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Update to latest upstream develop

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Stan Gerald Moore
2021-11-10 15:14:24 -07:00
parent 3f42e97405 a4ceda9706
commit 7625b9707b
6905 changed files with 214584 additions and 133407 deletions
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.gitattributes vendored
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@ -2,3 +2,4 @@
.gitignore export-ignore
.github export-ignore
.lgtm.yml export-ignore
SECURITY.md export-ignore

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.github/CODEOWNERS vendored
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@ -13,43 +13,51 @@ lib/kim/* @ellio167
lib/mesont/* @iafoss
# whole packages
src/COMPRESS/* @akohlmey
src/COMPRESS/* @rbberger
src/GPU/* @ndtrung81
src/KOKKOS/* @stanmoore1
src/KIM/* @ellio167
src/LATTE/* @cnegre
src/MESSAGE/* @sjplimp
src/MLIAP/* @athomps
src/SNAP/* @athomps
src/SPIN/* @julient31
src/USER-CGDNA/* @ohenrich
src/USER-CGSDK/* @akohlmey
src/USER-COLVARS/* @giacomofiorin
src/USER-INTEL/* @wmbrownintel
src/USER-MANIFOLD/* @Pakketeretet2
src/USER-MEAMC/* @martok
src/USER-MESONT/* @iafoss
src/USER-MOFFF/* @hheenen
src/USER-MOLFILE/* @akohlmey
src/USER-NETCDF/* @pastewka
src/USER-PLUMED/* @gtribello
src/USER-PHONON/* @lingtikong
src/USER-PTM/* @pmla
src/USER-OMP/* @akohlmey
src/USER-QMMM/* @akohlmey
src/USER-REAXC/* @hasanmetin
src/USER-SCAFACOS/* @rhalver
src/USER-TALLY/* @akohlmey
src/USER-UEF/* @danicholson
src/USER-VTK/* @rbberger
src/BROWNIAN/* @samueljmcameron
src/CG-DNA/* @ohenrich
src/CG-SDK/* @akohlmey
src/COLVARS/* @giacomofiorin
src/DIELECTRIC/* @ndtrung81
src/FEP/* @agiliopadua
src/ML-HDNNP/* @singraber
src/INTEL/* @wmbrownintel
src/MANIFOLD/* @Pakketeretet2
src/MDI/* @taylor-a-barnes
src/MEAM/* @martok
src/MESONT/* @iafoss
src/MOFFF/* @hheenen
src/MOLFILE/* @akohlmey
src/NETCDF/* @pastewka
src/ML-PACE/* @yury-lysogorskiy
src/PLUMED/* @gtribello
src/PHONON/* @lingtikong
src/PTM/* @pmla
src/OPENMP/* @akohlmey
src/QMMM/* @akohlmey
src/REAXFF/* @hasanmetin @stanmoore1
src/REACTION/* @jrgissing
src/SCAFACOS/* @rhalver
src/TALLY/* @akohlmey
src/UEF/* @danicholson
src/VTK/* @rbberger
# individual files in packages
src/GPU/pair_vashishta_gpu.* @andeplane
src/KOKKOS/pair_vashishta_kokkos.* @andeplane
src/MANYBODY/pair_vashishta_table.* @andeplane
src/MANYBODY/pair_atm.* @sergeylishchuk
src/USER-REACTION/fix_bond_react.* @jrgissing
src/USER-MISC/*_grem.* @dstelter92
src/USER-MISC/compute_stress_mop*.* @RomainVermorel
src/REPLICA/*_grem.* @dstelter92
src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
src/MISC/*_tracker.* @jtclemm
# core LAMMPS classes
src/lammps.* @sjplimp
@ -73,8 +81,9 @@ src/kspace.* @sjplimp
src/lmptyp.h @sjplimp
src/library.* @sjplimp
src/main.cpp @sjplimp
src/min_*.* @sjplimp
src/memory.* @sjplimp
src/modify.* @sjplimp
src/modify.* @sjplimp @stanmoore1
src/molecule.* @sjplimp
src/my_page.h @sjplimp
src/my_pool_chunk.h @sjplimp
@ -101,7 +110,6 @@ src/thermo.* @sjplimp
src/universe.* @sjplimp
src/update.* @sjplimp
src/variable.* @sjplimp
src/verlet.* @sjplimp
src/velocity.* @sjplimp
src/write_data.* @sjplimp
src/write_restart.* @sjplimp
@ -114,23 +122,26 @@ src/info.* @akohlmey @rbberger
src/timer.* @akohlmey
src/min* @sjplimp @stanmoore1
src/utils.* @akohlmey @rbberger
src/verlet.* @sjplimp @stanmoore1
src/math_eigen_impl.h @jewettaij
# tools
tools/msi2lmp/* @akohlmey
tools/emacs/* @HaoZeke
tools/singularity/* @akohlmey @rbberger
tools/code_standard/* @rbberger
tools/coding_standard/* @rbberger
tools/valgrind/* @akohlmey
tools/swig/* @akohlmey
tools/offline/* @rbberger
# tests
unittest/* @akohlmey @rbberger
# cmake
cmake/* @junghans @rbberger
cmake/Modules/Packages/USER-COLVARS.cmake @junghans @rbberger @giacomofiorin
cmake/Modules/Packages/COLVARS.cmake @junghans @rbberger @giacomofiorin
cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
cmake/presets/*.cmake @junghans @rbberger @akohlmey
cmake/presets/*.cmake @akohlmey
# python
python/* @rbberger
@ -142,6 +153,7 @@ fortran/* @akohlmey
doc/utils/*/* @rbberger
doc/Makefile @rbberger
doc/README @rbberger
examples/plugin/* @akohlmey
# for releases
src/version.h @sjplimp

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.github/CONTRIBUTING.md vendored
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@ -5,8 +5,9 @@ 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 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](https://lammps.sandia.gov/doc/Modify_contribute.html)
* [The LAMMPS GitHub Tutorial in the Manual](http://lammps.sandia.gov/doc/Howto_github.html)
* [The guide for submitting new features in the LAMMPS manual](https://lammps.sandia.gov/doc/Modify_contribute.html)
* [The guide on programming style and requirement in the LAMMPS manual](https://lammps.sandia.gov/doc/Modify_contribute.html)
* [The GitHub tutorial in the LAMMPS manual](http://lammps.sandia.gov/doc/Howto_github.html)
## Table of Contents
@ -26,11 +27,11 @@ __
## 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 either the ['lammps-users' mailing list](https://lammps.sandia.gov/mail.html) or the [LAMMPS Material Science Discourse forum](https://matsci.org/lammps). 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. The LAMMPS forum was recently created as part of a larger effort to build a materials science community and have discussions not just about using LAMMPS. Thus the forum may be also used for discussions that would be off-topic for the mailing list. Those will just have to be moved to a more general category.
> **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 either the ['lammps-users' mailing list](https://lammps.sandia.gov/mail.html) or the [LAMMPS Material Science Discourse forum](https://matsci.org/lammps). 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. The LAMMPS forum was recently created as part of a larger effort to build a materials science community and have discussions not just about using LAMMPS. Thus the forum may be also used for discussions that would be off-topic for the mailing list. Those will just have to be posted to a more general category.
## 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 or posting in the LAMMPS Materials Science Discourse forum), and you can contribute by submitting pull requests on GitHub or e-mail your code
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 or the forum, you can report bugs or suggest enhancements by creating issues on GitHub (or posting them to the lammps-users mailing list or posting in the LAMMPS Materials Science Discourse forum), and you can contribute by submitting pull requests on GitHub or e-mail your code
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
@ -62,37 +63,12 @@ To be able to submit an issue on GitHub, you have to register for an account (fo
### Contributing Code
We encourage users to submit new features or modifications for LAMMPS to the core developers so they can be added to the LAMMPS distribution. The preferred way to manage and coordinate this is by submitting a pull request at the LAMMPS project on GitHub. For any larger modifications or programming project, you are encouraged to contact the LAMMPS developers ahead of time, in order to discuss implementation strategies and coding guidelines, that will make it easier to integrate your contribution and result in less work for everybody involved. You are also encouraged to search through the list of open issues on GitHub and submit a new issue for a planned feature, so you would not duplicate the work of others (and possibly get scooped by them) or have your work duplicated by others.
We encourage users to submit new features or modifications for LAMMPS. Instructions, guidelines, requirements,
and recommendations are in the following sections of the LAMMPS manual:
* [The guide for submitting new features in the LAMMPS manual](https://lammps.sandia.gov/doc/Modify_contribute.html)
* [The guide on programming style and requirement in the LAMMPS manual](https://lammps.sandia.gov/doc/Modify_contribute.html)
* [The GitHub tutorial in the LAMMPS manual](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.
* C++ source code must be compatible with the C++-11 standard. Packages may require a later standard, if justified.
* 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 trailing whitespace, no lines over 80 characters. I/O is done via the C-style stdio library, style class header files should not import any system headers, STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. There MUST NOT be any "using namespace XXX;" statements in headers. In the implementation file (<name>.cpp) system includes should be placed in angular brackets (<>) and for c-library functions the C++ style header files should be included (<cstdio> instead of <stdio.h>, or <cstring> instead of <string.h>). This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages.
* Source, style name, and documentation file should follow the following naming convention: style names should be lowercase and words separated by a forward slash; for a new fix style 'foo/bar', the class should be named FixFooBar, the name of the source files should be 'fix_foo_bar.h' and 'fix_foo_bar.cpp' and the corresponding documentation should be in a file 'fix_foo_bar.rst'.
* If you want your contribution to be added as a user-contributed feature, and it is a single file (actually a `<name>.cpp` and `<name>.h` file) it can be rapidly added to the USER-MISC directory. Include the one-line entry to add to the USER-MISC/README file in that directory, along with the 2 source files. You can do this multiple times if you wish to contribute several individual features.
* If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like USER-FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this USER-FOO directory.
* Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code.
* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). The text files can include mathematical expressions and symbol in ".. math::" sections or ":math:" expressions or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html`, `make pdf` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file. For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`.
* For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/USER for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind
* For new utility functions or class (i.e. anything that does not depend on a LAMMPS object), new unit tests should be added to the unittest tree.
* When adding a new LAMMPS style, a .yaml file with a test configuration and reference data should be added for the styles where a suitable tester program already exists (e.g. pair styles, bond styles, etc.).
* If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the <name>.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide.
Finally, as a general rule-of-thumb, the more clear and self-explanatory you make your documentation and README files, and the easier you make it for people to get started, e.g. by providing example scripts, the more likely it is that users will try out your new feature.
If the new features/files are broadly useful we may add them as core files to LAMMPS or as part of a standard package. Else we will add them as a user-contributed file or package. Examples of user packages are in src sub-directories that start with USER. The USER-MISC package is simply a collection of (mostly) unrelated single files, which is the simplest way to have your contribution quickly added to the LAMMPS distribution. You can see a list of the both standard and user packages by typing "make package" in the LAMMPS src directory.
Note that by providing us files to release, you are agreeing to make them open-source, i.e. we can release them under the terms of the GPL, used as a license for the rest of LAMMPS. See Section 1.4 for details.
With user packages and files, all we are really providing (aside from the fame and fortune that accompanies having your name in the source code and on the Authors page of the LAMMPS WWW site), is a means for you to distribute your work to the LAMMPS user community, and a mechanism for others to easily try out your new feature. This may help you find bugs or make contact with new collaborators. Note that you are also implicitly agreeing to support your code which means answer questions, fix bugs, and maintain it if LAMMPS changes in some way that breaks it (an unusual event).
To be able to submit an issue on GitHub, you have to register for an account (for GitHub in general). If you do not want to do that, or have other reservations or difficulties to submit a pull request, you can - as an alternative - contact one or more of the core LAMMPS developers and ask if one of them would be interested in manually merging your code into LAMMPS and send them your source code. Since the effort to merge a pull request is a small fraction of the effort of integrating source code manually (which would usually be done by converting the contribution into a pull request), your chances to have your new code included quickly are the best with a pull request.
If you prefer to submit patches or full files, you should first make certain, that your code works correctly with the latest patch-level version of LAMMPS and contains all bug fixes from it. Then create a gzipped tar file of all changed or added files or a corresponding patch file using 'diff -u' or 'diff -c' and compress it with gzip. Please only use gzip compression, as this works well on all platforms.
## GitHub Workflows
@ -102,17 +78,17 @@ This section briefly summarizes the steps that will happen **after** you have su
After submitting an issue, one or more of the LAMMPS developers will review it and categorize it by assigning labels. Confirmed bug reports will be labeled `bug`; if the bug report also contains a suggestion for how to fix it, it will be labeled `bugfix`; if the issue is a feature request, it will be labeled `enhancement`. Other labels may be attached as well, depending on which parts of the LAMMPS code are affected. If the assessment is, that the issue does not warrant any changes, the `wontfix` label will be applied and if the submission is incorrect or something that should not be submitted as an issue, the `invalid` label will be applied. In both of the last two cases, the issue will then be closed without further action.
For feature requests, what happens next is that developers may comment on the viability or relevance of the request, discuss and make suggestions for how to implement it. If a LAMMPS developer or user is planning to implement the feature, the issue will be assigned to that developer. For developers, that are not yet listed as LAMMPS project collaborators, they will receive an invitation to be added to the LAMMPS project as a collaborator so they can get assigned. If the requested feature or enhancement is implemented, it will usually be submitted as a pull request, which will contain a reference to the issue number. And once the pull request is reviewed and accepted for inclusion into LAMMPS, the issue will be closed. For details on how pull requests are processed, please see below.
For feature requests, what happens next is that developers may comment on the viability or relevance of the request, discuss and make suggestions for how to implement it. If a LAMMPS developer or user is planning to implement the feature, the issue will be assigned to that developer. For developers, that are not yet listed as LAMMPS project collaborators, they will receive an invitation to be added to the LAMMPS project as a collaborator so they can get assigned. If the requested feature or enhancement is implemented, it will be submitted as a pull request, which will contain a reference to the issue number. And once the pull request is reviewed and accepted for inclusion into LAMMPS, the issue will be closed. For details on how pull requests are processed, please see below. Feature requests may be labeled with `volunteer_needed` if none of the LAMMPS developers has the time and the required knowledge implement the feature.
For bug reports, the next step is that one of the core LAMMPS developers will self-assign to the issue and try to confirm the bug. If confirmed, the `bug` label and potentially other labels are added to classify the issue and its impact to LAMMPS. Before confirming, further questions may be asked or requests for providing additional input files or details about the steps required to reproduce the issue. Any bugfix is likely to be submitted as a pull request (more about that below) and since most bugs require only local changes, the bugfix may be included in a pull request specifically set up to collect such local bugfixes or small enhancements. Once the bugfix is included in the master branch, the issue will be closed.
For bug reports, the next step is that one of the core LAMMPS developers will self-assign to the issue and try to confirm the bug. If confirmed, the `bug` label and potentially other labels are added to classify the issue and its impact to LAMMPS. Otherwise the `unconfirmed` label will be applied and some comment about what was tried to confirm the bug added. Before confirming, further questions may be asked or requests for providing additional input files or details about the steps required to reproduce the issue. Any bugfix will be submitted as a pull request (more about that below) and since most bugs require only local changes, the bugfix may be included in a pull request specifically set up to collect such local bugfixes or small enhancements. Once the bugfix is included in the master branch, the issue will be closed.
### Pull Requests
For submitting pull requests, there is a [detailed tutorial](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. As part of the assessment, 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).
Pull requests are the **only** way that changes get made to the LAMMPS distribution. So also the LAMMPS core developers will submit pull requests for their own changes and discuss them on GitHub. Thus if you submit a pull request it will be treated in a similar fashion. When you submit a pull request you may opt to submit a "Draft" pull request. That means your changes are visible and will be subject to testing, but reviewers will not be (auto-)assigned and comments will take into account that this is not complete. On the other hand, this is a perfect way to ask the LAMMPS developers for comments on non-obvious changes and get feedback and possible suggestions for improvements or recommendations about what to avoid.
Immediately after the submission, the LAMMPS continuing integration server at ci.lammps.org will download your submitted branch and perform a number of tests: it will tests whether it compiles cleanly under various conditions, it will also do a check on whether your included documentation translates cleanly and run some unit tests and other checks. 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 time the pull request is updated with a push to the remote branch on GitHub. If you are unsure about what you need to change, ask a question in the discussion area of the pull request.
Next a LAMMPS core developer will self-assign and do an overall technical assessment of the submission. If you submitted a draft pull request, this will not happen unless you mark it "ready for review". If you are not yet invited as a LAMMPS collaborator, and your contribution seems significant, you may also receive an invitation for collaboration on the LAMMPS repository. As part of the assessment, 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.
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. The minimum requirement to merge a pull request is that all automated tests have to pass and at least one LAMMPS developer has approved integrating the submitted code. Since the approver will not be the person merging a pull request, you will have at least two LAMMPS developers that looked at your contribution.
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 work flow may be adjusted.

2
.github/workflows/codeql-analysis.yml vendored
View File

@ -3,7 +3,7 @@ name: "CodeQL Code Analysis"
on:
push:
branches: [master]
branches: [develop]
jobs:
analyze:

33
.github/workflows/compile-msvc.yml vendored Normal file
View File

@ -0,0 +1,33 @@
# GitHub action to build LAMMPS on Windows with Visual C++
name: "Native Windows Compilation"
on:
push:
branches: [develop]
jobs:
build:
name: Windows Compilation Test
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: windows-latest
steps:
- name: Checkout repository
uses: actions/checkout@v2
with:
fetch-depth: 2
- name: Building LAMMPS via CMake
shell: bash
run: |
cmake -C cmake/presets/windows.cmake \
-S cmake -B build \
-D BUILD_SHARED_LIBS=on \
-D LAMMPS_EXCEPTIONS=on
cmake --build build --config Release
- name: Run LAMMPS executable
shell: bash
run: |
./build/Release/lmp.exe -h
./build/Release/lmp.exe -in bench/in.lj

2
.github/workflows/unittest-macos.yml vendored
View File

@ -3,7 +3,7 @@ name: "Unittest for MacOS"
on:
push:
branches: [master]
branches: [develop]
jobs:
build:

10
.gitignore vendored
View File

@ -12,6 +12,7 @@
*.sif
*.dll
*.pyc
a.out
__pycache__
Obj_*
@ -36,13 +37,20 @@ vgcore.*
.Trashes
ehthumbs.db
Thumbs.db
.clang-format
.lammps_history
.vs
#cmake
/build*
/CMakeCache.txt
/CMakeFiles/
/Testing
/Makefile
/Testing
/cmake_install.cmake
/lmp
out/Debug
out/RelWithDebInfo
out/Release
out/x86
out/x64

2
.lgtm.yml
View File

@ -4,7 +4,7 @@ extraction:
command:
- "mkdir build"
- "cd build"
- "cmake -G Ninja -C ../cmake/presets/minimal.cmake ../cmake"
- "cmake -G Ninja -C ../cmake/presets/most.cmake ../cmake"
index:
build_command:
- "cd build"

20
README
View File

@ -14,10 +14,10 @@ LAMMPS is a classical molecular dynamics simulation code designed to
run efficiently on parallel computers. It was developed at Sandia
National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL).
under the terms of the GNU Public License (GPL) version 2.
The primary author of the code is Steve Plimpton, who can be emailed
at sjplimp@sandia.gov. The LAMMPS WWW Site at lammps.sandia.gov has
at sjplimp@sandia.gov. The LAMMPS WWW Site at www.lammps.org has
more information about the code and its uses.
The LAMMPS distribution includes the following files and directories:
@ -37,14 +37,14 @@ tools pre- and post-processing tools
Point your browser at any of these files to get started:
https://lammps.sandia.gov/doc/Manual.html LAMMPS manual
https://lammps.sandia.gov/doc/Intro.html hi-level introduction
https://lammps.sandia.gov/doc/Build.html how to build LAMMPS
https://lammps.sandia.gov/doc/Run_head.html how to run LAMMPS
https://lammps.sandia.gov/doc/Commands_all.html Table of available commands
https://lammps.sandia.gov/doc/Library.html LAMMPS library interfaces
https://lammps.sandia.gov/doc/Modify.html how to modify and extend LAMMPS
https://lammps.sandia.gov/doc/Developer.html LAMMPS developer info
https://docs.lammps.org/Manual.html LAMMPS manual
https://docs.lammps.org/Intro.html hi-level introduction
https://docs.lammps.org/Build.html how to build LAMMPS
https://docs.lammps.org/Run_head.html how to run LAMMPS
https://docs.lammps.org/Commands_all.html Table of available commands
https://docs.lammps.org/Library.html LAMMPS library interfaces
https://docs.lammps.org/Modify.html how to modify and extend LAMMPS
https://docs.lammps.org/Developer.html LAMMPS developer info
You can also create these doc pages locally:

39
SECURITY.md Normal file
View File

@ -0,0 +1,39 @@
# Security Policy
LAMMPS is designed as a user-level application to conduct computer
simulations for research using classical mechanics. As such LAMMPS
depends to some degrees on users providing correctly formatted input and
LAMMPS needs to read and write files based on uncontrolled user input.
As a parallel application for use in high-performance computing
environments, performance critical steps are also done without checking
data.
LAMMPS also is interfaced to a number of external libraries, including
libraries with experimental research software, that are not validated
and tested by the LAMMPS developers, so it is easy to import bad
behavior from calling functions in one of those libraries.
Thus is is quite easy to crash LAMMPS through malicious input and do all
kinds of filesystem manipulations. And because of that LAMMPS should
**NEVER** be compiled or **run** as superuser, either from a "root" or
"administrator" account directly or indirectly via "sudo" or "su".
Therefore what could be seen as a security vulnerability is usually
either a user mistake or a bug in the code. Bugs can be reported in
the LAMMPS project
[issue tracker on GitHub](https://github.com/lammps/lammps/issues).
To mitigate issues with using homoglyphs or bidirectional reordering in
unicode, which have been demonstrated as a vector to obfuscate and hide
malicious changes to the source code, all LAMMPS submissions are checked
for unicode characters and only all-ASCII source code is accepted.
# Version Updates
LAMMPS follows continuous release development model. We aim to keep all
release versions (stable or patch) fully functional and employ a variety
of automatic testing procedures to detect failures of existing
functionality from adding new features before releases are made. Thus
bugfixes and updates are only integrated into the current development
branch and thus the next (patch) release and users are recommended to
update regularly.

2
bench/POTENTIALS/README
View File

@ -1,7 +1,7 @@
These are input scripts used to run benchmark tests for many of the
interatomic potentials in LAMMPS. The results of running these
scripts on different machines are shown on the Potentials section of
the Benchmark page of the LAMMPS WWW site (lammps.sandia.gov/bench).
the Benchmark page of the LAMMPS WWW site (https://www.lammps.org/bench.html).
Examples are shown below of how to run these scripts. Log files for
running them on 1 and 4 processors of a Linux box are included in the

2
bench/POTENTIALS/in.meamc → bench/POTENTIALS/in.meam
View File

@ -8,7 +8,7 @@ region box block 0 20 0 20 0 20
create_box 1 box
create_atoms 1 box
pair_style meam/c
pair_style meam
pair_coeff * * library.meam Ni4 Ni.meam Ni4
velocity all create 1600.0 376847 loop geom

6
bench/POTENTIALS/log.9Oct20.meamc.1 → bench/POTENTIALS/log.9Oct20.meam.1
View File

@ -15,7 +15,7 @@ create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.002 seconds
pair_style meam/c
pair_style meam
pair_coeff * * library.meam Ni4 Ni.meam Ni4
Reading potential file library.meam with DATE: 2012-06-29
Reading potential file Ni.meam with DATE: 2007-06-11
@ -38,12 +38,12 @@ Neighbor list info ...
ghost atom cutoff = 5
binsize = 2.5, bins = 29 29 29
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam/c, perpetual
(1) pair meam, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam/c, perpetual, half/full from (1)
(2) pair meam, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none

6
bench/POTENTIALS/log.9Oct20.meamc.4 → bench/POTENTIALS/log.9Oct20.meam.4
View File

@ -15,7 +15,7 @@ create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.001 seconds
pair_style meam/c
pair_style meam
pair_coeff * * library.meam Ni4 Ni.meam Ni4
Reading potential file library.meam with DATE: 2012-06-29
Reading potential file Ni.meam with DATE: 2007-06-11
@ -38,12 +38,12 @@ Neighbor list info ...
ghost atom cutoff = 5
binsize = 2.5, bins = 29 29 29
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam/c, perpetual
(1) pair meam, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam/c, perpetual, half/full from (1)
(2) pair meam, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none

2
bench/POTENTIALS/log.9Oct20.reaxc.1
View File

@ -24,7 +24,7 @@ velocity all create 300.0 9999
pair_style reax/c NULL
pair_coeff * * ffield.reax C H O N
WARNING: Changed valency_val to valency_boc for X (src/USER-REAXC/reaxc_ffield.cpp:315)
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxc_ffield.cpp:315)
timestep 0.1
fix 1 all nve

2
bench/POTENTIALS/log.9Oct20.reaxc.4
View File

@ -24,7 +24,7 @@ velocity all create 300.0 9999
pair_style reax/c NULL
pair_coeff * * ffield.reax C H O N
WARNING: Changed valency_val to valency_boc for X (src/USER-REAXC/reaxc_ffield.cpp:315)
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxc_ffield.cpp:315)
timestep 0.1
fix 1 all nve

4
bench/README
View File

@ -2,7 +2,7 @@ LAMMPS benchmark problems
This directory contains 5 benchmark problems which are discussed in
the Benchmark section of the LAMMPS documentation, and on the
Benchmark page of the LAMMPS WWW site (lammps.sandia.gov/bench).
Benchmark page of the LAMMPS WWW site (https://www.lammps.org/bench.html).
This directory also has several sub-directories:
@ -11,7 +11,7 @@ KEPLER benchmark scripts for GPU cluster with Kepler GPUs
POTENTIALS benchmarks scripts for various potentials in LAMMPS
The results for all of these benchmarks are displayed and discussed on
the Benchmark page of the LAMMPS WWW site: lammps.sandia.gov/bench.
the Benchmark page of the LAMMPS WWW site: https://www.lammps.org/bench.html
The remainder of this file refers to the 5 problems in the top-level
of this directory and how to run them on CPUs, either in serial or

10
cmake/.coveragerc.in Normal file
View File

@ -0,0 +1,10 @@
[run]
source = @LAMMPS_PYTHON_DIR@
parallel=True
branch=True
omit=*/install.py
*/setup.py
[paths]
sources = python
@LAMMPS_PYTHON_DIR@

299
cmake/CMakeLists.txt
View File

@ -7,6 +7,11 @@ cmake_minimum_required(VERSION 3.10)
if(POLICY CMP0074)
cmake_policy(SET CMP0074 NEW)
endif()
# set policy to silence warnings about missing executable permissions in
# pythonx.y-config when cross-compiling. review occasionally if it may be set to NEW
if(POLICY CMP0109)
cmake_policy(SET CMP0109 OLD)
endif()
########################################
project(lammps CXX)
@ -31,7 +36,11 @@ 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)
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (NOT CMAKE_CROSSCOMPILING))
set(CMAKE_INSTALL_PREFIX "$ENV{USERPROFILE}/LAMMPS" CACHE PATH "Default install path" FORCE)
else()
set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE)
endif()
endif()
# If enabled, no need to use LD_LIBRARY_PATH / DYLD_LIBRARY_PATH when installed
@ -72,19 +81,46 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
include(CheckIncludeFileCXX)
# set required compiler flags and compiler/CPU arch specific optimizations
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /Qrestrict")
endif()
if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
set(CMAKE_TUNE_DEFAULT "/QxCOMMON-AVX512")
else()
set(CMAKE_TUNE_DEFAULT "/QxHost")
endif()
else()
set(CMAKE_TUNE_DEFAULT "-xHost")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
else()
set(CMAKE_TUNE_DEFAULT "-xHost")
endif()
endif()
endif()
# we require C++11 without extensions
# we require C++11 without extensions. Kokkos requires at least C++14 (currently)
set(CMAKE_CXX_STANDARD 11)
if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 14))
set(CMAKE_CXX_STANDARD 14)
endif()
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
# and prints lots of pointless warnings about "unsafe" functions
if(MSVC)
add_compile_options(/Zc:__cplusplus)
add_compile_options(/wd4244)
add_compile_options(/wd4267)
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
# export all symbols when building a .dll file on windows
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND BUILD_SHARED_LIBS)
set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
endif()
########################################################################
# User input options #
@ -97,18 +133,27 @@ endif()
set(LAMMPS_BINARY lmp${LAMMPS_MACHINE})
option(BUILD_SHARED_LIBS "Build shared library" OFF)
if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
endif()
option(CMAKE_POSITION_INDEPENDENT_CODE "Create object compatible with shared libraries" ON)
option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
option(BUILD_LAMMPS_SHELL "Build and install the LAMMPS shell" OFF)
# allow enabling clang-tidy for C++ files
set(ENABLE_CLANG_TIDY OFF CACHE BOOL "Include clang-tidy processing when compiling")
if(ENABLE_CLANG_TIDY)
set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=*-header-filter=.*" CACHE STRING "")
endif()
include(GNUInstallDirs)
file(GLOB ALL_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
file(GLOB MAIN_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})
add_library(lammps ${ALL_SOURCES})
# tell CMake to export all symbols to a .dll on Windows with MinGW cross-compilers
if(BUILD_SHARED_LIBS AND (CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
set_target_properties(lammps PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols")
endif()
add_executable(lmp ${MAIN_SOURCES})
target_link_libraries(lmp PRIVATE lammps)
set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})
@ -116,17 +161,92 @@ install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS
PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE USER-BROWNIAN)
set(STANDARD_PACKAGES
ADIOS
ASPHERE
ATC
AWPMD
BOCS
BODY
BROWNIAN
CG-DNA
CG-SDK
CLASS2
COLLOID
COLVARS
COMPRESS
DIELECTRIC
DIFFRACTION
DIPOLE
DPD-BASIC
DPD-MESO
DPD-REACT
DPD-SMOOTH
DRUDE
EFF
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
EXTRA-MOLECULE
EXTRA-PAIR
FEP
GRANULAR
H5MD
INTERLAYER
KIM
KSPACE
LATBOLTZ
LATTE
MACHDYN
MANIFOLD
MANYBODY
MC
MDI
MEAM
MESONT
MESSAGE
MGPT
MISC
ML-HDNNP
ML-IAP
ML-PACE
ML-QUIP
ML-RANN
ML-SNAP
MOFFF
MOLECULE
MOLFILE
MPIIO
MSCG
NETCDF
ORIENT
PERI
PHONON
PLUGIN
PLUMED
POEMS
PTM
PYTHON
QEQ
QMMM
QTB
REACTION
REAXFF
REPLICA
RIGID
SCAFACOS
SHOCK
SMTBQ
SPH
SPIN
SRD
TALLY
UEF
VORONOI
VTK
YAFF)
set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP)
set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT INTEL OPENMP)
foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
option(PKG_${PKG} "Build ${PKG} Package" OFF)
@ -137,7 +257,7 @@ endforeach()
######################################################
target_include_directories(lammps PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}>)
if(PKG_USER-ADIOS)
if(PKG_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
@ -147,7 +267,6 @@ if(PKG_USER-ADIOS)
endif()
if(NOT CMAKE_CROSSCOMPILING)
set(MPI_CXX_SKIP_MPICXX TRUE)
find_package(MPI QUIET)
option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
else()
@ -155,8 +274,11 @@ else()
endif()
if(BUILD_MPI)
# do not include the (obsolete) MPI C++ bindings which makes
# for leaner object files and avoids namespace conflicts
set(MPI_CXX_SKIP_MPICXX TRUE)
# We use a non-standard procedure to cross-compile with MPI on Windows
if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
include(MPI4WIN)
target_link_libraries(lammps PUBLIC MPI::MPI_CXX)
else()
@ -174,9 +296,16 @@ else()
target_include_directories(mpi_stubs PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
if(BUILD_SHARED_LIBS)
target_link_libraries(lammps PRIVATE mpi_stubs)
if(MSVC)
target_link_libraries(lmp PRIVATE mpi_stubs)
target_include_directories(lmp INTERFACE $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
target_compile_definitions(lmp INTERFACE $<INSTALL_INTERFACE:LAMMPS_LIB_NO_MPI>)
endif()
target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
target_compile_definitions(lammps INTERFACE $<INSTALL_INTERFACE:LAMMPS_LIB_NO_MPI>)
else()
target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
target_compile_definitions(lammps INTERFACE $<INSTALL_INTERFACE:LAMMPS_LIB_NO_MPI>)
target_link_libraries(lammps PUBLIC mpi_stubs)
endif()
add_library(MPI::MPI_CXX ALIAS mpi_stubs)
@ -190,7 +319,7 @@ string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
target_compile_definitions(lammps PUBLIC -DLAMMPS_${LAMMPS_SIZES})
# posix_memalign is not available on Windows
if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
set(LAMMPS_MEMALIGN "0" CACHE STRING "posix_memalign() is not available on Windows" FORCE)
else()
set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS. Set to 0 to disable")
@ -206,12 +335,16 @@ endif()
# "hard" dependencies between packages resulting
# in an error instead of skipping over files
pkg_depends(MLIAP SNAP)
pkg_depends(ML-IAP ML-SNAP)
pkg_depends(MPIIO MPI)
pkg_depends(USER-ATC MANYBODY)
pkg_depends(USER-LB MPI)
pkg_depends(USER-PHONON KSPACE)
pkg_depends(USER-SCAFACOS MPI)
pkg_depends(ATC MANYBODY)
pkg_depends(LATBOLTZ MPI)
pkg_depends(PHONON KSPACE)
pkg_depends(SCAFACOS MPI)
pkg_depends(DIELECTRIC KSPACE)
pkg_depends(DIELECTRIC EXTRA-PAIR)
pkg_depends(CG-DNA MOLECULE)
pkg_depends(CG-DNA ASPHERE)
# detect if we may enable OpenMP support by default
set(BUILD_OMP_DEFAULT OFF)
@ -232,8 +365,10 @@ if(BUILD_OMP)
message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
endif()
if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR
(CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR
if(((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR
(CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR (CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR
(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM") OR (CMAKE_CXX_COMPILER_ID STREQUAL "XLClang") OR
((CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
# GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
@ -245,7 +380,7 @@ if(BUILD_OMP)
target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
endif()
if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE)
enable_language(C)
find_package(LAPACK)
find_package(BLAS)
@ -265,6 +400,8 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
endif()
endif()
# tweak jpeg library names to avoid linker errors with MinGW cross-compilation
set(JPEG_NAMES libjpeg libjpeg-62)
find_package(JPEG QUIET)
option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND})
if(WITH_JPEG)
@ -296,7 +433,7 @@ find_program(GZIP_EXECUTABLE gzip)
find_package_handle_standard_args(GZIP REQUIRED_VARS GZIP_EXECUTABLE)
option(WITH_GZIP "Enable GZIP support" ${GZIP_FOUND})
if(WITH_GZIP)
if(GZIP_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING))
if(GZIP_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING))
target_compile_definitions(lammps PRIVATE -DLAMMPS_GZIP)
else()
message(FATAL_ERROR "gzip executable not found")
@ -307,7 +444,7 @@ find_program(FFMPEG_EXECUTABLE ffmpeg)
find_package_handle_standard_args(FFMPEG REQUIRED_VARS FFMPEG_EXECUTABLE)
option(WITH_FFMPEG "Enable FFMPEG support" ${FFMPEG_FOUND})
if(WITH_FFMPEG)
if(FFMPEG_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING))
if(FFMPEG_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING))
target_compile_definitions(lammps PRIVATE -DLAMMPS_FFMPEG)
else()
message(FATAL_ERROR "ffmpeg executable not found")
@ -324,10 +461,10 @@ else()
set(CUDA_REQUEST_PIC)
endif()
foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MDI USER-MOLFILE USER-NETCDF USER-PLUMED
USER-QMMM USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE)
foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM LATTE MESSAGE MSCG COMPRESS ML-PACE)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()
endforeach()
@ -353,9 +490,12 @@ foreach(HEADER cmath)
endif(NOT FOUND_${HEADER})
endforeach(HEADER)
set(MATH_LIBRARIES "m" CACHE STRING "math library")
mark_as_advanced( MATH_LIBRARIES )
target_link_libraries(lammps PRIVATE ${MATH_LIBRARIES})
# make the standard math library overrideable and autodetected (for systems that don't have it)
find_library(STANDARD_MATH_LIB m DOC "Standard Math library")
mark_as_advanced(STANDARD_MATH_LIB)
if(STANDARD_MATH_LIB)
target_link_libraries(lammps PRIVATE ${STANDARD_MATH_LIB})
endif()
######################################
# Generate Basic Style files
@ -418,11 +558,10 @@ endforeach()
##############################################
# add lib sources of (simple) enabled packages
############################################
foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT)
if(PKG_${SIMPLE_LIB})
string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
foreach(PKG_LIB POEMS ATC AWPMD H5MD MESONT)
if(PKG_${PKG_LIB})
string(TOLOWER "${PKG_LIB}" PKG_LIB)
if(PKG_LIB STREQUAL mesont)
if(PKG_LIB STREQUAL "mesont")
enable_language(Fortran)
file(GLOB_RECURSE ${PKG_LIB}_SOURCES
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.f90)
@ -434,9 +573,9 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT)
add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE})
target_link_libraries(lammps PRIVATE ${PKG_LIB})
if(PKG_LIB STREQUAL awpmd)
if(PKG_LIB STREQUAL "awpmd")
target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include)
elseif(PKG_LIB STREQUAL h5md)
elseif(PKG_LIB STREQUAL "h5md")
target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include ${HDF5_INCLUDE_DIRS})
else()
target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB})
@ -444,13 +583,13 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT)
endif()
endforeach()
if(PKG_USER-AWPMD)
if(PKG_AWPMD)
target_link_libraries(awpmd PRIVATE ${LAPACK_LIBRARIES})
endif()
if(PKG_USER-ATC)
if(LAMMPS_SIZES STREQUAL BIGBIG)
message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG")
if(PKG_ATC)
if(LAMMPS_SIZES STREQUAL "BIGBIG")
message(FATAL_ERROR "The ATC Package is not compatible with -DLAMMPS_BIGBIG")
endif()
target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES})
if(BUILD_MPI)
@ -462,30 +601,27 @@ if(PKG_USER-ATC)
target_compile_definitions(atc PRIVATE -DLAMMPS_${LAMMPS_SIZES})
endif()
if(PKG_USER-H5MD)
include(Packages/USER-H5MD)
if(PKG_H5MD)
include(Packages/H5MD)
endif()
######################################################################
# packages which selectively include variants based on enabled styles
# e.g. accelerator packages
######################################################################
foreach(PKG_WITH_INCL CORESHELL QEQ USER-OMP USER-SDPD KOKKOS OPT USER-INTEL GPU)
foreach(PKG_WITH_INCL CORESHELL QEQ OPENMP DPD-SMOOTH KOKKOS OPT INTEL GPU)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()
endforeach()
if(PKG_PLUGIN)
if(BUILD_SHARED_LIBS)
target_compile_definitions(lammps PRIVATE -DLMP_PLUGIN)
else()
message(WARNING "Plugin loading will not work unless BUILD_SHARED_LIBS is enabled")
endif()
# link with -ldl or equivalent for plugin loading; except on Windows
if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
target_link_libraries(lammps PRIVATE ${CMAKE_DL_LIBS})
endif()
target_compile_definitions(lammps PRIVATE -DLMP_PLUGIN)
endif()
# link with -ldl or equivalent for plugin loading; except on Windows
if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
target_link_libraries(lammps PRIVATE ${CMAKE_DL_LIBS})
endif()
######################################################################
@ -493,8 +629,8 @@ endif()
# and the MPI library - if use - has to be linked right before those
# and after everything else that is compiled locally
######################################################################
if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
target_link_libraries(lammps PRIVATE -lwsock32 -lpsapi)
if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
target_link_libraries(lammps PRIVATE "wsock32;psapi")
endif()
######################################################
@ -542,8 +678,8 @@ add_dependencies(lammps gitversion)
# Actually add executable and lib to build
############################################
get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
list (FIND LANGUAGES "Fortran" _index)
if(${_index} GREATER -1)
list(FIND LANGUAGES "Fortran" _index)
if(_index GREATER -1)
target_link_libraries(lammps PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
endif()
set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h compute.h dihedral.h domain.h error.h fix.h force.h group.h improper.h
@ -621,7 +757,7 @@ if(BUILD_SHARED_LIBS)
else()
find_package(Python COMPONENTS Interpreter)
endif()
if (Python_EXECUTABLE)
if(Python_EXECUTABLE)
add_custom_target(
install-python ${CMAKE_COMMAND} -E remove_directory build
COMMAND ${Python_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
@ -654,7 +790,7 @@ if(BUILD_SHARED_LIBS OR PKG_PYTHON)
else()
find_package(Python COMPONENTS Interpreter)
endif()
if (Python_EXECUTABLE)
if(Python_EXECUTABLE)
file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python)
install(CODE "execute_process(COMMAND ${Python_EXECUTABLE} setup.py build -b ${CMAKE_BINARY_DIR}/python install --prefix=${CMAKE_INSTALL_PREFIX} --root=\$ENV{DESTDIR}/ WORKING_DIRECTORY ${LAMMPS_PYTHON_DIR})")
endif()
@ -663,13 +799,26 @@ endif()
include(Testing)
include(CodeCoverage)
include(CodingStandard)
find_package(ClangFormat 8.0)
if(ClangFormat_FOUND)
add_custom_target(format-src
COMMAND ${ClangFormat_EXECUTABLE} --verbose -i -style=file *.cpp *.h */*.cpp */*.h
WORKING_DIRECTORY ${LAMMPS_SOURCE_DIR})
endif()
get_target_property(DEFINES lammps COMPILE_DEFINITIONS)
get_property(BUILD_IS_MULTI_CONFIG GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
if(BUILD_IS_MULTI_CONFIG)
set(LAMMPS_BUILD_TYPE "Multi-Config")
else()
set(LAMMPS_BUILD_TYPE ${CMAKE_BUILD_TYPE})
endif()
include(FeatureSummary)
feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND)
message(STATUS "<<< Build configuration >>>
Operating System: ${CMAKE_SYSTEM_NAME} ${CMAKE_LINUX_DISTRO} ${CMAKE_DISTRO_VERSION}
Build type: ${CMAKE_BUILD_TYPE}
Build type: ${LAMMPS_BUILD_TYPE}
Install path: ${CMAKE_INSTALL_PREFIX}
Generator: ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}")
###############################################################################
@ -699,15 +848,15 @@ if(OPTIONS)
message(" Options: ${OPTIONS}")
endif()
get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
list (FIND LANGUAGES "Fortran" _index)
if(${_index} GREATER -1)
list(FIND LANGUAGES "Fortran" _index)
if(_index GREATER -1)
message(STATUS "Fortran Compiler: ${CMAKE_Fortran_COMPILER}
Type: ${CMAKE_Fortran_COMPILER_ID}
Version: ${CMAKE_Fortran_COMPILER_VERSION}
Fortran Flags:${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}")
endif()
list (FIND LANGUAGES "C" _index)
if(${_index} GREATER -1)
list(FIND LANGUAGES "C" _index)
if(_index GREATER -1)
message(STATUS "C compiler: ${CMAKE_C_COMPILER}
Type: ${CMAKE_C_COMPILER_ID}
Version: ${CMAKE_C_COMPILER_VERSION}
@ -772,7 +921,7 @@ if(PKG_KSPACE)
endif()
if(PKG_KOKKOS)
if(Kokkos_ENABLE_CUDA)
if (${FFT} STREQUAL "KISS")
if(FFT STREQUAL "KISS")
message(STATUS "Kokkos FFT: KISS")
else()
message(STATUS "Kokkos FFT: cuFFT")

111
cmake/CMakeSettings.json Normal file
View File

@ -0,0 +1,111 @@
{
"configurations": [
{
"name": "x64-Debug-MSVC",
"generator": "Ninja",
"configurationType": "Debug",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-S ${workspaceRoot}\\cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DENABLE_TESTING=on",
"buildCommandArgs": "",
"ctestCommandArgs": "",
"inheritEnvironments": [ "msvc_x64_x64" ],
"variables": [
{
"name": "BUILD_SHARED_LIBS",
"value": "True",
"type": "BOOL"
},
{
"name": "BUILD_TOOLS",
"value": "True",
"type": "BOOL"
},
{
"name": "LAMMPS_EXCEPTIONS",
"value": "True",
"type": "BOOL"
}
]
},
{
"name": "x64-Debug-Clang",
"generator": "Ninja",
"configurationType": "Debug",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-S ${workspaceRoot}\\cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DENABLE_TESTING=on",
"buildCommandArgs": "",
"ctestCommandArgs": "",
"inheritEnvironments": [ "clang_cl_x64" ],
"variables": [
{
"name": "BUILD_TOOLS",
"value": "True",
"type": "BOOL"
},
{
"name": "LAMMPS_EXCEPTIONS",
"value": "True",
"type": "BOOL"
}
]
},
{
"name": "x64-Debug-OneAPI",
"generator": "Ninja",
"configurationType": "Debug",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-S ${workspaceRoot}\\cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DENABLE_TESTING=on -DCMAKE_CXX_COMPILER=icx -DCMAKE_C_COMPILER=icx -DBUILD_MPI=off",
"buildCommandArgs": "",
"ctestCommandArgs": "",
"inheritEnvironments": [ "msvc_x64_x64" ],
"variables": [
{
"name": "BUILD_SHARED_LIBS",
"value": "True",
"type": "BOOL"
},
{
"name": "BUILD_TOOLS",
"value": "True",
"type": "BOOL"
},
{
"name": "LAMMPS_EXCEPTIONS",
"value": "True",
"type": "BOOL"
}
]
},
{
"name": "x64-Debug-Intel",
"generator": "Ninja",
"configurationType": "Debug",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-S ${workspaceRoot}\\cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DENABLE_TESTING=off -DCMAKE_CXX_COMPILER=icl -DCMAKE_C_COMPILER=icl -DCMAKE_Fortran_COMPILER=ifort -DBUILD_MPI=off",
"buildCommandArgs": "",
"ctestCommandArgs": "",
"inheritEnvironments": [ "msvc_x64_x64" ],
"variables": [
{
"name": "BUILD_SHARED_LIBS",
"value": "True",
"type": "BOOL"
},
{
"name": "BUILD_TOOLS",
"value": "True",
"type": "BOOL"
},
{
"name": "LAMMPS_EXCEPTIONS",
"value": "True",
"type": "BOOL"
}
]
}
]
}

10
cmake/Modules/CodeCoverage.cmake
View File

@ -54,6 +54,8 @@ if(ENABLE_COVERAGE)
if(COVERAGE_FOUND)
set(PYTHON_COVERAGE_HTML_DIR ${CMAKE_BINARY_DIR}/python_coverage_html)
configure_file(.coveragerc.in ${CMAKE_BINARY_DIR}/.coveragerc @ONLY)
add_custom_command(
OUTPUT ${CMAKE_BINARY_DIR}/unittest/python/.coverage
COMMAND ${COVERAGE_BINARY} combine
@ -63,16 +65,16 @@ if(ENABLE_COVERAGE)
add_custom_target(
gen_python_coverage_html
COMMAND ${COVERAGE_BINARY} html -d ${PYTHON_COVERAGE_HTML_DIR}
DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage
COMMAND ${COVERAGE_BINARY} html --rcfile=${CMAKE_BINARY_DIR}/.coveragerc -d ${PYTHON_COVERAGE_HTML_DIR}
DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage ${CMAKE_BINARY_DIR}/.coveragerc
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
COMMENT "Generating HTML Python coverage report..."
)
add_custom_target(
gen_python_coverage_xml
COMMAND ${COVERAGE_BINARY} xml -o ${CMAKE_BINARY_DIR}/python_coverage.xml
DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage
COMMAND ${COVERAGE_BINARY} xml --rcfile=${CMAKE_BINARY_DIR}/.coveragerc -o ${CMAKE_BINARY_DIR}/python_coverage.xml
DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage ${CMAKE_BINARY_DIR}/.coveragerc
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
COMMENT "Generating XML Python coverage report..."
)

10
cmake/Modules/CodingStandard.cmake
View File

@ -15,6 +15,11 @@ if(Python3_EXECUTABLE)
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Check for whitespace errors")
add_custom_target(
check-homepage
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Check for homepage URL errors")
add_custom_target(
check-permissions
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py .
@ -25,6 +30,11 @@ if(Python3_EXECUTABLE)
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py -f .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix whitespace errors")
add_custom_target(
fix-homepage
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py -f .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix homepage URL errors")
add_custom_target(
fix-permissions
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py -f .

33
cmake/Modules/ExternalCMakeProject.cmake Normal file
View File

@ -0,0 +1,33 @@
# Build a CMake based external library as subdirectory.
# The sources will be unpacked to ${CMAKE_BINARY_DIR}/_deps/${target}-src
# The binaries will be built in ${CMAKE_BINARY_DIR}/_deps/${target}-build
#
function(ExternalCMakeProject target url hash basedir cmakedir cmakefile)
# change settings locally
set(BUILD_SHARED_LIBS OFF)
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
get_filename_component(archive ${url} NAME)
file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/_deps/src)
message(STATUS "Downloading ${url}")
file(DOWNLOAD ${url} ${CMAKE_BINARY_DIR}/_deps/${archive} EXPECTED_HASH MD5=${hash} SHOW_PROGRESS)
message(STATUS "Unpacking and configuring ${archive}")
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf ${CMAKE_BINARY_DIR}/_deps/${archive}
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/_deps/src)
file(GLOB TARGET_SOURCE "${CMAKE_BINARY_DIR}/_deps/src/${basedir}*")
list(LENGTH TARGET_SOURCE _num)
if(_num GREATER 1)
message(FATAL_ERROR "Inconsistent ${target} library sources. "
"Please delete ${CMAKE_BINARY_DIR}/_deps/src and re-run cmake")
endif()
file(REMOVE_RECURSE ${CMAKE_BINARY_DIR}/_deps/${target}-src)
file(RENAME ${TARGET_SOURCE} ${CMAKE_BINARY_DIR}/_deps/${target}-src)
if(NOT (cmakefile STREQUAL ""))
file(COPY ${cmakefile} DESTINATION ${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}/)
get_filename_component(_cmakefile ${cmakefile} NAME)
file(RENAME "${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}/${_cmakefile}"
"${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}/CMakeLists.txt")
endif()
add_subdirectory("${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}"
"${CMAKE_BINARY_DIR}/_deps/${target}-build")
endfunction(ExternalCMakeProject)

2
cmake/Modules/FindFFTW3.cmake
View File

@ -38,7 +38,7 @@ if(FFTW3_FOUND)
add_library(FFTW3::FFTW3_OMP UNKNOWN IMPORTED)
set_target_properties(FFTW3::FFTW3_OMP PROPERTIES
IMPORTED_LINK_INTERFACE_LANGUAGES "C"
IMPORTED_LOCATION "${FFTW3_OMP_LIBRARY}"
IMPORTED_LOCATION "${FFTW3_OMP_LIBRARY}"
INTERFACE_INCLUDE_DIRECTORIES "${FFTW3_INCLUDE_DIRS}")
endif()
endif()

2
cmake/Modules/FindFFTW3F.cmake
View File

@ -37,7 +37,7 @@ if(FFTW3F_FOUND)
add_library(FFTW3F::FFTW3F_OMP UNKNOWN IMPORTED)
set_target_properties(FFTW3F::FFTW3F_OMP PROPERTIES
IMPORTED_LINK_INTERFACE_LANGUAGES "C"
IMPORTED_LOCATION "${FFTW3F_OMP_LIBRARY}"
IMPORTED_LOCATION "${FFTW3F_OMP_LIBRARY}"
INTERFACE_INCLUDE_DIRECTORIES "${FFTW3F_INCLUDE_DIRS}")
endif()
endif()

61
cmake/Modules/FindN2P2.cmake Normal file
View File

@ -0,0 +1,61 @@
include(FindPackageHandleStandardArgs)
# Check if N2P2_DIR is set manually.
if (DEFINED ENV{N2P2_DIR})
set(N2P2_DIR "${N2P2_DIR}")
# If not, try if directory "lib/hdnnp/n2p2" exists.
else()
get_filename_component(_fullpath "${LAMMPS_LIB_SOURCE_DIR}/hdnnp/n2p2" REALPATH)
if (EXISTS ${_fullpath})
set(N2P2_DIR "${_fullpath}")
endif()
endif()
# Set path to include directory.
find_path(N2P2_INCLUDE_DIR InterfaceLammps.h HINTS "${N2P2_DIR}/include")
# Two libraries need to be linked: libnnp and libnnpif.
find_library(N2P2_LIBNNP NAMES nnp HINTS "${N2P2_DIR}/lib")
find_library(N2P2_LIBNNPIF NAMES nnpif HINTS "${N2P2_DIR}/lib")
# Users could compile n2p2 with extra flags which are then also required for
# pair_hdnnp.cpp compilation. To forward them to the LAMMPS build process n2p2
# writes a file with cmake commands, e.g.
#
# target_compile_definitions(lammps PRIVATE -DN2P2_NO_SF_GROUPS)
#
# to "lib/lammps-extra.cmake" which is then included by ML-HDNNP.cmake.
find_file(N2P2_CMAKE_EXTRA NAMES lammps-extra.cmake HINTS "${N2P2_DIR}/lib")
find_package_handle_standard_args(N2P2 DEFAULT_MSG
N2P2_DIR
N2P2_INCLUDE_DIR
N2P2_LIBNNP
N2P2_LIBNNPIF
N2P2_CMAKE_EXTRA)
if(N2P2_FOUND)
if (NOT TARGET N2P2::N2P2)
# n2p2 core library "libnnp"
add_library(N2P2::LIBNNP UNKNOWN IMPORTED)
set_target_properties(N2P2::LIBNNP PROPERTIES
INTERFACE_INCLUDE_DIRECTORIES ${N2P2_INCLUDE_DIR}
IMPORTED_LOCATION ${N2P2_LIBNNP})
# n2p2 interface library "libnnpif"
add_library(N2P2::LIBNNPIF UNKNOWN IMPORTED)
set_target_properties(N2P2::LIBNNPIF PROPERTIES
INTERFACE_INCLUDE_DIRECTORIES ${N2P2_INCLUDE_DIR}
IMPORTED_LOCATION ${N2P2_LIBNNPIF})
# Put libnnp, libnnpif and include directory together.
add_library(N2P2::N2P2 INTERFACE IMPORTED)
set_property(TARGET N2P2::N2P2 PROPERTY
INTERFACE_LINK_LIBRARIES N2P2::LIBNNPIF N2P2::LIBNNP)
set(N2P2_CMAKE_EXTRAS ${N2P2_CMAKE_EXTRA})
endif()
endif()
mark_as_advanced(
N2P2_DIR
N2P2_INCLUDE_DIR
N2P2_LIBNNP
N2P2_LIBNNPIF
N2P2_CMAKE_EXTRA
)

81
cmake/Modules/GTest.cmake
View File

@ -1,81 +0,0 @@
message(STATUS "Downloading and building Google Test library")
if(CMAKE_BUILD_TYPE STREQUAL Debug)
set(GTEST_LIB_POSTFIX d)
else()
set(GTEST_LIB_POSTFIX)
endif()
include(ExternalProject)
set(GTEST_URL "https://github.com/google/googletest/archive/release-1.10.0.tar.gz" CACHE STRING "URL for GTest tarball")
set(GTEST_MD5 "ecd1fa65e7de707cd5c00bdac56022cd" CACHE STRING "MD5 checksum of GTest tarball")
mark_as_advanced(GTEST_URL)
mark_as_advanced(GTEST_MD5)
ExternalProject_Add(googletest
URL ${GTEST_URL}
URL_MD5 ${GTEST_MD5}
SOURCE_DIR "${CMAKE_BINARY_DIR}/gtest-src"
BINARY_DIR "${CMAKE_BINARY_DIR}/gtest-build"
CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_GTEST_OPTS}
-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
BUILD_BYPRODUCTS <BINARY_DIR>/lib/libgtest${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
<BINARY_DIR>/lib/libgmock${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
<BINARY_DIR>/lib/libgtest_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
<BINARY_DIR>/lib/libgmock_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
LOG_DOWNLOAD ON
LOG_CONFIGURE ON
LOG_BUILD ON
INSTALL_COMMAND ""
TEST_COMMAND "")
ExternalProject_Get_Property(googletest SOURCE_DIR)
set(GTEST_INCLUDE_DIR ${SOURCE_DIR}/googletest/include)
set(GMOCK_INCLUDE_DIR ${SOURCE_DIR}/googlemock/include)
# workaround for CMake 3.10 on ubuntu 18.04
file(MAKE_DIRECTORY ${GTEST_INCLUDE_DIR})
file(MAKE_DIRECTORY ${GMOCK_INCLUDE_DIR})
ExternalProject_Get_Property(googletest BINARY_DIR)
set(GTEST_LIBRARY_PATH ${BINARY_DIR}/lib/libgtest${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
set(GMOCK_LIBRARY_PATH ${BINARY_DIR}/lib/libgmock${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
set(GTEST_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/libgtest_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
set(GMOCK_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/libgmock_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
# Prevent GoogleTest from overriding our compiler/linker options
# when building with Visual Studio
set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
find_package(Threads QUIET)
add_library(GTest::GTest UNKNOWN IMPORTED)
set_target_properties(GTest::GTest PROPERTIES
IMPORTED_LOCATION ${GTEST_LIBRARY_PATH}
INTERFACE_INCLUDE_DIRECTORIES ${GTEST_INCLUDE_DIR}
INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
add_dependencies(GTest::GTest googletest)
add_library(GTest::GMock UNKNOWN IMPORTED)
set_target_properties(GTest::GMock PROPERTIES
IMPORTED_LOCATION ${GMOCK_LIBRARY_PATH}
INTERFACE_INCLUDE_DIRECTORIES ${GMOCK_INCLUDE_DIR}
INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
add_dependencies(GTest::GMock googletest)
add_library(GTest::GTestMain UNKNOWN IMPORTED)
set_target_properties(GTest::GTestMain PROPERTIES
IMPORTED_LOCATION ${GTEST_MAIN_LIBRARY_PATH}
INTERFACE_INCLUDE_DIRECTORIES ${GTEST_INCLUDE_DIR}
INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
add_dependencies(GTest::GTestMain googletest)
add_library(GTest::GMockMain UNKNOWN IMPORTED)
set_target_properties(GTest::GMockMain PROPERTIES
IMPORTED_LOCATION ${GMOCK_MAIN_LIBRARY_PATH}
INTERFACE_INCLUDE_DIRECTORIES ${GMOCK_INCLUDE_DIR}
INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
add_dependencies(GTest::GMockMain googletest)

6
cmake/Modules/LAMMPSUtils.cmake
View File

@ -67,7 +67,7 @@ endfunction()
macro(pkg_depends PKG1 PKG2)
if(PKG_${PKG1} AND NOT (PKG_${PKG2} OR BUILD_${PKG2}))
message(FATAL_ERROR "${PKG1} package needs LAMMPS to be build with ${PKG2}")
message(FATAL_ERROR "The ${PKG1} package needs LAMMPS to be build with the ${PKG2} package")
endif()
endmacro()
@ -85,7 +85,7 @@ endfunction(GenerateBinaryHeader)
# fetch missing potential files
function(FetchPotentials pkgfolder potfolder)
if (EXISTS "${pkgfolder}/potentials.txt")
if(EXISTS "${pkgfolder}/potentials.txt")
file(STRINGS "${pkgfolder}/potentials.txt" linelist REGEX "^[^#].")
foreach(line ${linelist})
string(FIND ${line} " " blank)
@ -106,7 +106,7 @@ function(FetchPotentials pkgfolder potfolder)
endfunction(FetchPotentials)
# set CMAKE_LINUX_DISTRO and CMAKE_DISTRO_VERSION on Linux
if((CMAKE_SYSTEM_NAME STREQUAL Linux) AND (EXISTS /etc/os-release))
if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (EXISTS /etc/os-release))
file(STRINGS /etc/os-release distro REGEX "^NAME=")
string(REGEX REPLACE "NAME=\"?([^\"]*)\"?" "\\1" distro "${distro}")
file(STRINGS /etc/os-release disversion REGEX "^VERSION_ID=")

4
cmake/Modules/OpenCLLoader.cmake
View File

@ -1,6 +1,6 @@
message(STATUS "Downloading and building OpenCL loader library")
set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.05.02.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "29180b05056578afda92f0d394c3a373" CACHE STRING "MD5 checksum of OpenCL loader tarball")
set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.09.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "3b3882627964bd02e5c3b02065daac3c" CACHE STRING "MD5 checksum of OpenCL loader tarball")
mark_as_advanced(OPENCL_LOADER_URL)
mark_as_advanced(OPENCL_LOADER_MD5)

0
cmake/Modules/Packages/USER-COLVARS.cmake → cmake/Modules/Packages/COLVARS.cmake
View File

8
cmake/Modules/Packages/USER-SDPD.cmake → cmake/Modules/Packages/DPD-SMOOTH.cmake
View File

@ -1,13 +1,13 @@
# Fix rigid/meso requires RIGID to be installed
set(USER-SDPD_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-SDPD)
set(DPD-SMOOTH_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/DPD-SMOOTH)
get_property(hlist GLOBAL PROPERTY FIX)
if(NOT PKG_RIGID)
list(REMOVE_ITEM hlist ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.h)
list(REMOVE_ITEM hlist ${DPD-SMOOTH_SOURCES_DIR}/fix_rigid_meso.h)
get_target_property(LAMMPS_SOURCES lammps SOURCES)
list(REMOVE_ITEM LAMMPS_SOURCES ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.cpp)
list(REMOVE_ITEM LAMMPS_SOURCES ${DPD-SMOOTH_SOURCES_DIR}/fix_rigid_meso.cpp)
set_property(TARGET lammps PROPERTY SOURCES ${LAMMPS_SOURCES})
endif()
set_property(GLOBAL PROPERTY FIX "${hlist}")
target_include_directories(lammps PRIVATE ${USER-SDPD_SOURCES_DIR})
target_include_directories(lammps PRIVATE ${DPD-SMOOTH_SOURCES_DIR})

102
cmake/Modules/Packages/GPU.cmake
View File

@ -48,7 +48,7 @@ if(GPU_API STREQUAL "CUDA")
# ensure that no *cubin.h files exist from a compile in the lib/gpu folder
file(GLOB GPU_LIB_OLD_CUBIN_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h)
if (GPU_LIB_OLD_CUBIN_HEADERS)
if(GPU_LIB_OLD_CUBIN_HEADERS)
message(FATAL_ERROR "########################################################################\n"
"Found file(s) generated by the make-based build system in lib/gpu\n"
"Please run\n"
@ -71,44 +71,47 @@ if(GPU_API STREQUAL "CUDA")
# build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH}")
# Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
if((CUDA_VERSION VERSION_GREATER_EQUAL "3.2") AND (CUDA_VERSION VERSION_LESS "9.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_20,code=[sm_20,compute_20] ")
endif()
# Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] ")
endif()
# Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_35,code=[sm_35,compute_35]")
endif()
# Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")
endif()
# Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "8.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")
endif()
# Volta (GPU Arch 7.0) is supported by CUDA 9 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")
endif()
# Turing (GPU Arch 7.5) is supported by CUDA 10 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
endif()
# Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
endif()
# Ampere (GPU Arch 8.6) is supported by CUDA 11.1 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
endif()
# apply the following to build "fat" CUDA binaries only for known CUDA toolkits
if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
message(WARNING "Unsupported CUDA version. Use at your own risk.")
message(WARNING "Untested CUDA Toolkit version. Use at your own risk")
else()
# Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
if((CUDA_VERSION VERSION_GREATER_EQUAL "3.2") AND (CUDA_VERSION VERSION_LESS "9.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_20,code=[sm_20,compute_20] ")
endif()
# Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] ")
endif()
# Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_35,code=[sm_35,compute_35]")
endif()
# Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")
endif()
# Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "8.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")
endif()
# Volta (GPU Arch 7.0) is supported by CUDA 9 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")
endif()
# Turing (GPU Arch 7.5) is supported by CUDA 10 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
endif()
# Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
endif()
# Ampere (GPU Arch 8.6) is supported by CUDA 11.1 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
endif()
endif()
cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
@ -154,7 +157,7 @@ elseif(GPU_API STREQUAL "OPENCL")
endif()
option(USE_STATIC_OPENCL_LOADER "Download and include a static OpenCL ICD loader" ${_opencl_static_default})
mark_as_advanced(USE_STATIC_OPENCL_LOADER)
if (USE_STATIC_OPENCL_LOADER)
if(USE_STATIC_OPENCL_LOADER)
include(OpenCLLoader)
else()
find_package(OpenCL REQUIRED)
@ -214,13 +217,20 @@ elseif(GPU_API STREQUAL "OPENCL")
elseif(GPU_API STREQUAL "HIP")
if(NOT DEFINED HIP_PATH)
if(NOT DEFINED ENV{HIP_PATH})
set(HIP_PATH "/opt/rocm/hip" CACHE PATH "Path to which HIP has been installed")
set(HIP_PATH "/opt/rocm/hip" CACHE PATH "Path to HIP installation")
else()
set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to which HIP has been installed")
set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to HIP installation")
endif()
endif()
set(CMAKE_MODULE_PATH "${HIP_PATH}/cmake" ${CMAKE_MODULE_PATH})
find_package(HIP REQUIRED)
if(NOT DEFINED ROCM_PATH)
if(NOT DEFINED ENV{ROCM_PATH})
set(ROCM_PATH "/opt/rocm" CACHE PATH "Path to ROCm installation")
else()
set(ROCM_PATH $ENV{ROCM_PATH} CACHE PATH "Path to ROCm installation")
endif()
endif()
list(APPEND CMAKE_PREFIX_PATH ${HIP_PATH} ${ROCM_PATH})
find_package(hip REQUIRED)
option(HIP_USE_DEVICE_SORT "Use GPU sorting" ON)
if(NOT DEFINED HIP_PLATFORM)
@ -322,10 +332,11 @@ elseif(GPU_API STREQUAL "HIP")
set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "${LAMMPS_LIB_BINARY_DIR}/gpu/*_cubin.h ${LAMMPS_LIB_BINARY_DIR}/gpu/*.cu.cpp")
hip_add_library(gpu STATIC ${GPU_LIB_SOURCES})
add_library(gpu STATIC ${GPU_LIB_SOURCES})
target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu)
target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT)
target_compile_definitions(gpu PRIVATE -DUSE_HIP)
target_link_libraries(gpu PRIVATE hip::host)
if(HIP_USE_DEVICE_SORT)
# add hipCUB
@ -374,8 +385,9 @@ elseif(GPU_API STREQUAL "HIP")
endif()
endif()
hip_add_executable(hip_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
add_executable(hip_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
target_compile_definitions(hip_get_devices PRIVATE -DUCL_HIP)
target_link_libraries(hip_get_devices hip::host)
if(HIP_PLATFORM STREQUAL "nvcc")
target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_NVCC__)

0
cmake/Modules/Packages/USER-H5MD.cmake → cmake/Modules/Packages/H5MD.cmake
View File

48
cmake/Modules/Packages/USER-INTEL.cmake → cmake/Modules/Packages/INTEL.cmake
View File

@ -3,9 +3,9 @@ if(NOT FOUND_IMMINTRIN)
message(FATAL_ERROR "immintrin.h header not found, Intel package won't work without it")
endif()
target_compile_definitions(lammps PRIVATE -DLMP_USER_INTEL)
target_compile_definitions(lammps PRIVATE -DLMP_INTEL)
set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)")
set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by INTEL (cpu or knl)")
set(INTEL_ARCH_VALUES cpu knl)
set_property(CACHE INTEL_ARCH PROPERTY STRINGS ${INTEL_ARCH_VALUES})
validate_option(INTEL_ARCH INTEL_ARCH_VALUES)
@ -40,10 +40,10 @@ endif()
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
message(FATAL_ERROR "USER-INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
message(FATAL_ERROR "INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
endif()
else()
message(WARNING "USER-INTEL gives best performance with Intel compilers")
message(WARNING "INTEL gives best performance with Intel compilers")
endif()
find_package(TBB_MALLOC QUIET)
@ -52,7 +52,7 @@ if(TBB_MALLOC_FOUND)
else()
target_compile_definitions(lammps PRIVATE -DLMP_INTEL_NO_TBB)
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
message(WARNING "USER-INTEL with Intel compilers should use TBB malloc libraries")
message(WARNING "INTEL with Intel compilers should use TBB malloc libraries")
endif()
endif()
@ -65,12 +65,12 @@ else()
endif()
if((NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "64") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "128") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "256"))
message(FATAL_ERROR "USER-INTEL only supports memory alignment of 64, 128 or 256 on this platform")
message(FATAL_ERROR "INTEL only supports memory alignment of 64, 128 or 256 on this platform")
endif()
if(INTEL_ARCH STREQUAL "KNL")
if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
message(FATAL_ERROR "Must use Intel compiler with USER-INTEL for KNL architecture")
message(FATAL_ERROR "Must use Intel compiler with INTEL for KNL architecture")
endif()
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload")
set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"")
@ -91,26 +91,26 @@ else()
endif()
# collect sources
set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/fix_intel.cpp
${USER-INTEL_SOURCES_DIR}/fix_nh_intel.cpp
${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp
${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp
${USER-INTEL_SOURCES_DIR}/npair_intel.cpp)
set(INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/INTEL)
set(INTEL_SOURCES ${INTEL_SOURCES_DIR}/fix_intel.cpp
${INTEL_SOURCES_DIR}/fix_nh_intel.cpp
${INTEL_SOURCES_DIR}/intel_buffers.cpp
${INTEL_SOURCES_DIR}/nbin_intel.cpp
${INTEL_SOURCES_DIR}/npair_intel.cpp)
set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")
set_property(GLOBAL PROPERTY "INTEL_SOURCES" "${INTEL_SOURCES}")
# detect styles which have a USER-INTEL version
RegisterStylesExt(${USER-INTEL_SOURCES_DIR} intel USER-INTEL_SOURCES)
RegisterNBinStyle(${USER-INTEL_SOURCES_DIR}/nbin_intel.h)
RegisterNPairStyle(${USER-INTEL_SOURCES_DIR}/npair_intel.h)
RegisterFixStyle(${USER-INTEL_SOURCES_DIR}/fix_intel.h)
# detect styles which have a INTEL version
RegisterStylesExt(${INTEL_SOURCES_DIR} intel INTEL_SOURCES)
RegisterNBinStyle(${INTEL_SOURCES_DIR}/nbin_intel.h)
RegisterNPairStyle(${INTEL_SOURCES_DIR}/npair_intel.h)
RegisterFixStyle(${INTEL_SOURCES_DIR}/fix_intel.h)
get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES)
get_property(INTEL_SOURCES GLOBAL PROPERTY INTEL_SOURCES)
if(PKG_KSPACE)
list(APPEND USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
RegisterIntegrateStyle(${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
list(APPEND INTEL_SOURCES ${INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
RegisterIntegrateStyle(${INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
endif()
target_sources(lammps PRIVATE ${USER-INTEL_SOURCES})
target_include_directories(lammps PRIVATE ${USER-INTEL_SOURCES_DIR})
target_sources(lammps PRIVATE ${INTEL_SOURCES})
target_include_directories(lammps PRIVATE ${INTEL_SOURCES_DIR})

19
cmake/Modules/Packages/KOKKOS.cmake
View File

@ -1,6 +1,8 @@
########################################################################
# As of version 3.3.0 Kokkos requires C++14
set(CMAKE_CXX_STANDARD 14)
if(CMAKE_CXX_STANDARD LESS 14)
message(FATAL_ERROR "The KOKKOS package requires the C++ standard to be set to at least C++14")
endif()
########################################################################
# consistency checks and Kokkos options/settings required by LAMMPS
if(Kokkos_ENABLE_CUDA)
@ -37,8 +39,8 @@ if(DOWNLOAD_KOKKOS)
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
include(ExternalProject)
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.4.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "c2fdcedb6953e6160c765366f6045abb" CACHE STRING "MD5 checksum of KOKKOS tarball")
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.4.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "4c84698917c93a18985b311bb6caf84f" CACHE STRING "MD5 checksum of KOKKOS tarball")
mark_as_advanced(KOKKOS_URL)
mark_as_advanced(KOKKOS_MD5)
ExternalProject_Add(kokkos_build
@ -58,7 +60,7 @@ if(DOWNLOAD_KOKKOS)
target_link_libraries(lmp PRIVATE LAMMPS::KOKKOS)
add_dependencies(LAMMPS::KOKKOS kokkos_build)
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 3.4.00 REQUIRED CONFIG)
find_package(Kokkos 3.4.01 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
target_link_libraries(lmp PRIVATE Kokkos::kokkos)
else()
@ -74,11 +76,12 @@ else()
target_link_libraries(lammps PRIVATE kokkos)
target_link_libraries(lmp PRIVATE kokkos)
endif()
target_compile_definitions(lammps PRIVATE -DLMP_KOKKOS)
target_compile_definitions(lammps PUBLIC $<BUILD_INTERFACE:LMP_KOKKOS>)
set(KOKKOS_PKG_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/KOKKOS)
set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/atom_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/atom_map_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp
@ -99,7 +102,7 @@ if(PKG_KSPACE)
${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
if(Kokkos_ENABLE_CUDA)
if(NOT ${FFT} STREQUAL "KISS")
if(NOT (FFT STREQUAL "KISS"))
target_compile_definitions(lammps PRIVATE -DFFT_CUFFT)
target_link_libraries(lammps PRIVATE cufft)
endif()
@ -116,7 +119,7 @@ RegisterNBinStyle(${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.h)
RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.h)
RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_halffull_kokkos.h)
if(PKG_USER-DPD)
if(PKG_DPD-REACT)
get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.cpp)
RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.h)
@ -126,4 +129,4 @@ endif()
get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
target_sources(lammps PRIVATE ${KOKKOS_PKG_SOURCES})
target_include_directories(lammps PRIVATE ${KOKKOS_PKG_SOURCES_DIR})
target_include_directories(lammps PUBLIC $<BUILD_INTERFACE:${KOKKOS_PKG_SOURCES_DIR}>)

8
cmake/Modules/Packages/LATTE.cmake
View File

@ -19,6 +19,14 @@ if(DOWNLOAD_LATTE)
set(LATTE_MD5 "820e73a457ced178c08c71389a385de7" CACHE STRING "MD5 checksum of LATTE tarball")
mark_as_advanced(LATTE_URL)
mark_as_advanced(LATTE_MD5)
# CMake cannot pass BLAS or LAPACK library variable to external project if they are a list
list(LENGTH BLAS_LIBRARIES} NUM_BLAS)
list(LENGTH LAPACK_LIBRARIES NUM_LAPACK)
if((NUM_BLAS GREATER 1) OR (NUM_LAPACK GREATER 1))
message(FATAL_ERROR "Cannot compile downloaded LATTE library due to a technical limitation")
endif()
include(ExternalProject)
ExternalProject_Add(latte_build
URL ${LATTE_URL}

10
cmake/Modules/Packages/USER-SMD.cmake → cmake/Modules/Packages/MACHDYN.cmake
View File

@ -7,8 +7,9 @@ endif()
option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT})
if(DOWNLOAD_EIGEN3)
message(STATUS "Eigen3 download requested - we will build our own")
set(EIGEN3_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz" CACHE STRING "URL for Eigen3 tarball")
set(EIGEN3_MD5 "9e30f67e8531477de4117506fe44669b" CACHE STRING "MD5 checksum of Eigen3 tarball")
set(EIGEN3_URL "${LAMMPS_THIRDPARTY_URL}/eigen-3.4.0.tar.gz" CACHE STRING "URL for Eigen3 tarball")
set(EIGEN3_MD5 "4c527a9171d71a72a9d4186e65bea559" CACHE STRING "MD5 checksum of Eigen3 tarball")
mark_as_advanced(EIGEN3_URL)
mark_as_advanced(EIGEN3_MD5)
include(ExternalProject)
@ -30,3 +31,8 @@ else()
endif()
target_link_libraries(lammps PRIVATE Eigen3::Eigen)
endif()
# PGI/Nvidia compiler internals collide with vector intrinsics support in Eigen3
if((CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR (CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC"))
target_compile_definitions(lammps PRIVATE -DEIGEN_DONT_VECTORIZE)
endif()

118
cmake/Modules/Packages/MDI.cmake Normal file
View File

@ -0,0 +1,118 @@
find_package(mdi QUIET)
if(${mdi_FOUND})
set(DOWNLOAD_MDI_DEFAULT OFF)
else()
set(DOWNLOAD_MDI_DEFAULT ON)
endif()
option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an already installed one" ${DOWNLOAD_MDI_DEFAULT})
if(DOWNLOAD_MDI)
message(STATUS "MDI download requested - we will build our own")
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.2.9.tar.gz" CACHE STRING "URL for MDI tarball")
set(MDI_MD5 "ddfa46d6ee15b4e59cfd527ec7212184" CACHE STRING "MD5 checksum for MDI tarball")
mark_as_advanced(MDI_URL)
mark_as_advanced(MDI_MD5)
enable_language(C)
# only ON/OFF are allowed for "mpi" flag when building MDI library
# so translate boolean value of BUILD_MPI
# always disable MPI when cross-compiling to Windows.
if((BUILD_MPI) AND NOT((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING))
set(MDI_USE_MPI ON)
else()
set(MDI_USE_MPI OFF)
endif()
# detect if we have python development support and thus can enable python plugins
set(MDI_USE_PYTHON_PLUGINS OFF)
if(CMAKE_VERSION VERSION_LESS 3.12)
find_package(PythonLibs QUIET) # Deprecated since version 3.12
if(PYTHONLIBS_FOUND)
set(MDI_USE_PYTHON_PLUGINS ON)
endif()
else()
find_package(Python QUIET COMPONENTS Development)
if(Python_Development_FOUND)
set(MDI_USE_PYTHON_PLUGINS ON)
endif()
endif()
# download/ build MDI library
# always build static library with -fpic
# support cross-compilation and ninja-build
include(ExternalProject)
ExternalProject_Add(mdi_build
URL ${MDI_URL}
URL_MD5 ${MDI_MD5}
CMAKE_ARGS ${CMAKE_REQUEST_PIC}
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
-Dlanguage=C
-Dlibtype=STATIC
-Dmpi=${MDI_USE_MPI}
-Dpython_plugins=${MDI_USE_PYTHON_PLUGINS}
UPDATE_COMMAND ""
INSTALL_COMMAND ""
BUILD_BYPRODUCTS "<BINARY_DIR>/MDI_Library/libmdi.a"
)
# where is the compiled library?
ExternalProject_get_property(mdi_build BINARY_DIR)
set(MDI_BINARY_DIR "${BINARY_DIR}/MDI_Library")
# workaround for older CMake versions
file(MAKE_DIRECTORY ${MDI_BINARY_DIR})
# create imported target for the MDI library
add_library(LAMMPS::MDI UNKNOWN IMPORTED)
add_dependencies(LAMMPS::MDI mdi_build)
set_target_properties(LAMMPS::MDI PROPERTIES
IMPORTED_LOCATION "${MDI_BINARY_DIR}/libmdi.a"
INTERFACE_INCLUDE_DIRECTORIES ${MDI_BINARY_DIR}
)
set(MDI_DEP_LIBS "")
# if compiling with python plugins we need
# to add python libraries as dependency.
if(MDI_USE_PYTHON_PLUGINS)
if(CMAKE_VERSION VERSION_LESS 3.12)
list(APPEND MDI_DEP_LIBS ${PYTHON_LIBRARIES})
else()
list(APPEND MDI_DEP_LIBS Python::Python)
endif()
endif()
# need to add support for dlopen/dlsym, except when compiling for Windows.
if(NOT (CMAKE_SYSTEM_NAME STREQUAL "Windows"))
list(APPEND MDI_DEP_LIBS "${CMAKE_DL_LIBS}")
endif()
if(MDI_DEP_LIBS)
set_target_properties(LAMMPS::MDI PROPERTIES
IMPORTED_LINK_INTERFACE_LIBRARIES "${MDI_DEP_LIBS}")
endif()
target_link_libraries(lammps PRIVATE LAMMPS::MDI)
target_link_libraries(lmp PRIVATE LAMMPS::MDI)
else()
find_package(mdi)
if(NOT mdi_FOUND)
message(FATAL_ERROR "MDI library not found. Help CMake to find it "
"by setting mdi_LIBRARY and mdi_INCLUDE_DIR, or set DOWNLOAD_MDI=ON "
"to download and compile it")
endif()
# Link the lammps library against MDI
target_include_directories(lammps PRIVATE ${mdi_INCLUDE_DIR})
target_link_libraries(lammps PRIVATE ${mdi_LIBRARY})
# Link the lammps executable against MDI
target_include_directories(lmp PRIVATE ${mdi_INCLUDE_DIR})
target_link_libraries(lmp PRIVATE ${mdi_LIBRARY})
endif()
target_compile_definitions(lammps PRIVATE -DLMP_MDI)
target_compile_definitions(lmp PRIVATE -DLMP_MDI)

2
cmake/Modules/Packages/MESSAGE.cmake
View File

@ -1,4 +1,4 @@
if(LAMMPS_SIZES STREQUAL BIGBIG)
if(LAMMPS_SIZES STREQUAL "BIGBIG")
message(FATAL_ERROR "The MESSAGE Package is not compatible with -DLAMMPS_BIGBIG")
endif()
option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)

133
cmake/Modules/Packages/ML-HDNNP.cmake Normal file
View File

@ -0,0 +1,133 @@
find_package(N2P2 QUIET)
if(N2P2_FOUND)
set(DOWNLOAD_N2P2_DEFAULT OFF)
else()
set(DOWNLOAD_N2P2_DEFAULT ON)
endif()
option(DOWNLOAD_N2P2 "Download n2p2 library instead of using an already installed one)" ${DOWNLOAD_N2P2_DEFAULT})
if(DOWNLOAD_N2P2)
set(N2P2_URL "https://github.com/CompPhysVienna/n2p2/archive/v2.1.4.tar.gz" CACHE STRING "URL for n2p2 tarball")
set(N2P2_MD5 "9595b066636cd6b90b0fef93398297a5" CACHE STRING "MD5 checksum of N2P2 tarball")
mark_as_advanced(N2P2_URL)
mark_as_advanced(N2P2_MD5)
# adjust settings from detected compiler to compiler platform in n2p2 library
# set compiler specific flag to turn on C++11 syntax (required on macOS and CentOS 7)
if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang"))
set(N2P2_COMP llvm)
set(N2P2_CXX_STD "-std=c++11")
elseif((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM"))
set(N2P2_COMP intel)
set(N2P2_CXX_STD "-std=c++11")
elseif(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
set(N2P2_COMP gnu)
set(N2P2_CXX_STD "-std=gnu++11")
elseif((CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR (CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC"))
set(N2P2_COMP gnu)
set(N2P2_CXX_STD "--c++11")
else() # default
set(N2P2_COMP "")
endif()
# pass on archive creator command. prefer compiler specific version, if set.
# important when using cross compiler.
if(CMAKE_CXX_COMPILER_AR)
set(N2P2_AR ${CMAKE_CXX_COMPILER_AR})
else()
set(N2P2_AR ${CMAKE_AR})
endif()
# adjust compilation of n2p2 library to whether MPI is requested in LAMMPS or not
# need special care for compiling for MPICH2 with Linux-to-Windows cross compiler.
if(NOT BUILD_MPI)
set(N2P2_PROJECT_OPTIONS "-DN2P2_NO_MPI")
else()
# get path to MPI include directory when cross-compiling to windows
if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)
get_target_property(N2P2_MPI_INCLUDE MPI::MPI_CXX INTERFACE_INCLUDE_DIRECTORIES)
set(N2P2_PROJECT_OPTIONS "-I${N2P2_MPI_INCLUDE}")
set(MPI_CXX_COMPILER ${CMAKE_CXX_COMPILER})
endif()
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
get_target_property(N2P2_MPI_INCLUDE MPI::MPI_CXX INTERFACE_INCLUDE_DIRECTORIES)
set(N2P2_PROJECT_OPTIONS "-I${N2P2_MPI_INCLUDE}")
set(MPI_CXX_COMPILER ${CMAKE_CXX_COMPILER})
endif()
endif()
# prefer GNU make, if available. N2P2 lib seems to need it.
find_program(N2P2_MAKE NAMES gmake make)
# override compiler (optimization) flags in n2p2 library to flags used for LAMMPS
# specifically -march=native can result in problems when compiling on HPC clusters or with a cross compiler
# this convoluted way gets correct quoting/escaping when configuring the external project
string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
set(N2P2_BUILD_FLAGS "${CMAKE_SHARED_LIBRARY_CXX_FLAGS} ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}} ${N2P2_CXX_STD}")
set(N2P2_BUILD_OPTIONS INTERFACES=LAMMPS COMP=${N2P2_COMP} "PROJECT_OPTIONS=${N2P2_PROJECT_OPTIONS}" "PROJECT_DEBUG="
"PROJECT_CC=${CMAKE_CXX_COMPILER}" "PROJECT_MPICC=${MPI_CXX_COMPILER}" "PROJECT_CFLAGS=${N2P2_BUILD_FLAGS}"
"PROJECT_AR=${N2P2_AR}")
# echo final flag for debugging
message(STATUS "N2P2 BUILD OPTIONS: ${N2P2_BUILD_OPTIONS}")
# must have "sed" command to compile n2p2 library (for now)
find_program(HAVE_SED sed)
if(NOT HAVE_SED)
message(FATAL_ERROR "Must have 'sed' program installed to compile 'n2p2' library for ML-HDNNP package")
endif()
# download compile n2p2 library. much patch MPI calls in LAMMPS interface to accommodate MPI-2 (e.g. for cross-compiling)
include(ExternalProject)
ExternalProject_Add(n2p2_build
URL ${N2P2_URL}
URL_MD5 ${N2P2_MD5}
UPDATE_COMMAND ""
CONFIGURE_COMMAND ""
PATCH_COMMAND sed -i -e "s/\\(MPI_\\(P\\|Unp\\)ack(\\)/\\1(void *) /" src/libnnpif/LAMMPS/InterfaceLammps.cpp
BUILD_COMMAND ${N2P2_MAKE} -f makefile libnnpif ${N2P2_BUILD_OPTIONS}
BUILD_ALWAYS YES
INSTALL_COMMAND ""
BUILD_IN_SOURCE 1
LOG_BUILD ON
SOURCE_SUBDIR src/
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libnnp.a <SOURCE_DIR>/lib/libnnpif.a
)
# create imported target LAMMPS::N2P2 from two libraries nnp and nnpif
ExternalProject_get_property(n2p2_build SOURCE_DIR)
# n2p2 core library "libnnp"
add_library(LAMMPS::N2P2::LIBNNP UNKNOWN IMPORTED)
set_target_properties(LAMMPS::N2P2::LIBNNP PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libnnp.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include")
# n2p2 interface library "libnnpif"
add_library(LAMMPS::N2P2::LIBNNPIF UNKNOWN IMPORTED)
set_target_properties(LAMMPS::N2P2::LIBNNPIF PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libnnpif.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include")
# nnpif library has MPI calls if MPI is enabled, so we must link with MPI libs
if(BUILD_MPI)
set_target_properties(LAMMPS::N2P2::LIBNNPIF PROPERTIES
INTERFACE_LINK_LIBRARIES MPI::MPI_CXX)
if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)
add_dependencies(LAMMPS::N2P2::LIBNNPIF MPI::MPI_CXX)
endif()
endif()
# final step to define imported target
add_library(LAMMPS::N2P2 INTERFACE IMPORTED)
set_property(TARGET LAMMPS::N2P2 PROPERTY
INTERFACE_LINK_LIBRARIES LAMMPS::N2P2::LIBNNPIF LAMMPS::N2P2::LIBNNP)
target_link_libraries(lammps PRIVATE LAMMPS::N2P2)
add_dependencies(LAMMPS::N2P2 n2p2_build)
# work around issues with older CMake versions
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
file(MAKE_DIRECTORY "${SOURCE_DIR}/lib")
else()
find_package(N2P2)
if(NOT N2P2_FOUND)
message(FATAL_ERROR "n2p2 not found, help CMake to find it by setting N2P2_DIR, or set DOWNLOAD_N2P2=ON to download it")
endif()
target_link_libraries(lammps PRIVATE N2P2::N2P2)
include(${N2P2_CMAKE_EXTRAS})
endif()

12
cmake/Modules/Packages/MLIAP.cmake → cmake/Modules/Packages/ML-IAP.cmake
View File

@ -1,4 +1,4 @@
# if PYTHON package is included we may also include Python support in MLIAP
# if PYTHON package is included we may also include Python support in ML-IAP
set(MLIAP_ENABLE_PYTHON_DEFAULT OFF)
if(PKG_PYTHON)
find_package(Cythonize QUIET)
@ -7,25 +7,25 @@ if(PKG_PYTHON)
endif()
endif()
option(MLIAP_ENABLE_PYTHON "Build MLIAP package with Python support" ${MLIAP_ENABLE_PYTHON_DEFAULT})
option(MLIAP_ENABLE_PYTHON "Build ML-IAP package with Python support" ${MLIAP_ENABLE_PYTHON_DEFAULT})
if(MLIAP_ENABLE_PYTHON)
find_package(Cythonize REQUIRED)
if(NOT PKG_PYTHON)
message(FATAL_ERROR "Must enable PYTHON package for including Python support in MLIAP")
message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP")
endif()
if(CMAKE_VERSION VERSION_LESS 3.12)
if(PYTHONLIBS_VERSION_STRING VERSION_LESS 3.6)
message(FATAL_ERROR "Python support in MLIAP requires Python 3.6 or later")
message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later")
endif()
else()
if(Python_VERSION VERSION_LESS 3.6)
message(FATAL_ERROR "Python support in MLIAP requires Python 3.6 or later")
message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later")
endif()
endif()
set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
set(MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/MLIAP/mliap_model_python_couple.pyx)
set(MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/ML-IAP/mliap_model_python_couple.pyx)
get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_SRC} NAME_WE)
file(MAKE_DIRECTORY ${MLIAP_BINARY_DIR})
add_custom_command(OUTPUT ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h

22
cmake/Modules/Packages/USER-PACE.cmake → cmake/Modules/Packages/ML-PACE.cmake
View File

@ -1,11 +1,11 @@
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.10.25.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.4.9.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_MD5 "4db54962fbd6adcf8c18d46e1798ceb5" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
set(PACELIB_MD5 "a2ac3315c41a1a4a5c912bcb1bc9c5cc" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
mark_as_advanced(PACELIB_URL)
mark_as_advanced(PACELIB_MD5)
# download library sources to build folder
file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz SHOW_PROGRESS EXPECTED_HASH MD5=${PACELIB_MD5})
file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5}) #SHOW_PROGRESS
# uncompress downloaded sources
execute_process(
@ -14,13 +14,19 @@ execute_process(
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
)
file(GLOB lib-pace ${CMAKE_BINARY_DIR}/lammps-user-pace-*)
add_subdirectory(${lib-pace}/yaml-cpp build-yaml-cpp)
set(YAML_CPP_INCLUDE_DIR ${lib-pace}/yaml-cpp/include)
file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE)
file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE/*.cpp)
file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${lib-pace}/ML-PACE)
file(GLOB PACE_EVALUATOR_SOURCES ${lib-pace}/ML-PACE/*.cpp)
list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp)
add_library(pace STATIC ${PACE_EVALUATOR_SOURCES})
set_target_properties(pace PROPERTIES OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR})
target_link_libraries(lammps PRIVATE pace)
set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR} ${YAML_CPP_INCLUDE_DIR})
target_link_libraries(pace PRIVATE yaml-cpp-pace)
target_link_libraries(lammps PRIVATE pace)

71
cmake/Modules/Packages/ML-QUIP.cmake Normal file
View File

@ -0,0 +1,71 @@
enable_language(Fortran)
find_package(QUIP QUIET)
if(QUIP_FOUND)
set(DOWNLOAD_QUIP_DEFAULT OFF)
else()
set(DOWNLOAD_QUIP_DEFAULT ON)
endif()
option(DOWNLOAD_QUIP "Download the QUIP library instead of using an already installed one" ${DOWNLOAD_QUIP_DEFAULT})
if(DOWNLOAD_QUIP)
string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
set(temp "F77 = ${CMAKE_Fortran_COMPILER}\nF90 = ${CMAKE_Fortran_COMPILER}\nF95 = ${CMAKE_Fortran_COMPILER}\n")
set(temp "${temp}CC=${CMAKE_C_COMPILER}\nCPLUSPLUS=${CMAKE_CXX_COMPILER}\nLINKER=${CMAKE_Fortran_COMPILER}\n")
if(CMAKE_Fortran_COMPILER_ID STREQUAL Intel)
set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E\nOPTIM=${CMAKE_Fortran_FLAGS_${BTYPE}}\n")
set(temp "${temp}DEFINES += -DGETARG_F2003 -DFORTRAN_UNDERSCORE\n")
set(temp "${temp}F95FLAGS += -fpp -free -fPIC\n")
set(temp "${temp}F77FLAGS += -fpp -fixed -fPIC\n")
elseif(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E -x f95-cpp-input\nOPTIM=${CMAKE_Fortran_FLAGS_${BTYPE}}\n")
set(temp "${temp}DEFINES += -DGETARG_F2003 -DGETENV_F2003 -DGFORTRAN -DFORTRAN_UNDERSCORE\n")
set(temp "${temp}F95FLAGS += -x f95-cpp-input -ffree-line-length-none -ffree-form -fno-second-underscore -fPIC\n")
set(temp "${temp}F77FLAGS += -x f77-cpp-input -fno-second-underscore -fPIC\n")
else()
message(FATAL_ERROR "The ${CMAKE_Fortran_COMPILER_ID} Fortran compiler is not (yet) supported for building QUIP")
endif()
set(temp "${temp}CFLAGS += -fPIC \nCPLUSPLUSFLAGS += -fPIC\nAR_ADD=src\n")
set(temp "${temp}MATH_LINKOPTS=")
foreach(flag ${BLAS_LIBRARIES})
set(temp "${temp} ${flag}")
endforeach()
foreach(flag ${LAPACK_LIBRARIES})
set(temp "${temp} ${flag}")
endforeach()
# Fix cmake crashing when MATH_LINKOPTS not set, required for e.g. recent Cray Programming Environment
set(temp "${temp} -L/_DUMMY_PATH_\n")
set(temp "${temp}PYTHON=python\nPIP=pip\nEXTRA_LINKOPTS=\n")
set(temp "${temp}HAVE_CP2K=0\nHAVE_VASP=0\nHAVE_TB=0\nHAVE_PRECON=1\nHAVE_LOTF=0\nHAVE_ONIOM=0\n")
set(temp "${temp}HAVE_LOCAL_E_MIX=0\nHAVE_QC=0\nHAVE_GAP=1\nHAVE_DESCRIPTORS_NONCOMMERCIAL=1\n")
set(temp "${temp}HAVE_TURBOGAP=0\nHAVE_QR=1\nHAVE_THIRDPARTY=0\nHAVE_FX=0\nHAVE_SCME=0\nHAVE_MTP=0\n")
set(temp "${temp}HAVE_MBD=0\nHAVE_TTM_NF=0\nHAVE_CH4=0\nHAVE_NETCDF4=0\nHAVE_MDCORE=0\nHAVE_ASAP=0\n")
set(temp "${temp}HAVE_CGAL=0\nHAVE_METIS=0\nHAVE_LMTO_TBE=0\nHAVE_SCALAPACK=0\n")
file(WRITE ${CMAKE_BINARY_DIR}/quip.config "${temp}")
message(STATUS "QUIP download via git requested - we will build our own")
# QUIP has no releases (except for a tag marking the end of Python 2 support). We use the current "public" branch
# The LAMMPS interface wrapper has a compatibility constant that is being checked at runtime.
include(ExternalProject)
ExternalProject_Add(quip_build
GIT_REPOSITORY "https://github.com/libAtoms/QUIP/"
GIT_TAG origin/public
GIT_SHALLOW YES
GIT_PROGRESS YES
PATCH_COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_BINARY_DIR}/quip.config <SOURCE_DIR>/arch/Makefile.lammps
CONFIGURE_COMMAND env QUIP_ARCH=lammps make config
BUILD_COMMAND env QUIP_ARCH=lammps make libquip
INSTALL_COMMAND ""
BUILD_IN_SOURCE YES
BUILD_BYPRODUCTS <SOURCE_DIR>/build/lammps/libquip.a
)
ExternalProject_get_property(quip_build SOURCE_DIR)
add_library(LAMMPS::QUIP UNKNOWN IMPORTED)
set_target_properties(LAMMPS::QUIP PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/build/lammps/libquip.a"
INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
target_link_libraries(lammps PRIVATE LAMMPS::QUIP)
add_dependencies(LAMMPS::QUIP quip_build)
else()
find_package(QUIP REQUIRED)
target_link_libraries(lammps PRIVATE QUIP::QUIP ${LAPACK_LIBRARIES})
endif()

6
cmake/Modules/Packages/USER-MOLFILE.cmake → cmake/Modules/Packages/MOLFILE.cmake
View File

@ -1,5 +1,7 @@
set(MOLFILE_INCLUDE_DIR "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
set(MOLFILE_INCLUDE_DIRS "${MOLFILE_INCLUDE_DIR}")
add_library(molfile INTERFACE)
target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIR})
if(NOT (CMAKE_SYSTEM_NAME STREQUAL "Windows"))
target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
endif()
target_link_libraries(lammps PRIVATE molfile)

34
cmake/Modules/Packages/MSCG.cmake
View File

@ -12,34 +12,12 @@ if(DOWNLOAD_MSCG)
mark_as_advanced(MSCG_URL)
mark_as_advanced(MSCG_MD5)
include(ExternalProject)
ExternalProject_Add(mscg_build
URL ${MSCG_URL}
URL_MD5 ${MSCG_MD5}
SOURCE_SUBDIR src/CMake
CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${EXTRA_MSCG_OPTS}
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
-DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}
-DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
BUILD_COMMAND ${CMAKE_COMMAND} --build . --target mscg
INSTALL_COMMAND ""
BUILD_BYPRODUCTS <BINARY_DIR>/libmscg.a
)
ExternalProject_get_property(mscg_build BINARY_DIR)
ExternalProject_get_property(mscg_build SOURCE_DIR)
file(MAKE_DIRECTORY ${SOURCE_DIR}/src)
add_library(LAMMPS::MSCG UNKNOWN IMPORTED)
set_target_properties(LAMMPS::MSCG PROPERTIES
IMPORTED_LOCATION "${BINARY_DIR}/libmscg.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/src"
INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
target_link_libraries(lammps PRIVATE LAMMPS::MSCG)
add_dependencies(LAMMPS::MSCG mscg_build)
include(ExternalCMakeProject)
ExternalCMakeProject(mscg ${MSCG_URL} ${MSCG_MD5} MSCG-release src/CMake "")
# set include and link library
target_include_directories(lammps PRIVATE "${CMAKE_BINARY_DIR}/_deps/mscg-src/src")
target_link_libraries(lammps PRIVATE mscg)
else()
find_package(MSCG)
if(NOT MSCG_FOUND)

2
cmake/Modules/Packages/USER-NETCDF.cmake → cmake/Modules/Packages/NETCDF.cmake
View File

@ -1,4 +1,4 @@
# USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
# NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
# NetCDF library enables dump style "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
# may use NetCDF or PNetCDF with MPI, but must have NetCDF without

40
cmake/Modules/Packages/OPENMP.cmake Normal file
View File

@ -0,0 +1,40 @@
set(OPENMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/OPENMP)
set(OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/thr_data.cpp
${OPENMP_SOURCES_DIR}/thr_omp.cpp
${OPENMP_SOURCES_DIR}/fix_omp.cpp
${OPENMP_SOURCES_DIR}/fix_nh_omp.cpp
${OPENMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp
${OPENMP_SOURCES_DIR}/domain_omp.cpp)
target_compile_definitions(lammps PRIVATE -DLMP_OPENMP)
set_property(GLOBAL PROPERTY "OMP_SOURCES" "${OPENMP_SOURCES}")
# detects styles which have OPENMP version
RegisterStylesExt(${OPENMP_SOURCES_DIR} omp OMP_SOURCES)
RegisterFixStyle(${OPENMP_SOURCES_DIR}/fix_omp.h)
get_property(OPENMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
# manually add package dependent source files from OPENMP that do not provide styles
if(PKG_ASPHERE)
list(APPEND OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/fix_nh_asphere_omp.cpp)
endif()
if(PKG_RIGID)
list(APPEND OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp)
endif()
if(PKG_REAXFF)
list(APPEND OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/reaxff_bond_orders_omp.cpp
${OPENMP_SOURCES_DIR}/reaxff_hydrogen_bonds_omp.cpp
${OPENMP_SOURCES_DIR}/reaxff_nonbonded_omp.cpp
${OPENMP_SOURCES_DIR}/reaxff_bonds_omp.cpp
${OPENMP_SOURCES_DIR}/reaxff_init_md_omp.cpp
${OPENMP_SOURCES_DIR}/reaxff_torsion_angles_omp.cpp
${OPENMP_SOURCES_DIR}/reaxff_forces_omp.cpp
${OPENMP_SOURCES_DIR}/reaxff_multi_body_omp.cpp
${OPENMP_SOURCES_DIR}/reaxff_valence_angles_omp.cpp)
endif()
target_sources(lammps PRIVATE ${OPENMP_SOURCES})
target_include_directories(lammps PRIVATE ${OPENMP_SOURCES_DIR})

4
cmake/Modules/Packages/USER-PLUMED.cmake → cmake/Modules/Packages/PLUMED.cmake
View File

@ -54,8 +54,8 @@ if(DOWNLOAD_PLUMED)
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
endif()
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.1/plumed-src-2.7.1.tgz" CACHE STRING "URL for PLUMED tarball")
set(PLUMED_MD5 "4eac6a462ec84dfe0cec96c82421b8e8" CACHE STRING "MD5 checksum of PLUMED tarball")
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.2/plumed-src-2.7.2.tgz" CACHE STRING "URL for PLUMED tarball")
set(PLUMED_MD5 "cfa0b4dd90a81c25d3302e8d97bfeaea" CACHE STRING "MD5 checksum of PLUMED tarball")
mark_as_advanced(PLUMED_URL)
mark_as_advanced(PLUMED_MD5)

17
cmake/Modules/Packages/QEQ.cmake
View File

@ -1,18 +1,13 @@
# Fix qeq/fire requires MANYBODY (i.e. COMB and COMB3) to be installed
set(QEQ_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/QEQ)
file(GLOB QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix*.h)
file(GLOB QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix*.cpp)
get_property(hlist GLOBAL PROPERTY FIX)
if(NOT PKG_MANYBODY)
list(REMOVE_ITEM QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix_qeq_fire.h)
list(REMOVE_ITEM QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix_qeq_fire.cpp)
list(REMOVE_ITEM hlist ${QEQ_SOURCES_DIR}/fix_qeq_fire.h)
get_target_property(LAMMPS_SOURCES lammps SOURCES)
list(REMOVE_ITEM LAMMPS_SOURCES ${QEQ_SOURCES_DIR}/fix_qeq_fire.cpp)
set_property(TARGET lammps PROPERTY SOURCES ${LAMMPS_SOURCES})
endif()
set_property(GLOBAL PROPERTY "QEQ_SOURCES" "${QEQ_SOURCES}")
set_property(GLOBAL PROPERTY FIX "${hlist}")
foreach(MY_HEADER ${QEQ_HEADERS})
AddStyleHeader(${MY_HEADER} FIX)
endforeach()
get_property(QEQ_SOURCES GLOBAL PROPERTY QEQ_SOURCES)
target_sources(lammps PRIVATE ${QEQ_SOURCES})
target_include_directories(lammps PRIVATE ${QEQ_SOURCES_DIR})

0
cmake/Modules/Packages/USER-QMMM.cmake → cmake/Modules/Packages/QMMM.cmake
View File

5
cmake/Modules/Packages/USER-SCAFACOS.cmake → cmake/Modules/Packages/SCAFACOS.cmake
View File

@ -23,6 +23,11 @@ if(DOWNLOAD_SCAFACOS)
file(DOWNLOAD ${LAMMPS_THIRDPARTY_URL}/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
EXPECTED_HASH MD5=4baa1333bb28fcce102d505e1992d032)
find_program(HAVE_PATCH patch)
if(NOT HAVE_PATCH)
message(FATAL_ERROR "The 'patch' program is required to build the ScaFaCoS library")
endif()
include(ExternalProject)
ExternalProject_Add(scafacos_build
URL ${SCAFACOS_URL}

66
cmake/Modules/Packages/USER-MDI.cmake
View File

@ -1,66 +0,0 @@
find_package(mdi QUIET)
if(${mdi_FOUND})
set(DOWNLOAD_MDI_DEFAULT OFF)
else()
set(DOWNLOAD_MDI_DEFAULT ON)
endif()
option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an already installed one" ${DOWNLOAD_MDI_DEFAULT})
if(DOWNLOAD_MDI)
message(STATUS "MDI download requested - we will build our own")
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.2.9.tar.gz" CACHE STRING "URL for MDI tarball")
set(MDI_MD5 "ddfa46d6ee15b4e59cfd527ec7212184" CACHE STRING "MD5 checksum for MDI tarball")
mark_as_advanced(MDI_URL)
mark_as_advanced(MDI_MD5)
set(LAMMPS_LIB_MDI_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/mdi)
include(ExternalProject)
message(STATUS "Building mdi.")
ExternalProject_Add(mdi_external
URL ${MDI_URL}
URL_MD5 ${MDI_MD5}
UPDATE_COMMAND ""
CMAKE_ARGS ${CMAKE_REQUEST_PIC}
-DCMAKE_INSTALL_PREFIX=${LAMMPS_LIB_MDI_BIN_DIR}
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_INSTALL_LIBDIR=${CMAKE_INSTALL_LIBDIR}
-DCMAKE_INSTALL_INCLUDEDIR=${CMAKE_INSTALL_INCLUDEDIR}
-DBUILD_SHARED_LIBS=${BUILD_SHARED_LIBS}
-Dlanguage=C
CMAKE_CACHE_ARGS -DCMAKE_C_FLAGS:STRING=${CMAKE_C_FLAGS}
-DCMAKE_CXX_FLAGS:STRING=${CMAKE_CXX_FLAGS}
-DTargetOpenMP_FIND_COMPONENTS:STRING=C;CXX)
# Link the lammps library against MDI
target_include_directories(lammps PRIVATE ${LAMMPS_LIB_MDI_BIN_DIR}/${CMAKE_INSTALL_INCLUDEDIR}/mdi)
target_link_directories(lammps PRIVATE ${LAMMPS_LIB_MDI_BIN_DIR}/${CMAKE_INSTALL_LIBDIR}/mdi)
target_link_libraries(lammps PRIVATE mdi)
add_dependencies(lammps mdi_external)
# Link the lammps executable against MDI
target_include_directories(lmp PRIVATE ${LAMMPS_LIB_MDI_BIN_DIR}/${CMAKE_INSTALL_INCLUDEDIR}/mdi)
target_link_directories(lmp PRIVATE ${LAMMPS_LIB_MDI_BIN_DIR}/${CMAKE_INSTALL_LIBDIR}/mdi)
target_link_libraries(lmp PRIVATE mdi)
add_dependencies(lmp mdi_external)
else()
find_package(mdi)
if(NOT mdi_FOUND)
message(FATAL_ERROR "MDI library not found. Help CMake to find it "
"by setting mdi_LIBRARY and mdi_INCLUDE_DIR, or set DOWNLOAD_MDI=ON "
"to download and compile it")
endif()
# Link the lammps library against MDI
target_include_directories(lammps PRIVATE ${mdi_INCLUDE_DIR})
target_link_libraries(lammps PRIVATE ${mdi_LIBRARY})
# Link the lammps executable against MDI
target_include_directories(lmp PRIVATE ${mdi_INCLUDE_DIR})
target_link_libraries(lmp PRIVATE ${mdi_LIBRARY})
endif()
target_compile_definitions(lammps PRIVATE -DLMP_USER_MDI)
target_compile_definitions(lmp PRIVATE -DLMP_USER_MDI)

40
cmake/Modules/Packages/USER-OMP.cmake
View File

@ -1,40 +0,0 @@
set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP)
set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
${USER-OMP_SOURCES_DIR}/thr_omp.cpp
${USER-OMP_SOURCES_DIR}/fix_omp.cpp
${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp
${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp
${USER-OMP_SOURCES_DIR}/domain_omp.cpp)
target_compile_definitions(lammps PRIVATE -DLMP_USER_OMP)
set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}")
# detects styles which have USER-OMP version
RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
RegisterFixStyle(${USER-OMP_SOURCES_DIR}/fix_omp.h)
get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
# manually add package dependent source files from USER-OMP that do not provide styles
if(PKG_ASPHERE)
list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_nh_asphere_omp.cpp)
endif()
if(PKG_RIGID)
list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp)
endif()
if(PKG_USER-REAXC)
list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/reaxc_bond_orders_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_hydrogen_bonds_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_bonds_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_init_md_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_torsion_angles_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_forces_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp)
endif()
target_sources(lammps PRIVATE ${USER-OMP_SOURCES})
target_include_directories(lammps PRIVATE ${USER-OMP_SOURCES_DIR})

3
cmake/Modules/Packages/USER-QUIP.cmake
View File

@ -1,3 +0,0 @@
enable_language(Fortran)
find_package(QUIP REQUIRED)
target_link_libraries(lammps PRIVATE QUIP::QUIP ${LAPACK_LIBRARIES})

5
cmake/Modules/Packages/VORONOI.cmake
View File

@ -26,6 +26,11 @@ if(DOWNLOAD_VORO)
set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
endif()
find_program(HAVE_PATCH patch)
if(NOT HAVE_PATCH)
message(FATAL_ERROR "The 'patch' program is required to build the voro++ library")
endif()
ExternalProject_Add(voro_build
URL ${VORO_URL}
URL_MD5 ${VORO_MD5}

0
cmake/Modules/Packages/USER-VTK.cmake → cmake/Modules/Packages/VTK.cmake
View File

2
cmake/Modules/PreventInSourceBuilds.cmake
View File

@ -9,7 +9,7 @@ function(prevent_in_source_builds)
get_filename_component(bindir "${CMAKE_BINARY_DIR}" REALPATH)
# disallow in-source builds
if("${srcdir}" STREQUAL "${bindir}" OR "${srcdir2}" STREQUAL "${bindir}" OR "${srcdir3}" STREQUAL "${bindir}")
if(("${srcdir}" STREQUAL "${bindir}") OR ("${srcdir2}" STREQUAL "${bindir}") OR ("${srcdir3}" STREQUAL "${bindir}"))
message(FATAL_ERROR "\
CMake must not to be run in the source directory. \

16
cmake/Modules/Testing.cmake
View File

@ -19,11 +19,11 @@ if(ENABLE_TESTING)
# we need to build and link a LOT of tester executables, so it is worth checking if
# a faster linker is available. requires GNU or Clang compiler, newer CMake.
# also only verified with Fedora Linux > 30 and Ubuntu <= 18.04 (Ubuntu 20.04 fails)
if((CMAKE_SYSTEM_NAME STREQUAL Linux) AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
AND ((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")))
if (((CMAKE_LINUX_DISTRO STREQUAL Ubuntu) AND (CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04))
OR ((CMAKE_LINUX_DISTRO STREQUAL Fedora) AND (CMAKE_DISTRO_VERSION VERSION_GREATER 30)))
if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
AND ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
if(((CMAKE_LINUX_DISTRO STREQUAL "Ubuntu") AND (CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04))
OR ((CMAKE_LINUX_DISTRO STREQUAL "Fedora") AND (CMAKE_DISTRO_VERSION VERSION_GREATER 30)))
include(CheckCXXCompilerFlag)
set(CMAKE_CUSTOM_LINKER_DEFAULT default)
check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG)
@ -58,7 +58,7 @@ if(ENABLE_TESTING)
endif()
# Compiler specific features for testing
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
mark_as_advanced(ENABLE_COVERAGE)
if(ENABLE_COVERAGE)
@ -83,7 +83,7 @@ mark_as_advanced(ENABLE_IWYU)
if(ENABLE_IWYU)
# enforce these settings
set(CMAKE_EXPORT_COMPILE_COMMANDS ON CACHE BOOL "Enable reporting compilation commands to compile_commands.json" FORCE)
if (NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")))
if(NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")))
message(FATAL_ERROR "IWYU is only supported with Clang or GNU compilers")
endif()
# detect the "native" header folder so we can include them first
@ -91,7 +91,7 @@ if(ENABLE_IWYU)
string(REGEX REPLACE ".*libraries: *=([^:]+):.*" "\\1/include" IWYU_EXTRA_INCLUDE_DIR ${IWYU_SEARCH_PATHS})
find_program(IWYU_EXE NAMES include-what-you-use iwyu)
find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py)
if (IWYU_EXE AND IWYU_TOOL)
if(IWYU_EXE AND IWYU_TOOL)
add_custom_target(
iwyu
${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -I${IWYU_EXTRA_INCLUDE_DIR} -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp

16
cmake/Modules/Tools.cmake
View File

@ -9,21 +9,25 @@ if(BUILD_TOOLS)
check_language(Fortran)
if(CMAKE_Fortran_COMPILER)
enable_language(Fortran)
add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f90)
target_link_libraries(chain.x PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR})
add_executable(micelle2d.x ${LAMMPS_TOOLS_DIR}/micelle2d.f90)
target_link_libraries(micelle2d.x PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
install(TARGETS chain.x micelle2d.x DESTINATION ${CMAKE_INSTALL_BINDIR})
else()
message(WARNING "No suitable Fortran compiler found, skipping build of 'chain.x'")
message(WARNING "No suitable Fortran compiler found, skipping build of 'chain.x' and 'micelle2d.x'")
endif()
else()
message(WARNING "CMake build doesn't support fortran, skipping build of 'chain.x'")
message(WARNING "CMake build doesn't support Fortran, skipping build of 'chain.x' and 'micelle2d.x'")
endif()
enable_language(C)
get_filename_component(MSI2LMP_SOURCE_DIR ${LAMMPS_TOOLS_DIR}/msi2lmp/src ABSOLUTE)
file(GLOB MSI2LMP_SOURCES ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
add_executable(msi2lmp ${MSI2LMP_SOURCES})
target_link_libraries(msi2lmp PRIVATE ${MATH_LIBRARIES})
if(STANDARD_MATH_LIB)
target_link_libraries(msi2lmp PRIVATE ${STANDARD_MATH_LIB})
endif()
install(TARGETS msi2lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
install(FILES ${LAMMPS_DOC_DIR}/msi2lmp.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
endif()
@ -45,7 +49,7 @@ if(BUILD_LAMMPS_SHELL)
target_include_directories(lammps-shell PRIVATE ${LAMMPS_TOOLS_DIR}/lammps-shell)
# workaround for broken readline pkg-config file on FreeBSD
if(CMAKE_SYSTEM_NAME STREQUAL FreeBSD)
if(CMAKE_SYSTEM_NAME STREQUAL "FreeBSD")
target_include_directories(lammps-shell PRIVATE /usr/local/include)
endif()
target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE)

35
cmake/Modules/YAML.cmake
View File

@ -1,35 +0,0 @@
message(STATUS "Downloading and building YAML library")
include(ExternalProject)
set(YAML_URL "https://pyyaml.org/download/libyaml/yaml-0.2.5.tar.gz" CACHE STRING "URL for libyaml tarball")
set(YAML_MD5 "bb15429d8fb787e7d3f1c83ae129a999" CACHE STRING "MD5 checksum of libyaml tarball")
mark_as_advanced(YAML_URL)
mark_as_advanced(YAML_MD5)
ExternalProject_Add(libyaml
URL ${YAML_URL}
URL_MD5 ${YAML_MD5}
SOURCE_DIR "${CMAKE_BINARY_DIR}/yaml-src"
BINARY_DIR "${CMAKE_BINARY_DIR}/yaml-build"
CONFIGURE_COMMAND <SOURCE_DIR>/configure ${CONFIGURE_REQUEST_PIC}
CXX=${CMAKE_CXX_COMPILER}
CC=${CMAKE_C_COMPILER}
--prefix=<INSTALL_DIR> --disable-shared
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libyaml${CMAKE_STATIC_LIBRARY_SUFFIX}
TEST_COMMAND "")
ExternalProject_Get_Property(libyaml INSTALL_DIR)
set(YAML_INCLUDE_DIR ${INSTALL_DIR}/include)
set(YAML_LIBRARY_DIR ${INSTALL_DIR}/lib)
# workaround for CMake 3.10 on ubuntu 18.04
file(MAKE_DIRECTORY ${YAML_INCLUDE_DIR})
file(MAKE_DIRECTORY ${YAML_LIBRARY_DIR})
set(YAML_LIBRARY_PATH ${INSTALL_DIR}/lib/libyaml${CMAKE_STATIC_LIBRARY_SUFFIX})
add_library(Yaml::Yaml UNKNOWN IMPORTED)
set_target_properties(Yaml::Yaml PROPERTIES
IMPORTED_LOCATION ${YAML_LIBRARY_PATH}
INTERFACE_INCLUDE_DIRECTORIES ${YAML_INCLUDE_DIR})
add_dependencies(Yaml::Yaml libyaml)

25
cmake/iwyu/iwyu-extra-map.imp
View File

@ -1,7 +1,28 @@
[
{ include: [ "<bits/types/struct_rusage.h>", private, "<sys/resource.h>", public ] },
{ include: [ "<bits/exception.h>", public, "<exception>", public ] },
{ include: [ "@<Eigen/.*>", private, "<Eigen/Eigen>", public ] },
{ include: [ "@<gtest/.*>", private, "\"gtest/gtest.h\"", public ] },
{ include: [ "@<gmock/.*>", private, "\"gmock/gmock.h\"", public ] },
{ include: [ "@<gmock/.*>", private, "\"gmock/gmock.h\"", public ] },
{ include: [ "@<(cell|c_loops|container).hh>", private, "<voro++.hh>", public ] },
{ include: [ "@\"atom_vec_.*.h\"", public, "\"style_atom.h\"", public ] },
{ include: [ "@\"body_.*.h\"", public, "\"style_body.h\"", public ] },
{ include: [ "@\"compute_.*.h\"", public, "\"style_compute.h\"", public ] },
{ include: [ "@\"fix_.*.h\"", public, "\"style_fix.h\"", public ] },
{ include: [ "@\"dump_.*.h\"", public, "\"style_dump.h\"", public ] },
{ include: [ "@\"min_.*.h\"", public, "\"style_minimize.h\"", public ] },
{ include: [ "@\"reader_.*.h\"", public, "\"style_reader.h\"", public ] },
{ include: [ "@\"region_.*.h\"", public, "\"style_region.h\"", public ] },
{ include: [ "@\"pair_.*.h\"", public, "\"style_pair.h\"", public ] },
{ include: [ "@\"angle_.*.h\"", public, "\"style_angle.h\"", public ] },
{ include: [ "@\"bond_.*.h\"", public, "\"style_bond.h\"", public ] },
{ include: [ "@\"dihedral_.*.h\"", public, "\"style_dihedral.h\"", public ] },
{ include: [ "@\"improper_.*.h\"", public, "\"style_improper.h\"", public ] },
{ include: [ "@\"kspace_.*.h\"", public, "\"style_kspace.h\"", public ] },
{ include: [ "@\"nbin_.*.h\"", public, "\"style_nbin.h\"", public ] },
{ include: [ "@\"npair_.*.h\"", public, "\"style_npair.h\"", public ] },
{ include: [ "@\"nstenci_.*.h\"", public, "\"style_nstencil.h\"", public ] },
{ include: [ "@\"ntopo_.*.h\"", public, "\"style_ntopo.h\"", public ] },
{ include: [ "<float.h>", public, "<cfloat>", public ] },
{ include: [ "<limits.h>", public, "<climits>", public ] },
{ include: [ "<bits/types/struct_tm.h>", private, "<ctime>", public ] },
]

2
cmake/pkgconfig/liblammps.pc.in
View File

@ -24,7 +24,7 @@ includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
Name: liblammps@LAMMPS_MACHINE@
Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library
URL: http://lammps.sandia.gov
URL: https://www.lammps.org
Version: @PROJECT_VERSION@
Requires:
Libs: -L${libdir} -llammps@LAMMPS_MACHINE@

103
cmake/presets/all_off.cmake
View File

@ -1,17 +1,96 @@
# preset that turns on all existing packages off. can be used to reset
# Preset that turns on all existing packages off. Can be used to reset
# an existing package selection without losing any other settings
set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE
MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-INTEL
USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MESONT USER-MGPT
USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE USER-PHONON
USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION USER-REAXC
USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
USER-VTK USER-YAFF)
set(ALL_PACKAGES
ADIOS
ASPHERE
ATC
AWPMD
BOCS
BODY
BROWNIAN
CG-DNA
CG-SDK
CLASS2
COLLOID
COLVARS
COMPRESS
CORESHELL
DIELECTRIC
DIFFRACTION
DIPOLE
DPD-BASIC
DPD-MESO
DPD-REACT
DPD-SMOOTH
DRUDE
EFF
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
EXTRA-MOLECULE
EXTRA-PAIR
FEP
GPU
GRANULAR
H5MD
INTEL
INTERLAYER
KIM
KOKKOS
KSPACE
LATBOLTZ
LATTE
MACHDYN
MANIFOLD
MANYBODY
MC
MDI
MEAM
MESONT
MESSAGE
MGPT
MISC
ML-HDNNP
ML-IAP
ML-PACE
ML-QUIP
ML-RANN
ML-SNAP
MOFFF
MOLECULE
MOLFILE
MPIIO
MSCG
NETCDF
OPENMP
OPT
ORIENT
PERI
PHONON
PLUGIN
PLUMED
POEMS
PTM
PYTHON
QEQ
QMMM
QTB
REACTION
REAXFF
REPLICA
RIGID
SCAFACOS
SHOCK
SMTBQ
SPH
SPIN
SRD
TALLY
UEF
VORONOI
VTK
YAFF)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

107
cmake/presets/all_on.cmake
View File

@ -1,19 +1,98 @@
# preset that turns on all existing packages. using the combination
# this preset followed by the nolib.cmake preset should configure a
# LAMMPS binary, with as many packages included, that can be compiled
# Preset that turns on all existing packages. Using the combination
# of this preset followed by the nolib.cmake preset should configure
# a LAMMPS binary, with as many packages included, that can be compiled
# with just a working C++ compiler and an MPI library.
set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE
MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-INTEL
USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MESONT USER-MGPT
USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE USER-PHONON
USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION USER-REAXC
USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
USER-VTK USER-YAFF)
set(ALL_PACKAGES
ADIOS
ASPHERE
ATC
AWPMD
BOCS
BODY
BROWNIAN
CG-DNA
CG-SDK
CLASS2
COLLOID
COLVARS
COMPRESS
CORESHELL
DIELECTRIC
DIFFRACTION
DIPOLE
DPD-BASIC
DPD-MESO
DPD-REACT
DPD-SMOOTH
DRUDE
EFF
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
EXTRA-MOLECULE
EXTRA-PAIR
FEP
GPU
GRANULAR
H5MD
INTEL
INTERLAYER
KIM
KOKKOS
KSPACE
LATBOLTZ
LATTE
MACHDYN
MANIFOLD
MANYBODY
MC
MDI
MEAM
MESONT
MESSAGE
MGPT
MISC
ML-HDNNP
ML-IAP
ML-PACE
ML-QUIP
ML-RANN
ML-SNAP
MOFFF
MOLECULE
MOLFILE
MPIIO
MSCG
NETCDF
OPENMP
OPT
ORIENT
PERI
PHONON
PLUGIN
PLUMED
POEMS
PTM
PYTHON
QEQ
QMMM
QTB
REACTION
REAXFF
REPLICA
RIGID
SCAFACOS
SHOCK
SMTBQ
SPH
SPIN
SRD
TALLY
UEF
VORONOI
VTK
YAFF)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)

0
cmake/presets/minimal.cmake → cmake/presets/basic.cmake
View File

15
cmake/presets/clang.cmake
View File

@ -1,13 +1,26 @@
# preset that will enable clang/clang++ with support for MPI and OpenMP (on Linux boxes)
# prefer flang over gfortran, if available
find_program(CLANG_FORTRAN NAMES flang gfortran f95)
set(ENV{OMPI_FC} ${CLANG_FORTRAN})
set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
set(CMAKE_Fortran_COMPILER ${CLANG_FORTRAN} CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_CXX "clang++" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "clang" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)

8
cmake/presets/download.cmake
View File

@ -1,7 +1,7 @@
# preset that turns on packages with automatic downloads of sources of potentials
# compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time.
# Preset that turns on packages with automatic downloads of sources or potentials.
# Compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time.
set(ALL_PACKAGES KIM LATTE MSCG VORONOI USER-PLUMED USER-SCAFACOS USER-SMD USER-MESONT)
set(ALL_PACKAGES KIM LATTE MSCG VORONOI PLUMED SCAFACOS MACHDYN MESONT MDI ML-PACE)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)
@ -9,9 +9,11 @@ endforeach()
set(DOWNLOAD_KIM ON CACHE BOOL "" FORCE)
set(DOWNLOAD_LATTE ON CACHE BOOL "" FORCE)
set(DOWNLOAD_MDI ON CACHE BOOL "" FORCE)
set(DOWNLOAD_MSCG ON CACHE BOOL "" FORCE)
set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
set(DOWNLOAD_PACE ON CACHE BOOL "" FORCE)
set(DOWNLOAD_PLUMED ON CACHE BOOL "" FORCE)
set(DOWNLOAD_SCAFACOS ON CACHE BOOL "" FORCE)

18
cmake/presets/gcc.cmake
View File

@ -1,11 +1,23 @@
# preset that will restore gcc/g++ with support for MPI and OpenMP (on Linux boxes)
# preset that will explicitly request gcc/g++ compilers with support for MPI and OpenMP
set(CMAKE_CXX_COMPILER "g++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_COMPILER "gfortran" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_CXX "g++" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
set(MPI_C "gcc" CACHE STRING "" FORCE)
set(MPI_C_COMPILER "mpicc" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_Fortran "gfortran" CACHE STRING "" FORCE)
set(MPI_Fortran_COMPILER "mpifort" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -g -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "gcc" CACHE STRING "" FORCE)

20
cmake/presets/hip.cmake
View File

@ -1,12 +1,26 @@
# preset that will enable hipcc plus gcc with support for MPI and OpenMP (on Linux boxes)
# preset that will enable hipcc plus gcc/gfortran with support for MPI and OpenMP (on Linux boxes)
set(CMAKE_CXX_COMPILER "hipcc" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)
set(CMAKE_Fortran_COMPILER gfortran CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(OpenMP_CXX "hipcc" CACHE STRING "" FORCE)
set(MPI_CXX "hipcc" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "gcc" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "gomp" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_CXX "hipcc" CACHE STRING "" FORCE)
set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)

30
cmake/presets/hip_amd.cmake Normal file
View File

@ -0,0 +1,30 @@
# preset that will enable hip (clang/clang++) with support for MPI and OpenMP (on Linux boxes)
# prefer flang over gfortran, if available
find_program(CLANG_FORTRAN NAMES flang gfortran f95)
set(ENV{OMPI_FC} ${CLANG_FORTRAN})
set(CMAKE_CXX_COMPILER "hipcc" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "hipcc" CACHE STRING "" FORCE)
set(CMAKE_Fortran_COMPILER ${CLANG_FORTRAN} CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_CXX "hipcc" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "hipcc" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_CXX "hipcc" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)

12
cmake/presets/intel.cmake
View File

@ -3,10 +3,20 @@
set(CMAKE_CXX_COMPILER "icpc" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "icc" CACHE STRING "" FORCE)
set(CMAKE_Fortran_COMPILER "ifort" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_CXX "icpc" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "icc" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-qopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)

85
cmake/presets/mingw-cross.cmake
View File

@ -1,13 +1,76 @@
set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KSPACE LATTE MANYBODY MC MISC MLIAP MOLECULE OPT
PERI POEMS QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
USER-FEP USER-INTEL USER-MANIFOLD USER-MEAMC USER-MESODPD
USER-MESONT USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE USER-OMP
USER-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC
USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
USER-YAFF)
set(WIN_PACKAGES
ASPHERE
ATC
AWPMD
BOCS
BODY
BROWNIAN
CG-DNA
CG-SDK
CLASS2
COLLOID
COLVARS
COMPRESS
CORESHELL
DIELECTRIC
DIFFRACTION
DIPOLE
DPD-BASIC
DPD-MESO
DPD-REACT
DPD-SMOOTH
DRUDE
EFF
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
EXTRA-MOLECULE
EXTRA-PAIR
FEP
GPU
GRANULAR
INTEL
INTERLAYER
KSPACE
LATTE
MACHDYN
MANIFOLD
MANYBODY
MC
MDI
MEAM
MESONT
MGPT
MISC
ML-HDNNP
ML-IAP
ML-SNAP
ML-RANN
MOFFF
MOLECULE
MOLFILE
OPENMP
OPT
ORIENT
PERI
PHONON
POEMS
PTM
QEQ
QTB
REACTION
REAXFF
REPLICA
RIGID
SHOCK
SMTBQ
SPH
SPIN
SRD
TALLY
UEF
VORONOI
YAFF)
foreach(PKG ${WIN_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)
@ -16,7 +79,7 @@ endforeach()
# these two packages require a full MPI implementation
if(BUILD_MPI)
set(PKG_MPIIO ON CACHE BOOL "" FORCE)
set(PKG_USER-LB ON CACHE BOOL "" FORCE)
set(PKG_LATBOLTZ ON CACHE BOOL "" FORCE)
endif()
set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)

67
cmake/presets/most.cmake
View File

@ -2,13 +2,66 @@
# external libraries. Compared to all_on.cmake some more unusual packages
# are removed. The resulting binary should be able to run most inputs.
set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
GRANULAR KSPACE MANYBODY MC MISC MLIAP MOLECULE OPT PERI
PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC
USER-MESODPD USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION
USER-REAXC USER-SDPD USER-SPH USER-SMD USER-UEF USER-YAFF)
set(ALL_PACKAGES
ASPHERE
BOCS
BODY
BROWNIAN
CG-DNA
CG-SDK
CLASS2
COLLOID
COLVARS
COMPRESS
CORESHELL
DIELECTRIC
DIFFRACTION
DIPOLE
DPD-BASIC
DPD-MESO
DPD-REACT
DPD-SMOOTH
DRUDE
EFF
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
EXTRA-MOLECULE
EXTRA-PAIR
FEP
GRANULAR
INTERLAYER
KSPACE
MACHDYN
MANYBODY
MC
MEAM
MISC
ML-IAP
ML-SNAP
MOFFF
MOLECULE
OPENMP
OPT
ORIENT
PERI
PHONON
PLUGIN
POEMS
PYTHON
QEQ
REACTION
REAXFF
REPLICA
RIGID
SHOCK
SPH
SPIN
SRD
TALLY
UEF
VORONOI
YAFF)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)

33
cmake/presets/nolib.cmake
View File

@ -1,11 +1,34 @@
# preset that turns off all packages that require some form of external
# library or special compiler (fortran or cuda) or equivalent.
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MESSAGE MPIIO MSCG
PYTHON VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB USER-MOLFILE USER-MESONT
USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS
USER-SMD USER-VTK)
set(PACKAGES_WITH_LIB
ADIOS
ATC
AWPMD
COMPRESS
GPU
H5MD
KIM
KOKKOS
LATBOLTZ
LATTE
MACHDYN
MDI
MESONT
MESSAGE
ML-HDNNP
ML-PACE
ML-QUIP
MOLFILE
MPIIO
MSCG
NETCDF
PLUMED
PYTHON
QMMM
SCAFACOS
VORONOI
VTK)
foreach(PKG ${PACKAGES_WITH_LIB})
set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

14
cmake/presets/oneapi.cmake
View File

@ -1,12 +1,22 @@
# preset that will enable the LLVM based Intel compilers with support for MPI and OpenMP (on Linux boxes)
# preset that will enable the LLVM based Intel compilers with support for MPI and OpenMP and Fortran (on Linux boxes)
set(CMAKE_CXX_COMPILER "icpx" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "icx" CACHE STRING "" FORCE)
set(CMAKE_Fortran_COMPILER "ifx" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_CXX "icpx" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "icx" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-qopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)

26
cmake/presets/pedantic.cmake Normal file
View File

@ -0,0 +1,26 @@
# preset that will restore gcc/g++ with support for MPI and OpenMP (on Linux boxes)
set(CMAKE_CXX_COMPILER "g++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)
set(CMAKE_Fortran_COMPILER "gfortran" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -Werror=vla -Wno-maybe-uninitialized -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -Werror=vla -Wno-maybe-uninitialized -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-Wall -O3 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_CXX "g++" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
set(MPI_C "gcc" CACHE STRING "" FORCE)
set(MPI_C_COMPILER "mpicc" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -Wno-maybe-uninitialized -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -Wno-maybe-uninitialized -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-Wall -O3 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_Fortran "gfortran" CACHE STRING "" FORCE)
set(MPI_Fortran_COMPILER "mpifort" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "gcc" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "gomp" CACHE STRING "" FORCE)
set(OpenMP_CXX "g++" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_CXX_LIB_NAMES "gomp" CACHE STRING "" FORCE)
set(OpenMP_omp_LIBRARY "libgomp.so" CACHE PATH "" FORCE)

64
cmake/presets/windows.cmake Normal file
View File

@ -0,0 +1,64 @@
set(WIN_PACKAGES
ASPHERE
BOCS
BODY
BROWNIAN
CG-DNA
CG-SDK
CLASS2
COLLOID
COLVARS
CORESHELL
DIELECTRIC
DIFFRACTION
DIPOLE
DPD-BASIC
DPD-MESO
DPD-REACT
DPD-SMOOTH
DRUDE
EFF
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
EXTRA-MOLECULE
EXTRA-PAIR
FEP
GRANULAR
INTERLAYER
KSPACE
MANIFOLD
MANYBODY
MC
MEAM
MISC
ML-IAP
ML-SNAP
MOFFF
MOLECULE
MOLFILE
OPENMP
ORIENT
PERI
PHONON
POEMS
PTM
QEQ
QTB
REACTION
REAXFF
REPLICA
RIGID
SHOCK
SMTBQ
SPH
SPIN
SRD
TALLY
UEF
YAFF)
foreach(PKG ${WIN_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)
endforeach()

18
doc/Makefile
View File

@ -10,7 +10,6 @@ endif
BUILDDIR = ${CURDIR}
RSTDIR = $(BUILDDIR)/src
VENV = $(BUILDDIR)/docenv
TXT2RST = $(VENV)/bin/txt2rst
ANCHORCHECK = $(VENV)/bin/rst_anchor_check
SPHINXCONFIG = $(BUILDDIR)/utils/sphinx-config
MATHJAX = $(SPHINXCONFIG)/_static/mathjax
@ -59,7 +58,7 @@ SPHINXEXTRA = -E -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiproc
# we only want to use explicitly listed files.
DOXYFILES = $(shell sed -n -e 's/\#.*$$//' -e '/^ *INPUT \+=/,/^[A-Z_]\+ \+=/p' doxygen/Doxyfile.in | sed -e 's/@LAMMPS_SOURCE_DIR@/..\/src/g' -e 's/\\//g' -e 's/ \+/ /' -e 's/[A-Z_]\+ \+= *\(YES\|NO\|\)//')
.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check xmlgen
.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check char_check xmlgen
# ------------------------------------------
@ -68,7 +67,6 @@ help:
@echo "Please use \`make <target>' where <target> is one of"
@echo " html create HTML pages in html dir"
@echo " pdf create Manual.pdf in this dir"
@echo " fetch fetch HTML and PDF files from LAMMPS web site"
@echo " epub create ePUB format manual for e-book readers"
@echo " mobi convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
@echo " (requires ebook-convert tool from calibre)"
@ -185,13 +183,6 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
@rm -rf latex/PDF/.[sg]*
@echo "Build finished. Manual.pdf is in this directory."
fetch:
@rm -rf html_www Manual_www.pdf
@curl -s -o Manual_www.pdf http://lammps.sandia.gov/doc/Manual.pdf
@curl -s -o lammps-doc.tar.gz http://lammps.sandia.gov/tars/lammps-doc.tar.gz
@tar xzf lammps-doc.tar.gz
@rm -f lammps-doc.tar.gz
anchor_check : $(ANCHORCHECK)
@(\
. $(VENV)/bin/activate ;\
@ -213,6 +204,9 @@ package_check : $(VENV)
deactivate ;\
)
char_check :
@( env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst && exit 1 || : )
xmlgen : doxygen/xml/index.xml
doxygen/Doxyfile: doxygen/Doxyfile.in
@ -236,9 +230,9 @@ $(VENV):
)
$(MATHJAX):
@git clone -b 3.1.4 -c advice.detachedHead=0 --depth 1 git://github.com/mathjax/MathJax.git $@
@git clone -b 3.2.0 -c advice.detachedHead=0 --depth 1 https://github.com/mathjax/MathJax.git $@
$(TXT2RST) $(ANCHORCHECK): $(VENV)
$(ANCHORCHECK): $(VENV)
@( \
. $(VENV)/bin/activate; \
(cd utils/converters;\

13
doc/README
View File

@ -25,16 +25,11 @@ github-development-workflow.md notes on the LAMMPS development workflow
include-file-conventions.md notes on LAMMPS' include file conventions
documentation_conventions.md notes on writing documentation for LAMMPS
If you downloaded a LAMMPS tarball from lammps.sandia.gov, then the html
If you downloaded a LAMMPS tarball from www.lammps.org, then the html
folder and the PDF manual should be included. If you downloaded LAMMPS
from GitHub then you either need to download them or build them.
from GitHub then you either need to build them.
(a) You can "fetch" the current HTML and PDF files from the LAMMPS web
site. Just type "make fetch". This should create a html_www directory
and Manual_www.pdf file. These will always represent the latest published
patch/development version of LAMMPS.
(b) You can build the HTML and PDF files yourself, by typing "make html"
You can build the HTML and PDF files yourself, by typing "make html"
or by "make pdf", respectively. This requires various tools and files.
Some of them have to be installed (more on that below). For the rest the
build process will attempt to download and install into a python virtual
@ -78,4 +73,4 @@ the tool 'ebook-convert' from the 'calibre' e-book management software
----------------
More details this can be found in the manual itself. The online
version is at: https://lammps.sandia.gov/doc/Manual_build.html
version is at: https://docs.lammps.org/Build_manual.html

2
doc/doxygen/Doxyfile.in
View File

@ -435,6 +435,8 @@ INPUT = @LAMMPS_SOURCE_DIR@/utils.cpp \
@LAMMPS_SOURCE_DIR@/my_pool_chunk.cpp \
@LAMMPS_SOURCE_DIR@/my_pool_chunk.h \
@LAMMPS_SOURCE_DIR@/math_eigen.h \
@LAMMPS_SOURCE_DIR@/platform.h \
@LAMMPS_SOURCE_DIR@/platform.cpp \
# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
# directories that are symbolic links (a Unix file system feature) are excluded

141
doc/github-development-workflow.md
View File

@ -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 2018-12-19.
adapt accordingly. Last change 2021-09-02.
## Table of Contents
@ -23,19 +23,19 @@ adapt accordingly. Last change 2018-12-19.
In the interest of consistency, ONLY ONE of the core LAMMPS developers
should doing the merging itself. This is currently
[@akohlmey](https://github.com/akohlmey) (Axel Kohlmeyer).
If this assignment needs to be changed, it shall be done right after a
stable release. If the currently assigned developer cannot merge outstanding pull
requests in a timely manner, or in other extenuating circumstances,
[@akohlmey](https://github.com/akohlmey) (Axel Kohlmeyer). If this
assignment needs to be changed, it shall be done right after a stable
release. If the currently assigned developer cannot merge outstanding
pull requests in a timely manner, or in other extenuating circumstances,
other core LAMMPS developers with merge rights can merge pull requests,
when necessary.
## Pull Requests
ALL changes to the LAMMPS code and documentation, however trivial, MUST
be submitted as a pull request to GitHub. All changes to the "master"
be submitted as a pull request to GitHub. All changes to the "develop"
branch must be made exclusively through merging pull requests. The
"unstable" and "stable" branches, respectively are only to be updated
"release" and "stable" branches, respectively are only to be updated
upon patch or stable releases with fast-forward merges based on the
associated tags. Pull requests may also be submitted to (long-running)
feature branches created by LAMMPS developers inside the LAMMPS project,
@ -55,13 +55,14 @@ the required changes or ask the submitter of the pull request to implement
them. Even though, all LAMMPS developers may have write access to pull
requests (if enabled by the submitter, which is the default), only the
submitter or the assignee of a pull request may do so. During this
period the `work_in_progress` label shall be applied to the pull
period the `work_in_progress` label may be applied to the pull
request. The assignee gets to decide what happens to the pull request
next, e.g. whether it should be assigned to a different developer for
additional checks and changes, or is recommended to be merged. Removing
the `work_in_progress` label and assigning the pull request to the
developer tasked with merging signals that a pull request is ready to be
merged.
merged. In addition, a `ready_for_merge` label may also be assigned
to signal urgency to merge this pull request quickly.
### Pull Request Reviews
@ -97,108 +98,50 @@ rationale behind choices made. Exceptions to this policy are technical
discussions, that are centered on tools or policies themselves
(git, GitHub, c++) rather than on the content of the pull request.
### Checklist for Pull Requests
Here are some items to check:
* source and text files should not have CR/LF line endings (use dos2unix to remove)
* every new command or style should have documentation. The names of
source files (c++ and manual) should follow the name of the style.
(example: `src/fix_nve.cpp`, `src/fix_nve.h` for `fix nve` command,
implementing the class `FixNVE`, documented in `doc/src/fix_nve.rst`)
* all new style names should be lower case, the must be no dashes,
blanks, or underscores separating words, only forward slashes.
* new style docs should be added to the "overview" files in
`doc/src/Commands_*.rst`, `doc/src/{fixes,computes,pairs,bonds,...}.rst`
* check whether manual cleanly translates with `make html` and `make pdf`
* if documentation is (still) provided as a .txt file, convert to .rst
and remove the .txt file. For files in doc/txt the conversion is automatic.
* remove all .txt files in `doc/txt` that are out of sync with their .rst counterparts in `doc/src`
* check spelling of manual with `make spelling` in doc folder
* check style tables and command lists with `make style_check`
* new source files in packages should be added to `src/.gitignore`
* removed or renamed files in packages should be added to `src/Purge.list`
* C++ source files should use C++ style include files for accessing
C-library APIs, e.g. `#include <cstdlib>` instead of `#include <stdlib.h>`.
And they should use angular brackets instead of double quotes. Full list:
* assert.h -> cassert
* ctype.h -> cctype
* errno.h -> cerrno
* float.h -> cfloat
* limits.h -> climits
* math.h -> cmath
* complex.h -> complex
* setjmp.h -> csetjmp
* signal.h -> csignal
* stddef.h -> cstddef
* stdint.h -> cstdint
* stdio.h -> cstdio
* stdlib.h -> cstdlib
* string.h -> cstring
* time.h -> ctime
* Do NOT replace (as they are C++-11): `inttypes.h` and `stdint.h`.
* Code must follow the C++-11 standard. C++98-only is no longer accepted
* Code should use `nullptr` instead of `NULL` where applicable.
in individual special purpose packages
* indentation is 2 spaces per level
* there should be NO tabs and no trailing whitespace (review the "checkstyle" test on pull requests)
* 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.
exception is <string>, but it won't need to be explicitly included
since pointers.h already includes it. so std::string can be used directly.
* there MUST NOT be any "using namespace XXX;" statements in headers.
* static class members should be avoided at all cost.
* anything storing atom IDs should be using `tagint` and not `int`.
This can be flagged by the compiler only for pointers and only when
compiling LAMMPS with `-DLAMMPS_BIGBIG`.
* when including both `lmptype.h` (and using defines or macros from it)
and `mpi.h`, `lmptype.h` must be included first.
* see https://github.com/lammps/lammps/blob/master/doc/include-file-conventions.md
for general include file conventions and best practices
* when pair styles are added, check if settings for flags like
`single_enable`, `writedata`, `reinitflag`, `manybody_flag`
and others are correctly set and supported.
## GitHub Issues
The GitHub issue tracker is the location where the LAMMPS developers
and other contributors or LAMMPS users can report issues or bugs with
the LAMMPS code or request new features to be added. Feature requests
are usually indicated by a `[Feature Request]` marker in the subject.
Issues are assigned to a person, if this person is working on this
feature or working to resolve an issue. Issues that have nobody working
on them at the moment, have the label `volunteer needed` attached.
the LAMMPS code or request new features to be added. Bug reports have
a `[Bug]` marker in the subject line; suggestions for changes or
adding new functionality are indicated by a `[Feature Request]`
marker in the subject. This is automatically done when using the
corresponding template for submitting an issue. Issues may be assigned
to one or more developers, if they are working on this feature or
working to resolve an issue. Issues that have nobody working
on them at the moment or in the near future, have the label
`volunteer needed` attached.
When an issue, say `#125` is resolved by a specific pull request,
the comment for the pull request shall contain the text `closes #125`
or `fixes #125`, so that the issue is automatically deleted when
the pull request is merged.
the pull request is merged. The template for pull requests includes
a header where connections between pull requests and issues can be listed
and thus were this comment should be placed.
## Milestones and Release Planning
LAMMPS uses a continuous release development model with incremental
changes, i.e. significant effort is made - including automated pre-merge
testing - that the code in the branch "master" does not get broken.
More extensive testing (including regression testing) is performed after
code is merged to the "master" branch. There are patch releases of
LAMMPS every 1-3 weeks at a point, when the LAMMPS developers feel, that
a sufficient amount of changes have happened, and the post-merge testing
has been successful. These patch releases are marked with a
`patch_<version date>` tag and the "unstable" branch follows only these
versions (and thus is always supposed to be of production quality,
unlike "master", which may be temporary broken, in the case of larger
change sets or unexpected incompatibilities or side effects.
testing - that the code in the branch "develop" does not get easily
broken. These tests are run after every update to a pull request. More
extensive and time consuming tests (including regression testing) are
performed after code is merged to the "develop" branch. There are patch
releases of LAMMPS every 3-5 weeks at a point, when the LAMMPS
developers feel, that a sufficient amount of changes have happened, and
the post-merge testing has been successful. These patch releases are
marked with a `patch_<version date>` tag and the "release" branch
follows only these versions (and thus is always supposed to be of
production quality, unlike "develop", which may be temporary broken, in
the case of larger change sets or unexpected incompatibilities or side
effects.
About 3-4 times each year, there are going to be "stable" releases
of LAMMPS. These have seen additional, manual testing and review of
About 1-2 times each year, there are going to be "stable" releases of
LAMMPS. These have seen additional, manual testing and review of
results from testing with instrumented code and static code analysis.
Also, in the last 2-3 patch releases before a stable release are
"release candidate" versions which only contain bugfixes and
documentation updates. For release planning and the information of
code contributors, issues and pull requests being actively worked on
are assigned a "milestone", which corresponds to the next stable
release or the stable release after that, with a tentative release
date.
Also, the last 1-3 patch releases before a stable release are "release
candidate" versions which only contain bugfixes and documentation
updates. For release planning and the information of code contributors,
issues and pull requests being actively worked on are assigned a
"milestone", which corresponds to the next stable release or the stable
release after that, with a tentative release date.

128
doc/include-file-conventions.md
View File

@ -1,128 +0,0 @@
# Outline of include file conventions in LAMMPS
This purpose of this document is to provide a point of reference
for LAMMPS developers and contributors as to what include files
and definitions to put where into LAMMPS source.
Last change 2020-08-31
## Table of Contents
* [Motivation](#motivation)
* [Rules](#rules)
* [Tools](#tools)
* [Legacy Code](#legacy-code)
## Motivation
The conventions outlined in this document are supposed to help make
maintenance of the LAMMPS software easier. By trying to achieve
consistency across files contributed by different developers, it will
become easier for the code maintainers to modify and adjust files and,
overall, the chance for errors or portability issues will be reduced.
The rules employed are supposed to minimize naming conflicts and
simplify dependencies between files and thus speed up compilation. They
may, as well, make otherwise hidden dependencies visible.
## Rules
Below are the various rules that are applied. Not all are enforced
strictly and automatically. If there are no significant side effects,
exceptions may be possible for cases where a full compliance to the
rules may require a large effort compared to the benefit.
### Core Files Versus Package Files
All rules listed below are most strictly observed for core LAMMPS files,
which are the files that are not part of a package, and the files of the
packages MOLECULE, MANYBODY, KSPACE, and RIGID. On the other end of
the spectrum are USER packages and legacy packages that predate these
rules and thus may not be fully compliant. Also, new contributions
will be checked more closely, while existing code will be incrementally
adapted to the rules as time and required effort permits.
### System Versus Local Header Files
All system- or library-provided include files are included with angular
brackets (examples: `#include <cstring>` or `#include <mpi.h>`) while
include files provided with LAMMPS are included with double quotes
(examples: `#include "pointers.h"` or `#include "compute_temp.h"`).
For headers declaring functions of the C-library, the corresponding
C++ versions should be included (examples: `#include <cstdlib>` or
`#include <cctypes>` instead of `#include <stdlib.h>` or
`#include<ctypes.h>` ).
### C++ Standard Compliance
LAMMPS core files use standard conforming C++ compatible with the
C++11 standard, unless explicitly noted. Also, LAMMPS uses the C-style
stdio library for I/O instead of iostreams. Since using both at the
same time can cause problems, iostreams should be avoided where possible.
### Lean Header Files
Header files will typically contain the definition of a (single) class.
These header files should have as few include statements as possible.
This is particularly important for classes that implement a "style" and
thus use a macro of the kind `SomeStyle(some/name,SomeName)`. These will
all be included in the auto-generated `"some_style.h"` files which
results in a high potential for direct or indirect symbol name clashes.
In the ideal case, the header would only include one file defining the
parent class. That would typically be either `#include "pointers.h"` for
the `Pointers` class, or a header of a class derived from it like
`#include "pair.h"` for the `Pair` class and so on. References to other
classes inside the class should be make through pointers, for which forward
declarations (inside the `LAMMPS_NS` or the new class' namespace) can
be employed. The full definition will then be included into the corresponding
implementation file. In the given example from above, the header file
would be called `some_name.h` and the implementation `some_name.cpp` (all
lower case with underscores, while the class itself would be in camel case
and no underscores `SomeName`, and the style name with lower case names separated by
a forward slash).
### Implementation Files
In the implementation files (typically, those would have the same base name
as the corresponding header with a .cpp extension instead of .h) include
statements should follow the "include what you use" principle.
### Order of Include Statements
Include files should be included in this order:
* the header matching the implementation (`some_class.h` for file `some_class.cpp`)
* mpi.h (only if needed)
* LAMMPS local headers (preferably in alphabetical order)
* system and library headers (anything that is using angular brackets; preferably in alphabetical order)
* conditional include statements (i.e. anything bracketed with ifdefs)
### Special Cases and Exceptions
#### pointers.h
The `pointer.h` header file also includes (in this order) `lmptype.h`,
`mpi.h`, `cstddef`, `cstdio`, `string`, `utils.h`, and `fmt/format.h`
and through `lmptype.h` indirectly also `climits`, `cstdlib`, `cinttypes`.
This means any header including `pointers.h` can assume that `FILE`,
`NULL`, `INT_MAX` are defined, and the may freely use the std::string
for arguments. Corresponding implementation files do not need to include
those headers.
## Tools
The [Include What You Use tool](https://include-what-you-use.org/)
can be used to provide supporting information about compliance with
the rules listed here. Through setting `-DENABLE_IWYU=on` when running
CMake, a custom build target is added that will enable recording
the compilation commands and then run the `iwyu_tool` using the
recorded compilation commands information when typing `make iwyu`.
## Legacy Code
A lot of code predates the application of the rules in this document
and the rules themselves are a moving target. So there are going to be
significant chunks of code that do not fully comply. This applies
for example to the USER-REAXC, or the USER-ATC package. The LAMMPS
developers are dedicated to make an effort to improve the compliance
and welcome volunteers wanting to help with the process.

59
doc/lammps.1
View File

@ -1,4 +1,4 @@
.TH LAMMPS "8 April 2021" "2021-04-08"
.TH LAMMPS "1" "27 October 2021" "2021-10-27"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator.
@ -34,7 +34,7 @@ semiconductors) and coarse-grained or mesoscopic systems. It can be used to
model atoms or, more generically, as a parallel particle simulator at the
atomic, meso, or continuum scale.
See https://lammps.sandia.gov/ for more information and documentation.
See https://www.lammps.org/ for more information and documentation.
.SH EXECUTABLE NAME
The
@ -54,7 +54,7 @@ using
this <machine name> parameter can be chosen arbitrarily at configuration
time, but more common is to just use
.B lmp
without a suffix. In this manpage we will use
without a suffix. In this man page we will use
.B lmp
to represent any of those names.
@ -94,7 +94,7 @@ Enable or disable general KOKKOS support, as provided by the KOKKOS
package. Even if LAMMPS is built with this package, this switch must
be set to \fBon\fR to enable running with KOKKOS-enabled styles. More
details on this switch and its optional keyword value pairs are discussed
at: https://lammps.sandia.gov/doc/Run_options.html
at: https://docs.lammps.org/Run_options.html
.TP
\fB\-l <log file>\fR or \fB\-log <log file>\fR
Specify a log file for LAMMPS to write status information to.
@ -122,6 +122,38 @@ to perform client/server messaging with another application.
.B LAMMPS
can act as either a client or server (or both).
.TP
\fB\-mdi '<mdi_flags>'\fR
This flag is only recognized and used when
.B LAMMPS
has support for the MolSSI
Driver Interface (MDI) included as part of the MDI package. This flag is
specific to the MDI library and controls how
.B LAMMPS
interacts with MDI. There are usually multiple flags that have to follow it
and those have to be placed in quotation marks. For more information about
how to launch LAMMPS in MDI client/server mode please refer to the
MDI How-to at https://docs.lammps.org/Howto_mdi.html
.TP
\fB\-c\fR or \fB\-cite <style or filename>\fR
Select how and where to output a reminder about citing contributions
to the
.B LAMMPS
code that were used during the run. Available keywords
for styles are "both", "none", "screen", or "log". Any other keyword
will be considered a file name to write the detailed citation info to
instead of logfile or screen. Default is the "log" style where there
is a short summary in the screen output and detailed citations
in BibTeX format in the logfile. The option "both" selects the detailed
output for both, "none", the short output for both, and "screen" will
write the detailed info to the screen and the short version to the log
file. If a dedicated citation info file is requested, the screen and
log file output will be in the short format (same as with "none").
See https://docs.lammps.org/Intro_citing.html for more details on
how to correctly reference and cite
.B LAMMPS
.
.TP
\fB\-nc\fR or \fB\-nocite\fR
Disable writing the "log.cite" file which is normally written to
list references for specific cite-able features used during a
@ -135,7 +167,7 @@ For example "-pk gpu 2" is the same as "package gpu 2" in the input
script. The possible styles and options are discussed in the
.B LAMMPS
manual for the "package" command. This switch can be used multiple
times, e.g. to set options for the USER-INTEL and USER-OMP packages
times, e.g. to set options for the INTEL and OPENMP packages
when used together. Along with the "-sf" or "-suffix" switch, this
is a convenient mechanism for invoking accelerator packages and their
options without having to edit an input script.
@ -202,7 +234,7 @@ the standard output. If <file name> is "none", (most) screen
output will be suppressed. In multi-partition mode only
some high-level all-partition information is written to the
screen or "<file name>" file, the remainder is written in a
per-partition file "screen.N" or "<file name>.N"
per-partition file "screen.N" or "<file name>.N"
with "N" being the respective partition number, and unless
overridden by the \-pscreen flag (see above).
.TP
@ -218,8 +250,19 @@ and then "omp") and thus requires two arguments. Along with the
"-package" command-line switch, this is a convenient mechanism for
invoking styles from accelerator packages and setting their options
without having to edit an input script.
.TP
\fB\-sr\fR or \fB\-skiprun\fR
Insert the command "timer timeout 0 every 1" at the
beginning of an input file or after a "clear" command.
This has the effect that the entire
.B LAMMPS
input script is processed without executing actual
"run" or "minimize" or similar commands (their main loops are skipped).
This can be helpful and convenient to test input scripts of long running
calculations for correctness to avoid having them crash after a
long time due to a typo or syntax error in the middle or at the end.
See https://lammps.sandia.gov/doc/Run_options.html for additional
See https://docs.lammps.org/Run_options.html for additional
details and discussions on command-line options.
.SH LAMMPS BASICS
@ -254,7 +297,7 @@ the chapter on errors in the
manual gives some additional information about error messages, if possible.
.SH COPYRIGHT
© 2003--2020 Sandia Corporation
© 2003--2021 Sandia Corporation
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License version 2 as

4
doc/msi2lmp.1
View File

@ -1,4 +1,4 @@
.TH MSI2LMP "v3.9.9" "2018-11-05"
.TH MSI2LMP "1" "v3.9.9" "2018-11-05"
.SH NAME
.B MSI2LMP
\- Converter for Materials Studio files to LAMMPS
@ -98,7 +98,7 @@ msi2lmp decane -c 0 -f oplsaa
.SH COPYRIGHT
© 2003--2019 Sandia Corporation
© 2003--2021 Sandia Corporation
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License version 2 as

10
doc/src/Bibliography.rst
View File

@ -191,7 +191,7 @@ Bibliography
A.\ Calhoun, M. Pavese, G. Voth, Chem Phys Letters, 262, 415 (1996).
**(Campana)**
C.\ Campana and M. H. Muser, *Practical Green's function approach to the simulation of elastic semi-infinite solids*\ , `Phys. Rev. B [74], 075420 (2006) <https://doi.org/10.1103/PhysRevB.74.075420>`_
C.\ Campana and M. H. Muser, *Practical Green's function approach to the simulation of elastic semi-infinite solids*, `Phys. Rev. B [74], 075420 (2006) <https://doi.org/10.1103/PhysRevB.74.075420>`_
**(Cao1)**
J.\ Cao and B. Berne, J Chem Phys, 99, 2902 (1993).
@ -767,7 +767,7 @@ Bibliography
Morris, Fox, Zhu, J Comp Physics, 136, 214-226 (1997).
**(Moustafa)**
Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, *Very fast averaging of thermal properties of crystals by molecular simulation*\ , `Phys. Rev. E [92], 043303 (2015) <https://link.aps.org/doi/10.1103/PhysRevE.92.043303>`_
Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, *Very fast averaging of thermal properties of crystals by molecular simulation*, `Phys. Rev. E [92], 043303 (2015) <https://link.aps.org/doi/10.1103/PhysRevE.92.043303>`_
**(Muller-Plathe1)**
Muller-Plathe, J Chem Phys, 106, 6082 (1997).
@ -1129,6 +1129,9 @@ Bibliography
**(Sutmann)**
Sutmann, Arnold, Fahrenberger, et. al., Physical review / E 88(6), 063308 (2013)
**(Sutmann)** G. Sutmann. ScaFaCoS - a Scalable library of Fast Coulomb Solvers for particle Systems.
In Bajaj, Zavattieri, Koslowski, Siegmund, Proceedings of the Society of Engineering Science 51st Annual Technical Meeting. 2014.
**(Swinburne)**
Swinburne and Marinica, Physical Review Letters, 120, 1 (2018)
@ -1285,9 +1288,6 @@ Bibliography
**(Wennberg)**
Wennberg, Murtola, Hess, Lindahl, J Chem Theory Comput, 9, 3527 (2013).
**(Who)**
Who, Author2, Author3, J of Long Range Solvers, 35, 164-177 (2012).
**(Wicaksono1)**
Wicaksono, Sinclair, Militzer, Computational Materials Science, 117, 397-405 (2016).

1
doc/src/Build.rst
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@ -22,4 +22,5 @@ page.
Build_extras
Build_manual
Build_windows
Build_diskspace
Build_development

22
doc/src/Build_basics.rst
View File

@ -90,7 +90,7 @@ standard. A more detailed discussion of that is below.
directory, or ``make`` from the ``src/STUBS`` dir. If the build
fails, you may need to edit the ``STUBS/Makefile`` for your
platform. The stubs library does not provide MPI/IO functions
required by some LAMMPS packages, e.g. ``MPIIO`` or ``USER-LB``,
required by some LAMMPS packages, e.g. ``MPIIO`` or ``LATBOLTZ``,
and thus is not compatible with those packages.
.. note::
@ -120,19 +120,19 @@ self-installed MPICH or OpenMPI, so you should study the provided
documentation to find out how to build and link with it.
The majority of OpenMP (threading) support in LAMMPS is provided by the
``USER-OMP`` package; see the :doc:`Speed_omp`
page for details. The ``USER-INTEL`` package also includes OpenMP
threading (it is compatible with ``USER-OMP`` and will usually fall
back on styles from that package, if a ``USER-INTEL`` does not exist)
``OPENMP`` package; see the :doc:`Speed_omp`
page for details. The ``INTEL`` package also includes OpenMP
threading (it is compatible with ``OPENMP`` and will usually fall
back on styles from that package, if a ``INTEL`` does not exist)
and adds vectorization support when compiled with compatible compilers,
in particular the Intel compilers on top of OpenMP. Also, the ``KOKKOS``
package can be compiled to include OpenMP threading.
In addition, there are a few commands in LAMMPS that have native OpenMP
support included as well. These are commands in the ``MPIIO``,
``SNAP``, ``USER-DIFFRACTION``, and ``USER-DPD`` packages. In addition
``ML-SNAP``, ``DIFFRACTION``, and ``DPD-REACT`` packages. In addition
some packages support OpenMP threading indirectly through the libraries
they interface to: e.g. ``LATTE``, ``KSPACE``, and ``USER-COLVARS``.
they interface to: e.g. ``LATTE``, ``KSPACE``, and ``COLVARS``.
See the :doc:`Packages details <Packages_details>` page for more
info on these packages and the pages for their respective commands
for OpenMP threading info.
@ -176,7 +176,7 @@ performance. Vendor provided compilers for a specific hardware can
produce faster code than open-source compilers like the GNU compilers.
On the most common x86 hardware most popular C++ compilers are quite
similar in performance of C/C++ code at high optimization levels. When
using the ``USER-INTEL`` package, there is a distinct advantage in using
using the ``INTEL`` package, there is a distinct advantage in using
the `Intel C++ compiler <intel_>`_ due to much improved vectorization
through SSE and AVX instructions on compatible hardware as the source
code includes changes and Intel compiler specific directives to enable
@ -325,9 +325,9 @@ LAMMPS.
.. code-block:: bash
Makefile.opt # OPT package
Makefile.omp # USER-OMP package
Makefile.intel_cpu # USER-INTEL package for CPUs
Makefile.intel_coprocessor # USER-INTEL package for KNLs
Makefile.omp # OPENMP package
Makefile.intel_cpu # INTEL package for CPUs
Makefile.intel_coprocessor # INTEL package for KNLs
Makefile.gpu # GPU package
Makefile.kokkos_cuda_mpi # KOKKOS package for GPUs
Makefile.kokkos_omp # KOKKOS package for CPUs (OpenMP)

38
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@ -140,7 +140,7 @@ can be used several times in one command.
For your convenience we provide :ref:`CMake presets <cmake_presets>`
that combine multiple settings to enable optional LAMMPS packages or use
a different compiler tool chain. Those are loaded with the *-C* flag
(``-C ../cmake/presets/minimal.cmake``). This step would only be needed
(``-C ../cmake/presets/basic.cmake``). This step would only be needed
once, as the settings from the preset files are stored in the
``CMakeCache.txt`` file. It is also possible to customize the build
by adding one or more *-D* flags to the CMake command line.
@ -150,6 +150,42 @@ for IDEs like Eclipse, CodeBlocks, or Kate can be selected using the *-G*
command line flag. A list of available generator settings for your
specific CMake version is given when running ``cmake --help``.
.. _cmake_multiconfig:
Multi-configuration build systems
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Throughout this manual it is mostly assumed that LAMMPS is being built
on a Unix-like operating system with "make" as the underlying "builder",
since this is the most common case. In this case the build "configuration"
is chose using ``-D CMAKE_BUILD_TYPE=<configuration>`` with ``<configuration>``
being one of "Release", "Debug", "RelWithDebInfo", or "MinSizeRel".
Some build tools, however, can also use or even require to have a so-called
multi-configuration build system setup. For those the built type (or
configuration) is chosen at compile time using the same build files. E.g.
with:
.. code-block:: bash
cmake --build build-multi --config Release
In that case the resulting binaries are not in the build folder directly
but in sub-directories corresponding to the build type (i.e. Release in
the example from above). Similarly, for running unit tests the
configuration is selected with the *-C* flag:
.. code-block:: bash
ctest -C Debug
The CMake scripts in LAMMPS have basic support for being compiled using a
multi-config build system, but not all of it has been ported. This is in
particular applicable to compiling packages that require additional libraries
that would be downloaded and compiled by CMake. The "windows" preset file
tries to keep track of which packages can be compiled natively with the
MSVC compilers out-of-the box. Not all of those external libraries are
portable to Windows either.
Installing CMake
^^^^^^^^^^^^^^^^

121
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@ -1,15 +1,15 @@
Development build options (CMake only)
======================================
Development build options
=========================
The CMake build procedure of LAMMPS offers a few extra options which are
The build procedures in LAMMPS offers a few extra options which are
useful during development, testing or debugging.
----------
.. _compilation:
Monitor compilation flags
-------------------------
Monitor compilation flags (CMake only)
--------------------------------------
Sometimes it is necessary to verify the complete sequence of compilation flags
generated by the CMake build. To enable a more verbose output during
@ -28,22 +28,46 @@ variable VERBOSE set to 1:
----------
.. _clang-tidy:
Enable static code analysis with clang-tidy (CMake only)
--------------------------------------------------------
The `clang-tidy tool <https://clang.llvm.org/extra/clang-tidy/>`_ is a
static code analysis tool to diagnose (and potentially fix) typical
programming errors or coding style violations. It has a modular framework
of tests that can be adjusted to help identifying problems before they
become bugs and also assist in modernizing large code bases (like LAMMPS).
It can be enabled for all C++ code with the following CMake flag
.. code-block:: bash
-D ENABLE_CLANG_TIDY=value # value = no (default) or yes
With this flag enabled all source files will be processed twice, first to
be compiled and then to be analyzed. Please note that the analysis can be
significantly more time consuming than the compilation itself.
----------
.. _iwyu_processing:
Report missing and unneeded '#include' statements
-------------------------------------------------
Report missing and unneeded '#include' statements (CMake only)
--------------------------------------------------------------
The conventions for how and when to use and order include statements in
LAMMPS are `documented in a separate file <https://github.com/lammps/lammps/blob/master/doc/include-file-conventions.md>`_
(also included in the source code distribution). To assist with following
LAMMPS are documented in :doc:`Modify_style`. To assist with following
these conventions one can use the `Include What You Use tool <https://include-what-you-use.org/>`_.
This is still under development and for large and complex projects like LAMMPS
This tool is still under development and for large and complex projects like LAMMPS
there are some false positives, so suggested changes need to be verified manually.
It is recommended to use at least version 0.14, which has much fewer incorrect
reports than earlier versions.
It is recommended to use at least version 0.16, which has much fewer incorrect
reports than earlier versions. To install the IWYU toolkit, you need to have
the clang compiler **and** its development package installed. Download the IWYU
version that matches the version of the clang compiler, configure, build, and
install it.
The necessary steps to generate the report can be enabled via a
CMake variable:
The necessary steps to generate the report can be enabled via a CMake variable
during CMake configuration.
.. code-block:: bash
@ -64,8 +88,8 @@ on recording all commands required to do the compilation.
.. _sanitizer:
Address, Undefined Behavior, and Thread Sanitizer Support
---------------------------------------------------------
Address, Undefined Behavior, and Thread Sanitizer Support (CMake only)
----------------------------------------------------------------------
Compilers such as GCC and Clang support generating instrumented binaries
which use different sanitizer libraries to detect problems in the code
@ -94,8 +118,8 @@ compilation and linking stages. This is done through setting the
.. _testing:
Code Coverage and Unit Testing
------------------------------
Code Coverage and Unit Testing (CMake only)
-------------------------------------------
The LAMMPS code is subject to multiple levels of automated testing
during development: integration testing (i.e. whether the code compiles
@ -288,7 +312,7 @@ and working.
parameter needs to be adjusted. Typically a value around 1.0e-13
can be used, but it may need to be as large as 1.0e-8 in some
cases.
- The tests for pair styles from OPT, USER-OMP and USER-INTEL are
- The tests for pair styles from OPT, OPENMP and INTEL are
performed with automatically rescaled epsilon to account for
additional loss of precision from code optimizations and different
summation orders.
@ -323,7 +347,7 @@ and compared. If the fix is a thermostat and thus the internal property
``t_target`` can be extracted, then this is compared to the reference
data. The tests are repeated with the respa run style.
If the fix has a multi-threaded version in the USER-OMP package, then
If the fix has a multi-threaded version in the OPENMP package, then
the entire set of tests is repeated for that version as well.
For this to work, some additional conditions have to be met by the
@ -442,17 +466,56 @@ Coding style utilities
To aid with enforcing some of the coding style conventions in LAMMPS
some additional build targets have been added. These require Python 3.5
or later and will only work on Unix-like operating and file systems.
or later and will only work properly on Unix-like operating and file systems.
The following options are available.
.. code-block:: bash
make check-whitespace # generate coverage report in HTML format
make fix-whitespace # generate coverage report in XML format
make check-permissions # delete folder with HTML format coverage report
make fix-permissions # delete all collected coverage data and HTML output
make check-whitespace # search for files with whitespace issues
make fix-whitespace # correct whitespace issues in files
make check-homepage # search for files with old LAMMPS homepage URLs
make fix-homepage # correct LAMMPS homepage URLs in files
make check-permissions # search for files with permissions issues
make fix-permissions # correct permissions issues in files
For the code in the ``unittest`` tree we are using the `clang-format`
tool (Clang version 8.0 or later is required). If available, the source
code files in the ``unittest`` tree can be updated to conform to the
formatting settings using ``make format-tests``.
These should help to replace all TAB characters with blanks and remove
any trailing whitespace. Also all LAMMPS homepage URL references can be
updated to the location change from Sandia to the lammps.org domain.
And the permission check can remove executable permissions from non-executable
files (like source code).
Clang-format support
--------------------
For the code in the ``unittest`` and ``src`` trees we are transitioning
to use the `clang-format` tool to assist with having a consistent source
code formatting style. The `clang-format` command bundled with Clang
version 8.0 or later is required. The configuration is in files called
``.clang-format`` in the respective folders. Since the modifications
from `clang-format` can be significant and - especially for "legacy
style code" - they are not always improving readability, a large number
of files currently have a ``// clang-format off`` at the top, which will
disable the processing. As of fall 2021 all files have been either
"protected" this way or are enabled for full or partial `clang-format`
processing. Over time, the "protected" files will be refactored and
updated so that `clang-format` may be applied to them as well.
It is recommended for all newly contributed files to use the clang-format
processing while writing the code or do the coding style processing
(including the scripts mentioned in the previous paragraph)
If `clang-format` is available, files can be updated individually with
commands like the following:
.. code-block:: bash
$ clang-format -i some_file.cpp
The following target are available for both, GNU make and CMake:
.. code-block:: bash
make format-src # apply clang-format to all files in src and the package folders
make format-tests # apply clang-format to all files in the unittest tree

45
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@ -0,0 +1,45 @@
Notes for saving disk space when building LAMMPS from source
------------------------------------------------------------
LAMMPS is a large software project with a large number of source files,
extensive documentation, and a large collection of example files.
When downloading LAMMPS by cloning the
`git repository from GitHub <https://github.com/lammps/lammps>`_ this
will by default also download the entire commit history since September 2006.
Compiling LAMMPS will add the storage requirements of the compiled object
files and libraries to the tally.
In a user account on an HPC cluster with filesystem quotas or in other
environments with restricted disk space capacity it may be needed to
reduce the storage requirements. Here are some suggestions:
- Create a so-called shallow repository by cloning only the last commit
instead of the full project history by using ``git clone git@github.com:lammps/lammps --depth=1 --branch=develop``.
This reduces the downloaded size to about half. With ``--depth=1`` it is not possible to check out different
versions/branches of LAMMPS, using ``--depth=1000`` will make multiple recent versions available at little
extra storage needs (the entire git history had nearly 30,000 commits in fall 2021).
- Download a tar archive from either the `download section on the LAMMPS homepage <https://www.lammps.org/download.html>`_
or from the `LAMMPS releases page on GitHub <https://github.com/lammps/lammps/releases>`_ these will not
contain the git history at all.
- Build LAMMPS without the debug flag (remove ``-g`` from the machine makefile or use ``-DCMAKE_BUILD_TYPE=Release``)
or use the ``strip`` command on the LAMMPS executable when no more debugging would be needed. The strip command
may also be applied to the LAMMPS shared library. The static library may be deleted entirely.
- Delete compiled object files and libraries after copying the LAMMPS executable to a permanent location.
When using the traditional build process, one may use ``make clean-<machine>`` or ``make clean-all``
to delete object files in the src folder. For CMake based builds, one may use ``make clean`` or just
delete the entire build folder.
- The folders containing the documentation tree (doc), the examples (examples) are not needed to build and
run LAMMPS and can be safely deleted. Some files in the potentials folder are large and may be deleted,
if not needed. The largest of those files (occupying about 120 MBytes combined) will only be downloaded on
demand, when the corresponding package is installed.
- When using the CMake build procedure, the compilation can be done on a (local) scratch storage that will not
count toward the quota. A local scratch file system may offer the additional benefit of speeding up creating
object files and linking with libraries compared to a networked file system. Also with CMake (and unlike with
the traditional make) it is possible to compile LAMMPS executables with different settings and packages included
from the same source tree since all the configuration information is stored in the build folder. So it is
not necessary to have multiple copies of LAMMPS.

298
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@ -31,36 +31,37 @@ This is the list of packages that may require additional steps.
.. table_from_list::
:columns: 6
* :ref:`ADIOS <adios>`
* :ref:`ATC <atc>`
* :ref:`AWPMD <awpmd>`
* :ref:`COLVARS <colvars>`
* :ref:`COMPRESS <compress>`
* :ref:`GPU <gpu>`
* :ref:`H5MD <h5md>`
* :ref:`INTEL <intel>`
* :ref:`KIM <kim>`
* :ref:`KOKKOS <kokkos>`
* :ref:`LATTE <latte>`
* :ref:`MACHDYN <machdyn>`
* :ref:`MDI <mdi>`
* :ref:`MESONT <mesont>`
* :ref:`MESSAGE <message>`
* :ref:`MLIAP <mliap>`
* :ref:`ML-HDNNP <ml-hdnnp>`
* :ref:`ML-IAP <mliap>`
* :ref:`ML-PACE <ml-pace>`
* :ref:`ML-QUIP <ml-quip>`
* :ref:`MOLFILE <molfile>`
* :ref:`MSCG <mscg>`
* :ref:`NETCDF <netcdf>`
* :ref:`OPENMP <openmp>`
* :ref:`OPT <opt>`
* :ref:`PLUMED <plumed>`
* :ref:`POEMS <poems>`
* :ref:`PYTHON <python>`
* :ref:`QMMM <qmmm>`
* :ref:`SCAFACOS <scafacos>`
* :ref:`VORONOI <voronoi>`
* :ref:`USER-ADIOS <user-adios>`
* :ref:`USER-ATC <user-atc>`
* :ref:`USER-AWPMD <user-awpmd>`
* :ref:`USER-COLVARS <user-colvars>`
* :ref:`USER-H5MD <user-h5md>`
* :ref:`USER-INTEL <user-intel>`
* :ref:`USER-MDI <user-mdi>`
* :ref:`USER-MESONT <user-mesont>`
* :ref:`USER-MOLFILE <user-molfile>`
* :ref:`USER-NETCDF <user-netcdf>`
* :ref:`USER-PACE <user-pace>`
* :ref:`USER-PLUMED <user-plumed>`
* :ref:`USER-OMP <user-omp>`
* :ref:`USER-QMMM <user-qmmm>`
* :ref:`USER-QUIP <user-quip>`
* :ref:`USER-SCAFACOS <user-scafacos>`
* :ref:`USER-SMD <user-smd>`
* :ref:`USER-VTK <user-vtk>`
* :ref:`VTK <vtk>`
----------
@ -73,7 +74,8 @@ To build with this package you must have the `zlib compression library
<https://zlib.net>`_ available on your system to build dump styles with
a '/gz' suffix. There are also styles using the
`Zstandard <https://facebook.github.io/zstd/>`_ library which have a
'/zstd' suffix.
'/zstd' suffix. The zstd library version must be at least 1.4. Older
versions use an incompatible API and thus LAMMPS will fail to compile.
.. tabs::
@ -456,6 +458,9 @@ They must be specified in uppercase.
* - ZEN2
- HOST
- AMD Zen2 class CPU (AVX 2)
* - ZEN3
- HOST
- AMD Zen3 class CPU (AVX 2)
* - ARMV80
- HOST
- ARMv8.0 Compatible CPU
@ -559,7 +564,7 @@ They must be specified in uppercase.
- GPU
- Intel GPUs Gen9+
This list was last updated for version 3.4 of the Kokkos library.
This list was last updated for version 3.4.1 of the Kokkos library.
.. tabs::
@ -618,7 +623,7 @@ This list was last updated for version 3.4 of the Kokkos library.
mkdir build-kokkos-cuda
cd build-kokkos-cuda
cmake -C ../cmake/presets/minimal.cmake -C ../cmake/presets/kokkos-cuda.cmake ../cmake
cmake -C ../cmake/presets/basic.cmake -C ../cmake/presets/kokkos-cuda.cmake ../cmake
cmake --build .
.. tab:: Basic traditional make settings:
@ -807,16 +812,17 @@ be installed on your system.
.. _mliap:
MLIAP package
ML-IAP package
---------------------------
Building the MLIAP package requires including the :ref:`SNAP <PKG-SNAP>`
package. There will be an error message if this requirement is not satisfied.
Using the *mliappy* model also requires enabling Python support, which
in turn requires the :ref:`PYTHON <PKG-PYTHON>`
package **and** requires you have the `cython <https://cython.org>`_ software
installed and with it a working ``cythonize`` command. This feature requires
compiling LAMMPS with Python version 3.6 or later.
Building the ML-IAP package requires including the :ref:`ML-SNAP
<PKG-ML-SNAP>` package. There will be an error message if this requirement
is not satisfied. Using the *mliappy* model also requires enabling
Python support, which in turn requires to include the :ref:`PYTHON
<PKG-PYTHON>` package **and** requires to have the `cython
<https://cython.org>`_ software installed and with it a working
``cythonize`` command. This feature requires compiling LAMMPS with
Python version 3.6 or later.
.. tabs::
@ -830,9 +836,9 @@ compiling LAMMPS with Python version 3.6 or later.
suitable Python version and the ``cythonize`` command and choose
the default accordingly. During the build procedure the provided
.pyx file(s) will be automatically translated to C++ code and compiled.
Please do **not** run ``cythonize`` manually in the ``src/MLIAP`` folder,
Please do **not** run ``cythonize`` manually in the ``src/ML-IAP`` folder,
as that can lead to compilation errors if Python support is not enabled.
If you did by accident, please remove the generated .cpp and .h files.
If you did it by accident, please remove the generated .cpp and .h files.
.. tab:: Traditional make
@ -841,15 +847,16 @@ compiling LAMMPS with Python version 3.6 or later.
the ``cythonize`` command in case the corresponding .pyx file(s) were
modified. You may need to modify ``lib/python/Makefile.lammps``
if the LAMMPS build fails.
To manually enforce building MLIAP with Python support enabled,
you can add
``-DMLIAP_PYTHON`` to the ``LMP_INC`` variable in your machine makefile.
You may have to manually run the ``cythonize`` command on .pyx file(s)
in the ``src`` folder, if this is not automatically done during
installing the MLIAP package. Please do **not** run ``cythonize``
in the ``src/MLIAP`` folder, as that can lead to compilation errors
if Python support is not enabled.
If you did by accident, please remove the generated .cpp and .h files.
To enable building the ML-IAP package with Python support enabled,
you need to add ``-DMLIAP_PYTHON`` to the ``LMP_INC`` variable in
your machine makefile. You may have to manually run the
``cythonize`` command on .pyx file(s) in the ``src`` folder, if
this is not automatically done during installing the ML-IAP
package. Please do **not** run ``cythonize`` in the ``src/ML-IAP``
folder, as that can lead to compilation errors if Python support
is not enabled. If you did this by accident, please remove the
generated .cpp and .h files.
----------
@ -1050,12 +1057,12 @@ binary package provided by your operating system.
----------
.. _user-adios:
.. _adios:
USER-ADIOS package
ADIOS package
-----------------------------------
The USER-ADIOS package requires the `ADIOS I/O library
The 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
@ -1071,38 +1078,38 @@ systems.
.. code-block:: bash
-D ADIOS2_DIR=path # path is where ADIOS 2.x is installed
-D PKG_USER-ADIOS=yes
-D PKG_ADIOS=yes
.. tab:: Traditional make
Turn on the USER-ADIOS package before building LAMMPS. If the
Turn on the ADIOS package before building LAMMPS. If the
ADIOS 2.x software is installed in PATH, there is nothing else to
do:
.. code-block:: bash
$ make yes-user-adios
$ make yes-adios
otherwise, set ADIOS2_DIR environment variable when turning on the package:
.. code-block:: bash
$ ADIOS2_DIR=path make yes-user-adios # path is where ADIOS 2.x is installed
$ ADIOS2_DIR=path make yes-adios # path is where ADIOS 2.x is installed
----------
.. _user-atc:
.. _atc:
USER-ATC package
ATC package
-------------------------------
The USER-ATC package requires the MANYBODY package also be installed.
The ATC package requires the MANYBODY package also be installed.
.. tabs::
.. tab:: CMake build
No additional settings are needed besides ``-D PKG_USER-ATC=yes``
No additional settings are needed besides ``-D PKG_ATC=yes``
and ``-D PKG_MANYBODY=yes``.
.. tab:: Traditional make
@ -1145,16 +1152,16 @@ The USER-ATC package requires the MANYBODY package also be installed.
----------
.. _user-awpmd:
.. _awpmd:
USER-AWPMD package
AWPMD package
------------------
.. tabs::
.. tab:: CMake build
No additional settings are needed besides ``-D PKG_USER-AQPMD=yes``.
No additional settings are needed besides ``-D PKG_AQPMD=yes``.
.. tab:: Traditional make
@ -1196,9 +1203,9 @@ USER-AWPMD package
----------
.. _user-colvars:
.. _colvars:
USER-COLVARS package
COLVARS package
---------------------------------------
This package includes the `Colvars library
@ -1212,7 +1219,7 @@ be built for the most part with all major versions of the C++ language.
This is the recommended build procedure for using Colvars in
LAMMPS. No additional settings are normally needed besides
``-D PKG_USER-COLVARS=yes``.
``-D PKG_COLVARS=yes``.
.. tab:: Traditional make
@ -1255,9 +1262,9 @@ be built for the most part with all major versions of the C++ language.
----------
.. _user-pace:
.. _ml-pace:
USER-PACE package
ML-PACE package
-----------------------------
This package requires a library that can be downloaded and built
@ -1270,8 +1277,8 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
.. tab:: CMake build
By default the library will be downloaded from the git repository
and built automatically when the USER-PACE package is enabled with
``-D PKG_USER-PACE=yes``. The location for the sources may be
and built automatically when the ML-PACE package is enabled with
``-D PKG_ML-PACE=yes``. The location for the sources may be
customized by setting the variable ``PACELIB_URL`` when
configuring with CMake (e.g. to use a local archive on machines
without internet access). Since CMake checks the validity of the
@ -1282,7 +1289,7 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
.. tab:: Traditional make
You can download and build the USER-PACE library
You can download and build the ML-PACE library
in one step from the ``lammps/src`` dir, using these commands,
which invoke the ``lib/pace/Install.py`` script.
@ -1295,9 +1302,9 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
----------
.. _user-plumed:
.. _plumed:
USER-PLUMED package
PLUMED package
-------------------------------------
.. _plumedinstall: https://plumed.github.io/doc-master/user-doc/html/_installation.html
@ -1305,7 +1312,7 @@ USER-PLUMED package
Before building LAMMPS with this package, you must first build PLUMED.
PLUMED can be built as part of the LAMMPS build or installed separately
from LAMMPS using the generic `PLUMED installation instructions <plumedinstall_>`_.
The USER-PLUMED package has been tested to work with Plumed versions
The PLUMED package has been tested to work with Plumed versions
2.4.x, 2.5.x, and 2.6.x and will error out, when trying to run calculations
with a different version of the Plumed kernel.
@ -1341,7 +1348,7 @@ LAMMPS build.
.. tab:: CMake build
When the ``-D PKG_USER-PLUMED=yes`` flag is included in the cmake
When the ``-D PKG_PLUMED=yes`` flag is included in the cmake
command you must ensure that GSL is installed in locations that
are specified in your environment. There are then two additional
variables that control the manner in which PLUMED is obtained and
@ -1374,7 +1381,7 @@ LAMMPS build.
.. tab:: Traditional make
PLUMED needs to be installed before the USER-PLUMED package is
PLUMED needs to be installed before the PLUMED package is
installed so that LAMMPS can find the right settings when
compiling and linking the LAMMPS executable. You can either
download and build PLUMED inside the LAMMPS plumed library folder
@ -1399,12 +1406,12 @@ LAMMPS build.
build to use. A new file ``lib/plumed/Makefile.lammps`` is also
created with settings suitable for LAMMPS to compile and link
PLUMED using the desired linkage mode. After this step is
completed, you can install the USER-PLUMED package and compile
completed, you can install the PLUMED package and compile
LAMMPS in the usual manner:
.. code-block:: bash
$ make yes-user-plumed
$ make yes-plumed
$ make machine
Once this compilation completes you should be able to run LAMMPS
@ -1419,15 +1426,15 @@ LAMMPS build.
If you want to change the linkage mode, you have to re-run "make
lib-plumed" with the desired settings **and** do a re-install if
the USER-PLUMED package with "make yes-user-plumed" to update the
the PLUMED package with "make yes-plumed" to update the
required makefile settings with the changes in the lib/plumed
folder.
----------
.. _user-h5md:
.. _h5md:
USER-H5MD package
H5MD package
---------------------------------
To build with this package you must have the HDF5 software package
@ -1438,7 +1445,7 @@ the HDF5 library.
.. tab:: CMake build
No additional settings are needed besides ``-D PKG_USER-H5MD=yes``.
No additional settings are needed besides ``-D PKG_H5MD=yes``.
This should auto-detect the H5MD library on your system. Several
advanced CMake H5MD options exist if you need to specify where it
@ -1470,24 +1477,78 @@ the HDF5 library.
----------
.. _user-intel:
.. _ml-hdnnp:
USER-INTEL package
ML-HDNNP package
----------------
To build with the ML-HDNNP package it is required to download and build the
external `n2p2 <https://github.com/CompPhysVienna/n2p2>`_ library ``v2.1.4``
(or higher). The LAMMPS build process offers an automatic download and
compilation of *n2p2* or allows you to choose the installation directory of
*n2p2* manually. Please see the boxes below for the CMake and traditional build
system for detailed information.
In case of a manual installation of *n2p2* you only need to build the *n2p2* core
library ``libnnp`` and interface library ``libnnpif``. When using GCC it should
suffice to execute ``make libnnpif`` in the *n2p2* ``src`` directory. For more
details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
<https://compphysvienna.github.io/n2p2/topics/build.html>`_.
.. tabs::
.. tab:: CMake build
.. code-block:: bash
-D DOWNLOAD_N2P2=value # download n2p2 for build, value = no (default) or yes
-D N2P2_DIR=path # n2p2 base directory (only needed if a custom location)
If ``DOWNLOAD_N2P2`` is set, the *n2p2* library will be downloaded and
built inside the CMake build directory. If the *n2p2* library is already
on your system (in a location CMake cannot find it), set the ``N2P2_DIR``
to path where *n2p2* is located. If *n2p2* is located directly in
``lib/hdnnp/n2p2`` it will be automatically found by CMake.
.. tab:: Traditional make
You can download and build the *n2p2* library manually if you prefer;
follow the instructions in ``lib/hdnnp/README``\ . You can also do it in
one step from the ``lammps/src`` dir, using a command like these, which
simply invoke the ``lib/hdnnp/Install.py`` script with the specified args:
.. code-block:: bash
$ make lib-hdnnp # print help message
$ make lib-hdnnp args="-b" # download and build in lib/hdnnp/n2p2-...
$ make lib-hdnnp args="-b -v 2.1.4" # download and build specific version
$ make lib-hdnnp args="-p /usr/local/n2p2" # use the existing n2p2 installation in /usr/local/n2p2
Note that 3 symbolic (soft) links, ``includelink``, ``liblink`` and
``Makefile.lammps``, will be created in ``lib/hdnnp`` to point to
``n2p2/include``, ``n2p2/lib`` and ``n2p2/lib/Makefile.lammps-extra``,
respectively. When LAMMPS is built in ``src`` it will use these links.
----------
.. _intel:
INTEL package
-----------------------------------
To build with this package, you must choose which hardware you want to
build for, either x86 CPUs or Intel KNLs in offload mode. You should
also typically :ref:`install the USER-OMP package <user-omp>`, as it can be
used in tandem with the USER-INTEL package to good effect, as explained
also typically :ref:`install the OPENMP package <openmp>`, as it can be
used in tandem with the INTEL package to good effect, as explained
on the :doc:`Speed_intel` page.
When using Intel compilers version 16.0 or later is required. You can
also use the GNU or Clang compilers and they will provide performance
improvements over regular styles and USER-OMP styles, but less so than
improvements over regular styles and OPENMP styles, but less so than
with the Intel compilers. Please also note, that some compilers have
been found to apply memory alignment constraints incompletely or
incorrectly and thus can cause segmentation faults in otherwise correct
code when using features from the USER-INTEL package.
code when using features from the INTEL package.
.. tabs::
@ -1504,7 +1565,7 @@ code when using features from the USER-INTEL package.
Choose which hardware to compile for in Makefile.machine via the
following settings. See ``src/MAKE/OPTIONS/Makefile.intel_cpu*``
and ``Makefile.knl`` files for examples. and
``src/USER-INTEL/README`` for additional information.
``src/INTEL/README`` for additional information.
For CPUs:
@ -1540,9 +1601,9 @@ TBB and MKL.
----------
.. _user-mdi:
.. _mdi:
USER-MDI package
MDI package
-----------------------------
.. tabs::
@ -1569,9 +1630,9 @@ USER-MDI package
----------
.. _user-mesont:
.. _mesont:
USER-MESONT package
MESONT package
-------------------------
This package includes a library written in Fortran 90 in the
@ -1584,7 +1645,7 @@ they will be downloaded the first time this package is installed.
.. tab:: CMake build
No additional settings are needed besides ``-D PKG_USER-MESONT=yes``
No additional settings are needed besides ``-D PKG_MESONT=yes``
.. tab:: Traditional make
@ -1611,9 +1672,9 @@ they will be downloaded the first time this package is installed.
----------
.. _user-molfile:
.. _molfile:
USER-MOLFILE package
MOLFILE package
---------------------------------------
.. tabs::
@ -1623,9 +1684,9 @@ USER-MOLFILE package
.. code-block:: bash
-D MOLFILE_INCLUDE_DIR=path # (optional) path where VMD molfile plugin headers are installed
-D PKG_USER-MOLFILE=yes
-D PKG_MOLFILE=yes
Using ``-D PKG_USER-MOLFILE=yes`` enables the package, and setting
Using ``-D PKG_MOLFILE=yes`` enables the package, and setting
``-D MOLFILE_INCLUDE_DIR`` allows to provide a custom location for
the molfile plugin header files. These should match the ABI of the
plugin files used, and thus one typically sets them to include
@ -1649,9 +1710,9 @@ USER-MOLFILE package
----------
.. _user-netcdf:
.. _netcdf:
USER-NETCDF package
NETCDF package
-------------------------------------
To build with this package you must have the NetCDF library installed
@ -1661,7 +1722,7 @@ on your system.
.. tab:: CMake build
No additional settings are needed besides ``-D PKG_USER-NETCDF=yes``.
No additional settings are needed besides ``-D PKG_NETCDF=yes``.
This should auto-detect the NETCDF library if it is installed on
your system at standard locations. Several advanced CMake NETCDF
@ -1680,9 +1741,9 @@ on your system.
----------
.. _user-omp:
.. _openmp:
USER-OMP package
OPENMP package
-------------------------------
.. tabs::
@ -1690,13 +1751,13 @@ USER-OMP package
.. tab:: CMake build
No additional settings are required besides ``-D
PKG_USER-OMP=yes``. If CMake detects OpenMP compiler support, the
USER-OMP code will be compiled with multi-threading support
PKG_OPENMP=yes``. If CMake detects OpenMP compiler support, the
OPENMP code will be compiled with multi-threading support
enabled, otherwise as optimized serial code.
.. tab:: Traditional make
To enable multi-threading support in the USER-OMP package (and
To enable multi-threading support in the OPENMP package (and
other styles supporting OpenMP) the following compile and link
flags must be added to your Makefile.machine file. See
``src/MAKE/OPTIONS/Makefile.omp`` for an example.
@ -1713,12 +1774,12 @@ USER-OMP package
----------
.. _user-qmmm:
.. _qmmm:
USER-QMMM package
QMMM package
---------------------------------
For using LAMMPS to do QM/MM simulations via the USER-QMMM package you
For using LAMMPS to do QM/MM simulations via the QMMM package you
need to build LAMMPS as a library. A LAMMPS executable with :doc:`fix
qmmm <fix_qmmm>` included can be built, but will not be able to do a
QM/MM simulation on as such. You must also build a QM code - currently
@ -1741,11 +1802,11 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
libqmmm.a) are not included in the static LAMMPS library and
(currently) not installed, while their code is included in the
shared LAMMPS library. Thus a typical command line to configure
building LAMMPS for USER-QMMM would be:
building LAMMPS for QMMM would be:
.. code-block:: bash
cmake -C ../cmake/presets/minimal.cmake -D PKG_USER-QMMM=yes \
cmake -C ../cmake/presets/basic.cmake -D PKG_QMMM=yes \
-D BUILD_LIB=yes -DBUILD_SHARED_LIBS=yes ../cmake
After completing the LAMMPS build and also configuring and
@ -1788,16 +1849,16 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
----------
.. _user-quip:
.. _ml-quip:
USER-QUIP package
ML-QUIP package
---------------------------------
To build with this package, you must download and build the QUIP
library. It can be obtained from GitHub. For support of GAP
potentials, additional files with specific licensing conditions need
to be downloaded and configured. See step 1 and step 1.1 in the
``lib/quip/README`` file for details on how to do this.
to be downloaded and configured. The automatic download will from
within CMake will download the non-commercial use version.
.. tabs::
@ -1805,11 +1866,14 @@ to be downloaded and configured. See step 1 and step 1.1 in the
.. code-block:: bash
-D DOWNLOAD_QUIP=value # download OpenKIM API v2 for build, value = no (default) or yes
-D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location)
CMake will **not** download and build the QUIP library. But once you have
done that, a CMake build of LAMMPS with ``-D PKG_USER-QUIP=yes`` should
work. Set the ``QUIP_LIBRARY`` variable if CMake cannot find the QUIP library.
CMake will try to download and build the QUIP library from GitHub, if it is not
found on the local machine. This requires to have git installed. It will use the same compilers
and flags as used for compiling LAMMPS. Currently this is only supported for the GNU and the
Intel compilers. Set the ``QUIP_LIBRARY`` variable if you want to use a previously compiled
and installed QUIP library and CMake cannot find it.
.. tab:: Traditional make
@ -1823,9 +1887,9 @@ to be downloaded and configured. See step 1 and step 1.1 in the
----------
.. _user-scafacos:
.. _scafacos:
USER-SCAFACOS package
SCAFACOS package
-----------------------------------------
To build with this package, you must download and build the
@ -1870,9 +1934,9 @@ To build with this package, you must download and build the
----------
.. _user-smd:
.. _machdyn:
USER-SMD package
MACHDYN package
-------------------------------
To build with this package, you must download the Eigen3 library.
@ -1914,9 +1978,9 @@ Eigen3 is a template library, so you do not need to build it.
----------
.. _user-vtk:
.. _vtk:
USER-VTK package
VTK package
-------------------------------
To build with this package you must have the VTK library installed on
@ -1926,7 +1990,7 @@ your system.
.. tab:: CMake build
No additional settings are needed besides ``-D PKG_USER-VTK=yes``.
No additional settings are needed besides ``-D PKG_VTK=yes``.
This should auto-detect the VTK library if it is installed on your
system at standard locations. Several advanced VTK options exist

6
doc/src/Build_make.rst
View File

@ -117,10 +117,10 @@ settings may become outdated:
make mac # build serial LAMMPS on a Mac
make mac_mpi # build parallel LAMMPS on a Mac
make intel_cpu # build with the USER-INTEL package optimized for CPUs
make knl # build with the USER-INTEL package optimized for KNLs
make intel_cpu # build with the INTEL package optimized for CPUs
make knl # build with the INTEL package optimized for KNLs
make opt # build with the OPT package optimized for CPUs
make omp # build with the USER-OMP package optimized for OpenMP
make omp # build with the OPENMP package optimized for OpenMP
make kokkos_omp # build with the KOKKOS package for OpenMP
make kokkos_cuda_mpi # build with the KOKKOS package for GPUs
make kokkos_phi # build with the KOKKOS package for KNLs

49
doc/src/Build_manual.rst
View File

@ -22,35 +22,26 @@ files. Here is a list with descriptions:
.gitignore # list of files and folders to be ignored by git
doxygen-warn.log # logfile with warnings from running doxygen
github-development-workflow.md # notes on the LAMMPS development workflow
include-file-conventions.md # notes on LAMMPS' include file conventions
If you downloaded LAMMPS as a tarball from `the LAMMPS website <lws_>`_,
the html folder and the PDF files should be included.
If you downloaded LAMMPS from the public git repository, then the HTML
and PDF files are not included. Instead you need to create them, in one
of two ways:
and PDF files are not included. You can build the HTML or PDF files yourself,
by typing ``make html`` or ``make pdf`` in the ``doc`` folder. This requires
various tools and files. Some of them have to be installed (see below). For
the rest the build process will attempt to download and install them into
a python virtual environment and local folders.
a. You can "fetch" the current HTML and PDF files from the LAMMPS web
site. Just type ``make fetch``. This should download a ``html_www``
directory and a ``Manual_www.pdf`` file. Note that if new LAMMPS features
have been added more recently than the date of your LAMMPS version, the
fetched documentation will include those changes (but your source code
will not, unless you update your local repository).
b. You can build the HTML or PDF files yourself, by typing ``make html``
or ``make pdf`` in the ``doc`` folder. This requires various tools
and files. Some of them have to be installed (see below). For the
rest the build process will attempt to download and install them into
a python virtual environment and local folders.
A current version of the manual (latest patch release, aka unstable
branch) is is available online at:
`https://lammps.sandia.gov/doc/Manual.html
<https://lammps.sandia.gov/doc/Manual.html>`_ A version of the manual
corresponding to the ongoing development (aka master branch) is
available online at: `https://docs.lammps.org/
<https://docs.lammps.org/>`_
A current version of the manual (latest patch release, that is the state
of the *release* branch) is is available online at:
`https://docs.lammps.org/ <https://docs.lammps.org/>`_.
A version of the manual corresponding to the ongoing development (that is
the state of the *develop* branch) is available online at:
`https://docs.lammps.org/latest/ <https://docs.lammps.org/latest/>`_
A version of the manual corresponding to the latest stable LAMMPS release
(that is the state of the *stable* branch) is available online at:
`https://docs.lammps.org/stable/ <https://docs.lammps.org/stable/>`_
Build using GNU make
--------------------
@ -86,8 +77,8 @@ folder. The following ``make`` commands are available:
.. code-block:: bash
make html # generate HTML in html dir using Sphinx
make pdf # generate PDF as Manual.pdf using Sphinx and pdflatex
make fetch # fetch HTML pages and PDF files from LAMMPS web site
make pdf # generate PDF as Manual.pdf using Sphinx and PDFLaTeX
make fetch # fetch HTML pages and PDF files from LAMMPS website
# and unpack into the html_www folder and Manual_www.pdf
make epub # generate LAMMPS.epub in ePUB format using Sphinx
make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert
@ -215,9 +206,9 @@ be multiple tests run automatically:
.. parsed-literal::
Found 33 standard and 41 user packages
Standard package NEWPACKAGE missing in Packages_standard.rst
Standard package NEWPACKAGE missing in Packages_details.rst
Found 88 packages
Package NEWPACKAGE missing in Packages_list.rst
Package NEWPACKAGE missing in Packages_details.rst
- A test that only standard, printable ASCII text characters are used.
This runs the command ``env LC_ALL=C grep -n '[^ -~]' src/*.rst`` and
@ -257,4 +248,4 @@ the file ``lammps/doc/utils/sphinx-config/false_positives.txt``.
.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
.. _lws: https://lammps.sandia.gov
.. _lws: https://www.lammps.org

85
doc/src/Build_package.rst
View File

@ -30,17 +30,37 @@ steps, as explained on the :doc:`Build extras <Build_extras>` page.
These links take you to the extra instructions for those select
packages:
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`COMPRESS <compress>` | :ref:`GPU <gpu>` | :ref:`KIM <kim>` | :ref:`KOKKOS <kokkos>` | :ref:`LATTE <latte>` | :ref:`MESSAGE <message>` |
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`MSCG <mscg>` | :ref:`OPT <opt>` | :ref:`POEMS <poems>` | :ref:`PYTHON <python>` | :ref:`VORONOI <voronoi>` | :ref:`USER-ADIOS <user-adios>` |
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`USER-ATC <user-atc>` | :ref:`USER-AWPMD <user-awpmd>` | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>` | :ref:`USER-INTEL <user-intel>` | :ref:`USER-MOLFILE <user-molfile>` |
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`USER-NETCDF <user-netcdf>` | :ref:`USER-PACE <user-pace>` | :ref:`USER-PLUMED <user-plumed>` | :ref:`USER-OMP <user-omp>` | :ref:`USER-QMMM <user-qmmm>` | :ref:`USER-QUIP <user-quip>` |
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`USER-SCAFACOS <user-scafacos>` | :ref:`USER-SMD <user-smd>` | :ref:`USER-VTK <user-vtk>` | | | |
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
.. table_from_list::
:columns: 6
* :ref:`ADIOS <adios>`
* :ref:`ATC <atc>`
* :ref:`AWPMD <awpmd>`
* :ref:`COLVARS <colvars>`
* :ref:`COMPRESS <compress>`
* :ref:`GPU <gpu>`
* :ref:`H5MD <h5md>`
* :ref:`INTEL <intel>`
* :ref:`KIM <kim>`
* :ref:`KOKKOS <kokkos>`
* :ref:`LATTE <latte>`
* :ref:`MACHDYN <machdyn>`
* :ref:`MESSAGE <message>`
* :ref:`ML-HDNNP <ml-hdnnp>`
* :ref:`ML-PACE <ml-pace>`
* :ref:`ML-QUIP <ml-quip>`
* :ref:`MOLFILE <molfile>`
* :ref:`MSCG <mscg>`
* :ref:`NETCDF <netcdf>`
* :ref:`OPENMP <openmp>`
* :ref:`OPT <opt>`
* :ref:`PLUMED <plumed>`
* :ref:`POEMS <poems>`
* :ref:`PYTHON <python>`
* :ref:`QMMM <qmmm>`
* :ref:`SCAFACOS <scafacos>`
* :ref:`VORONOI <voronoi>`
* :ref:`VTK <vtk>`
The mechanism for including packages is simple but different for CMake
versus make.
@ -58,14 +78,10 @@ versus make.
.. code-block:: csh
-D PKG_MANYBODY=yes
-D PKG_USER-INTEL=yes
-D PKG_INTEL=yes
All standard and user packages are included the same way. Note
that USER packages have a hyphen between USER and the rest of the
package name, not an underscore.
See the shortcut section below for how to install many packages at
once with CMake.
All packages are included the same way. See the shortcut section
below for how to install many packages at once with CMake.
.. note::
@ -89,12 +105,10 @@ versus make.
.. code-block:: bash
make no-rigid
make yes-user-intel
make yes-intel
All standard and user packages are included the same way.
See the shortcut section below for how to install many packages at
once with make.
All packages are included the same way. See the shortcut section
below for how to install many packages at once with make.
.. note::
@ -126,7 +140,7 @@ other files dependent on that package are also excluded.
.. note::
By default no package is installed. Prior to August 2018, however,
By default no packages are installed. Prior to August 2018, however,
if you downloaded a tarball, 3 packages (KSPACE, MANYBODY, MOLECULE)
were pre-installed via the traditional make procedure in the ``src``
directory. That is no longer the case, so that CMake will build
@ -153,7 +167,7 @@ one of them as a starting point and customize it to your needs.
.. code-block:: bash
cmake -C ../cmake/presets/minimal.cmake [OPTIONS] ../cmake # enable just a few core packages
cmake -C ../cmake/presets/basic.cmake [OPTIONS] ../cmake # enable just a few core packages
cmake -C ../cmake/presets/most.cmake [OPTIONS] ../cmake # enable most packages
cmake -C ../cmake/presets/download.cmake [OPTIONS] ../cmake # enable packages which download sources or potential files
cmake -C ../cmake/presets/nolib.cmake [OPTIONS] ../cmake # disable packages that do require extra libraries or tools
@ -208,10 +222,10 @@ These commands install/un-install sets of packages:
make yes-all # install all packages
make no-all # uninstall all packages
make yes-standard or make yes-std # install standard packages
make no-standard or make no-std # uninstall standard packages
make yes-user # install user packages
make no-user # uninstall user packages
make yes-basic # install a few commonly used packages'
make no-basic # remove a few commonly used packages'
make yes-most # install most packages w/o libs'
make no-most # remove most packages w/o libs'
make yes-lib # install packages that require extra libraries
make no-lib # uninstall packages that require extra libraries
make yes-ext # install packages that require external libraries
@ -225,15 +239,14 @@ package`` will list all the these commands.
Installing or un-installing a package for the make based build process
works by simply copying files back and forth between the main source
directory src and the sub-directories with the package name (e.g.
src/KSPACE, src/USER-ATC), so that the files are included or excluded
src/KSPACE, src/ATC), so that the files are included or excluded
when LAMMPS is built. Only source files in the src folder will be
compiled.
The following make commands help manage files that exist in both the
src directory and in package sub-directories. You do not normally
need to use these commands unless you are editing LAMMPS files or are
:doc:`installing a patch <Install_patch>` downloaded from the LAMMPS web
site.
updating LAMMPS via git.
Type ``make package-status`` or ``make ps`` to show which packages are
currently installed. For those that are installed, it will list any
@ -245,10 +258,10 @@ currently installed, without listing the status of packages that are
not installed.
Type ``make package-update`` or ``make pu`` to overwrite src files with
files from the package sub-directories if the package is installed.
It should be used after a :doc:`patch has been applied <Install_patch>`,
since patches only update the files in the package sub-directory, but
not the src files.
files from the package sub-directories if the package is installed. It
should be used after the checkout has been :doc:`updated or changed
withy git <Install_git>`, this will only update the files in the package
sub-directories, but not the copies in the src folder.
Type ``make package-overwrite`` to overwrite files in the package
sub-directories with src files.

41
doc/src/Build_settings.rst
View File

@ -64,14 +64,15 @@ LAMMPS can use them if they are available on your system.
selected, then CMake will try to detect, if threaded FFTW
libraries are available and enable them by default. This setting
is independent of whether OpenMP threads are enabled and a
packages like KOKKOS or USER-OMP is used. If CMake cannot detect
packages like KOKKOS or OPENMP is used. If CMake cannot detect
the FFT library, you can set these variables to assist:
.. code-block:: bash
-D FFTW3_INCLUDE_DIR=path # path to FFTW3 include files
-D FFTW3_LIBRARY=path # path to FFTW3 libraries
-D FFT_FFTW_THREADS=on # enable using threaded FFTW3 libraries
-D FFTW3_OMP_LIBRARY=path # path to FFTW3 OpenMP wrapper libraries
-D FFT_FFTW_THREADS=on # enable using OpenMP threaded FFTW3 libraries
-D MKL_INCLUDE_DIR=path # ditto for Intel MKL library
-D FFT_MKL_THREADS=on # enable using threaded FFTs with MKL libraries
-D MKL_LIBRARY=path # path to MKL libraries
@ -242,8 +243,8 @@ does not support 64-bit integers or incurs performance penalties when
using them.
These are limits for the core of the LAMMPS code, specific features or
some styles may impose additional limits. The :ref:`USER-ATC
<PKG-USER-ATC>` package cannot be compiled with the "bigbig" setting.
some styles may impose additional limits. The :ref:`ATC
<PKG-ATC>` package cannot be compiled with the "bigbig" setting.
Also, there are limitations when using the library interface where some
functions with known issues have been replaced by dummy calls printing a
corresponding error message rather than crashing randomly or corrupting
@ -320,9 +321,7 @@ following settings:
.. code-block:: make
LMP_INC = -DLAMMPS_JPEG
LMP_INC = -DLAMMPS_PNG
LMP_INC = -DLAMMPS_FFMPEG
LMP_INC = -DLAMMPS_JPEG -DLAMMPS_PNG -DLAMMPS_FFMPEG <other LMP_INC settings>
JPG_INC = -I/usr/local/include # path to jpeglib.h, png.h, zlib.h header files if make cannot find them
JPG_PATH = -L/usr/lib # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them
@ -353,8 +352,10 @@ Read or write compressed files
-----------------------------------------
If this option is enabled, large files can be read or written with
gzip compression by several LAMMPS commands, including
:doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
compression by ``gzip`` or similar tools by several LAMMPS commands,
including :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and
:doc:`dump <dump>`. Currently supported compression tools are:
``gzip``, ``bzip2``, ``zstd``, and ``lzma``.
.. tabs::
@ -363,23 +364,23 @@ gzip compression by several LAMMPS commands, including
.. code-block:: bash
-D WITH_GZIP=value # yes or no
# default is yes if CMake can find gzip, else no
-D GZIP_EXECUTABLE=path # path to gzip executable if CMake cannot find it
# default is yes if CMake can find the gzip program, else no
.. tab:: Traditional make
.. code-block:: make
LMP_INC = -DLAMMPS_GZIP
LMP_INC = -DLAMMPS_GZIP <other LMP_INC settings>
This option requires that your operating system fully supports the "popen()"
function in the standard runtime library and that a ``gzip`` executable can be
found by LAMMPS during a run.
This option requires that your operating system fully supports the
"popen()" function in the standard runtime library and that a ``gzip``
or other executable can be found by LAMMPS in the standard search path
during a run.
.. note::
On some clusters with high-speed networks, using the "fork()" library
call (required by "popen()") can interfere with the fast communication
On clusters with high-speed networks, using the "fork()" library call
(required by "popen()") can interfere with the fast communication
library and lead to simulations using compressed output or input to
hang or crash. For selected operations, compressed file I/O is also
available using a compression library instead, which is what the
@ -451,7 +452,7 @@ those systems:
.. code-block:: make
LMP_INC = -DLAMMPS_LONGLONG_TO_LONG
LMP_INC = -DLAMMPS_LONGLONG_TO_LONG <other LMP_INC settings>
----------
@ -478,7 +479,7 @@ e.g. to Python. Of course, the calling code has to be set up to
.. code-block:: make
LMP_INC = -DLAMMPS_EXCEPTIONS
LMP_INC = -DLAMMPS_EXCEPTIONS <other LMP_INC settings>
.. note::
@ -519,7 +520,7 @@ executable, not the library.
.. code-block:: make
LMP_INC = -DLAMMPS_TRAP_FPE
LMP_INC = -DLAMMPS_TRAP_FPE <other LMP_INC settings>
After compilation with this flag set, the LAMMPS executable will stop
and produce a core dump when a division by zero, overflow, illegal math

49
doc/src/Build_windows.rst
View File

@ -4,6 +4,7 @@ Notes for building LAMMPS on Windows
* :ref:`General remarks <generic>`
* :ref:`Running Linux on Windows <linux>`
* :ref:`Using GNU GCC ported to Windows <gnu>`
* :ref:`Using Visual Studio <msvc>`
* :ref:`Using a cross-compiler <cross>`
----------
@ -31,13 +32,13 @@ pre-compiled Windows binary packages are sufficient for your needs. If
it is necessary for you to compile LAMMPS on a Windows machine
(e.g. because it is your main desktop), please also consider using a
virtual machine software and compile and run LAMMPS in a Linux virtual
machine, or - if you have a sufficiently up-to-date Windows 10
installation - consider using the Windows subsystem for Linux. This
optional Windows feature allows you to run the bash shell from Ubuntu
from within Windows and from there on, you can pretty much use that
shell like you are running on an Ubuntu Linux machine (e.g. installing
software via apt-get and more). For more details on that, please see
:doc:`this tutorial <Howto_wsl>`.
machine, or - if you have a sufficiently up-to-date Windows 10 or
Windows 11 installation - consider using the Windows subsystem for
Linux. This optional Windows feature allows you to run the bash shell
from Ubuntu from within Windows and from there on, you can pretty much
use that shell like you are running on an Ubuntu Linux machine
(e.g. installing software via apt-get and more). For more details on
that, please see :doc:`this tutorial <Howto_wsl>`.
.. _gnu:
@ -67,6 +68,40 @@ requiring changes to the LAMMPS source code, or figure out corrections
yourself, please report them on the lammps-users mailing list, or file
them as an issue or pull request on the LAMMPS GitHub project.
.. _msvc:
Using Microsoft Visual Studio
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Following the integration of the :doc:`platform namespace
<Developer_platform>` into the LAMMPS code base, portability of LAMMPS
to be compiled on Windows using Visual Studio has been significantly
improved. This has been tested with Visual Studio 2019 (aka version
16). Not all features and packages in LAMMPS are currently supported
out of the box, but a preset ``cmake/presets/windows.cmake`` is provided
that contains the packages that have been compiled successfully. You
must use the CMake based build procedure, and either use the integrated
CMake support of Visual Studio or use an external CMake installation to
create build files for the Visual Studio build system. Please note that
on launching Visual Studio it will scan the directory tree and likely
miss the correct master ``CMakeLists.txt``. Try to open the
``cmake/CMakeSettings.json`` and use those CMake configurations as a
starting point. It is also possible to configure and compile LAMMPS
from the command line with a CMake binary from `cmake.org <https://cmake.org>`_.
Please note, that for either approach CMake will create a so-called
:ref:`"multi-configuration" build environment <cmake_multiconfig>`, and
the command lines for building and testing LAMMPS must be adjusted
accordingly.
To support running in parallel you can compile with OpenMP enabled using
the OPENMP package or install Microsoft MPI (including the SDK) and compile
LAMMPS with MPI enabled.
This is work in progress and you should contact the LAMMPS developers
via GitHub, the forum, or the mailing list, if you have questions or
LAMMPS specific problems.
.. _cross:
Using a cross-compiler

8
doc/src/Commands_bond.rst
View File

@ -18,7 +18,7 @@ Bond_style potentials
All LAMMPS :doc:`bond_style <bond_style>` commands. Some styles have
accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
@ -57,7 +57,7 @@ Angle_style potentials
All LAMMPS :doc:`angle_style <angle_style>` commands. Some styles have
accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
@ -99,7 +99,7 @@ Dihedral_style potentials
All LAMMPS :doc:`dihedral_style <dihedral_style>` commands. Some styles
have accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
@ -135,7 +135,7 @@ Improper_style potentials
All LAMMPS :doc:`improper_style <improper_style>` commands. Some styles
have accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::

2
doc/src/Commands_category.rst
View File

@ -2,7 +2,7 @@ Commands by category
====================
This page lists most of the LAMMPS commands, grouped by category. The
:doc:`General commands <Commands_all>` doc page lists all general commands
:doc:`General commands <Commands_all>` page lists all general commands
alphabetically. Style options for entries like fix, compute, pair etc.
have their own pages where they are listed alphabetically.

10
doc/src/Commands_compute.rst
View File

@ -16,8 +16,8 @@ Compute commands
An alphabetic list of all LAMMPS :doc:`compute <compute>` commands.
Some styles have accelerated versions. This is indicated by
additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
additional letters in parenthesis: g = GPU, i = INTEL, k =
KOKKOS, o = OPENMP, t = OPT.
.. table_from_list::
:columns: 5
@ -47,17 +47,20 @@ KOKKOS, o = USER-OMP, t = OPT.
* :doc:`dihedral <compute_dihedral>`
* :doc:`dihedral/local <compute_dihedral_local>`
* :doc:`dilatation/atom <compute_dilatation_atom>`
* :doc:`dipole <compute_dipole>`
* :doc:`dipole/chunk <compute_dipole_chunk>`
* :doc:`displace/atom <compute_displace_atom>`
* :doc:`dpd <compute_dpd>`
* :doc:`dpd/atom <compute_dpd_atom>`
* :doc:`edpd/temp/atom <compute_edpd_temp_atom>`
* :doc:`efield/atom <compute_efield_atom>`
* :doc:`entropy/atom <compute_entropy_atom>`
* :doc:`erotate/asphere <compute_erotate_asphere>`
* :doc:`erotate/rigid <compute_erotate_rigid>`
* :doc:`erotate/sphere <compute_erotate_sphere>`
* :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>`
* :doc:`event/displace <compute_event_displace>`
* :doc:`fabric <compute_fabric>`
* :doc:`fep <compute_fep>`
* :doc:`force/tally <compute_tally>`
* :doc:`fragment/atom <compute_cluster_atom>`
@ -69,6 +72,7 @@ KOKKOS, o = USER-OMP, t = OPT.
* :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>`
* :doc:`heat/flux <compute_heat_flux>`
* :doc:`heat/flux/tally <compute_tally>`
* :doc:`heat/flux/virial/tally <compute_tally>`
* :doc:`hexorder/atom <compute_hexorder_atom>`
* :doc:`hma <compute_hma>`
* :doc:`improper <compute_improper>`
@ -148,7 +152,7 @@ KOKKOS, o = USER-OMP, t = OPT.
* :doc:`temp/chunk <compute_temp_chunk>`
* :doc:`temp/com <compute_temp_com>`
* :doc:`temp/cs <compute_temp_cs>`
* :doc:`temp/deform <compute_temp_deform>`
* :doc:`temp/deform (k) <compute_temp_deform>`
* :doc:`temp/deform/eff <compute_temp_deform_eff>`
* :doc:`temp/drude <compute_temp_drude>`
* :doc:`temp/eff <compute_temp_eff>`

17
doc/src/Commands_fix.rst
View File

@ -16,13 +16,14 @@ Fix commands
An alphabetic list of all LAMMPS :doc:`fix <fix>` commands. Some styles
have accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 5
* :doc:`accelerate/cos <fix_accelerate_cos>`
* :doc:`acks2/reaxff (k) <fix_acks2_reaxff>`
* :doc:`adapt <fix_adapt>`
* :doc:`adapt/fep <fix_adapt_fep>`
* :doc:`addforce <fix_addforce>`
@ -103,6 +104,7 @@ OPT.
* :doc:`manifoldforce <fix_manifoldforce>`
* :doc:`mdi/engine <fix_mdi_engine>`
* :doc:`meso/move <fix_meso_move>`
* :doc:`mol/swap <fix_mol_swap>`
* :doc:`momentum (k) <fix_momentum>`
* :doc:`momentum/chunk <fix_momentum>`
* :doc:`move <fix_move>`
@ -148,7 +150,7 @@ OPT.
* :doc:`nvt/body <fix_nvt_body>`
* :doc:`nvt/eff <fix_nh_eff>`
* :doc:`nvt/manifold/rattle <fix_nvt_manifold_rattle>`
* :doc:`nvt/sllod (io) <fix_nvt_sllod>`
* :doc:`nvt/sllod (iko) <fix_nvt_sllod>`
* :doc:`nvt/sllod/eff <fix_nvt_sllod_eff>`
* :doc:`nvt/sphere (o) <fix_nvt_sphere>`
* :doc:`nvt/uef <fix_nh_uef>`
@ -157,11 +159,15 @@ OPT.
* :doc:`orient/fcc <fix_orient>`
* :doc:`orient/eco <fix_orient_eco>`
* :doc:`pafi <fix_pafi>`
* :doc:`pair/tracker <fix_pair_tracker>`
* :doc:`phonon <fix_phonon>`
* :doc:`pimd <fix_pimd>`
* :doc:`planeforce <fix_planeforce>`
* :doc:`plumed <fix_plumed>`
* :doc:`poems <fix_poems>`
* :doc:`polarize/bem/gmres <fix_polarize>`
* :doc:`polarize/bem/icc <fix_polarize>`
* :doc:`polarize/functional <fix_polarize>`
* :doc:`pour <fix_pour>`
* :doc:`precession/spin <fix_precession_spin>`
* :doc:`press/berendsen <fix_press_berendsen>`
@ -175,14 +181,14 @@ OPT.
* :doc:`qeq/dynamic <fix_qeq>`
* :doc:`qeq/fire <fix_qeq>`
* :doc:`qeq/point <fix_qeq>`
* :doc:`qeq/reax (ko) <fix_qeq_reax>`
* :doc:`qeq/reaxff (ko) <fix_qeq_reaxff>`
* :doc:`qeq/shielded <fix_qeq>`
* :doc:`qeq/slater <fix_qeq>`
* :doc:`qmmm <fix_qmmm>`
* :doc:`qtb <fix_qtb>`
* :doc:`rattle <fix_shake>`
* :doc:`reax/c/bonds (k) <fix_reaxc_bonds>`
* :doc:`reax/c/species (k) <fix_reaxc_species>`
* :doc:`reaxff/bonds (k) <fix_reaxff_bonds>`
* :doc:`reaxff/species (k) <fix_reaxff_species>`
* :doc:`recenter <fix_recenter>`
* :doc:`restrain <fix_restrain>`
* :doc:`rhok <fix_rhok>`
@ -232,6 +238,7 @@ OPT.
* :doc:`ti/spring <fix_ti_spring>`
* :doc:`tmd <fix_tmd>`
* :doc:`ttm <fix_ttm>`
* :doc:`ttm/grid <fix_ttm>`
* :doc:`ttm/mod <fix_ttm>`
* :doc:`tune/kspace <fix_tune_kspace>`
* :doc:`vector <fix_vector>`

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