic"_bond_harmonic.html - harmonic bond
"harmonic/shift"_bond_harmonic_shift.html - shifted harmonic bond
"harmonic/shift/cut"_bond_harmonic_shift_cut.html - shifted harmonic bond with a cutoff
"mm3"_bond_mm3.html - MM3 anharmonic bond
"morse"_bond_morse.html - Morse bond
"nonlinear"_bond_nonlinear.html - nonlinear bond
"oxdna/fene"_bond_oxdna.html - modified FENE bond suitable for DNA modeling

1
doc/src/bonds.txt
View File

@ -13,6 +13,7 @@ Bond Styles :h1
bond_harmonic_shift
bond_harmonic_shift_cut
bond_hybrid
bond_mm3
bond_morse
bond_none
bond_nonlinear

2
doc/src/commands_list.txt
View File

@ -32,6 +32,7 @@ Commands :h1
dimension
displace_atoms
dump
dump_adios
dump_cfg_uef
dump_h5md
dump_image
@ -39,6 +40,7 @@ Commands :h1
dump_molfile
dump_netcdf
dump_vtk
dynamical_matrix
echo
fix
fix_modify

2
doc/src/compute_angmom_chunk.txt
View File

@ -37,7 +37,7 @@ they can be used to measure properties of a system.
This compute calculates the 3 components of the angular momentum
vector for each chunk, due to the velocity/momentum of the individual
atoms in the chunk around the center-of-mass of the chunk. The
calculation includes all effects due to atoms passing thru periodic
calculation includes all effects due to atoms passing through periodic
boundaries.
Note that only atoms in the specified group contribute to the

2
doc/src/compute_com.txt
View File

@ -22,7 +22,7 @@ compute 1 all com :pre
[Description:]
Define a computation that calculates the center-of-mass of the group
of atoms, including all effects due to atoms passing thru periodic
of atoms, including all effects due to atoms passing through periodic
boundaries.
A vector of three quantities is calculated by this compute, which

2
doc/src/compute_com_chunk.txt
View File

@ -35,7 +35,7 @@ doc pages for details of how chunks can be defined and examples of how
they can be used to measure properties of a system.
This compute calculates the x,y,z coordinates of the center-of-mass
for each chunk, which includes all effects due to atoms passing thru
for each chunk, which includes all effects due to atoms passing through
periodic boundaries.
Note that only atoms in the specified group contribute to the

2
doc/src/compute_dipole_chunk.txt
View File

@ -38,7 +38,7 @@ they can be used to measure properties of a system.
This compute calculates the x,y,z coordinates of the dipole vector
and the total dipole moment for each chunk, which includes all effects
due to atoms passing thru periodic boundaries. For chunks with a net
due to atoms passing through periodic boundaries. For chunks with a net
charge the resulting dipole is made position independent by subtracting
the position vector of the center of mass or geometric center times the
net charge from the computed dipole vector.

2
doc/src/compute_displace_atom.txt
View File

@ -29,7 +29,7 @@ compute 1 all displace/atom refresh myVar :pre
Define a computation that calculates the current displacement of each
atom in the group from its original (reference) coordinates, including
all effects due to atoms passing thru periodic boundaries.
all effects due to atoms passing through periodic boundaries.
A vector of four quantities per atom is calculated by this compute.
The first 3 elements of the vector are the dx,dy,dz displacements.

43
doc/src/compute_fep.txt
View File

@ -128,24 +128,39 @@ commands to be changed, if the pair style supports it.
The {pstyle} argument is the name of the pair style. For example,
{pstyle} could be specified as "lj/cut". The {pparam} argument is the
name of the parameter to change. This is a (non-exclusive) list of
name of the parameter to change. This is a list of
pair styles and parameters that can be used with this compute. See
the doc pages for individual pair styles and their energy formulas for
the meaning of these parameters:
"lj/cut"_pair_lj.html: epsilon,sigma: type pairs:
"lj/cut/coul/cut"_pair_lj.html: epsilon,sigma: type pairs:
"lj/cut/coul/long"_pair_lj.html: epsilon,sigma: type pairs:
"lj/cut/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
"coul/cut/soft"_pair_lj_soft.html: lambda: type pairs:
"coul/long/soft"_pair_lj_soft.html: lambda: type pairs:
"lj/cut/coul/cut/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
"lj/cut/coul/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
"lj/cut/tip4p/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
"tip4p/long/soft"_pair_lj_soft.html: lambda: type pairs:
"lj/charmm/coul/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
"born"_pair_born.html: a,b,c: type pairs:
"buck"_pair_buck.html: a,c : type pairs :tb(c=3,s=:)
"buck"_pair_buck.html: a,c: type pairs:
"buck/mdf"_pair_mdf.html: a,c: type pairs:
"coul/cut"_pair_coul.html: scale: type pairs:
"coul/cut/soft"_pair_fep_soft.html: lambda: type pairs:
"coul/long, coul/msm"_pair_coul.html: scale: type pairs:
"coul/long/soft"_pair_fep_soft.html: scale, lambda: type pairs:
"eam"_pair_eam.html: scale: type pairs:
"gauss"_pair_gauss.html: a: type pairs:
"lennard/mdf"_pair_mdf.html: a,b: type pairs:
"lj/class2"_pair_class2.html: epsilon,sigma: type pairs:
"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma: type pairs:
"lj/cut"_pair_lj.html: epsilon,sigma: type pairs:
"lj/cut/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs:
"lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma: type pairs:
"lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs:
"lj/cut/tip4p/cut, lj/cut/tip4p/long"_pair_lj.html: epsilon,sigma: type pairs:
"lj/cut/tip4p/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs:
"lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs:
"lj/mdf"_pair_mdf.html: epsilon,sigma: type pairs:
"lj/sf/dipole/sf"_pair_dipole.html: epsilon,sigma,scale: type pairs:
"mie/cut"_pair_mie.html: epsilon,sigma,gamR,gamA: type pairs:
"morse, morse/smooth/linear"_pair_morse.html: d0,r0,alpha: type pairs:
"morse/soft"_pair_morse.html: d0,r0,alpha,lambda: type pairs:
"nm/cut"_pair_nm.html: e0,r0,nn,mm: type pairs:
"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: e0,r0,nn,mm: type pairs:
"ufm"_pair_ufm.html: epsilon,sigma,scale: type pairs:
"soft"_pair_soft.html: a: type pairs :tb(c=3,s=:)
Note that it is easy to add new potentials and their parameters to
this list. All it typically takes is adding an extract() method to
@ -236,7 +251,7 @@ package"_Build_package.html doc page for more info.
[Related commands:]
"fix adapt/fep"_fix_adapt_fep.html, "fix ave/time"_fix_ave_time.html,
"pair_style lj/soft/coul/soft"_pair_lj_soft.html
"pair_fep_soft"_pair_fep_soft.html
[Default:]

9
doc/src/compute_group_group.txt
View File

@ -137,11 +137,12 @@ Not all pair styles can be evaluated in a pairwise mode as required by
this compute. For example, 3-body and other many-body potentials,
such as "Tersoff"_pair_tersoff.html and
"Stillinger-Weber"_pair_sw.html cannot be used. "EAM"_pair_eam.html
potentials only include the pair potential portion of the EAM
interaction when used by this compute, not the embedding term.
potentials will re-use previously computed embedding term contributions,
so the computed pairwise forces and energies are based on the whole
system and not valid if particles have been moved since.
Not all Kspace styles support calculation of group/group interactions.
The {ewald} and {pppm} styles do.
Not all "Kspace styles"_kspace_style.html support the calculation of
group/group interactions. The regular {ewald} and {pppm} styles do.
[Related commands:] none

2
doc/src/compute_gyration.txt
View File

@ -22,7 +22,7 @@ compute 1 molecule gyration :pre
[Description:]
Define a computation that calculates the radius of gyration Rg of the
group of atoms, including all effects due to atoms passing thru
group of atoms, including all effects due to atoms passing through
periodic boundaries.
Rg is a measure of the size of the group of atoms, and is computed as

2
doc/src/compute_gyration_chunk.txt
View File

@ -40,7 +40,7 @@ doc pages for details of how chunks can be defined and examples of how
they can be used to measure properties of a system.
This compute calculates the radius of gyration Rg for each chunk,
which includes all effects due to atoms passing thru periodic
which includes all effects due to atoms passing through periodic
boundaries.
Rg is a measure of the size of a chunk, and is computed by this

2
doc/src/compute_inertia_chunk.txt
View File

@ -36,7 +36,7 @@ they can be used to measure properties of a system.
This compute calculates the 6 components of the symmetric inertia
tensor for each chunk, ordered Ixx,Iyy,Izz,Ixy,Iyz,Ixz. The
calculation includes all effects due to atoms passing thru periodic
calculation includes all effects due to atoms passing through periodic
boundaries.
Note that only atoms in the specified group contribute to the

2
doc/src/compute_msd.txt
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@ -29,7 +29,7 @@ compute 1 upper msd com yes average yes :pre
Define a computation that calculates the mean-squared displacement
(MSD) of the group of atoms, including all effects due to atoms
passing thru periodic boundaries. For computation of the non-Gaussian
passing through periodic boundaries. For computation of the non-Gaussian
parameter of mean-squared displacement, see the "compute
msd/nongauss"_compute_msd_nongauss.html command.

2
doc/src/compute_msd_chunk.txt
View File

@ -38,7 +38,7 @@ Four quantities are calculated by this compute for each chunk. The
first 3 quantities are the squared dx,dy,dz displacements of the
center-of-mass. The 4th component is the total squared displacement,
i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass. These
calculations include all effects due to atoms passing thru periodic
calculations include all effects due to atoms passing through periodic
boundaries.
Note that only atoms in the specified group contribute to the

2
doc/src/compute_msd_nongauss.txt
View File

@ -28,7 +28,7 @@ compute 1 upper msd/nongauss com yes :pre
Define a computation that calculates the mean-squared displacement
(MSD) and non-Gaussian parameter (NGP) of the group of atoms,
including all effects due to atoms passing thru periodic boundaries.
including all effects due to atoms passing through periodic boundaries.
A vector of three quantities is calculated by this compute. The first
element of the vector is the total squared dx,dy,dz displacements

2
doc/src/compute_omega_chunk.txt
View File

@ -38,7 +38,7 @@ This compute calculates the 3 components of the angular velocity
vector for each chunk, via the formula L = Iw where L is the angular
momentum vector of the chunk, I is its moment of inertia tensor, and w
is omega = angular velocity of the chunk. The calculation includes
all effects due to atoms passing thru periodic boundaries.
all effects due to atoms passing through periodic boundaries.
Note that only atoms in the specified group contribute to the
calculation. The "compute chunk/atom"_compute_chunk_atom.html command

6
doc/src/compute_pair.txt
View File

@ -24,7 +24,7 @@ nsub = {n}-instance of a sub-style, if a pair style is used multiple times in a
compute 1 all pair gauss
compute 1 all pair lj/cut/coul/cut ecoul
compute 1 all pair tersoff 2 epair
compute 1 all pair reax :pre
compute 1 all pair reax/c :pre
[Description:]
@ -60,8 +60,8 @@ corrections, even if they are enabled via the
"pair_modify"_pair_modify.html command.
Some pair styles tally additional quantities, e.g. a breakdown of
potential energy into a dozen or so components is tallied by the
"pair_style reax"_pair_reax.html command. These values (1 or more)
potential energy into 14 components is tallied by the "pair_style
reax/c"_pair_reaxc.html command. These values (1 or more)
are stored as a global vector by this compute. See the doc page for
"individual pair styles"_pair_style.html for info on these values.

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