update to current master

.github/CODEOWNERS

@@ -22,7 +22,6 @@ src/SPIN/*            @julient31
 src/USER-CGDNA/*      @ohenrich
 src/USER-CGSDK/*      @akohlmey
 src/USER-COLVARS/*    @giacomofiorin
-src/USER-DPD/*        @timattox
 src/USER-INTEL/*      @wmbrownintel
 src/USER-MANIFOLD/*   @Pakketeretet2
 src/USER-MEAMC/*      @martok
@@ -46,7 +45,7 @@ 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-MISC/fix_bond_react.*      @jrgissing
+src/USER-REACTION/fix_bond_react.*  @jrgissing
 src/USER-MISC/*_grem.*              @dstelter92
 src/USER-MISC/compute_stress_mop*.* @RomainVermorel
 
@@ -111,6 +110,7 @@ src/exceptions.h          @rbberger
 src/fix_nh.*              @athomps
 src/info.*                @akohlmey @rbberger
 src/timer.*               @akohlmey
+src/min*                  @sjplimp @stanmoore1
 
 # tools
 tools/msi2lmp/*       @akohlmey
@@ -118,6 +118,7 @@ tools/emacs/*         @HaoZeke
 
 # cmake
 cmake/*               @junghans @rbberger
+cmake/Modules/Packages/USER-COLVARS.cmake @junghans @rbberger @giacomofiorin
 
 # python
 python/*              @rbberger

.github/CONTRIBUTING.md

@@ -68,12 +68,12 @@ How quickly your contribution will be integrated depends largely on how much eff
 Here is a checklist of steps you need to follow to submit a single file or user package for our consideration. Following these steps will save both you and us time. See existing files in packages in the source directory for examples. If you are uncertain, please ask on the lammps-users mailing list.
 
 * All source files you provide must compile with the most current version of LAMMPS with multiple configurations. In particular you need to test compiling LAMMPS from scratch with `-DLAMMPS_BIGBIG` set in addition to the default `-DLAMMPS_SMALLBIG` setting. Your code will need to work correctly in serial and in parallel using MPI.
-* For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no lines over 80 characters. I/O is done via the C-style stdio library, 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.
+* 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.txt'.
+* 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 simple text files with a specific markup language, that are then auto-converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.txt` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. A description of the markup can also be found in `lammps/doc/utils/txt2html/README.html` As appropriate, the text files can include links to equations (see doc/Eqs/*.tex for examples, we auto-create the associated JPG files), or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.txt for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv, the requirement for generating the PDF format manual is the htmldoc software. Please run at least "make html" and carefully inspect and proofread the resulting HTML format doc page before submitting your code.
+* 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
 * If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the *.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide.
 

.github/ISSUE_TEMPLATE/bug_report.md

@@ -9,24 +9,24 @@ assignees: ''
 
 **Summary**
 
-_Please provide a clear and concise description of what the bug is._
+<!--Please provide a clear and concise description of what the bug is.-->
 
 **LAMMPS Version and Platform**
 
-_Please specify precisely which LAMMPS version this issue was detected with (the first line of the output) and what platform (operating system and its version, hardware) you are running on. If possible, test with the most recent LAMMPS patch version_
+<!--Please specify precisely which LAMMPS version this issue was detected with (the first line of the output) and what platform (operating system and its version, hardware) you are running on. If possible, test with the most recent LAMMPS patch version-->
 
 **Expected Behavior**
 
-_Describe the expected behavior.  Quote from the LAMMPS manual where needed, or explain why the expected behavior is meaningful, especially when it differs from the manual_
+<!--Describe the expected behavior.  Quote from the LAMMPS manual where needed, or explain why the expected behavior is meaningful, especially when it differs from the manual-->
 
 **Actual Behavior**
 
-_Describe the actual behavior, how it differs from the expected behavior, and how this can be observed.  Try to be specific and do **not** use vague terms like "doesn't work" or "wrong result".  Do not assume that the person reading this has any experience with or knowledge of your specific area of research._
+<!--Describe the actual behavior, how it differs from the expected behavior, and how this can be observed.  Try to be specific and do **not** use vague terms like "doesn't work" or "wrong result".  Do not assume that the person reading this has any experience with or knowledge of your specific area of research.-->
 
 **Steps to Reproduce**
 
-_Describe the steps required to (quickly) reproduce the issue. You can attach (small) files to the section below or add URLs where to download an archive with all necessary files. Please try to create an input set that is as minimal and small as possible and reproduces the bug as quickly as possible. **NOTE:** the less effort and time it takes to reproduce your reported bug, the more likely it becomes, that somebody will look into it and fix the problem._
+<!--Describe the steps required to (quickly) reproduce the issue. You can attach (small) files to the section below or add URLs where to download an archive with all necessary files. Please try to create an input set that is as minimal and small as possible and reproduces the bug as quickly as possible. **NOTE:** the less effort and time it takes to reproduce your reported bug, the more likely it becomes, that somebody will look into it and fix the problem.-->
 
 **Further Information, Files, and Links**
 
-_Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications_
+<!--Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications-->

.github/ISSUE_TEMPLATE/feature_request.md

@@ -9,12 +9,12 @@ assignees: ''
 
 **Summary**
 
-_Please provide a brief and concise description of the suggested feature or change_
+<!--Please provide a brief and concise description of the suggested feature or change-->
 
 **Detailed Description**
 
-_Please explain how you would like to see LAMMPS enhanced, what feature(s) you are looking for, what specific problems this will solve. If possible, provide references to relevant background information like publications or web pages, and whether you are planning to implement the enhancement yourself or would like to participate in the implementation. If applicable add a reference to an existing bug report or issue that this will address._
+<!--Please explain how you would like to see LAMMPS enhanced, what feature(s) you are looking for, what specific problems this will solve. If possible, provide references to relevant background information like publications or web pages, and whether you are planning to implement the enhancement yourself or would like to participate in the implementation. If applicable add a reference to an existing bug report or issue that this will address.-->
 
 **Further Information, Files, and Links**
 
-_Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications_
+<!--Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications-->

.github/ISSUE_TEMPLATE/generic.md

@@ -9,13 +9,13 @@ assignees: ''
 
 **Summary**
 
-_Please provide a clear and concise description of what this issue report is about._
+<!--Please provide a clear and concise description of what this issue report is about.-->
 
 **LAMMPS Version and Platform**
 
-_Please specify precisely which LAMMPS version this issue was detected with (the first line of the output) and what platform (operating system and its version, hardware) you are running on. If possible, test with the most recent LAMMPS patch version_
+<!--Please specify precisely which LAMMPS version this issue was detected with (the first line of the output) and what platform (operating system and its version, hardware) you are running on. If possible, test with the most recent LAMMPS patch version-->
 
 **Details**
 
-_Please explain the issue in detail here_
+<!--Please explain the issue in detail here-->
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,14 +1,14 @@
 **Summary**
 
-_Briefly describe the new feature(s), enhancement(s), or bugfix(es) included in this pull request._
+<!--Briefly describe the new feature(s), enhancement(s), or bugfix(es) included in this pull request.-->
 
 **Related Issues**
 
-_If this addresses an open GitHub issue for this project, please mention the issue number here, and describe the relation. Use the phrases `fixes #221` or `closes #135`, when you want an issue to be automatically closed when the pull request is merged_
+<!--If this addresses an open GitHub issue for this project, please mention the issue number here, and describe the relation. Use the phrases `fixes #221` or `closes #135`, when you want an issue to be automatically closed when the pull request is merged-->
 
 **Author(s)**
 
-_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request. If this pull request adds new files to the distribution, please also provide a suitable "long-lived" e-mail address (ideally something that can outlive your institution's e-mail, in case you change jobs) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this contributed code._
+<!--Please state name and affiliation of the author or authors that should be credited with the changes in this pull request. If this pull request adds new files to the distribution, please also provide a suitable "long-lived" e-mail address (ideally something that can outlive your institution's e-mail, in case you change jobs) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this contributed code.-->
 
 **Licensing**
 
@@ -16,15 +16,15 @@ By submitting this pull request, I agree, that my contribution will be included
 
 **Backward Compatibility**
 
-_Please state whether any changes in the pull request will break backward compatibility for inputs, and - if yes - explain what has been changed and why_
+<!--Please state whether any changes in the pull request will break backward compatibility for inputs, and - if yes - explain what has been changed and why-->
 
 **Implementation Notes**
 
-_Provide any relevant details about how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected_
+<!--Provide any relevant details about how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected-->
 
 **Post Submission Checklist**
 
-_Please check the fields below as they are completed **after** the pull request has been submitted. Delete lines that don't apply_
+<!--Please check the fields below as they are completed **after** the pull request has been submitted. Delete lines that don't apply-->
 
 - [ ] The feature or features in this pull request is complete
 - [ ] Licensing information is complete
@@ -39,6 +39,6 @@ _Please check the fields below as they are completed **after** the pull request
 
 **Further Information, Files, and Links**
 
-_Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)_
+<!--Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)-->
 
 

.github/PULL_REQUEST_TEMPLATE/bug_fix.md

@@ -9,15 +9,15 @@ assignees: ''
 
 **Summary**
 
-_Briefly describe the bug or bugs, that are eliminated by this pull request._
+<!--Briefly describe the bug or bugs, that are eliminated by this pull request.-->
 
 **Related Issue(s)**
 
-_If this request addresses or is related to an existing (open) GitHub issue, e.g. a bug report, mention the issue number number here following a pound sign (aka hashmark), e.g.`#222`._
+<!--If this request addresses or is related to an existing (open) GitHub issue, e.g. a bug report, mention the issue number number here following a pound sign (aka hashmark), e.g.`#222`.-->
 
 **Author(s)**
 
-_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request_
+<!--Please state name and affiliation of the author or authors that should be credited with the changes in this pull request-->
 
 **Licensing**
 
@@ -25,18 +25,18 @@ By submitting this pull request I implicitly accept, that my submission is subje
 
 **Backward Compatibility**
 
-_Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why_
+<!--Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why-->
 
 **Detailed Description**
 
-_Provide any relevant details about how the fixed bug can be reproduced, how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected_
+<!--Provide any relevant details about how the fixed bug can be reproduced, how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected-->
 
 ## Post Submission Checklist
 
-_Please check the fields below as they are completed *after* the pull request is submitted_
+<!--Please check the fields below as they are completed *after* the pull request is submitted-->
 - [ ] The code in this pull request is complete
 - [ ] The source code follows the LAMMPS formatting guidelines
 
 ## Further Information, Files, and Links
 
-_Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. to download input decks for testing)_
+<!--Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. to download input decks for testing)-->

.github/PULL_REQUEST_TEMPLATE/maintenance_refactoring.md

@@ -9,15 +9,15 @@ assignees: ''
 
 **Summary**
 
-_Briefly describe the included changes._
+<!--Briefly describe the included changes.-->
 
 **Related Issue(s)**
 
-_If this request addresses or is related to an existing (open) GitHub issue, e.g. a bug report, mention the issue number number here following a pound sign (aka hashmark), e.g.`#222`.
+<!--If this request addresses or is related to an existing (open) GitHub issue, e.g. a bug report, mention the issue number number here following a pound sign (aka hashmark), e.g.`#222`.
 
 **Author(s)**
 
-_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request_
+<!--Please state name and affiliation of the author or authors that should be credited with the changes in this pull request-->
 
 **Licensing**
 
@@ -25,11 +25,11 @@ By submitting this pull request I implicitly accept, that my submission is subje
 
 **Detailed Description**
 
-_Provide any relevant details about the included changes._
+<!--Provide any relevant details about the included changes.-->
 
 ## Post Submission Checklist
 
-_Please check the fields below as they are completed *after* the pull request is submitted_
+<!--Please check the fields below as they are completed *after* the pull request is submitted-->
 - [ ] The pull request is complete
 - [ ] The source code follows the LAMMPS formatting guidelines
 

.github/PULL_REQUEST_TEMPLATE/new_feature.md

@@ -9,34 +9,34 @@ assignees: ''
 
 **Summary**
 
-_Briefly describe the new feature(s) included in this pull request._
+<!--Briefly describe the new feature(s) included in this pull request.-->
 
 **Related Issues**
 
-_If this addresses an existing (open) GitHub issue, e.g. a feature request, mention the issue number here following a pound sign (aka hashmark), e.g. `#331`._
+<!--If this addresses an existing (open) GitHub issue, e.g. a feature request, mention the issue number here following a pound sign (aka hashmark), e.g. `#331`.-->
 
 **Author(s)**
 
-_Please state name and affiliation of the author or authors that should be credited with the features added in this pull request. Please provide a suitable "long-lived" e-mail address (e.g. from gmail, yahoo, outlook, etc.) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this code. now and in the future_
+<!--Please state name and affiliation of the author or authors that should be credited with the features added in this pull request. Please provide a suitable "long-lived" e-mail address (e.g. from gmail, yahoo, outlook, etc.) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this code. now and in the future-->
 
 **Licensing**
 
-_Please add *yes* or *no* to the following two statements (please contact @lammps/core if you have questions about this)_
+<!--Please add *yes* or *no* to the following two statements (please contact @lammps/core if you have questions about this)-->
 
 My contribution may be licensed as GPL v2 (default LAMMPS license):
 My contribution may be licensed as LGPL (for use as a library with proprietary software):
 
 **Backward Compatibility**
 
-_Please state if any of the changes in this pull request will affect backward compatibility for inputs, and - if yes - explain what has been changed and why_
+<!--Please state if any of the changes in this pull request will affect backward compatibility for inputs, and - if yes - explain what has been changed and why-->
 
 **Implementation Notes**
 
-_Provide any relevant details about how the new features are implemented, how correctness was verified, what platforms (OS, compiler, MPI, hardware, number of processors, accelerator(s)) it was tested on_
+<!--Provide any relevant details about how the new features are implemented, how correctness was verified, what platforms (OS, compiler, MPI, hardware, number of processors, accelerator(s)) it was tested on-->
 
 ## Post Submission Checklist
 
-_Please check the fields below as they are completed *after* the pull request has been submitted_
+<!--Please check the fields below as they are completed *after* the pull request has been submitted-->
 
 - [ ] The feature or features in this pull request is complete
 - [ ] Licensing information is complete
@@ -51,6 +51,6 @@ _Please check the fields below as they are completed *after* the pull request ha
 
 ## Further Information, Files, and Links
 
-_Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)_
+<!--Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)-->
 
 

.github/PULL_REQUEST_TEMPLATE/update_enhancement.md

@@ -9,11 +9,11 @@ assignees: ''
 
 **Summary**
 
-_Briefly describe what kind of updates or enhancements for a package or feature are included. If you are not the original author of the package or feature, please mention, whether your contribution was created independently or in collaboration/cooperation with the original author._
+<!--Briefly describe what kind of updates or enhancements for a package or feature are included. If you are not the original author of the package or feature, please mention, whether your contribution was created independently or in collaboration/cooperation with the original author.-->
 
 **Author(s)**
 
-_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request_
+<!--Please state name and affiliation of the author or authors that should be credited with the changes in this pull request-->
 
 **Licensing**
 
@@ -21,15 +21,15 @@ By submitting this pull request I implicitly accept, that my submission is subje
 
 **Backward Compatibility**
 
-_Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why_
+<!--Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why-->
 
 **Implementation Notes**
 
-_Provide any relevant details about how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected_
+<!--Provide any relevant details about how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected-->
 
 **Post Submission Checklist**
 
-_Please check the fields below as they are completed_
+<!--Please check the fields below as they are completed-->
 - [ ] The feature or features in this pull request is complete
 - [ ] Suitable updates to the existing docs are included
 - [ ] One or more example input decks are included
@@ -37,6 +37,6 @@ _Please check the fields below as they are completed_
 
 **Further Information, Files, and Links**
 
-_Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)_
+<!--Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)-->
 
 

.gitignore

@@ -9,6 +9,7 @@
 *.d
 *.x
 *.exe
+*.sif
 *.dll
 *.pyc
 __pycache__
@@ -26,6 +27,7 @@ vgcore.*
 .vagrant
 \#*#
 .#*
+.vscode
 
 .DS_Store
 .DS_Store?

cmake/CMakeLists.txt

@@ -2,7 +2,7 @@
 # CMake build system
 # This file is part of LAMMPS
 # Created by Christoph Junghans and Richard Berger
-cmake_minimum_required(VERSION 2.8.12)
+cmake_minimum_required(VERSION 3.10)
 
 project(lammps CXX)
 set(SOVERSION 0)
@@ -21,22 +21,16 @@ if (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
   set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "default install path" FORCE )
 endif()
 
-# To avoid conflicts with the conventional Makefile build system, we build everything here
-file(GLOB LIB_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
-file(GLOB LMP_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
-list(REMOVE_ITEM LIB_SOURCES ${LMP_SOURCES})
-
 # Cmake modules/macros are in a subdirectory to keep this file cleaner
 set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules)
 
 include(LAMMPSUtils)
 
-get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h LAMMPS_VERSION)
+get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h PROJECT_VERSION)
 
 include(PreventInSourceBuilds)
 
 if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
-  #release comes with -O3 by default
   set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
 endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
 string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
@@ -52,116 +46,85 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
 include(CheckCCompilerFlag)
 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 -std=c++11")
+  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()
 
-option(DISABLE_CXX11_REQUIREMENT "Disable check that requires C++11 for compiling LAMMPS" OFF)
+if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
-if(DISABLE_CXX11_REQUIREMENT)
+  set(CMAKE_TUNE_DEFAULT "-ffast-math -march=native")
-  add_definitions(-DLAMMPS_CXX98)
-# else()
-#  set(CMAKE_CXX_STANDARD 11)
 endif()
 
-# GNU compiler features
+if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")
+  set(CMAKE_TUNE_DEFAULT "-ffast-math -march=native")
+endif()
+
+# we require C++11 without extensions
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
+# GNU compiler specific features for testing
 if (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
-  option(ENABLE_COVERAGE "Enable code coverage" OFF)
+  option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
   mark_as_advanced(ENABLE_COVERAGE)
   if(ENABLE_COVERAGE)
     set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
   endif()
-  option(ENABLE_SANITIZE_ADDRESS "Enable address sanitizer" OFF)
-  mark_as_advanced(ENABLE_SANITIZE_ADDRESS)
-  if(ENABLE_SANITIZE_ADDRESS)
-    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=address")
-  endif()
-  option(ENABLE_SANITIZE_UNDEFINED "Enable undefined behavior sanitizer" OFF)
-  mark_as_advanced(ENABLE_SANITIZE_UNDEFINED)
-  if(ENABLE_SANITIZE_UNDEFINED)
-    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=undefined")
-  endif()
-  option(ENABLE_SANITIZE_THREAD "Enable thread sanitizer" OFF)
-  mark_as_advanced(ENABLE_SANITIZE_THREAD)
-  if(ENABLE_SANITIZE_THREAD)
-    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=thread")
-  endif()
 endif()
 
 ########################################################################
 # User input options                                                   #
 ########################################################################
-option(BUILD_EXE "Build lmp binary" ON)
+set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically")
-if(BUILD_EXE)
+mark_as_advanced(LAMMPS_MACHINE)
-  set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically")
+if(LAMMPS_MACHINE)
-  mark_as_advanced(LAMMPS_MACHINE)
+  set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}")
-  if(LAMMPS_MACHINE)
-    set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}")
-  endif()
-  set(LAMMPS_BINARY lmp${LAMMPS_MACHINE})
 endif()
+set(LAMMPS_BINARY lmp${LAMMPS_MACHINE})
 
-option(BUILD_LIB "Build LAMMPS library" OFF)
+option(BUILD_SHARED_LIBS "Build shared library" OFF)
-if(BUILD_LIB)
+if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
-  option(BUILD_SHARED_LIBS "Build shared library" OFF)
+  set(CMAKE_POSITION_INDEPENDENT_CODE ON)
-  if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
-    set(CMAKE_POSITION_INDEPENDENT_CODE ON)
-  endif()
-  set(LAMMPS_LIB_SUFFIX "" CACHE STRING "Suffix to append to liblammps and pkg-config file")
-  mark_as_advanced(LAMMPS_LIB_SUFFIX)
-  if(LAMMPS_LIB_SUFFIX)
-    set(LAMMPS_LIB_SUFFIX "_${LAMMPS_LIB_SUFFIX}")
-  endif()
 endif()
 
 option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
 
-if(NOT BUILD_EXE AND NOT BUILD_LIB)
+include(GNUInstallDirs)
-  message(FATAL_ERROR "You need to at least enable one of two following options: BUILD_LIB or BUILD_EXE")
+file(GLOB ALL_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
-endif()
+file(GLOB MAIN_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
+list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})
+add_library(lammps ${ALL_SOURCES})
+add_executable(lmp ${MAIN_SOURCES})
+target_link_libraries(lmp PRIVATE lammps)
+set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})
+install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
 
 option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
-include(GNUInstallDirs)
 
-set(LAMMPS_LINK_LIBS)
+set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
-set(LAMMPS_DEPS)
-set(LAMMPS_API_DEFINES)
-
-set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
   GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MOLECULE PERI POEMS QEQ
   REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
-  USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS
+  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-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
-  USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC
+  USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION
-  USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
+  USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
-  USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
+  USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
-set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
+set(SUFFIX_PACKAGES CORESHELL USER-OMP KOKKOS OPT USER-INTEL GPU)
-foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
+foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
   option(PKG_${PKG} "Build ${PKG} Package" OFF)
 endforeach()
 
-######################################################
-# download and unpack support binaries for compilation
-# of windows binaries.
-######################################################
-if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
-  set(LAMMPS_THIRDPARTY_URL "http://download.lammps.org/thirdparty")
-  file(DOWNLOAD "${LAMMPS_THIRDPARTY_URL}/opencl-win-devel.tar.gz" "${CMAKE_CURRENT_BINARY_DIR}/opencl-win-devel.tar.gz"
-          EXPECTED_MD5 2c00364888d5671195598b44c2e0d44d)
-  execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf opencl-win-devel.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
-  if(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86")
-    set(OpenCL_LIBRARY "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win32/libOpenCL.dll")
-  elseif(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86_64")
-    set(OpenCL_LIBRARY "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win64/libOpenCL.dll")
-  endif()
-  set(OpenCL_INCLUDE_DIR "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/include")
-endif()
-
-######################################################
 ######################################################
 # packages with special compiler needs or external libs
 ######################################################
-include_directories(${LAMMPS_SOURCE_DIR})
+target_include_directories(lammps PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}>)
 
 if(PKG_USER-ADIOS)
   # The search for ADIOS2 must come before MPI because
@@ -169,27 +132,47 @@ if(PKG_USER-ADIOS)
   # script that defines the MPI::MPI_C target
   enable_language(C)
   find_package(ADIOS2 REQUIRED)
-  list(APPEND LAMMPS_LINK_LIBS adios2::adios2)
+  target_link_libraries(lammps PRIVATE adios2::adios2)
+endif()
+
+if(NOT CMAKE_CROSSCOMPILING)
+  set(MPI_CXX_SKIP_MPICXX TRUE)
+  find_package(MPI QUIET)
+  option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
+else()
+  option(BUILD_MPI "Build MPI version" OFF)
 endif()
 
-# do MPI detection after language activation, if MPI for these language is required
-set(MPI_CXX_SKIP_MPICXX TRUE)
-find_package(MPI QUIET)
-option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
 if(BUILD_MPI)
-  find_package(MPI REQUIRED)
+  # We use a non-standard procedure to cross-compile with MPI on Windows
-  include_directories(${MPI_CXX_INCLUDE_PATH})
+  if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)
-  list(APPEND LAMMPS_LINK_LIBS ${MPI_CXX_LIBRARIES})
+    include(MPI4WIN)
-  option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
+    target_link_libraries(lammps PUBLIC MPI::MPI_CXX)
-  if(LAMMPS_LONGLONG_TO_LONG)
+  else()
-    add_definitions(-DLAMMPS_LONGLONG_TO_LONG)
+    find_package(MPI REQUIRED)
+    target_link_libraries(lammps PUBLIC MPI::MPI_CXX)
+    option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
+    if(LAMMPS_LONGLONG_TO_LONG)
+      target_compile_definitions(lammps PRIVATE -DLAMMPS_LONGLONG_TO_LONG)
+    endif()
   endif()
 else()
   enable_language(C)
   file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
   add_library(mpi_stubs STATIC ${MPI_SOURCES})
-  include_directories(${LAMMPS_SOURCE_DIR}/STUBS)
+  if(NOT BUILD_SHARED_LIBS)
-  list(APPEND LAMMPS_LINK_LIBS mpi_stubs)
+    install(TARGETS mpi_stubs EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+  endif()
+  set_target_properties(mpi_stubs PROPERTIES OUTPUT_NAME lammps_mpi_stubs${LAMMPS_MACHINE})
+  target_include_directories(mpi_stubs PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS> $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/lammps/mpi>)
+  install(FILES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps/mpi)
+  if(BUILD_SHARED_LIBS)
+    target_link_libraries(lammps PRIVATE mpi_stubs)
+    target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS> $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/lammps/mpi>)
+  else()
+    target_link_libraries(lammps PUBLIC mpi_stubs)
+  endif()
+  add_library(MPI::MPI_CXX ALIAS mpi_stubs)
 endif()
 
 set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
@@ -197,8 +180,7 @@ set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
 set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
 validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
 string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
-add_definitions(-DLAMMPS_${LAMMPS_SIZES})
+target_compile_definitions(lammps PUBLIC -DLAMMPS_${LAMMPS_SIZES})
-set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -DLAMMPS_${LAMMPS_SIZES}")
 
 # posix_memalign is not available on Windows
 if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
@@ -207,13 +189,12 @@ 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")
 endif()
 if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0")
-  add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
+  target_compile_definitions(lammps PRIVATE -DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
 endif()
 
 option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)
 if(LAMMPS_EXCEPTIONS)
-  add_definitions(-DLAMMPS_EXCEPTIONS)
+  target_compile_definitions(lammps PUBLIC -DLAMMPS_EXCEPTIONS)
-  set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -DLAMMPS_EXCEPTIONS")
 endif()
 
 # "hard" dependencies between packages resulting
@@ -224,27 +205,36 @@ pkg_depends(USER-LB MPI)
 pkg_depends(USER-PHONON KSPACE)
 pkg_depends(USER-SCAFACOS MPI)
 
+# detect if we may enable OpenMP support by default
+set(BUILD_OMP_DEFAULT OFF)
 find_package(OpenMP QUIET)
-
+if(OpenMP_FOUND)
-# TODO: this is a temporary workaround until a better solution is found. AK 2019-05-30
+  check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
-# GNU GCC 9.x uses settings incompatible with our use of 'default(none)' in OpenMP pragmas
+  if(HAVE_OMP_H_INCLUDE)
-# where we assume older GCC semantics. For the time being, we disable OpenMP by default
+    set(BUILD_OMP_DEFAULT ON)
-# for GCC 9.x and beyond. People may manually turn it on, but need to run the script
+  endif()
-# src/USER-OMP/hack_openmp_for_pgi_gcc9.sh on all sources to make it compatible with gcc 9.
-if ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 8.99.9))
-  option(BUILD_OMP "Build with OpenMP support" OFF)
-else()
-  option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})
 endif()
 
+option(BUILD_OMP "Build with OpenMP support" ${BUILD_OMP_DEFAULT})
+
 if(BUILD_OMP)
   find_package(OpenMP REQUIRED)
   check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
   if(NOT HAVE_OMP_H_INCLUDE)
-    message(FATAL_ERROR "Cannot find required 'omp.h' header file")
+    message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
   endif()
-  set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
+
-  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
+  if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 8.99.9)) OR
+      ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 9.99.9)) OR
+      ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 18.99.9))
+      )
+    # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
+    # Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe.
+    target_compile_definitions(lammps PRIVATE -DLAMMPS_OMP_COMPAT=4)
+  else()
+    target_compile_definitions(lammps PRIVATE -DLAMMPS_OMP_COMPAT=3)
+  endif()
+  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)
@@ -252,14 +242,19 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
   find_package(LAPACK)
   find_package(BLAS)
   if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
-    if(CMAKE_GENERATOR STREQUAL "Ninja")
+    include(CheckGeneratorSupport)
-      status(FATAL_ERROR "Cannot build internal linear algebra library with Ninja build tool due to lack for Fortran support")
+    if(NOT CMAKE_GENERATOR_SUPPORT_FORTRAN)
+      status(FATAL_ERROR "Cannot build internal linear algebra library as CMake build tool lacks Fortran support")
     endif()
     enable_language(Fortran)
     file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
     add_library(linalg STATIC ${LAPACK_SOURCES})
-    set(BLAS_LIBRARIES linalg)
+    if(NOT BUILD_SHARED_LIBS)
-    set(LAPACK_LIBRARIES linalg)
+      install(TARGETS linalg EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+    endif()
+    set_target_properties(linalg PROPERTIES OUTPUT_NAME lammps_linalg${LAMMPS_MACHINE})
+    set(BLAS_LIBRARIES "$<TARGET_FILE:linalg>")
+    set(LAPACK_LIBRARIES "$<TARGET_FILE:linalg>")
   else()
     list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
   endif()
@@ -270,9 +265,13 @@ find_package(JPEG QUIET)
 option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND})
 if(WITH_JPEG)
   find_package(JPEG REQUIRED)
-  add_definitions(-DLAMMPS_JPEG)
+  target_compile_definitions(lammps PRIVATE -DLAMMPS_JPEG)
-  include_directories(${JPEG_INCLUDE_DIR})
+  if(CMAKE_VERSION VERSION_LESS 3.12)
-  list(APPEND LAMMPS_LINK_LIBS ${JPEG_LIBRARIES})
+    target_include_directories(lammps PRIVATE ${JPEG_INCLUDE_DIR})
+    target_link_libraries(lammps PRIVATE ${JPEG_LIBRARIES})
+  else()
+    target_link_libraries(lammps PRIVATE JPEG::JPEG)
+  endif()
 endif()
 
 find_package(PNG QUIET)
@@ -285,9 +284,8 @@ endif()
 if(WITH_PNG)
   find_package(PNG REQUIRED)
   find_package(ZLIB REQUIRED)
-  include_directories(${PNG_INCLUDE_DIRS} ${ZLIB_INCLUDE_DIRS})
+  target_link_libraries(lammps PRIVATE PNG::PNG ZLIB::ZLIB)
-  list(APPEND LAMMPS_LINK_LIBS ${PNG_LIBRARIES} ${ZLIB_LIBRARIES})
+  target_compile_definitions(lammps PRIVATE -DLAMMPS_PNG)
-  add_definitions(-DLAMMPS_PNG)
 endif()
 
 find_program(GZIP_EXECUTABLE gzip)
@@ -297,7 +295,7 @@ if(WITH_GZIP)
   if(NOT GZIP_FOUND)
     message(FATAL_ERROR "gzip executable not found")
   endif()
-  add_definitions(-DLAMMPS_GZIP)
+  target_compile_definitions(lammps PRIVATE -DLAMMPS_GZIP)
 endif()
 
 find_program(FFMPEG_EXECUTABLE ffmpeg)
@@ -307,7 +305,7 @@ if(WITH_FFMPEG)
   if(NOT FFMPEG_FOUND)
     message(FATAL_ERROR "ffmpeg executable not found")
   endif()
-  add_definitions(-DLAMMPS_FFMPEG)
+  target_compile_definitions(lammps PRIVATE -DLAMMPS_FFMPEG)
 endif()
 
 if(BUILD_SHARED_LIBS)
@@ -320,29 +318,25 @@ else()
   set(CUDA_REQUEST_PIC)
 endif()
 
-include(Packages/KSPACE)
+foreach(PKG_WITH_INCL KSPACE PYTHON VORONOI USER-COLVARS USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM
-include(Packages/PYTHON)
+        USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS)
-include(Packages/VORONOI)
+  if(PKG_${PKG_WITH_INCL})
-include(Packages/USER-COLVARS)
+    include(Packages/${PKG_WITH_INCL})
-include(Packages/USER-MOLFILE)
+  endif()
-include(Packages/USER-NETCDF)
+endforeach()
-include(Packages/USER-PLUMED)
-include(Packages/USER-QMMM)
-include(Packages/USER-QUIP)
-include(Packages/USER-SCAFACOS)
-include(Packages/USER-SMD)
-include(Packages/USER-VTK)
-include(Packages/KIM)
-include(Packages/LATTE)
-include(Packages/MESSAGE)
-include(Packages/MSCG)
-include(Packages/COMPRESS)
-
-# the windows version of LAMMPS requires a couple extra libraries
-if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
-  list(APPEND LAMMPS_LINK_LIBS -lwsock32 -lpsapi)
-endif()
 
+set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler specific optimization or instrumentation")
+separate_arguments(CMAKE_TUNE_FLAGS)
+include(CheckCXXCompilerFlag)
+foreach(_FLAG ${CMAKE_TUNE_FLAGS})
+  string(REGEX REPLACE "[=\"]" "" _FLAGX ${_FLAG})
+  check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAGX})
+  if(COMPILER_SUPPORTS${_FLAGX})
+    target_compile_options(lammps PRIVATE ${_FLAG})
+  else()
+    message(WARNING "${_FLAG} found in CMAKE_TUNE_FLAGS, but not supported by the compiler, skipping")
+  endif()
+endforeach()
 ########################################################################
 # Basic system tests (standard libraries, headers, functions, types)   #
 ########################################################################
@@ -355,18 +349,7 @@ endforeach(HEADER)
 
 set(MATH_LIBRARIES "m" CACHE STRING "math library")
 mark_as_advanced( MATH_LIBRARIES )
-include(CheckLibraryExists)
+target_link_libraries(lammps PRIVATE ${MATH_LIBRARIES})
-if (CMAKE_VERSION VERSION_LESS "3.4")
-  enable_language(C) # check_library_exists isn't supported without a C compiler before v3.4
-endif()
-# RB: disabled this check because it breaks with KOKKOS CUDA enabled
-#foreach(FUNC sin cos)
-#  check_library_exists(${MATH_LIBRARIES} ${FUNC} "" FOUND_${FUNC}_${MATH_LIBRARIES})
-#  if(NOT FOUND_${FUNC}_${MATH_LIBRARIES})
-#    message(FATAL_ERROR "Could not find needed math function - ${FUNC}")
-#  endif(NOT FOUND_${FUNC}_${MATH_LIBRARIES})
-#endforeach(FUNC)
-list(APPEND LAMMPS_LINK_LIBS ${MATH_LIBRARIES})
 
 ######################################
 # Generate Basic Style files
@@ -377,7 +360,7 @@ RegisterStyles(${LAMMPS_SOURCE_DIR})
 ##############################################
 # add sources of enabled packages
 ############################################
-foreach(PKG ${DEFAULT_PACKAGES})
+foreach(PKG ${STANDARD_PACKAGES})
   set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
 
   file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
@@ -390,8 +373,8 @@ foreach(PKG ${DEFAULT_PACKAGES})
     # detects styles in package and adds them to global list
     RegisterStyles(${${PKG}_SOURCES_DIR})
 
-    list(APPEND LIB_SOURCES ${${PKG}_SOURCES})
+    target_sources(lammps PRIVATE ${${PKG}_SOURCES})
-    include_directories(${${PKG}_SOURCES_DIR})
+    target_include_directories(lammps PRIVATE ${${PKG}_SOURCES_DIR})
   endif()
 
   RegisterPackages(${${PKG}_SOURCES_DIR})
@@ -400,12 +383,12 @@ endforeach()
 # packages that need defines set
 foreach(PKG MPIIO)
   if(PKG_${PKG})
-    add_definitions(-DLMP_${PKG})
+    target_compile_definitions(lammps PRIVATE -DLMP_${PKG})
   endif()
 endforeach()
 
 # dedicated check for entire contents of accelerator packages
-foreach(PKG ${ACCEL_PACKAGES})
+foreach(PKG ${SUFFIX_PACKAGES})
   set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
 
   file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
@@ -420,16 +403,19 @@ endforeach()
 ##############################################
 # add lib sources of (simple) enabled packages
 ############################################
-foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-QMMM)
+foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD)
   if(PKG_${SIMPLE_LIB})
     string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
     string(TOLOWER "${PKG_LIB}" PKG_LIB)
     file(GLOB_RECURSE ${PKG_LIB}_SOURCES
-      ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.F
       ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c
       ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
     add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
-    list(APPEND LAMMPS_LINK_LIBS ${PKG_LIB})
+    if(NOT BUILD_SHARED_LIBS)
+      install(TARGETS ${PKG_LIB} EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+    endif()
+    set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE})
+    target_link_libraries(lammps PRIVATE ${PKG_LIB})
     if(PKG_LIB STREQUAL awpmd)
       target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include)
     elseif(PKG_LIB STREQUAL h5md)
@@ -441,30 +427,40 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-QMMM)
 endforeach()
 
 if(PKG_USER-AWPMD)
-  target_link_libraries(awpmd ${LAPACK_LIBRARIES})
+  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")
   endif()
-  target_link_libraries(atc ${LAPACK_LIBRARIES})
+  target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES} MPI::MPI_CXX)
+  target_include_directories(atc PRIVATE ${LAMMPS_SOURCE_DIR})
+  target_compile_definitions(atc PRIVATE -DLAMMPS_${LAMMPS_SIZES})
 endif()
 
-include(Packages/USER-H5MD)
+if(PKG_USER-H5MD)
+  include(Packages/USER-H5MD)
+endif()
 
 ######################################################################
 # packages which selectively include variants based on enabled styles
 # e.g. accelerator packages
 ######################################################################
-include(Packages/CORESHELL)
+foreach(PKG_WITH_INCL CORESHELL QEQ USER-OMP USER-SDPD KOKKOS OPT USER-INTEL GPU)
-include(Packages/QEQ)
+  if(PKG_${PKG_WITH_INCL})
-include(Packages/USER-OMP)
+    include(Packages/${PKG_WITH_INCL})
-include(Packages/USER-SDPD)
+  endif()
-include(Packages/KOKKOS)
+endforeach()
-include(Packages/OPT)
+
-include(Packages/USER-INTEL)
+######################################################################
-include(Packages/GPU)
+# the windows version of LAMMPS requires a couple extra libraries
+# 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)
+endif()
 
 ######################################################
 # Generate style headers based on global list of
@@ -476,14 +472,14 @@ set(LAMMPS_STYLE_HEADERS_DIR ${CMAKE_CURRENT_BINARY_DIR}/styles)
 GenerateStyleHeaders(${LAMMPS_STYLE_HEADERS_DIR})
 GeneratePackagesHeaders(${LAMMPS_STYLE_HEADERS_DIR})
 
-include_directories(${LAMMPS_STYLE_HEADERS_DIR})
+target_include_directories(lammps PRIVATE ${LAMMPS_STYLE_HEADERS_DIR})
 
 ######################################
 # Generate lmpinstalledpkgs.h
 ######################################
 set(temp "#ifndef LMP_INSTALLED_PKGS_H\n#define LMP_INSTALLED_PKGS_H\n")
 set(temp "${temp}const char * LAMMPS_NS::LAMMPS::installed_packages[] =  {\n")
-set(temp_PKG_LIST ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
+set(temp_PKG_LIST ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
 list(SORT temp_PKG_LIST)
 foreach(PKG ${temp_PKG_LIST})
     if(PKG_${PKG})
@@ -505,7 +501,7 @@ add_custom_target(gitversion COMMAND ${CMAKE_COMMAND}
   -DLAMMPS_STYLE_HEADERS_DIR="${LAMMPS_STYLE_HEADERS_DIR}"
   -P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/generate_lmpgitversion.cmake)
 set_property(DIRECTORY APPEND PROPERTY ADDITIONAL_MAKE_CLEAN_FILES ${LAMMPS_STYLE_HEADERS_DIR}/gitversion.h)
-list(APPEND LAMMPS_DEPS gitversion)
+add_dependencies(lammps gitversion)
 
 ###########################################
 # Actually add executable and lib to build
@@ -513,94 +509,64 @@ list(APPEND LAMMPS_DEPS gitversion)
 get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
 list (FIND LANGUAGES "Fortran" _index)
 if (${_index} GREATER -1)
-  list(APPEND LAMMPS_LINK_LIBS ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+  target_link_libraries(lammps PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
 endif()
-list(REMOVE_DUPLICATES LAMMPS_LINK_LIBS)
+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
-if(BUILD_LIB)
+  input.h info.h kspace.h lammps.h lattice.h library.h lmppython.h lmptype.h memory.h modify.h neighbor.h neigh_list.h output.h
-  add_library(lammps ${LIB_SOURCES})
+  pair.h pointers.h region.h timer.h universe.h update.h variable.h)
-  target_link_libraries(lammps ${LAMMPS_LINK_LIBS})
+if(LAMMPS_EXCEPTIONS)
-  if(LAMMPS_DEPS)
+  list(APPEND LAMMPS_CXX_HEADERS exceptions.h)
-    add_dependencies(lammps ${LAMMPS_DEPS})
-  endif()
-  set(LAMMPS_CXX_HEADERS
-    ${LAMMPS_SOURCE_DIR}/angle.h
-    ${LAMMPS_SOURCE_DIR}/atom.h
-    ${LAMMPS_SOURCE_DIR}/bond.h
-    ${LAMMPS_SOURCE_DIR}/citeme.h
-    ${LAMMPS_SOURCE_DIR}/comm.h
-    ${LAMMPS_SOURCE_DIR}/compute.h
-    ${LAMMPS_SOURCE_DIR}/dihedral.h
-    ${LAMMPS_SOURCE_DIR}/domain.h
-    ${LAMMPS_SOURCE_DIR}/error.h
-    ${LAMMPS_SOURCE_DIR}/fix.h
-    ${LAMMPS_SOURCE_DIR}/force.h
-    ${LAMMPS_SOURCE_DIR}/group.h
-    ${LAMMPS_SOURCE_DIR}/improper.h
-    ${LAMMPS_SOURCE_DIR}/input.h
-    ${LAMMPS_SOURCE_DIR}/kspace.h
-    ${LAMMPS_SOURCE_DIR}/lammps.h
-    ${LAMMPS_SOURCE_DIR}/lattice.h
-    ${LAMMPS_SOURCE_DIR}/lmppython.h
-    ${LAMMPS_SOURCE_DIR}/memory.h
-    ${LAMMPS_SOURCE_DIR}/modify.h
-    ${LAMMPS_SOURCE_DIR}/neighbor.h
-    ${LAMMPS_SOURCE_DIR}/neigh_list.h
-    ${LAMMPS_SOURCE_DIR}/output.h
-    ${LAMMPS_SOURCE_DIR}/pair.h
-    ${LAMMPS_SOURCE_DIR}/pointers.h
-    ${LAMMPS_SOURCE_DIR}/region.h
-    ${LAMMPS_SOURCE_DIR}/timer.h
-    ${LAMMPS_SOURCE_DIR}/universe.h
-    ${LAMMPS_SOURCE_DIR}/update.h
-    ${LAMMPS_SOURCE_DIR}/variable.h)
-
-  set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_LIB_SUFFIX})
-  set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
-  install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-  install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
-  install(FILES ${LAMMPS_CXX_HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
-  configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY)
-  install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
-  configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY)
-  install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Modules)
-else()
-  list(APPEND LMP_SOURCES ${LIB_SOURCES})
 endif()
 
-if(BUILD_EXE)
+set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
-  add_executable(lmp ${LMP_SOURCES})
+set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
-  if(BUILD_LIB)
+install(TARGETS lammps EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-    target_link_libraries(lmp lammps)
+target_include_directories(lammps PUBLIC $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>)
-  else()
+file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps)
-    target_link_libraries(lmp ${LAMMPS_LINK_LIBS})
+foreach(_HEADER ${LAMMPS_CXX_HEADERS})
-    if(LAMMPS_DEPS)
+  add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/${_HEADER})
-      add_dependencies(lmp ${LAMMPS_DEPS})
+  add_custom_target(${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER})
-    endif()
+  add_dependencies(lammps ${_HEADER})
-  endif()
+  install(FILES ${LAMMPS_SOURCE_DIR}/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
-
+endforeach()
-  set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})
+target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/includes>)
-  install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
+add_library(LAMMPS::lammps ALIAS lammps)
-  install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1)
+get_target_property(LAMMPS_DEFINES lammps INTERFACE_COMPILE_DEFINITIONS)
-endif()
+set(LAMMPS_API_DEFINES)
+foreach(_DEF ${LAMMPS_DEFINES})
+  set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${_DEF}")
+endforeach()
+configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+install(EXPORT LAMMPS_Targets FILE LAMMPS_Targets.cmake NAMESPACE LAMMPS:: DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
+file(GLOB MODULE_FILES ${CMAKE_CURRENT_SOURCE_DIR}/Modules/Find*.cmake)
+install(FILES ${MODULE_FILES} DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
+include(CMakePackageConfigHelpers)
+configure_file(LAMMPSConfig.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake @ONLY)
+write_basic_package_version_file("LAMMPSConfigVersion.cmake" VERSION ${PROJECT_VERSION} COMPATIBILITY ExactVersion)
+install(FILES "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake" "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfigVersion.cmake" DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
+install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1)
 
 if(BUILD_TOOLS)
   add_executable(binary2txt ${LAMMPS_TOOLS_DIR}/binary2txt.cpp)
+  target_compile_definitions(binary2txt PRIVATE -DLAMMPS_${LAMMPS_SIZES})
   install(TARGETS binary2txt DESTINATION ${CMAKE_INSTALL_BINDIR})
 
-  # ninja-build currently does not support fortran. thus we skip building this tool
+  include(CheckGeneratorSupport)
-  if(NOT CMAKE_GENERATOR STREQUAL "Ninja")
+  if(CMAKE_GENERATOR_SUPPORT_FORTRAN)
-    message(STATUS "Skipping building 'chain.x' with Ninja build tool due to lack of Fortran support")
     enable_language(Fortran)
     add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
-    target_link_libraries(chain.x ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+    target_link_libraries(chain.x PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
     install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR})
+  else()
+    message(WARNING "CMake build doesn't support fortran, skipping building 'chain.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 m)
+  target_link_libraries(msi2lmp PRIVATE ${MATH_LIBRARIES})
   install(TARGETS msi2lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
   install(FILES ${LAMMPS_DOC_DIR}/msi2lmp.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
 endif()
@@ -630,12 +596,19 @@ install(
 # conventional build.  Only available, if a shared library is built.
 # This is primarily for people that only want to use the Python wrapper.
 ###############################################################################
-if(BUILD_LIB AND BUILD_SHARED_LIBS)
+if(BUILD_SHARED_LIBS)
-  find_package(PythonInterp)
+  if(CMAKE_VERSION VERSION_LESS 3.12)
-  if (PYTHONINTERP_FOUND)
+    find_package(PythonInterp) # Deprecated since version 3.12
+    if(PYTHONINTERP_FOUND)
+        set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
+    endif()
+  else()
+    find_package(Python COMPONENTS Interpreter)
+  endif()
+  if (Python_EXECUTABLE)
     add_custom_target(
       install-python
-      ${PYTHON_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
+      ${Python_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
       -m ${LAMMPS_PYTHON_DIR}/lammps.py
       -l ${CMAKE_BINARY_DIR}/liblammps${CMAKE_SHARED_LIBRARY_SUFFIX}
       WORKING_DIRECTORY  ${LAMMPS_PYTHON_DIR}
@@ -656,10 +629,17 @@ endif()
 # LAMMPS for package managers and with different prefix settings.
 # This requires either a shared library or that the PYTHON package is included.
 ###############################################################################
-if((BUILD_LIB AND BUILD_SHARED_LIBS) OR (PKG_PYTHON))
+if(BUILD_SHARED_LIBS OR PKG_PYTHON)
-  find_package(PythonInterp)
+  if(CMAKE_VERSION VERSION_LESS 3.12)
-  if (PYTHONINTERP_FOUND)
+    find_package(PythonInterp) # Deprecated since version 3.12
-    execute_process(COMMAND ${PYTHON_EXECUTABLE}
+    if(PYTHONINTERP_FOUND)
+        set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
+    endif()
+  else()
+    find_package(Python COMPONENTS Interpreter)
+  endif()
+  if (Python_EXECUTABLE)
+    execute_process(COMMAND ${Python_EXECUTABLE}
       -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
       OUTPUT_VARIABLE PYTHON_DEFAULT_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
     set(PYTHON_INSTDIR ${PYTHON_DEFAULT_INSTDIR} CACHE PATH "Installation folder for LAMMPS Python module")
@@ -673,69 +653,103 @@ include(CodeCoverage)
 ###############################################################################
 # Print package summary
 ###############################################################################
-foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
+foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
   if(PKG_${PKG})
     message(STATUS "Building package: ${PKG}")
   endif()
 endforeach()
 
-get_directory_property(CPPFLAGS DIRECTORY ${CMAKE_SOURCE_DIR} COMPILE_DEFINITIONS)
+get_target_property(DEFINES lammps COMPILE_DEFINITIONS)
 include(FeatureSummary)
-feature_summary(DESCRIPTION "The following packages have been found:" WHAT PACKAGES_FOUND)
+feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND)
 message(STATUS "<<< Build configuration >>>
-   Build type       ${CMAKE_BUILD_TYPE}
+   Build type:       ${CMAKE_BUILD_TYPE}
-   Install path     ${CMAKE_INSTALL_PREFIX}
+   Install path:     ${CMAKE_INSTALL_PREFIX}
-   Compilers and Flags:
+   Generator:        ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}
-   C++ Compiler     ${CMAKE_CXX_COMPILER}
+-- <<< Compilers and Flags: >>>
-       Type         ${CMAKE_CXX_COMPILER_ID}
+-- C++ Compiler:     ${CMAKE_CXX_COMPILER}
-       Version      ${CMAKE_CXX_COMPILER_VERSION}
+      Type:          ${CMAKE_CXX_COMPILER_ID}
-   C++ Flags        ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}
+      Version:       ${CMAKE_CXX_COMPILER_VERSION}
-   Defines          ${CPPFLAGS}")
+      C++ Flags:    ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}
+      Defines:       ${DEFINES}")
+get_target_property(OPTIONS lammps COMPILE_OPTIONS)
+if(OPTIONS)
+  message("      Options:       ${OPTIONS}")
+endif()
 get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
 list (FIND LANGUAGES "Fortran" _index)
 if (${_index} GREATER -1)
-  message(STATUS "Fortran Compiler ${CMAKE_Fortran_COMPILER}
+  message(STATUS "Fortran Compiler: ${CMAKE_Fortran_COMPILER}
-           Type     ${CMAKE_Fortran_COMPILER_ID}
+      Type:          ${CMAKE_Fortran_COMPILER_ID}
-           Version  ${CMAKE_Fortran_COMPILER_VERSION}
+      Version:       ${CMAKE_Fortran_COMPILER_VERSION}
-   Fortran Flags    ${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}")
+      Fortran Flags:${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}")
 endif()
 list (FIND LANGUAGES "C" _index)
 if (${_index} GREATER -1)
-  message(STATUS "C Compiler ${CMAKE_C_COMPILER}
+  message(STATUS "C compiler:       ${CMAKE_C_COMPILER}
-     Type     ${CMAKE_C_COMPILER_ID}
+      Type:          ${CMAKE_C_COMPILER_ID}
-     Version  ${CMAKE_C_COMPILER_VERSION}
+      Version:       ${CMAKE_C_COMPILER_VERSION}
-     C Flags  ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${BTYPE}}")
+      C Flags:      ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${BTYPE}}")
 endif()
+message(STATUS "<<< Linker flags: >>>")
+message(STATUS "Executable name:  ${LAMMPS_BINARY}")
 if(CMAKE_EXE_LINKER_FLAGS)
-  message(STATUS "Linker flags:
+  message(STATUS "Executable linker flags: ${CMAKE_EXE_LINKER_FLAGS}")
-   Executable      ${CMAKE_EXE_LINKER_FLAGS}")
 endif()
 if(BUILD_SHARED_LIBS)
-  message(STATUS "Shared libraries  ${CMAKE_SHARED_LINKER_FLAGS}")
+  message(STATUS "Shared library flags:    ${CMAKE_SHARED_LINKER_FLAGS}")
 else()
-  message(STATUS "Static libraries  ${CMAKE_STATIC_LINKER_FLAGS}")
+  message(STATUS "Static library flags:    ${CMAKE_STATIC_LINKER_FLAGS}")
 endif()
-message(STATUS "Link libraries: ${LAMMPS_LINK_LIBS}")
 if(BUILD_MPI)
-  message(STATUS "Using mpi with headers in ${MPI_CXX_INCLUDE_PATH} and ${MPI_CXX_LIBRARIES}")
+  message(STATUS "<<< MPI flags >>>
+-- MPI_defines:      ${MPI_CXX_COMPILE_DEFINITIONS}
+-- MPI includes:     ${MPI_CXX_INCLUDE_PATH}
+-- MPI libraries:    ${MPI_CXX_LIBRARIES};${MPI_Fortran_LIBRARIES}")
 endif()
 if(PKG_GPU)
-  message(STATUS "GPU Api: ${GPU_API}")
+  message(STATUS "<<< GPU package settings >>>
+-- GPU API:          ${GPU_API}")
   if(GPU_API STREQUAL "CUDA")
-    message(STATUS "GPU Arch: ${GPU_ARCH}")
+    message(STATUS "GPU architecture: ${GPU_ARCH}")
   elseif(GPU_API STREQUAL "OPENCL")
-    message(STATUS "OCL Tune: ${OCL_TUNE}")
+    message(STATUS "OpenCL tuning:    ${OCL_TUNE}")
+  elseif(GPU_API STREQUAL "HIP")
+    message(STATUS "HIP platform:     ${HIP_PLATFORM}")
+    message(STATUS "HIP architecture: ${HIP_ARCH}")
+    if(HIP_USE_DEVICE_SORT)
+      message(STATUS "HIP GPU sorting: on")
+    else()
+      message(STATUS "HIP GPU sorting: off")
+    endif()
   endif()
-  message(STATUS "GPU Precision: ${GPU_PREC}")
+  message(STATUS "GPU precision:    ${GPU_PREC}")
 endif()
 if(PKG_KOKKOS)
   message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}")
 endif()
 if(PKG_KSPACE)
-  message(STATUS "Using ${FFT} as primary FFT library")
+  message(STATUS "<<< FFT settings >>>
+-- Primary FFT lib:  ${FFT}")
   if(FFT_SINGLE)
     message(STATUS "Using single precision FFTs")
   else()
     message(STATUS "Using double precision FFTs")
   endif()
+  if(FFT_FFTW_THREADS OR FFT_MKL_THREADS)
+    message(STATUS "Using threaded FFTs")
+  else()
+    message(STATUS "Using non-threaded FFTs")
+  endif()
+  if(PKG_KOKKOS)
+    if(Kokkos_ENABLE_CUDA)
+      if (${FFT} STREQUAL "KISS")
+        message(STATUS "Kokkos FFT: KISS")
+      else()
+        message(STATUS "Kokkos FFT: cuFFT")
+      endif()
+    else()
+      message(STATUS "Kokkos FFT: ${FFT}")
+    endif()
+  endif()
 endif()

cmake/FindLAMMPS.cmake.in

@@ -1,48 +0,0 @@
-# - Find liblammps
-# Find the native liblammps headers and libraries.
-#
-# The following variables will set:
-#  LAMMPS_INCLUDE_DIRS - where to find lammps/library.h, etc.
-#  LAMMPS_LIBRARIES    - List of libraries when using lammps.
-#  LAMMPS_API_DEFINES  - lammps library api defines
-#  LAMMPS_VERSION      - lammps library version 
-#  LAMMPS_FOUND        - True if liblammps found.
-#
-# In addition a LAMMPS::LAMMPS imported target is getting created.
-#
-#  LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-#  http://lammps.sandia.gov, Sandia National Laboratories
-#  Steve Plimpton, sjplimp@sandia.gov
-#
-#  Copyright (2003) Sandia Corporation.  Under the terms of Contract
-#  DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
-#  certain rights in this software.  This software is distributed under
-#  the GNU General Public License.
-#
-#  See the README file in the top-level LAMMPS directory.
-#
-
-find_package(PkgConfig)
-
-pkg_check_modules(PC_LAMMPS liblammps@LAMMPS_LIB_SUFFIX@)
-find_path(LAMMPS_INCLUDE_DIR lammps/library.h HINTS ${PC_LAMMPS_INCLUDE_DIRS} @CMAKE_INSTALL_FULL_INCLUDEDIR@)
-
-set(LAMMPS_VERSION @LAMMPS_VERSION@)
-set(LAMMPS_API_DEFINES @LAMMPS_API_DEFINES@)
-
-find_library(LAMMPS_LIBRARY NAMES lammps@LAMMPS_LIB_SUFFIX@ HINTS ${PC_LAMMPS_LIBRARY_DIRS} @CMAKE_INSTALL_FULL_LIBDIR@)
-
-set(LAMMPS_INCLUDE_DIRS "${LAMMPS_INCLUDE_DIR}")
-set(LAMMPS_LIBRARIES "${LAMMPS_LIBRARY}")
-
-include(FindPackageHandleStandardArgs)
-# handle the QUIETLY and REQUIRED arguments and set LAMMPS_FOUND to TRUE
-# if all listed variables are TRUE
-find_package_handle_standard_args(LAMMPS REQUIRED_VARS LAMMPS_LIBRARY LAMMPS_INCLUDE_DIR VERSION_VAR LAMMPS_VERSION)
-
-mark_as_advanced(LAMMPS_INCLUDE_DIR LAMMPS_LIBRARY)
-
-if(LAMMPS_FOUND AND NOT TARGET LAMMPS::LAMMPS)
-  add_library(LAMMPS::LAMMPS UNKNOWN IMPORTED)
-  set_target_properties(LAMMPS::LAMMPS PROPERTIES IMPORTED_LOCATION "${LAMMPS_LIBRARY}" INTERFACE_INCLUDE_DIRECTORIES "${LAMMPS_INCLUDE_DIR}" INTERFACE_COMPILE_DEFINITIONS "${LAMMPS_API_DEFINES}")
-endif()

cmake/LAMMPSConfig.cmake.in

@@ -0,0 +1,87 @@
+set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR})
+include(CMakeFindDependencyMacro)
+if(@BUILD_MPI@)
+  find_dependency(MPI REQUIRED CXX)
+endif()
+if(@PKG_KSPACE@)
+  if(@FFT@ STREQUAL "FFTW3")
+    find_dependency(@FFTW@ REQUIRED MODULE)
+  endif()
+endif()
+if(NOT @BUILD_SHARED_LIBS@)
+  if(@BUILD_OMP@)
+    find_dependency(OpenMP REQUIRED)
+  endif()
+  if(@WITH_JPEG@)
+    find_dependency(JPEG REQUIRED)
+  endif()
+  if(@WITH_PNG@)
+    find_dependency(PNG REQUIRED)
+    find_dependency(ZLIB REQUIRED)
+  endif()
+  if(@PKG_KIM@)
+    find_dependency(PkgConfig REQUIRED)
+    pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=@KIM-API_MIN_VERSION@)
+    if(@CURL_FOUND@)
+      find_dependency(CURL REQUIRED)
+    endif()
+  endif()
+  if(@PKG_USER-SMD@)
+    find_dependency(Eigen3 NO_MODULE REQUIRED)
+  endif()
+  if(@PKG_USER-SCAFACOS@)
+    find_dependency(PkgConfig REQUIRED)
+    find_ependency(GSL REQUIRED)
+    find_dependency(MPI REQUIRED C Fortran)
+    pkg_check_modules(SCAFACOS REQUIRED IMPORTED_TARGET scafacos)
+  endif()
+  if(@PKG_PYTHON@ AND NOT CMAKE_VERSION VERSION_LESS 3.12)
+    find_package(Python REQUIRED COMPONENTS Development)
+  endif()
+  if(@PKG_COMPRESS@)
+    find_dependency(ZLIB REQUIRED)
+  endif()
+  if(@PKG_KOKKOS@)
+    if(@EXTERNAL_KOKKOS@)
+      find_dependency(Kokkos 3 REQUIRED)
+    endif()
+  endif()
+  if(@PKG_VORONOI@)
+    find_dependency(VORO REQUIRED)
+  endif()
+  if(@PKG_USER-INTEL@)
+    if(@INTEL_LRT_MODE@ STREQUAL "THREADS")
+      find_dependency(Threads REQUIRED)
+    endif()
+    if(@TBB_MALLOC_FOUND@)
+      find_ependency(TBB_MALLOC REQUIRED)
+    endif()
+  endif()
+  if(@PKG_USER-ADIOS@)
+    find_ependency(ADIOS2 REQUIRED)
+  endif()
+  if(@PKG_LATTE@)
+    find_ependency(LATTE REQUIRED)
+  endif()
+  if(@PKG_MESSAGE@)
+    if(@MESSAGE_ZMQ@)
+      find_ependency(ZMQ REQUIRED)
+    endif()
+  endif()
+  if(@PKG_MSCG@)
+    find_ependency(GSL REQUIRED)
+    find_ependency(MSCG REQUIRED)
+  endif()
+  if(@USER-NETCDF@)
+    if(@NETCDF_FOUND@)
+      find_ependency(NetCDF REQUIRED)
+    endif()
+    if(@PNETCDF_FOUND@)
+      find_ependency(PNetCDF REQUIRED)
+    endif()
+  endif()
+  if(@PKG_QUIP@)
+    find_ependency(QUIP REQUIRED)
+  endif()
+endif()
+include("${CMAKE_CURRENT_LIST_DIR}/LAMMPS_Targets.cmake")

cmake/Modules/CheckGeneratorSupport.cmake

@@ -0,0 +1,21 @@
+# ninja-build<1.10 does not support fortran.
+if(CMAKE_GENERATOR STREQUAL "Ninja")
+  set(CMAKE_GENERATOR_SUPPORT_FORTRAN FALSE)
+  execute_process(COMMAND "${CMAKE_MAKE_PROGRAM}" --version
+    OUTPUT_VARIABLE NINJA_VERSION
+    OUTPUT_STRIP_TRAILING_WHITESPACE
+    RESULT_VARIABLE _Ninja_version_result
+  )
+  if(_Ninja_version_result)
+    message(WARNING "Unable to determine ninja version: ${_Ninja_version_result}, assuming fortran isn't supported")
+  elseif(NINJA_VERSION VERSION_LESS "1.10")
+    message(WARNING "Ninja build tool too old, to compile Fortran code, please install ninja-1.10 or newer")
+  else()
+    set(CMAKE_GENERATOR_SUPPORT_FORTRAN TRUE)
+  endif()
+else()
+  set(CMAKE_GENERATOR_SUPPORT_FORTRAN TRUE)
+  if(NOT CMAKE_GENERATOR STREQUAL "Unix Makefiles")
+    message(WARNING "Assuming fortran is supported for ${CMAKE_GENERATOR}")
+  endif()
+endif()

cmake/Modules/Documentation.cmake

@@ -1,10 +1,8 @@
 ###############################################################################
 # Build documentation
 ###############################################################################
-option(BUILD_DOC "Build LAMMPS documentation" OFF)
+option(BUILD_DOC "Build LAMMPS HTML documentation" OFF)
 if(BUILD_DOC)
-  include(ProcessorCount)
-  ProcessorCount(NPROCS)
   find_package(PythonInterp 3 REQUIRED)
 
   set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)
@@ -26,15 +24,49 @@ if(BUILD_DOC)
     COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
   )
 
+  # download mathjax distribution and unpack to folder "mathjax"
+  file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
+    "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
+    EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7)
+
+  if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax)
+    execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+    file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
+    execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${CMAKE_CURRENT_BINARY_DIR}/mathjax)
+  endif()
+  file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax)
+  file(COPY ${CMAKE_CURRENT_BINARY_DIR}/mathjax/es5 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax/)
+
+  # note, this may run in parallel with other tasks, so we must not use multiple processes here
   add_custom_command(
     OUTPUT html
     DEPENDS ${DOC_SOURCES} docenv requirements.txt
-    COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${LAMMPS_DOC_DIR}/src html
+    COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${LAMMPS_DOC_DIR}/src html
   )
 
+  # copy selected image files to html output tree
+  file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/html/JPG)
+  set(HTML_EXTRA_IMAGES balance_nonuniform.jpg balance_rcb.jpg
+    balance_uniform.jpg bow_tutorial_01.png bow_tutorial_02.png
+    bow_tutorial_03.png bow_tutorial_04.png bow_tutorial_05.png
+    dump1.jpg dump2.jpg examples_mdpd.gif gran_funnel.png gran_mixer.png
+    hop1.jpg hop2.jpg saed_ewald_intersect.jpg saed_mesh.jpg
+    screenshot_atomeye.jpg screenshot_gl.jpg screenshot_pymol.jpg
+    screenshot_vmd.jpg sinusoid.jpg xrd_mesh.jpg)
+  set(HTML_IMAGE_TARGETS "")
+  foreach(_IMG ${HTML_EXTRA_IMAGES})
+    string(PREPEND _IMG JPG/)
+    list(APPEND HTML_IMAGE_TARGETS "html/${_IMG}")
+    add_custom_command(
+      OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/html/${_IMG}
+      DEPENDS ${LAMMPS_DOC_DIR}/src/${_IMG} html/JPG
+      COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/src/${_IMG} ${CMAKE_BINARY_DIR}/html/${_IMG}
+    )
+  endforeach()
+
   add_custom_target(
     doc ALL
-    DEPENDS html
+    DEPENDS html html/_static/mathjax/es5 ${HTML_IMAGE_TARGETS}
     SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES}
   )
 

cmake/Modules/FindCUB.cmake

@@ -0,0 +1,16 @@
+# - Find CUB
+# Find the CUB header library
+#
+#  CUB_INCLUDE_DIRS - where to find cub/cub.cuh
+#  CUB_FOUND        - True if CUB found.
+#
+
+find_path(CUB_INCLUDE_DIR cub.cuh PATH_SUFFIXES cub)
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set CUB_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(CUB DEFAULT_MSG CUB_INCLUDE_DIR)
+
+mark_as_advanced(CUB_INCLUDE_DIR)

cmake/Modules/FindFFTW3.cmake

@@ -1,20 +1,18 @@
 # - Find fftw3
-# Find the native FFTW3 headers and libraries.
+# Find the native double precision FFTW3 headers and libraries.
 #
-#  FFTW3_INCLUDE_DIRS - where to find fftw3.h, etc.
+#  FFTW3_INCLUDE_DIRS  - where to find fftw3.h, etc.
-#  FFTW3_LIBRARIES    - List of libraries when using fftw3.
+#  FFTW3_LIBRARIES     - List of libraries when using fftw3.
-#  FFTW3_FOUND        - True if fftw3 found.
+#  FFTW3_OMP_LIBRARIES - List of libraries when using fftw3.
+#  FFTW3_FOUND         - True if fftw3 found.
 #
 
 find_package(PkgConfig)
 
 pkg_check_modules(PC_FFTW3 fftw3)
 find_path(FFTW3_INCLUDE_DIR fftw3.h HINTS ${PC_FFTW3_INCLUDE_DIRS})
-
 find_library(FFTW3_LIBRARY NAMES fftw3 HINTS ${PC_FFTW3_LIBRARY_DIRS})
-
+find_library(FFTW3_OMP_LIBRARY NAMES fftw3_omp HINTS ${PC_FFTW3_LIBRARY_DIRS})
-set(FFTW3_LIBRARIES ${FFTW3_LIBRARY})
-set(FFTW3_INCLUDE_DIRS ${FFTW3_INCLUDE_DIR})
 
 include(FindPackageHandleStandardArgs)
 # handle the QUIETLY and REQUIRED arguments and set FFTW3_FOUND to TRUE
@@ -22,4 +20,28 @@ include(FindPackageHandleStandardArgs)
 
 find_package_handle_standard_args(FFTW3 DEFAULT_MSG FFTW3_LIBRARY FFTW3_INCLUDE_DIR)
 
-mark_as_advanced(FFTW3_INCLUDE_DIR FFTW3_LIBRARY )
+# Copy the results to the output variables and target.
+if(FFTW3_FOUND)
+  set(FFTW3_LIBRARIES ${FFTW3_LIBRARY} )
+  set(FFTW3_INCLUDE_DIRS ${FFTW3_INCLUDE_DIR} )
+
+  if(NOT TARGET FFTW3::FFTW3)
+    add_library(FFTW3::FFTW3 UNKNOWN IMPORTED)
+    set_target_properties(FFTW3::FFTW3 PROPERTIES
+      IMPORTED_LINK_INTERFACE_LANGUAGES "C"
+      IMPORTED_LOCATION "${FFTW3_LIBRARY}"
+      INTERFACE_INCLUDE_DIRECTORIES "${FFTW3_INCLUDE_DIRS}")
+  endif()
+  if(FFTW3_OMP_LIBRARY)
+    set(FFTW3_OMP_LIBRARIES ${FFTW3_OMP_LIBRARY})
+    if(NOT TARGET FFTW3::FFTW3_OMP)
+      add_library(FFTW3::FFTW3_OMP UNKNOWN IMPORTED)
+      set_target_properties(FFTW3::FFTW3_OMP PROPERTIES
+        IMPORTED_LINK_INTERFACE_LANGUAGES "C"
+	IMPORTED_LOCATION "${FFTW3_OMP_LIBRARY}"
+        INTERFACE_INCLUDE_DIRECTORIES "${FFTW3_INCLUDE_DIRS}")
+    endif()
+  endif()
+endif()
+
+mark_as_advanced(FFTW3_INCLUDE_DIR FFTW3_LIBRARY FFTW3_OMP_LIBRARY)

cmake/Modules/FindFFTW3F.cmake

@@ -1,8 +1,8 @@
-# - Find fftw3f
+# Find the native single precision FFTW3 headers and libraries.
-# Find the native FFTW3F headers and libraries.
 #
 #  FFTW3F_INCLUDE_DIRS - where to find fftw3f.h, etc.
 #  FFTW3F_LIBRARIES    - List of libraries when using fftw3f.
+#  FFTW3F_OMP_LIBRARIES - List of libraries when using fftw3.
 #  FFTW3F_FOUND        - True if fftw3f found.
 #
 
@@ -10,11 +10,8 @@ find_package(PkgConfig)
 
 pkg_check_modules(PC_FFTW3F fftw3f)
 find_path(FFTW3F_INCLUDE_DIR fftw3.h HINTS ${PC_FFTW3F_INCLUDE_DIRS})
-
 find_library(FFTW3F_LIBRARY NAMES fftw3f HINTS ${PC_FFTW3F_LIBRARY_DIRS})
-
+find_library(FFTW3F_OMP_LIBRARY NAMES fftw3f_omp HINTS ${PC_FFTW3F_LIBRARY_DIRS})
-set(FFTW3F_LIBRARIES ${FFTW3F_LIBRARY})
-set(FFTW3F_INCLUDE_DIRS ${FFTW3F_INCLUDE_DIR})
 
 include(FindPackageHandleStandardArgs)
 # handle the QUIETLY and REQUIRED arguments and set FFTW3F_FOUND to TRUE
@@ -22,4 +19,28 @@ include(FindPackageHandleStandardArgs)
 
 find_package_handle_standard_args(FFTW3F DEFAULT_MSG FFTW3F_LIBRARY FFTW3F_INCLUDE_DIR)
 
-mark_as_advanced(FFTW3F_INCLUDE_DIR FFTW3F_LIBRARY )
+# Copy the results to the output variables and target.
+if(FFTW3F_FOUND)
+  set(FFTW3F_LIBRARIES ${FFTW3F_LIBRARY} )
+  set(FFTW3F_INCLUDE_DIRS ${FFTW3F_INCLUDE_DIR} )
+
+  if(NOT TARGET FFTW3F::FFTW3F)
+    add_library(FFTW3F::FFTW3F UNKNOWN IMPORTED)
+    set_target_properties(FFTW3F::FFTW3F PROPERTIES
+      IMPORTED_LINK_INTERFACE_LANGUAGES "C"
+      IMPORTED_LOCATION "${FFTW3F_LIBRARY}"
+      INTERFACE_INCLUDE_DIRECTORIES "${FFTW3F_INCLUDE_DIRS}")
+  endif()
+  if(FFTW3F_OMP_LIBRARY)
+    set(FFTW3F_OMP_LIBRARIES ${FFTW3F_OMP_LIBRARY})
+    if(NOT TARGET FFTW3F::FFTW3F_OMP)
+      add_library(FFTW3F::FFTW3F_OMP UNKNOWN IMPORTED)
+      set_target_properties(FFTW3F::FFTW3F_OMP PROPERTIES
+        IMPORTED_LINK_INTERFACE_LANGUAGES "C"
+	IMPORTED_LOCATION "${FFTW3F_OMP_LIBRARY}"
+        INTERFACE_INCLUDE_DIRECTORIES "${FFTW3F_INCLUDE_DIRS}")
+    endif()
+  endif()
+endif()
+
+mark_as_advanced(FFTW3F_INCLUDE_DIR FFTW3F_LIBRARY FFTW3F_OMP_LIBRARY)

cmake/Modules/FindKIM-API.cmake

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

cmake/Modules/FindLATTE.cmake

@@ -7,12 +7,21 @@
 
 find_library(LATTE_LIBRARY NAMES latte)
 
-set(LATTE_LIBRARIES ${LATTE_LIBRARY})
-
 include(FindPackageHandleStandardArgs)
 # handle the QUIETLY and REQUIRED arguments and set LATTE_FOUND to TRUE
 # if all listed variables are TRUE
 
 find_package_handle_standard_args(LATTE DEFAULT_MSG LATTE_LIBRARY)
 
+# Copy the results to the output variables and target.
+if(LATTE_FOUND)
+  set(LATTE_LIBRARIES ${LATTE_LIBRARY})
+
+  if(NOT TARGET LATTE::latte)
+    add_library(LATTE::latte UNKNOWN IMPORTED)
+    set_target_properties(LATTE::latte PROPERTIES
+      IMPORTED_LOCATION "${LATTE_LIBRARY}")
+  endif()
+endif()
+
 mark_as_advanced(LATTE_LIBRARY)

cmake/Modules/FindMKL.cmake

@@ -10,13 +10,22 @@ find_path(MKL_INCLUDE_DIR mkl_dfti.h HINTS $ENV{MKLROOT}/include)
 
 find_library(MKL_LIBRARY NAMES mkl_rt HINTS $ENV{MKLROOT}/lib $ENV{MKLROOT}/lib/intel64)
 
-set(MKL_LIBRARIES ${MKL_LIBRARY})
-set(MKL_INCLUDE_DIRS ${MKL_INCLUDE_DIR})
-
 include(FindPackageHandleStandardArgs)
 # handle the QUIETLY and REQUIRED arguments and set MKL_FOUND to TRUE
 # if all listed variables are TRUE
 
 find_package_handle_standard_args(MKL DEFAULT_MSG MKL_LIBRARY MKL_INCLUDE_DIR)
 
+if(MKL_FOUND)
+  set(MKL_LIBRARIES ${MKL_LIBRARY})
+  set(MKL_INCLUDE_DIRS ${MKL_INCLUDE_DIR})
+
+  if(NOT TARGET MKL::MKL)
+    add_library(MKL::MKL UNKNOWN IMPORTED)
+    set_target_properties(MKL::MKL PROPERTIES
+      IMPORTED_LOCATION "${MKL_LIBRARY}"
+      INTERFACE_INCLUDE_DIRECTORIES "${MKL_INCLUDE_DIR}")
+  endif()
+endif()
+
 mark_as_advanced(MKL_INCLUDE_DIR MKL_LIBRARY )

cmake/Modules/FindMSCG.cmake

@@ -10,13 +10,23 @@ find_path(MSCG_INCLUDE_DIR mscg.h PATH_SUFFIXES mscg)
 
 find_library(MSCG_LIBRARY NAMES mscg)
 
-set(MSCG_LIBRARIES ${MSCG_LIBRARY})
-set(MSCG_INCLUDE_DIRS ${MSCG_INCLUDE_DIR})
-
 include(FindPackageHandleStandardArgs)
 # handle the QUIETLY and REQUIRED arguments and set MSCG_FOUND to TRUE
 # if all listed variables are TRUE
 
 find_package_handle_standard_args(MSCG DEFAULT_MSG MSCG_LIBRARY MSCG_INCLUDE_DIR)
 
+# Copy the results to the output variables and target.
+if(MSCG_FOUND)
+  set(MSCG_LIBRARIES ${MSCG_LIBRARY})
+  set(MSCG_INCLUDE_DIRS ${MSCG_INCLUDE_DIR})
+
+  if(NOT TARGET MSCG::MSCG)
+    add_library(MSCG::MSCG UNKNOWN IMPORTED)
+    set_target_properties(MSCG::MSCG PROPERTIES
+      IMPORTED_LOCATION "${MSCG_LIBRARY}"
+      INTERFACE_INCLUDE_DIRECTORIES "${MSCG_INCLUDE_DIR}")
+  endif()
+endif()
+
 mark_as_advanced(MSCG_INCLUDE_DIR MSCG_LIBRARY )

cmake/Modules/FindNetCDF.cmake

@@ -46,10 +46,14 @@ endif()
 find_path (NETCDF_INCLUDE_DIR netcdf.h
   HINTS "${NETCDF_DIR}/include")
 mark_as_advanced (NETCDF_INCLUDE_DIR)
+
 set (NETCDF_C_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR})
 
+string(REGEX REPLACE "/include/?$" ""
+  NETCDF_LIB_HINT ${NETCDF_INCLUDE_DIR})
+
 find_library (NETCDF_LIBRARY NAMES netcdf
-  HINTS "${NETCDF_DIR}/lib")
+  HINTS "${NETCDF_DIR}" "${NETCDF_LIB_HINT}" PATH_SUFFIXES lib lib64)
 mark_as_advanced (NETCDF_LIBRARY)
 
 set (NETCDF_C_LIBRARIES ${NETCDF_LIBRARY})
@@ -116,3 +120,14 @@ set (NETCDF_INCLUDE_DIRS ${NetCDF_includes})
 include (FindPackageHandleStandardArgs)
 find_package_handle_standard_args (NetCDF
   DEFAULT_MSG NETCDF_LIBRARIES NETCDF_INCLUDE_DIRS NETCDF_HAS_INTERFACES)
+
+# Copy the results to the output variables and target.
+if(NetCDF_FOUND)
+  if(NOT TARGET NetCDF::NetCDF)
+    add_library(NetCDF::NetCDF UNKNOWN IMPORTED)
+    set_target_properties(NetCDF::NetCDF PROPERTIES
+      IMPORTED_LOCATION "${NETCDF_LIBRARY}"
+      INTERFACE_INCLUDE_DIRECTORIES "${NETCDF_INCLUDE_DIRS}"
+      INTERFACE_LINK_LIBRARIES "${NETCDF_LIBRARIES}")
+  endif()
+endif()

cmake/Modules/FindPNetCDF.cmake

@@ -0,0 +1,64 @@
+# source: https://ftp.space.dtu.dk/pub/Ioana/pism0.6.1-10/CMake/FindPNetCDF.cmake
+# license: GPL v3 (https://ftp.space.dtu.dk/pub/Ioana/pism0.6.1-10/COPYING)
+#
+# - Find PNetCDF
+# Find the native PNetCDF includes and library
+#
+#  PNETCDF_INCLUDES    - where to find netcdf.h, etc
+#  PNETCDF_LIBRARIES   - Link these libraries when using NetCDF
+#  PNETCDF_FOUND       - True if PNetCDF was found
+#
+# Normal usage would be:
+#  find_package (PNetCDF REQUIRED)
+#  target_link_libraries (uses_pnetcdf ${PNETCDF_LIBRARIES})
+
+if (PNETCDF_INCLUDES AND PNETCDF_LIBRARIES)
+  # Already in cache, be silent
+  set (PNETCDF_FIND_QUIETLY TRUE)
+endif (PNETCDF_INCLUDES AND PNETCDF_LIBRARIES)
+
+find_path (PNETCDF_INCLUDES pnetcdf.h
+  HINTS "${PNETCDF_ROOT}/include" "$ENV{PNETCDF_ROOT}/include")
+
+string(REGEX REPLACE "/include/?$" ""
+  PNETCDF_LIB_HINT ${PNETCDF_INCLUDES})
+
+find_library (PNETCDF_LIBRARIES
+  NAMES pnetcdf
+  HINTS ${PNETCDF_LIB_HINT} PATH_SUFFIXES lib lib64)
+
+if ((NOT PNETCDF_LIBRARIES) OR (NOT PNETCDF_INCLUDES))
+  message(STATUS "Trying to find PNetCDF using LD_LIBRARY_PATH (we're desperate)...")
+
+  file(TO_CMAKE_PATH "$ENV{LD_LIBRARY_PATH}" LD_LIBRARY_PATH)
+
+  find_library(PNETCDF_LIBRARIES
+    NAMES pnetcdf
+    HINTS ${LD_LIBRARY_PATH})
+
+  if (PNETCDF_LIBRARIES)
+    get_filename_component(PNETCDF_LIB_DIR ${PNETCDF_LIBRARIES} PATH)
+    string(REGEX REPLACE "/(lib|lib64)/?$" "/include"
+      PNETCDF_H_HINT ${PNETCDF_LIB_DIR})
+
+    find_path (PNETCDF_INCLUDES pnetcdf.h
+      HINTS ${PNETCDF_H_HINT}
+      DOC "Path to pnetcdf.h")
+  endif()
+endif()
+
+# handle the QUIETLY and REQUIRED arguments and set PNETCDF_FOUND to TRUE if
+# all listed variables are TRUE
+include (FindPackageHandleStandardArgs)
+find_package_handle_standard_args (PNetCDF DEFAULT_MSG PNETCDF_LIBRARIES PNETCDF_INCLUDES)
+
+mark_as_advanced (PNETCDF_LIBRARIES PNETCDF_INCLUDES)
+
+if(PNetCDF_FOUND)
+  if(NOT TARGET PNetCDF::PNetCDF)
+    add_library(PNetCDF::PNetCDF UNKNOWN IMPORTED)
+    set_target_properties(PNetCDF::PNetCDF PROPERTIES
+      IMPORTED_LOCATION "${PNETCDF_LIBRARIES}"
+      INTERFACE_INCLUDE_DIRECTORIES "${PNETCDF_INCLUDES}")
+  endif()
+endif()

cmake/Modules/FindQE.cmake

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

cmake/Modules/FindQUIP.cmake

@@ -7,12 +7,21 @@
 
 find_library(QUIP_LIBRARY NAMES quip)
 
-set(QUIP_LIBRARIES ${QUIP_LIBRARY})
-
 include(FindPackageHandleStandardArgs)
 # handle the QUIETLY and REQUIRED arguments and set QUIP_FOUND to TRUE
 # if all listed variables are TRUE
 
 find_package_handle_standard_args(QUIP DEFAULT_MSG QUIP_LIBRARY)
 
+# Copy the results to the output variables and target.
+if(QUIP_FOUND)
+  set(QUIP_LIBRARIES ${QUIP_LIBRARY})
+
+  if(NOT TARGET QUIP::QUIP)
+    add_library(QUIP::QUIP UNKNOWN IMPORTED)
+    set_target_properties(QUIP::QUIP PROPERTIES
+      IMPORTED_LOCATION "${QUIP_LIBRARY}")
+  endif()
+endif()
+
 mark_as_advanced(QUIP_LIBRARY)

cmake/Modules/FindTBB.cmake

@@ -1,46 +0,0 @@
-# - Find parts of TBB
-# Find the native TBB headers and libraries.
-#
-#  TBB_INCLUDE_DIRS - where to find tbb.h, etc.
-#  TBB_LIBRARIES    - List of libraries when using tbb.
-#  TBB_FOUND        - True if tbb found.
-#
-
-########################################################
-# TBB
-
-# TODO use more generic FindTBB
-
-find_path(TBB_INCLUDE_DIR NAMES tbb/tbb.h PATHS $ENV{TBBROOT}/include)
-find_library(TBB_LIBRARY NAMES tbb PATHS $ENV{TBBROOT}/lib/intel64/gcc4.7
-                                         $ENV{TBBROOT}/lib/intel64/gcc4.4
-                                         $ENV{TBBROOT}/lib/intel64/gcc4.1)
-set(TBB_LIBRARIES ${TBB_LIBRARY})
-set(TBB_INCLUDE_DIRS ${TBB_INCLUDE_DIR})
-
-include(FindPackageHandleStandardArgs)
-# handle the QUIETLY and REQUIRED arguments and set TBB_FOUND to TRUE
-# if all listed variables are TRUE
-
-find_package_handle_standard_args(TBB DEFAULT_MSG TBB_LIBRARY TBB_INCLUDE_DIR)
-
-mark_as_advanced(TBB_INCLUDE_DIR TBB_LIBRARY )
-
-########################################################
-# TBB Malloc
-
-find_path(TBB_MALLOC_INCLUDE_DIR NAMES tbb/tbb.h PATHS $ENV{TBBROOT}/include)
-find_library(TBB_MALLOC_LIBRARY NAMES tbbmalloc PATHS $ENV{TBBROOT}/lib/intel64/gcc4.7
-                                                      $ENV{TBBROOT}/lib/intel64/gcc4.4
-                                                      $ENV{TBBROOT}/lib/intel64/gcc4.1)
-
-set(TBB_MALLOC_LIBRARIES ${TBB_MALLOC_LIBRARY})
-set(TBB_MALLOC_INCLUDE_DIRS ${TBB_MALLOC_INCLUDE_DIR})
-
-include(FindPackageHandleStandardArgs)
-# handle the QUIETLY and REQUIRED arguments and set TBB_MALLOC_FOUND to TRUE
-# if all listed variables are TRUE
-
-find_package_handle_standard_args(TBB_MALLOC DEFAULT_MSG TBB_MALLOC_LIBRARY TBB_MALLOC_INCLUDE_DIR)
-
-mark_as_advanced(TBB_MALLOC_INCLUDE_DIR TBB_MALLOC_LIBRARY )

cmake/Modules/FindTBB_MALLOC.cmake

@@ -0,0 +1,36 @@
+# - Find parts of TBB_MALLOC
+# Find the native TBB_MALLOC headers and libraries.
+#
+#  TBB_MALLOC_INCLUDE_DIRS - where to find tbb.h, etc.
+#  TBB_MALLOC_LIBRARIES    - List of libraries when using tbb.
+#  TBB_MALLOC_FOUND        - True if tbb found.
+#
+
+
+########################################################
+# TBB Malloc
+
+find_path(TBB_MALLOC_INCLUDE_DIR NAMES tbb/tbb.h PATHS $ENV{TBBROOT}/include)
+find_library(TBB_MALLOC_LIBRARY NAMES tbbmalloc PATHS $ENV{TBBROOT}/lib/intel64/gcc4.7
+                                                      $ENV{TBBROOT}/lib/intel64/gcc4.4
+                                                      $ENV{TBBROOT}/lib/intel64/gcc4.1)
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set TBB_MALLOC_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(TBB_MALLOC DEFAULT_MSG TBB_MALLOC_LIBRARY TBB_MALLOC_INCLUDE_DIR)
+
+if(TBB_MALLOC_FOUND)
+  set(TBB_MALLOC_LIBRARIES ${TBB_MALLOC_LIBRARY})
+  set(TBB_MALLOC_INCLUDE_DIRS ${TBB_MALLOC_INCLUDE_DIR})
+
+  if(NOT TARGET TBB::TBB_MALLOC)
+    add_library(TBB::TBB_MALLOC UNKNOWN IMPORTED)
+    set_target_properties(TBB::TBB_MALLOC PROPERTIES
+      IMPORTED_LOCATION "${TBB_MALLOC_LIBRARY}"
+      INTERFACE_INCLUDE_DIRECTORIES "${TBB_MALLOC_INCLUDE_DIR}")
+  endif()
+endif()
+
+mark_as_advanced(TBB_MALLOC_INCLUDE_DIR TBB_MALLOC_LIBRARY )

cmake/Modules/FindVORO.cmake

@@ -10,13 +10,23 @@ find_path(VORO_INCLUDE_DIR voro++.hh PATH_SUFFIXES voro++)
 
 find_library(VORO_LIBRARY NAMES voro++)
 
-set(VORO_LIBRARIES ${VORO_LIBRARY})
-set(VORO_INCLUDE_DIRS ${VORO_INCLUDE_DIR})
-
 include(FindPackageHandleStandardArgs)
 # handle the QUIETLY and REQUIRED arguments and set VORO_FOUND to TRUE
 # if all listed variables are TRUE
 
 find_package_handle_standard_args(VORO DEFAULT_MSG VORO_LIBRARY VORO_INCLUDE_DIR)
 
+# Copy the results to the output variables and target.
+if(VORO_FOUND)
+  set(VORO_LIBRARIES ${VORO_LIBRARY})
+  set(VORO_INCLUDE_DIRS ${VORO_INCLUDE_DIR})
+
+  if(NOT TARGET VORO::VORO)
+    add_library(VORO::VORO UNKNOWN IMPORTED)
+    set_target_properties(VORO::VORO PROPERTIES
+      IMPORTED_LOCATION "${VORO_LIBRARY}"
+      INTERFACE_INCLUDE_DIRECTORIES "${VORO_INCLUDE_DIR}")
+  endif()
+endif()
+
 mark_as_advanced(VORO_INCLUDE_DIR VORO_LIBRARY )

cmake/Modules/FindZMQ.cmake

@@ -1,8 +1,19 @@
 find_path(ZMQ_INCLUDE_DIR zmq.h)
 find_library(ZMQ_LIBRARY NAMES zmq)
 
-set(ZMQ_LIBRARIES ${ZMQ_LIBRARY})
-set(ZMQ_INCLUDE_DIRS ${ZMQ_INCLUDE_DIR})
-
 include(FindPackageHandleStandardArgs)
 find_package_handle_standard_args(ZMQ DEFAULT_MSG ZMQ_LIBRARY ZMQ_INCLUDE_DIR)
+
+# Copy the results to the output variables and target.
+if(ZMQ_FOUND)
+  set(ZMQ_LIBRARIES ${ZMQ_LIBRARY})
+  set(ZMQ_INCLUDE_DIRS ${ZMQ_INCLUDE_DIR})
+
+  if(NOT TARGET ZMQ::ZMQ)
+    add_library(ZMQ::ZMQ UNKNOWN IMPORTED)
+    set_target_properties(ZMQ::ZMQ PROPERTIES
+      IMPORTED_LINK_INTERFACE_LANGUAGES "C"
+      IMPORTED_LOCATION "${ZMQ_LIBRARY}"
+      INTERFACE_INCLUDE_DIRECTORIES "${ZMQ_INCLUDE_DIR}")
+  endif()
+endif()

cmake/Modules/GenerateBinaryHeader.cmake

@@ -0,0 +1,3 @@
+# utility script to call GenerateBinaryHeader function
+include(${SOURCE_DIR}/Modules/LAMMPSUtils.cmake)
+GenerateBinaryHeader(${VARNAME} ${HEADER_FILE} ${SOURCE_FILES})

cmake/Modules/LAMMPSUtils.cmake

@@ -69,3 +69,19 @@ macro(pkg_depends PKG1 PKG2)
     message(FATAL_ERROR "${PKG1} package needs LAMMPS to be build with ${PKG2}")
   endif()
 endmacro()
+
+# CMake-only replacement for bin2c and xxd
+function(GenerateBinaryHeader varname outfile files)
+    message("Creating ${outfile}...")
+    file(WRITE ${outfile} "// CMake generated file\n")
+    math(EXPR ARG_END   "${ARGC}-1")
+
+    foreach(IDX RANGE 2 ${ARG_END})
+        list(GET ARGV ${IDX} filename)
+        file(READ ${filename} content HEX)
+        string(REGEX REPLACE "([0-9a-f][0-9a-f])" "0x\\1," content "${content}")
+        string(REGEX REPLACE ",$" "" content "${content}")
+        file(APPEND ${outfile} "const unsigned char ${varname}[] = { ${content} };\n")
+        file(APPEND ${outfile} "const unsigned int ${varname}_size = sizeof(${varname});\n")
+    endforeach()
+endfunction(GenerateBinaryHeader)

cmake/Modules/MPI4WIN.cmake

@@ -0,0 +1,30 @@
+# Download and configure custom MPICH files for Windows
+message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
+include(ExternalProject)
+if (CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+  ExternalProject_Add(mpi4win_build
+    URL https://download.lammps.org/thirdparty/mpich2-win64-devel.tar.gz
+    URL_MD5 4939fdb59d13182fd5dd65211e469f14
+    CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+    BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+else()
+  ExternalProject_Add(mpi4win_build
+    URL https://download.lammps.org/thirdparty/mpich2-win32-devel.tar.gz
+    URL_MD5 a61d153500dce44e21b755ee7257e031
+    CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+    BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+endif()
+
+ExternalProject_get_property(mpi4win_build SOURCE_DIR)
+file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
+add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
+set_target_properties(MPI::MPI_CXX PROPERTIES
+  IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
+  INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
+  INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+add_dependencies(MPI::MPI_CXX mpi4win_build)
+
+# set variables for status reporting at the end of CMake run
+set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
+set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")

cmake/Modules/Packages/COMPRESS.cmake

@@ -1,5 +1,2 @@
-if(PKG_COMPRESS)
+find_package(ZLIB REQUIRED)
-  find_package(ZLIB REQUIRED)
+target_link_libraries(lammps PRIVATE ZLIB::ZLIB)
-  include_directories(${ZLIB_INCLUDE_DIRS})
-  list(APPEND LAMMPS_LINK_LIBS ${ZLIB_LIBRARIES})
-endif()

cmake/Modules/Packages/CORESHELL.cmake

@@ -1,13 +1,11 @@
-if(PKG_CORESHELL)
+  set(CORESHELL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/CORESHELL)
-    set(CORESHELL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/CORESHELL)
+  set(CORESHELL_SOURCES)
-    set(CORESHELL_SOURCES)
+  set_property(GLOBAL PROPERTY "CORESHELL_SOURCES" "${CORESHELL_SOURCES}")
-    set_property(GLOBAL PROPERTY "CORESHELL_SOURCES" "${CORESHELL_SOURCES}")
 
-    # detects styles which have a CORESHELL version
+  # detects styles which have a CORESHELL version
-    RegisterStylesExt(${CORESHELL_SOURCES_DIR} cs CORESHELL_SOURCES)
+  RegisterStylesExt(${CORESHELL_SOURCES_DIR} cs CORESHELL_SOURCES)
 
-    get_property(CORESHELL_SOURCES GLOBAL PROPERTY CORESHELL_SOURCES)
+  get_property(CORESHELL_SOURCES GLOBAL PROPERTY CORESHELL_SOURCES)
 
-    list(APPEND LIB_SOURCES ${CORESHELL_SOURCES})
+  target_sources(lammps PRIVATE ${CORESHELL_SOURCES})
-    include_directories(${CORESHELL_SOURCES_DIR})
+  target_include_directories(lammps PRIVATE ${CORESHELL_SOURCES_DIR})
-endif()

cmake/Modules/Packages/GPU.cmake

@@ -1,194 +1,374 @@
-if(PKG_GPU)
+set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
-    if (CMAKE_VERSION VERSION_LESS "3.1")
+set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
-      message(FATAL_ERROR "For the GPU package you need at least cmake-3.1")
+                ${GPU_SOURCES_DIR}/fix_gpu.h
-    endif()
+                ${GPU_SOURCES_DIR}/fix_gpu.cpp)
-    set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
-    set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
-                    ${GPU_SOURCES_DIR}/fix_gpu.h
-                    ${GPU_SOURCES_DIR}/fix_gpu.cpp)
 
-    set(GPU_API "opencl" CACHE STRING "API used by GPU package")
+set(GPU_API "opencl" CACHE STRING "API used by GPU package")
-    set(GPU_API_VALUES opencl cuda)
+set(GPU_API_VALUES opencl cuda hip)
-    set_property(CACHE GPU_API PROPERTY STRINGS ${GPU_API_VALUES})
+set_property(CACHE GPU_API PROPERTY STRINGS ${GPU_API_VALUES})
-    validate_option(GPU_API GPU_API_VALUES)
+validate_option(GPU_API GPU_API_VALUES)
-    string(TOUPPER ${GPU_API} GPU_API)
+string(TOUPPER ${GPU_API} GPU_API)
 
-    set(GPU_PREC "mixed" CACHE STRING "LAMMPS GPU precision")
+set(GPU_PREC "mixed" CACHE STRING "LAMMPS GPU precision")
-    set(GPU_PREC_VALUES double mixed single)
+set(GPU_PREC_VALUES double mixed single)
-    set_property(CACHE GPU_PREC PROPERTY STRINGS ${GPU_PREC_VALUES})
+set_property(CACHE GPU_PREC PROPERTY STRINGS ${GPU_PREC_VALUES})
-    validate_option(GPU_PREC GPU_PREC_VALUES)
+validate_option(GPU_PREC GPU_PREC_VALUES)
-    string(TOUPPER ${GPU_PREC} GPU_PREC)
+string(TOUPPER ${GPU_PREC} GPU_PREC)
 
-    if(GPU_PREC STREQUAL "DOUBLE")
+if(GPU_PREC STREQUAL "DOUBLE")
-      set(GPU_PREC_SETTING "DOUBLE_DOUBLE")
+  set(GPU_PREC_SETTING "DOUBLE_DOUBLE")
-    elseif(GPU_PREC STREQUAL "MIXED")
+elseif(GPU_PREC STREQUAL "MIXED")
-      set(GPU_PREC_SETTING "SINGLE_DOUBLE")
+  set(GPU_PREC_SETTING "SINGLE_DOUBLE")
-    elseif(GPU_PREC STREQUAL "SINGLE")
+elseif(GPU_PREC STREQUAL "SINGLE")
-      set(GPU_PREC_SETTING "SINGLE_SINGLE")
+  set(GPU_PREC_SETTING "SINGLE_SINGLE")
-    endif()
-
-    file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
-    file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
-
-    if(GPU_API STREQUAL "CUDA")
-      find_package(CUDA REQUIRED)
-      find_program(BIN2C bin2c)
-      if(NOT BIN2C)
-        message(FATAL_ERROR "Could not find bin2c, use -DBIN2C=/path/to/bin2c to help cmake finding it.")
-      endif()
-      option(CUDPP_OPT "Enable CUDPP_OPT" ON)
-      option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF)
-      if(CUDA_MPS_SUPPORT)
-        set(GPU_CUDA_MPS_FLAGS "-DCUDA_PROXY")
-      endif()
-
-      set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
-
-      file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
-      list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
-
-      cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
-
-      if(CUDPP_OPT)
-        cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
-        file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
-        file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
-      endif()
-
-      # build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
-      # --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
-      set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH} ")
-      # Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
-      if((CUDA_VERSION VERSION_GREATER "3.1") AND (CUDA_VERSION VERSION_LESS "9.0"))
-        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_20,code=[sm_20,compute_20] ")
-      endif()
-      # Kepler (GPU Arch 3.x) is supported by CUDA 5 and later
-      if(CUDA_VERSION VERSION_GREATER "4.9")
-        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35] ")
-      endif()
-      # Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
-      if(CUDA_VERSION VERSION_GREATER "5.9")
-        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] ")
-      endif()
-      # Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
-      if(CUDA_VERSION VERSION_GREATER "7.9")
-        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] ")
-      endif()
-      # Volta (GPU Arch 7.0) is supported by CUDA 9 and later
-      if(CUDA_VERSION VERSION_GREATER "8.9")
-        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_70,code=[sm_70,compute_70] ")
-      endif()
-      # Turing (GPU Arch 7.5) is supported by CUDA 10 and later
-      if(CUDA_VERSION VERSION_GREATER "9.9")
-        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ")
-      endif()
-
-      cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
-              -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
-
-      cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
-              -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
-
-      foreach(CU_OBJ ${GPU_GEN_OBJS})
-        get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
-        string(REGEX REPLACE "^.*_lal_" "" CU_NAME "${CU_NAME}")
-        add_custom_command(OUTPUT ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
-          COMMAND ${BIN2C} -c -n ${CU_NAME} ${CU_OBJ} > ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
-          DEPENDS ${CU_OBJ}
-          COMMENT "Generating ${CU_NAME}_cubin.h")
-        list(APPEND GPU_LIB_SOURCES ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h)
-      endforeach()
-      set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "${LAMMPS_LIB_BINARY_DIR}/gpu/*_cubin.h")
-
-
-      add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
-      target_link_libraries(gpu ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
-      target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
-      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS})
-      if(CUDPP_OPT)
-        target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
-        target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
-      endif()
-
-      list(APPEND LAMMPS_LINK_LIBS gpu)
-
-      add_executable(nvc_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
-      target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR)
-      target_link_libraries(nvc_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
-      target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
-
-
-    elseif(GPU_API STREQUAL "OPENCL")
-      find_package(OpenCL REQUIRED)
-      set(OCL_TUNE "generic" CACHE STRING "OpenCL Device Tuning")
-      set(OCL_TUNE_VALUES intel fermi kepler cypress generic)
-      set_property(CACHE OCL_TUNE PROPERTY STRINGS ${OCL_TUNE_VALUES})
-      validate_option(OCL_TUNE OCL_TUNE_VALUES)
-      string(TOUPPER ${OCL_TUNE} OCL_TUNE)
-
-      include(OpenCLUtils)
-      set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
-
-      file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
-      list(REMOVE_ITEM GPU_LIB_CU
-        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu
-        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu
-        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu
-        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu
-        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu
-        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu
-        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu
-      )
-
-      foreach(GPU_KERNEL ${GPU_LIB_CU})
-          get_filename_component(basename ${GPU_KERNEL} NAME_WE)
-          string(SUBSTRING ${basename} 4 -1 KERNEL_NAME)
-          GenerateOpenCLHeader(${KERNEL_NAME} ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h ${OCL_COMMON_HEADERS} ${GPU_KERNEL})
-          list(APPEND GPU_LIB_SOURCES ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h)
-      endforeach()
-
-      GenerateOpenCLHeader(gayberne ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu)
-      GenerateOpenCLHeader(gayberne_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu)
-      GenerateOpenCLHeader(re_squared ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu)
-      GenerateOpenCLHeader(re_squared_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu)
-      GenerateOpenCLHeader(tersoff ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu)
-      GenerateOpenCLHeader(tersoff_zbl ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu)
-      GenerateOpenCLHeader(tersoff_mod ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu)
-
-      list(APPEND GPU_LIB_SOURCES
-        ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h
-        ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h
-        ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h
-        ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h
-        ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h
-        ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h
-        ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h
-      )
-
-      add_library(gpu STATIC ${GPU_LIB_SOURCES})
-      target_link_libraries(gpu ${OpenCL_LIBRARIES})
-      target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu ${OpenCL_INCLUDE_DIRS})
-      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -D${OCL_TUNE}_OCL -DMPI_GERYON -DUCL_NO_EXIT)
-      target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
-
-      list(APPEND LAMMPS_LINK_LIBS gpu)
-
-      add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
-      target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL)
-      target_link_libraries(ocl_get_devices PRIVATE ${OpenCL_LIBRARIES})
-      target_include_directories(ocl_get_devices PRIVATE ${OpenCL_INCLUDE_DIRS})
-    endif()
-
-    # GPU package
-    FindStyleHeaders(${GPU_SOURCES_DIR} FIX_CLASS fix_ FIX)
-
-    set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
-
-    # detects styles which have GPU version
-    RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)
-
-    get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
-
-    list(APPEND LIB_SOURCES ${GPU_SOURCES})
-    include_directories(${GPU_SOURCES_DIR})
 endif()
+
+file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
+file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
+
+if(GPU_API STREQUAL "CUDA")
+  find_package(CUDA REQUIRED)
+  find_program(BIN2C bin2c)
+  if(NOT BIN2C)
+    message(FATAL_ERROR "Could not find bin2c, use -DBIN2C=/path/to/bin2c to help cmake finding it.")
+  endif()
+  option(CUDPP_OPT "Enable CUDPP_OPT" ON)
+  option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF)
+  if(CUDA_MPS_SUPPORT)
+    set(GPU_CUDA_MPS_FLAGS "-DCUDA_PROXY")
+  endif()
+
+  set(GPU_ARCH "sm_50" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
+
+  file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
+  list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
+
+  cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
+
+  if(CUDPP_OPT)
+    cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
+    file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
+    file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
+  endif()
+
+  # build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
+  # --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
+  set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH} ")
+  # Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
+  if((CUDA_VERSION VERSION_GREATER "3.1") AND (CUDA_VERSION VERSION_LESS "9.0"))
+    string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_20,code=[sm_20,compute_20] ")
+  endif()
+  # Kepler (GPU Arch 3.x) is supported by CUDA 5 and later
+  if(CUDA_VERSION VERSION_GREATER "4.9")
+    string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35] ")
+  endif()
+  # Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
+  if(CUDA_VERSION VERSION_GREATER "5.9")
+    string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] ")
+  endif()
+  # Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
+  if(CUDA_VERSION VERSION_GREATER "7.9")
+    string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] ")
+  endif()
+  # Volta (GPU Arch 7.0) is supported by CUDA 9 and later
+  if(CUDA_VERSION VERSION_GREATER "8.9")
+    string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_70,code=[sm_70,compute_70] ")
+  endif()
+  # Turing (GPU Arch 7.5) is supported by CUDA 10 and later
+  if(CUDA_VERSION VERSION_GREATER "9.9")
+    string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ")
+  endif()
+
+  cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
+          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
+
+  cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
+          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
+
+  foreach(CU_OBJ ${GPU_GEN_OBJS})
+    get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
+    string(REGEX REPLACE "^.*_lal_" "" CU_NAME "${CU_NAME}")
+    add_custom_command(OUTPUT ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
+      COMMAND ${BIN2C} -c -n ${CU_NAME} ${CU_OBJ} > ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
+      DEPENDS ${CU_OBJ}
+      COMMENT "Generating ${CU_NAME}_cubin.h")
+    list(APPEND GPU_LIB_SOURCES ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h)
+  endforeach()
+  set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "${LAMMPS_LIB_BINARY_DIR}/gpu/*_cubin.h")
+
+  add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
+  target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
+  target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
+  target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS})
+  if(CUDPP_OPT)
+    target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
+    target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
+  endif()
+
+  target_link_libraries(lammps PRIVATE gpu)
+
+  add_executable(nvc_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
+  target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR)
+  target_link_libraries(nvc_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
+  target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
+
+elseif(GPU_API STREQUAL "OPENCL")
+  if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+    # download and unpack support binaries for compilation of windows binaries.
+    set(LAMMPS_THIRDPARTY_URL "http://download.lammps.org/thirdparty")
+    file(DOWNLOAD "${LAMMPS_THIRDPARTY_URL}/opencl-win-devel.tar.gz" "${CMAKE_CURRENT_BINARY_DIR}/opencl-win-devel.tar.gz"
+            EXPECTED_MD5 2c00364888d5671195598b44c2e0d44d)
+    execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf opencl-win-devel.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+    add_library(OpenCL::OpenCL UNKNOWN IMPORTED)
+    if(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86")
+      set_target_properties(OpenCL::OpenCL PROPERTIES IMPORTED_LOCATION "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win32/libOpenCL.dll")
+    elseif(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86_64")
+      set_target_properties(OpenCL::OpenCL PROPERTIES IMPORTED_LOCATION "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win64/libOpenCL.dll")
+    endif()
+    set_target_properties(OpenCL::OpenCL PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/include")
+  else()
+    find_package(OpenCL REQUIRED)
+  endif()
+  set(OCL_TUNE "generic" CACHE STRING "OpenCL Device Tuning")
+  set(OCL_TUNE_VALUES intel fermi kepler cypress generic)
+  set_property(CACHE OCL_TUNE PROPERTY STRINGS ${OCL_TUNE_VALUES})
+  validate_option(OCL_TUNE OCL_TUNE_VALUES)
+  string(TOUPPER ${OCL_TUNE} OCL_TUNE)
+
+  include(OpenCLUtils)
+  set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
+
+  file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
+  list(REMOVE_ITEM GPU_LIB_CU
+    ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu
+    ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu
+    ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu
+    ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu
+    ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu
+    ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu
+    ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu
+  )
+
+  foreach(GPU_KERNEL ${GPU_LIB_CU})
+      get_filename_component(basename ${GPU_KERNEL} NAME_WE)
+      string(SUBSTRING ${basename} 4 -1 KERNEL_NAME)
+      GenerateOpenCLHeader(${KERNEL_NAME} ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h ${OCL_COMMON_HEADERS} ${GPU_KERNEL})
+      list(APPEND GPU_LIB_SOURCES ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h)
+  endforeach()
+
+  GenerateOpenCLHeader(gayberne ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu)
+  GenerateOpenCLHeader(gayberne_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu)
+  GenerateOpenCLHeader(re_squared ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu)
+  GenerateOpenCLHeader(re_squared_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu)
+  GenerateOpenCLHeader(tersoff ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu)
+  GenerateOpenCLHeader(tersoff_zbl ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu)
+  GenerateOpenCLHeader(tersoff_mod ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu)
+
+  list(APPEND GPU_LIB_SOURCES
+    ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h
+    ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h
+    ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h
+    ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h
+    ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h
+    ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h
+    ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h
+  )
+
+  add_library(gpu STATIC ${GPU_LIB_SOURCES})
+  target_link_libraries(gpu PRIVATE OpenCL::OpenCL)
+  target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu)
+  target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -D${OCL_TUNE}_OCL -DMPI_GERYON -DUCL_NO_EXIT)
+  target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
+
+  target_link_libraries(lammps PRIVATE gpu)
+
+  add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
+  target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL)
+  target_link_libraries(ocl_get_devices PRIVATE OpenCL::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")
+      else()
+          set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to which HIP has been installed")
+      endif()
+  endif()
+  set(CMAKE_MODULE_PATH "${HIP_PATH}/cmake" ${CMAKE_MODULE_PATH})
+  find_package(HIP REQUIRED)
+  option(HIP_USE_DEVICE_SORT "Use GPU sorting" ON)
+
+  if(NOT DEFINED HIP_PLATFORM)
+      if(NOT DEFINED ENV{HIP_PLATFORM})
+          set(HIP_PLATFORM "hcc" CACHE PATH "HIP Platform to be used during compilation")
+      else()
+          set(HIP_PLATFORM $ENV{HIP_PLATFORM} CACHE PATH "HIP Platform used during compilation")
+      endif()
+  endif()
+
+  set(ENV{HIP_PLATFORM} ${HIP_PLATFORM})
+
+  if(HIP_PLATFORM STREQUAL "hcc")
+    set(HIP_ARCH "gfx906" CACHE STRING "HIP target architecture")
+  elseif(HIP_PLATFORM STREQUAL "nvcc")
+    find_package(CUDA REQUIRED)
+    set(HIP_ARCH "sm_50" CACHE STRING "HIP primary CUDA architecture (e.g. sm_60)")
+
+    # build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
+    # --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
+    set(HIP_CUDA_GENCODE "-arch=${HIP_ARCH} ")
+    # Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
+    if((CUDA_VERSION VERSION_GREATER "3.1") AND (CUDA_VERSION VERSION_LESS "9.0"))
+      string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_20,code=[sm_20,compute_20] ")
+    endif()
+    # Kepler (GPU Arch 3.x) is supported by CUDA 5 and later
+    if(CUDA_VERSION VERSION_GREATER "4.9")
+      string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35] ")
+    endif()
+    # Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
+    if(CUDA_VERSION VERSION_GREATER "5.9")
+      string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] ")
+    endif()
+    # Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
+    if(CUDA_VERSION VERSION_GREATER "7.9")
+      string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] ")
+    endif()
+    # Volta (GPU Arch 7.0) is supported by CUDA 9 and later
+    if(CUDA_VERSION VERSION_GREATER "8.9")
+      string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_70,code=[sm_70,compute_70] ")
+    endif()
+    # Turing (GPU Arch 7.5) is supported by CUDA 10 and later
+    if(CUDA_VERSION VERSION_GREATER "9.9")
+      string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ")
+    endif()
+  endif()
+
+  file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
+  list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
+
+  set(GPU_LIB_CU_HIP "")
+  foreach(CU_FILE ${GPU_LIB_CU})
+    get_filename_component(CU_NAME ${CU_FILE} NAME_WE)
+    string(REGEX REPLACE "^.*lal_" "" CU_NAME "${CU_NAME}")
+
+    set(CU_CPP_FILE  "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}.cu.cpp")
+    set(CUBIN_FILE   "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}.cubin")
+    set(CUBIN_H_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h")
+
+    if(HIP_PLATFORM STREQUAL "hcc")
+        configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY)
+
+        add_custom_command(OUTPUT ${CUBIN_FILE}
+          VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
+          DEPENDS ${CU_CPP_FILE}
+          COMMENT "Generating ${CU_NAME}.cubin")
+    elseif(HIP_PLATFORM STREQUAL "nvcc")
+        add_custom_command(OUTPUT ${CUBIN_FILE}
+          VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE}
+          DEPENDS ${CU_FILE}
+          COMMENT "Generating ${CU_NAME}.cubin")
+    endif()
+
+    add_custom_command(OUTPUT ${CUBIN_H_FILE}
+      COMMAND ${CMAKE_COMMAND} -D SOURCE_DIR=${CMAKE_CURRENT_SOURCE_DIR} -D VARNAME=${CU_NAME} -D HEADER_FILE=${CUBIN_H_FILE} -D SOURCE_FILES=${CUBIN_FILE} -P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/GenerateBinaryHeader.cmake
+      DEPENDS ${CUBIN_FILE}
+      COMMENT "Generating ${CU_NAME}_cubin.h")
+
+    list(APPEND GPU_LIB_SOURCES ${CUBIN_H_FILE})
+  endforeach()
+
+  set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "${LAMMPS_LIB_BINARY_DIR}/gpu/*_cubin.h ${LAMMPS_LIB_BINARY_DIR}/gpu/*.cu.cpp")
+
+  hip_add_library(gpu STATIC ${GPU_LIB_SOURCES})
+  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)
+
+  if(HIP_USE_DEVICE_SORT)
+    # add hipCUB
+    target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
+    target_compile_definitions(gpu PRIVATE -DUSE_HIP_DEVICE_SORT)
+
+    if(HIP_PLATFORM STREQUAL "nvcc")
+      find_package(CUB)
+
+      if(CUB_FOUND)
+        set(DOWNLOAD_CUB_DEFAULT OFF)
+      else()
+        set(DOWNLOAD_CUB_DEFAULT ON)
+      endif()
+
+      option(DOWNLOAD_CUB "Download and compile the CUB library instead of using an already installed one" ${DOWNLOAD_CUB_DEFAULT})
+
+      if(DOWNLOAD_CUB)
+        message(STATUS "CUB download requested")
+        include(ExternalProject)
+
+        ExternalProject_Add(CUB
+          GIT_REPOSITORY https://github.com/NVlabs/cub
+          TIMEOUT 5
+          PREFIX "${CMAKE_CURRENT_BINARY_DIR}"
+          CONFIGURE_COMMAND ""
+          BUILD_COMMAND ""
+          INSTALL_COMMAND ""
+          UPDATE_COMMAND ""
+        )
+        ExternalProject_get_property(CUB SOURCE_DIR)
+        set(CUB_INCLUDE_DIR ${SOURCE_DIR})
+      else()
+        find_package(CUB)
+        if(NOT CUB_FOUND)
+          message(FATAL_ERROR "CUB library not found. Help CMake to find it by setting CUB_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
+        endif()
+      endif()
+
+      target_include_directories(gpu PRIVATE ${CUB_INCLUDE_DIR})
+    endif()
+  endif()
+
+  hip_add_executable(hip_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
+  target_compile_definitions(hip_get_devices PRIVATE -DUCL_HIP)
+
+  if(HIP_PLATFORM STREQUAL "nvcc")
+    target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_NVCC__)
+    target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
+    target_include_directories(gpu PRIVATE ${CUDA_INCLUDE_DIRS})
+    target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
+
+    target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_NVCC__)
+    target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/include)
+    target_include_directories(hip_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
+    target_link_libraries(hip_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
+  elseif(HIP_PLATFORM STREQUAL "hcc")
+    target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_HCC__)
+    target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
+
+    target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_HCC__)
+    target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include)
+  endif()
+
+  target_link_libraries(lammps PRIVATE gpu)
+endif()
+
+# GPU package
+FindStyleHeaders(${GPU_SOURCES_DIR} FIX_CLASS fix_ FIX)
+
+set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
+
+# detects styles which have GPU version
+RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)
+
+get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
+
+if(NOT BUILD_MPI)
+  # mpistubs is aliased to MPI::MPI_CXX, but older versions of cmake won't work forward the include path
+  target_link_libraries(gpu PRIVATE mpi_stubs)
+else()
+  target_link_libraries(gpu PRIVATE MPI::MPI_CXX)
+endif()
+if(NOT BUILD_SHARED_LIBS)
+  install(TARGETS gpu EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+endif()
+target_compile_definitions(gpu PRIVATE -DLAMMPS_${LAMMPS_SIZES})
+set_target_properties(gpu PROPERTIES OUTPUT_NAME lammps_gpu${LAMMPS_MACHINE})
+target_sources(lammps PRIVATE ${GPU_SOURCES})
+target_include_directories(lammps PRIVATE ${GPU_SOURCES_DIR})

cmake/Modules/Packages/KIM.cmake

@@ -1,57 +1,66 @@
-if(PKG_KIM)
+set(KIM-API_MIN_VERSION 2.1.3)
-  set(KIM-API_MIN_VERSION 2.1)
+find_package(CURL)
-  find_package(CURL)
+if(CURL_FOUND)
-  if(CURL_FOUND)
+  if(CMAKE_VERSION VERSION_LESS 3.12)
-    include_directories(${CURL_INCLUDE_DIRS})
+    target_include_directories(lammps PRIVATE ${CURL_INCLUDE_DIRS})
-    list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES})
+    target_link_libraries(lammps PRIVATE ${CURL_LIBRARIES})
-    add_definitions(-DLMP_KIM_CURL)
-  endif()
-  find_package(KIM-API QUIET)
-  if(KIM-API_FOUND)
-    if (KIM-API_VERSION VERSION_LESS ${KIM-API_MIN_VERSION})
-      if ("${DOWNLOAD_KIM}" STREQUAL "")
-        message(WARNING "Unsuitable KIM-API version \"${KIM-API_VERSION}\" found, but required is at least \"${KIM-API_MIN_VERSION}\".  Default behavior set to download and build our own.")
-      endif()
-      set(DOWNLOAD_KIM_DEFAULT ON)
-    else()
-      set(DOWNLOAD_KIM_DEFAULT OFF)
-    endif()
   else()
-    if ("${DOWNLOAD_KIM}" STREQUAL "")
+    target_link_libraries(lammps PRIVATE CURL::libcurl)
-      message(WARNING "KIM-API package not found.  Default behavior set to download and build our own")
-    endif()
-    set(DOWNLOAD_KIM_DEFAULT ON)
   endif()
-  option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT})
+  target_compile_definitions(lammps PRIVATE -DLMP_KIM_CURL)
-  if(DOWNLOAD_KIM)
+  set(LMP_DEBUG_CURL OFF CACHE STRING "Set libcurl verbose mode on/off. If on, it displays a lot of verbose information about its operations.")
-    if(CMAKE_GENERATOR STREQUAL "Ninja")
+  mark_as_advanced(LMP_DEBUG_CURL)
-      message(FATAL_ERROR "Cannot build downloaded KIM-API library with Ninja build tool")
+  if(LMP_DEBUG_CURL)
-    endif()
+    target_compile_definitions(lammps PRIVATE -DLMP_DEBUG_CURL)
-    message(STATUS "KIM-API download requested - we will build our own")
+  endif()
-    include(CheckLanguage)
+  set(LMP_NO_SSL_CHECK OFF CACHE STRING "Tell libcurl to not verify the peer. If on, the connection succeeds regardless of the names in the certificate. Insecure - Use with caution!")
-    include(ExternalProject)
+  mark_as_advanced(LMP_NO_SSL_CHECK)
-    enable_language(C)
+  if(LMP_NO_SSL_CHECK)
-    check_language(Fortran)
+    target_compile_definitions(lammps PRIVATE -DLMP_NO_SSL_CHECK)
-    if(NOT CMAKE_Fortran_COMPILER)
-      message(FATAL_ERROR "Compiling the KIM-API library requires a Fortran compiler")
-    endif()
-    ExternalProject_Add(kim_build
-      URL https://s3.openkim.org/kim-api/kim-api-2.1.3.txz
-      URL_MD5 6ee829a1bbba5f8b9874c88c4c4ebff8
-      BINARY_DIR build
-      CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-                 -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
-                 -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}
-                 -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
-                 -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-      )
-    ExternalProject_get_property(kim_build INSTALL_DIR)
-    set(KIM-API_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api)
-    set(KIM-API_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX})
-    list(APPEND LAMMPS_DEPS kim_build)
-  else()
-    find_package(KIM-API ${KIM-API_MIN_VERSION} REQUIRED)
   endif()
-  list(APPEND LAMMPS_LINK_LIBS "${KIM-API_LDFLAGS}")
+endif()
-  include_directories(${KIM-API_INCLUDE_DIRS})
+find_package(PkgConfig QUIET)
+set(DOWNLOAD_KIM_DEFAULT ON)
+if(PKG_CONFIG_FOUND)
+  pkg_check_modules(KIM-API QUIET libkim-api>=${KIM-API_MIN_VERSION})
+  if(KIM-API_FOUND)
+    set(DOWNLOAD_KIM_DEFAULT OFF)
+  endif()
+endif()
+option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT})
+if(DOWNLOAD_KIM)
+  message(STATUS "KIM-API download requested - we will build our own")
+  include(ExternalProject)
+  enable_language(C)
+  enable_language(Fortran)
+  ExternalProject_Add(kim_build
+    URL https://s3.openkim.org/kim-api/kim-api-2.1.3.txz
+    URL_MD5 6ee829a1bbba5f8b9874c88c4c4ebff8
+    BINARY_DIR build
+    CMAKE_ARGS ${CMAKE_REQUEST_PIC}
+               -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+               -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+               -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}
+               -DCMAKE_INSTALL_LIBDIR=lib
+               -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+               -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+               -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
+               -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
+               BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX}
+    )
+  ExternalProject_get_property(kim_build INSTALL_DIR)
+  file(MAKE_DIRECTORY ${INSTALL_DIR}/include/kim-api)
+  add_library(LAMMPS::KIM UNKNOWN IMPORTED)
+  set_target_properties(LAMMPS::KIM PROPERTIES
+    IMPORTED_LOCATION "${INSTALL_DIR}/lib/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX}"
+    INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include/kim-api")
+  target_link_libraries(lammps PRIVATE LAMMPS::KIM)
+  add_dependencies(LAMMPS::KIM kim_build)
+  if(NOT BUILD_SHARED_LIBS)
+    install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
+  endif()
+else()
+  find_package(PkgConfig REQUIRED)
+  pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=${KIM-API_MIN_VERSION})
+  target_link_libraries(lammps PRIVATE PkgConfig::KIM-API)
 endif()

cmake/Modules/Packages/KOKKOS.cmake

@@ -1,66 +1,125 @@
-if(PKG_KOKKOS)
+########################################################################
-  # TODO: this option needs to be documented when this works with a
+# consistency checks and Kokkos options/settings required by LAMMPS
-  # regular release version of KOKKOS, and a version compatibility check
+if(Kokkos_ENABLE_CUDA)
-  # of external KOKKOS lib versus what the KOKKOS package needs is required.
+  message(STATUS "KOKKOS: Enabling CUDA LAMBDA function support")
-  option(EXTERNAL_KOKKOS "Build against external kokkos library")
+  set(Kokkos_ENABLE_CUDA_LAMBDA ON CACHE BOOL "" FORCE)
-  if(EXTERNAL_KOKKOS)
-    find_package(Kokkos REQUIRED)
-    list(APPEND LAMMPS_LINK_LIBS Kokkos::kokkos)
-  else()
-    set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
-    set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
-    add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
-  
-    set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
-                            ${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
-                            ${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src
-                            ${LAMMPS_LIB_KOKKOS_BIN_DIR})
-    include_directories(${Kokkos_INCLUDE_DIRS})
-    list(APPEND LAMMPS_LINK_LIBS kokkos)
-  endif()
-  add_definitions(-DLMP_KOKKOS)
-
-  set(KOKKOS_PKG_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/KOKKOS)
-  set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/atom_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/min_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/min_linesearch_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/neighbor_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/neigh_list_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/neigh_bond_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/fix_nh_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/npair_halffull_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
-
-  if(PKG_KSPACE)
-    list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp)
-  endif()
-
-  set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
-
-  # detects styles which have KOKKOS version
-  RegisterStylesExt(${KOKKOS_PKG_SOURCES_DIR} kokkos KOKKOS_PKG_SOURCES)
-
-  # register kokkos-only styles
-  RegisterNBinStyle(${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.h)
-  RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.h)
-  RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_halffull_kokkos.h)
-
-  if(PKG_USER-DPD)
-    get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
-    list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.cpp)
-    RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.h)
-    set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
-  endif()
-
-  get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
-
-  list(APPEND LIB_SOURCES ${KOKKOS_PKG_SOURCES})
-  include_directories(${KOKKOS_PKG_SOURCES_DIR})
 endif()
+# Adding OpenMP compiler flags without the checks done for
+# BUILD_OMP can result in compile failures. Enforce consistency.
+if(Kokkos_ENABLE_OPENMP AND NOT BUILD_OMP)
+  message(FATAL_ERROR "Must enable BUILD_OMP with Kokkos_ENABLE_OPENMP")
+endif()
+########################################################################
+
+option(EXTERNAL_KOKKOS "Build against external kokkos library" OFF)
+option(DOWNLOAD_KOKKOS "Download the KOKKOS library instead of using the bundled one" OFF)
+if(DOWNLOAD_KOKKOS)
+  # extract Kokkos-related variables and values so we can forward them to the Kokkos library build
+  get_cmake_property(_VARS VARIABLES)
+  list(FILTER _VARS INCLUDE REGEX ^Kokkos_)
+  foreach(_VAR IN LISTS _VARS)
+    list(APPEND KOKKOS_LIB_BUILD_ARGS "-D${_VAR}=${${_VAR}}")
+  endforeach()
+  message(STATUS "KOKKOS download requested - we will build our own")
+  list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>")
+  if(CMAKE_REQUEST_PIC)
+    list(APPEND KOKKOS_LIB_BUILD_ARGS ${CMAKE_REQUEST_PIC})
+  endif()
+  # append other CMake variables that need to be forwarded to CMAKE_ARGS
+  list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}")
+  list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_INSTALL_LIBDIR=lib")
+  list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}")
+  list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}")
+  list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_STANDARD=${CMAKE_CXX_STANDARD}")
+  list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
+  list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
+  include(ExternalProject)
+  ExternalProject_Add(kokkos_build
+    URL https://github.com/kokkos/kokkos/archive/3.1.00.tar.gz
+    URL_MD5 f638a6c786f748a602b26faa0e96ebab
+    CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
+    BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
+  )
+  ExternalProject_get_property(kokkos_build INSTALL_DIR)
+  file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
+  add_library(LAMMPS::KOKKOS UNKNOWN IMPORTED)
+  set_target_properties(LAMMPS::KOKKOS PROPERTIES
+    IMPORTED_LOCATION "${INSTALL_DIR}/lib/libkokkoscore.a"
+    INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include"
+    INTERFACE_LINK_LIBRARIES ${CMAKE_DL_LIBS})
+  target_link_libraries(lammps PRIVATE LAMMPS::KOKKOS)
+  add_dependencies(LAMMPS::KOKKOS kokkos_build)
+  if(NOT BUILD_SHARED_LIBS)
+    install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
+  endif()
+elseif(EXTERNAL_KOKKOS)
+  find_package(Kokkos 3.1)
+  if(NOT Kokkos_FOUND)
+    message(FATAL_ERROR "KOKKOS library version 3.1 or later not found, help CMake to find it by setting KOKKOS_LIBRARY, or set DOWNLOAD_KOKKOS=ON to download it")
+  endif()
+  target_link_libraries(lammps PRIVATE Kokkos::kokkos)
+else()
+  set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
+  set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
+  add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
+
+  set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
+                          ${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
+                          ${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src
+                          ${LAMMPS_LIB_KOKKOS_BIN_DIR})
+  target_include_directories(lammps PRIVATE ${Kokkos_INCLUDE_DIRS})
+  target_link_libraries(lammps PRIVATE kokkos)
+endif()
+target_compile_definitions(lammps PRIVATE -DLMP_KOKKOS)
+
+set(KOKKOS_PKG_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/KOKKOS)
+set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
+                       ${KOKKOS_PKG_SOURCES_DIR}/atom_kokkos.cpp
+                       ${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp
+                       ${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp
+                       ${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp
+                       ${KOKKOS_PKG_SOURCES_DIR}/min_kokkos.cpp
+                       ${KOKKOS_PKG_SOURCES_DIR}/min_linesearch_kokkos.cpp
+                       ${KOKKOS_PKG_SOURCES_DIR}/neighbor_kokkos.cpp
+                       ${KOKKOS_PKG_SOURCES_DIR}/neigh_list_kokkos.cpp
+                       ${KOKKOS_PKG_SOURCES_DIR}/neigh_bond_kokkos.cpp
+                       ${KOKKOS_PKG_SOURCES_DIR}/fix_nh_kokkos.cpp
+                       ${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.cpp
+                       ${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.cpp
+                       ${KOKKOS_PKG_SOURCES_DIR}/npair_halffull_kokkos.cpp
+                       ${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp
+                       ${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
+
+if(PKG_KSPACE)
+  list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/fft3d_kokkos.cpp
+                                 ${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp
+                                 ${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
+  if(Kokkos_ENABLE_CUDA)
+    if(NOT ${FFT} STREQUAL "KISS")
+      target_compile_definitions(lammps PRIVATE -DFFT_CUFFT)
+      target_link_libraries(lammps PRIVATE cufft)
+    endif()
+  endif()
+endif()
+
+set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
+
+# detects styles which have KOKKOS version
+RegisterStylesExt(${KOKKOS_PKG_SOURCES_DIR} kokkos KOKKOS_PKG_SOURCES)
+
+# register kokkos-only styles
+RegisterNBinStyle(${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.h)
+RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.h)
+RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_halffull_kokkos.h)
+
+if(PKG_USER-DPD)
+  get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
+  list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.cpp)
+  RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.h)
+  set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
+endif()
+
+get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
+
+target_sources(lammps PRIVATE ${KOKKOS_PKG_SOURCES})
+target_include_directories(lammps PRIVATE ${KOKKOS_PKG_SOURCES_DIR})

cmake/Modules/Packages/KSPACE.cmake

@@ -1,42 +1,56 @@
-if(PKG_KSPACE)
+option(FFT_SINGLE "Use single precision FFTs instead of double precision FFTs" OFF)
-  option(FFT_SINGLE "Use single precision FFTs instead of double precision FFTs" OFF)
+set(FFTW "FFTW3")
-  set(FFTW "FFTW3")
+if(FFT_SINGLE)
-  if(FFT_SINGLE)
+  set(FFTW "FFTW3F")
-    set(FFTW "FFTW3F")
+  target_compile_definitions(lammps PUBLIC -DFFT_SINGLE)
-    add_definitions(-DFFT_SINGLE)
+endif()
-  endif()
+find_package(${FFTW} QUIET)
-  find_package(${FFTW} QUIET)
+if(${FFTW}_FOUND)
-  if(${FFTW}_FOUND)
+  set(FFT "FFTW3" CACHE STRING "FFT library for KSPACE package")
-    set(FFT "FFTW3" CACHE STRING "FFT library for KSPACE package")
+else()
-  else()
+  set(FFT "KISS" CACHE STRING "FFT library for KSPACE package")
-    set(FFT "KISS" CACHE STRING "FFT library for KSPACE package")
+endif()
-  endif()
+set(FFT_VALUES KISS FFTW3 MKL)
-  set(FFT_VALUES KISS FFTW3 MKL)
+set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES})
-  set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES})
+validate_option(FFT FFT_VALUES)
-  validate_option(FFT FFT_VALUES)
+string(TOUPPER ${FFT} FFT)
-  string(TOUPPER ${FFT} FFT)
+
-
+if(FFT STREQUAL "FFTW3")
-  if(FFT STREQUAL "FFTW3")
+  find_package(${FFTW} REQUIRED)
-    find_package(${FFTW} REQUIRED)
+  target_compile_definitions(lammps PUBLIC -DFFT_FFTW3)
-    add_definitions(-DFFT_FFTW3)
+  target_link_libraries(lammps PUBLIC ${FFTW}::${FFTW})
-    include_directories(${${FFTW}_INCLUDE_DIRS})
+  if(FFTW3_OMP_LIBRARY OR FFTW3F_OMP_LIBRARY)
-    list(APPEND LAMMPS_LINK_LIBS ${${FFTW}_LIBRARIES})
+    option(FFT_FFTW_THREADS "Use threaded FFTW library" ON)
-  elseif(FFT STREQUAL "MKL")
+  else()
-    find_package(MKL REQUIRED)
+    option(FFT_FFTW_THREADS "Use threaded FFT library" OFF)
-    add_definitions(-DFFT_MKL)
+  endif()
-    include_directories(${MKL_INCLUDE_DIRS})
+
-    list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES})
+  if(FFT_FFTW_THREADS)
-  else()
+    if(FFTW3_OMP_LIBRARY OR FFTW3F_OMP_LIBRARY)
-    # last option is KISSFFT
+	target_compile_definitions(lammps PRIVATE -DFFT_FFTW_THREADS)
-    add_definitions(-DFFT_KISS)
+	target_link_libraries(lammps PRIVATE ${FFTW}::${FFTW}_OMP)
-  endif()
+    else()
-
+      message(FATAL_ERROR "Need OpenMP enabled FFTW3 library for FFT_THREADS")
-  set(FFT_PACK "array" CACHE STRING "Optimization for FFT")
+    endif()
-  set(FFT_PACK_VALUES array pointer memcpy)
+  endif()
-  set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES})
+elseif(FFT STREQUAL "MKL")
-  validate_option(FFT_PACK FFT_PACK_VALUES)
+  find_package(MKL REQUIRED)
-  if(NOT FFT_PACK STREQUAL "array")
+  target_compile_definitions(lammps PRIVATE -DFFT_MKL)
-    string(TOUPPER ${FFT_PACK} FFT_PACK)
+  option(FFT_MKL_THREADS "Use threaded MKL FFT" ON)
-    add_definitions(-DFFT_PACK_${FFT_PACK})
+  if(FFT_MKL_THREADS)
-  endif()
+    target_compile_definitions(lammps PRIVATE -DFFT_MKL_THREADS)
+  endif()
+  target_link_libraries(lammps PRIVATE MKL::MKL)
+else()
+  # last option is KISSFFT
+  target_compile_definitions(lammps PRIVATE -DFFT_KISS)
+endif()
+
+set(FFT_PACK "array" CACHE STRING "Optimization for FFT")
+set(FFT_PACK_VALUES array pointer memcpy)
+set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES})
+validate_option(FFT_PACK FFT_PACK_VALUES)
+if(NOT FFT_PACK STREQUAL "array")
+  string(TOUPPER ${FFT_PACK} FFT_PACK)
+  target_compile_definitions(lammps PRIVATE -DFFT_PACK_${FFT_PACK})
 endif()

cmake/Modules/Packages/LATTE.cmake

@@ -1,38 +1,47 @@
-if(PKG_LATTE)
+enable_language(Fortran)
-  enable_language(Fortran)
+
-  find_package(LATTE)
+# using lammps in a super-build setting
-  if(LATTE_FOUND)
+if(TARGET LATTE::latte)
-    set(DOWNLOAD_LATTE_DEFAULT OFF)
+  target_link_libraries(lammps PRIVATE LATTE::latte)
-  else()
+  return()
-    set(DOWNLOAD_LATTE_DEFAULT ON)
+endif()
-  endif()
+
-  option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
+find_package(LATTE)
-  if(DOWNLOAD_LATTE)
+if(LATTE_FOUND)
-    if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
+  set(DOWNLOAD_LATTE_DEFAULT OFF)
-      message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
+else()
-    endif()
+  set(DOWNLOAD_LATTE_DEFAULT ON)
-    if(CMAKE_GENERATOR STREQUAL "Ninja")
+endif()
-      message(FATAL_ERROR "Cannot build downloaded LATTE library with Ninja build tool")
+option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
-    endif()
+if(DOWNLOAD_LATTE)
-    message(STATUS "LATTE download requested - we will build our own")
+  message(STATUS "LATTE download requested - we will build our own")
-    include(ExternalProject)
+  include(ExternalProject)
-    ExternalProject_Add(latte_build
+  ExternalProject_Add(latte_build
-      URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz
+    URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz
-      URL_MD5 85ac414fdada2d04619c8f936344df14
+    URL_MD5 85ac414fdada2d04619c8f936344df14
-      SOURCE_SUBDIR cmake
+    SOURCE_SUBDIR cmake
-      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC}
+    CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} -DCMAKE_INSTALL_LIBDIR=lib
-      -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
+    -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
-      -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=${CMAKE_Fortran_FLAGS}
+    -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=${CMAKE_Fortran_FLAGS}
-      -DCMAKE_Fortran_FLAGS_${BTYPE}=${CMAKE_Fortran_FLAGS_${BTYPE}} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+    -DCMAKE_Fortran_FLAGS_${BTYPE}=${CMAKE_Fortran_FLAGS_${BTYPE}} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-    )
+    -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM} -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
-    ExternalProject_get_property(latte_build INSTALL_DIR)
+    BUILD_BYPRODUCTS <INSTALL_DIR>/lib/liblatte.a
-    set(LATTE_LIBRARIES ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/liblatte.a)
+  )
-    list(APPEND LAMMPS_DEPS latte_build)
+  ExternalProject_get_property(latte_build INSTALL_DIR)
-  else()
+  add_library(LAMMPS::LATTE UNKNOWN IMPORTED)
-    find_package(LATTE)
+  set_target_properties(LAMMPS::LATTE PROPERTIES
-    if(NOT LATTE_FOUND)
+    IMPORTED_LOCATION "${INSTALL_DIR}/lib/liblatte.a"
-      message(FATAL_ERROR "LATTE library not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
+    INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
-    endif()
+  target_link_libraries(lammps PRIVATE LAMMPS::LATTE)
-  endif()
+  add_dependencies(LAMMPS::LATTE latte_build)
-  list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES})
+  if(NOT BUILD_SHARED_LIBS)
+    install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
+  endif()
+else()
+  find_package(LATTE)
+  if(NOT LATTE_FOUND)
+    message(FATAL_ERROR "LATTE library not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
+  endif()
+  # latte needs lapack
+  target_link_libraries(lammps PRIVATE LATTE::latte ${LAPACK_LIBRARIES})
 endif()

cmake/Modules/Packages/MESSAGE.cmake

@@ -1,32 +1,35 @@
-if(PKG_MESSAGE)
+if(LAMMPS_SIZES STREQUAL BIGBIG)
-  if(LAMMPS_SIZES STREQUAL BIGBIG)
+  message(FATAL_ERROR "The MESSAGE Package is not compatible with -DLAMMPS_BIGBIG")
-    message(FATAL_ERROR "The MESSAGE Package is not compatible with -DLAMMPS_BIGBIG")
-  endif()
-  option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
-  file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F
-      ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c
-      ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
-
-  add_library(cslib STATIC ${cslib_SOURCES})
-  if(BUILD_MPI)
-    target_compile_definitions(cslib PRIVATE -DMPI_YES)
-    set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi")
-  else()
-    target_compile_definitions(cslib PRIVATE -DMPI_NO)
-    target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_MPI)
-    set_target_properties(cslib PROPERTIES OUTPUT_NAME "csnompi")
-  endif()
-
-  if(MESSAGE_ZMQ)
-    target_compile_definitions(cslib PRIVATE -DZMQ_YES)
-    find_package(ZMQ REQUIRED)
-    target_include_directories(cslib PRIVATE ${ZMQ_INCLUDE_DIRS})
-    target_link_libraries(cslib PUBLIC ${ZMQ_LIBRARIES})
-  else()
-    target_compile_definitions(cslib PRIVATE -DZMQ_NO)
-    target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_ZMQ)
-  endif()
-
-  list(APPEND LAMMPS_LINK_LIBS cslib)
-  include_directories(${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src)
 endif()
+option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
+file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F
+    ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c
+    ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
+
+add_library(cslib STATIC ${cslib_SOURCES})
+if(NOT BUILD_SHARED_LIBS)
+  install(TARGETS cslib EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+endif()
+target_compile_definitions(cslib PRIVATE -DLAMMPS_${LAMMPS_SIZES})
+set_target_properties(cslib PROPERTIES OUTPUT_NAME lammps_cslib${LAMMPS_MACHINE})
+if(BUILD_MPI)
+  target_compile_definitions(cslib PRIVATE -DMPI_YES)
+  set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi")
+  target_link_libraries(cslib PRIVATE MPI::MPI_CXX)
+else()
+  target_compile_definitions(cslib PRIVATE -DMPI_NO)
+  target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_MPI)
+  set_target_properties(cslib PROPERTIES OUTPUT_NAME "csnompi")
+endif()
+
+if(MESSAGE_ZMQ)
+  target_compile_definitions(cslib PRIVATE -DZMQ_YES)
+  find_package(ZMQ REQUIRED)
+  target_link_libraries(cslib PUBLIC ZMQ::ZMQ)
+else()
+  target_compile_definitions(cslib PRIVATE -DZMQ_NO)
+  target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_ZMQ)
+endif()
+
+target_link_libraries(lammps PRIVATE cslib)
+target_include_directories(lammps PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src)

cmake/Modules/Packages/MSCG.cmake

@@ -1,45 +1,48 @@
-if(PKG_MSCG)
+find_package(GSL REQUIRED)
-  find_package(GSL REQUIRED)
+find_package(MSCG QUIET)
-  find_package(MSCG QUIET)
+if(MSGC_FOUND)
-  if(MSGC_FOUND)
+  set(DOWNLOAD_MSCG_DEFAULT OFF)
-    set(DOWNLOAD_MSCG_DEFAULT OFF)
+else()
-  else()
+  set(DOWNLOAD_MSCG_DEFAULT ON)
-    set(DOWNLOAD_MSCG_DEFAULT ON)
-  endif()
-  option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
-  if(DOWNLOAD_MSCG)
-    if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
-      message(FATAL_ERROR "For downlading MSCG you need at least cmake-3.7")
-    endif()
-    if(CMAKE_GENERATOR STREQUAL "Ninja")
-      message(FATAL_ERROR "Cannot build downloaded MSCG library with Ninja build tool")
-    endif()
-    include(ExternalProject)
-    if(NOT LAPACK_FOUND)
-      set(EXTRA_MSCG_OPTS "-DLAPACK_LIBRARIES=${CMAKE_CURRENT_BINARY_DIR}/liblinalg.a")
-    endif()
-    ExternalProject_Add(mscg_build
-      URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz
-      URL_MD5 8c45e269ee13f60b303edd7823866a91
-      SOURCE_SUBDIR src/CMake
-      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} ${EXTRA_MSCG_OPTS}
-      BUILD_COMMAND make mscg INSTALL_COMMAND ""
-      )
-    ExternalProject_get_property(mscg_build BINARY_DIR)
-    set(MSCG_LIBRARIES ${BINARY_DIR}/libmscg.a)
-    ExternalProject_get_property(mscg_build SOURCE_DIR)
-    set(MSCG_INCLUDE_DIRS ${SOURCE_DIR}/src)
-    list(APPEND LAMMPS_DEPS mscg_build)
-    if(NOT LAPACK_FOUND)
-      file(MAKE_DIRECTORY ${MSCG_INCLUDE_DIRS})
-      add_dependencies(mscg_build linalg)
-    endif()
-  else()
-    find_package(MSCG)
-    if(NOT MSCG_FOUND)
-      message(FATAL_ERROR "MSCG not found, help CMake to find it by setting MSCG_LIBRARY and MSCG_INCLUDE_DIRS, or set DOWNLOAD_MSCG=ON to download it")
-    endif()
-  endif()
-  list(APPEND LAMMPS_LINK_LIBS ${MSCG_LIBRARIES} ${GSL_LIBRARIES} ${LAPACK_LIBRARIES})
-  include_directories(${MSCG_INCLUDE_DIRS})
 endif()
+option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
+if(DOWNLOAD_MSCG)
+  include(ExternalProject)
+  ExternalProject_Add(mscg_build
+    URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz
+    URL_MD5 8c45e269ee13f60b303edd7823866a91
+    SOURCE_SUBDIR src/CMake
+    CMAKE_ARGS ${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)
+  if(NOT BUILD_SHARED_LIBS)
+    install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
+  endif()
+else()
+  find_package(MSCG)
+  if(NOT MSCG_FOUND)
+    message(FATAL_ERROR "MSCG not found, help CMake to find it by setting MSCG_LIBRARY and MSCG_INCLUDE_DIRS, or set DOWNLOAD_MSCG=ON to download it")
+  endif()
+  target_link_libraries(lammps PRIVATE MSCG::MSCG)
+endif()
+target_link_libraries(lammps PRIVATE GSL::gsl ${LAPACK_LIBRARIES})

cmake/Modules/Packages/OPT.cmake

@@ -1,13 +1,11 @@
-if(PKG_OPT)
+  set(OPT_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/OPT)
-    set(OPT_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/OPT)
+  set(OPT_SOURCES)
-    set(OPT_SOURCES)
+  set_property(GLOBAL PROPERTY "OPT_SOURCES" "${OPT_SOURCES}")
-    set_property(GLOBAL PROPERTY "OPT_SOURCES" "${OPT_SOURCES}")
 
-    # detects styles which have OPT version
+  # detects styles which have OPT version
-    RegisterStylesExt(${OPT_SOURCES_DIR} opt OPT_SOURCES)
+  RegisterStylesExt(${OPT_SOURCES_DIR} opt OPT_SOURCES)
 
-    get_property(OPT_SOURCES GLOBAL PROPERTY OPT_SOURCES)
+  get_property(OPT_SOURCES GLOBAL PROPERTY OPT_SOURCES)
 
-    list(APPEND LIB_SOURCES ${OPT_SOURCES})
+  target_sources(lammps PRIVATE ${OPT_SOURCES})
-    include_directories(${OPT_SOURCES_DIR})
+  target_include_directories(lammps PRIVATE ${OPT_SOURCES_DIR})
-endif()

cmake/Modules/Packages/PYTHON.cmake

@@ -1,6 +1,9 @@
-if(PKG_PYTHON)
+if(CMAKE_VERSION VERSION_LESS 3.12)
-  find_package(PythonLibs REQUIRED)
+  find_package(PythonLibs REQUIRED) # Deprecated since version 3.12
-  add_definitions(-DLMP_PYTHON)
+  target_include_directories(lammps PRIVATE ${PYTHON_INCLUDE_DIR})
-  include_directories(${PYTHON_INCLUDE_DIR})
+  target_link_libraries(lammps PRIVATE ${PYTHON_LIBRARY})
-  list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY})
+else()
+  find_package(Python REQUIRED COMPONENTS Development)
+  target_link_libraries(lammps PRIVATE Python::Python)
 endif()
+target_compile_definitions(lammps PRIVATE -DLMP_PYTHON)

cmake/Modules/Packages/QEQ.cmake

@@ -1,20 +1,18 @@
 # Fix qeq/fire requires MANYBODY (i.e. COMB and COMB3) to be installed
-if(PKG_QEQ)
+set(QEQ_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/QEQ)
-  set(QEQ_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/QEQ)
+file(GLOB QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix*.h)
-  file(GLOB QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix*.h)
+file(GLOB QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix*.cpp)
-  file(GLOB QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix*.cpp)
 
-  if(NOT PKG_MANYBODY)
+if(NOT PKG_MANYBODY)
-    list(REMOVE_ITEM QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix_qeq_fire.h)
+  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 QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix_qeq_fire.cpp)
-  endif()
-  set_property(GLOBAL PROPERTY "QEQ_SOURCES" "${QEQ_SOURCES}")
-
-  foreach(MY_HEADER ${QEQ_HEADERS})
-    AddStyleHeader(${MY_HEADER} FIX)
-  endforeach()
-
-  get_property(QEQ_SOURCES GLOBAL PROPERTY QEQ_SOURCES)
-  list(APPEND LIB_SOURCES ${QEQ_SOURCES})
-  include_directories(${QEQ_SOURCES_DIR})
 endif()
+set_property(GLOBAL PROPERTY "QEQ_SOURCES" "${QEQ_SOURCES}")
+
+foreach(MY_HEADER ${QEQ_HEADERS})
+  AddStyleHeader(${MY_HEADER} FIX)
+endforeach()
+
+get_property(QEQ_SOURCES GLOBAL PROPERTY QEQ_SOURCES)
+target_sources(lammps PRIVATE ${QEQ_SOURCES})
+target_include_directories(lammps PRIVATE ${QEQ_SOURCES_DIR})

cmake/Modules/Packages/USER-COLVARS.cmake

@@ -1,42 +1,36 @@
-if(PKG_USER-COLVARS)
+set(COLVARS_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars)
 
-  set(COLVARS_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars)
+file(GLOB COLVARS_SOURCES ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
 
-  file(GLOB COLVARS_SOURCES ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
+# Build Lepton by default
+option(COLVARS_LEPTON "Build and link the Lepton library" ON)
 
-  # Build Lepton by default
+if(COLVARS_LEPTON)
-  set(COLVARS_LEPTON_DEFAULT ON)
+  set(LEPTON_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton)
-  # but not if C++11 is disabled per user request
+  file(GLOB LEPTON_SOURCES ${LEPTON_DIR}/src/[^.]*.cpp)
-  if(DEFINED DISABLE_CXX11_REQUIREMENT)
+  add_library(lepton STATIC ${LEPTON_SOURCES})
-    if(DISABLE_CXX11_REQUIREMENT)
+  if(NOT BUILD_SHARED_LIBS)
-      set(COLVARS_LEPTON_DEFAULT OFF)
+    install(TARGETS lepton EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-    endif()
   endif()
-
+  # Change the define below to LEPTON_BUILDING_SHARED_LIBRARY when linking Lepton as a DLL with MSVC
-  option(COLVARS_LEPTON "Build and link the Lepton library" ${COLVARS_LEPTON_DEFAULT})
+  target_compile_definitions(lepton PRIVATE -DLEPTON_BUILDING_STATIC_LIBRARY)
-
+  set_target_properties(lepton PROPERTIES OUTPUT_NAME lammps_lepton${LAMMPS_MACHINE})
-  # Verify that the user's choice is consistent
+  target_include_directories(lepton PRIVATE ${LEPTON_DIR}/include)
-  if(DEFINED DISABLE_CXX11_REQUIREMENT)
+endif()
-    if((DISABLE_CXX11_REQUIREMENT) AND (COLVARS_LEPTON))
+
-      message(FATAL_ERROR "Building the Lepton library requires C++11 or later.")
+add_library(colvars STATIC ${COLVARS_SOURCES})
-    endif()
+if(NOT BUILD_SHARED_LIBS)
-  endif()
+  install(TARGETS colvars EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-
+endif()
-  if(COLVARS_LEPTON)
+target_compile_definitions(colvars PRIVATE -DLAMMPS_${LAMMPS_SIZES})
-    set(LEPTON_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton)
+set_target_properties(colvars PROPERTIES OUTPUT_NAME lammps_colvars${LAMMPS_MACHINE})
-    file(GLOB LEPTON_SOURCES ${LEPTON_DIR}/src/[^.]*.cpp)
+target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
-    add_library(lepton STATIC ${LEPTON_SOURCES})
+target_link_libraries(lammps PRIVATE colvars)
-    target_include_directories(lepton PRIVATE ${LEPTON_DIR}/include)
+
-  endif()
+if(COLVARS_LEPTON)
-
+  target_link_libraries(lammps PRIVATE lepton)
-  add_library(colvars STATIC ${COLVARS_SOURCES})
+  target_compile_definitions(colvars PRIVATE -DLEPTON)
-  target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
+  # Disable the line below when linking Lepton as a DLL with MSVC
-  list(APPEND LAMMPS_LINK_LIBS colvars)
+  target_compile_definitions(colvars PRIVATE -DLEPTON_USE_STATIC_LIBRARIES)
-
+  target_include_directories(colvars PUBLIC ${LEPTON_DIR}/include)
-  if(COLVARS_LEPTON)
-    list(APPEND LAMMPS_LINK_LIBS lepton)
-    target_compile_options(colvars PRIVATE -DLEPTON)
-    target_include_directories(colvars PUBLIC ${LEPTON_DIR}/include)
-  endif()
-
 endif()

cmake/Modules/Packages/USER-H5MD.cmake

@@ -1,8 +1,5 @@
-if(PKG_USER-H5MD)
+enable_language(C)
-  enable_language(C)
 
-  find_package(HDF5 REQUIRED)
+find_package(HDF5 REQUIRED)
-  target_link_libraries(h5md ${HDF5_LIBRARIES})
+target_link_libraries(h5md PRIVATE ${HDF5_LIBRARIES})
-  target_include_directories(h5md PRIVATE ${HDF5_INCLUDE_DIRS})
+target_include_directories(h5md PUBLIC ${HDF5_INCLUDE_DIRS})
-  include_directories(${HDF5_INCLUDE_DIRS})
-endif()

cmake/Modules/Packages/USER-INTEL.cmake

@@ -1,118 +1,109 @@
-if(PKG_USER-INTEL)
+check_include_file_cxx(immintrin.h FOUND_IMMINTRIN)
-  check_include_file_cxx(immintrin.h FOUND_IMMINTRIN)
+if(NOT FOUND_IMMINTRIN)
-  if(NOT FOUND_IMMINTRIN)
+  message(FATAL_ERROR "immintrin.h header not found, Intel package won't work without it")
-    message(FATAL_ERROR "immintrin.h header not found, Intel package won't work without it")
-  endif()
-
-  add_definitions(-DLMP_USER_INTEL)
-
-  set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)")
-  set(INTEL_ARCH_VALUES cpu knl)
-  set_property(CACHE INTEL_ARCH PROPERTY STRINGS ${INTEL_ARCH_VALUES})
-  validate_option(INTEL_ARCH INTEL_ARCH_VALUES)
-  string(TOUPPER ${INTEL_ARCH} INTEL_ARCH)
-
-  find_package(Threads QUIET)
-  if(Threads_FOUND)
-    set(INTEL_LRT_MODE "threads" CACHE STRING "Long-range threads mode (none, threads, or c++11)")
-  else()
-    set(INTEL_LRT_MODE "none" CACHE STRING "Long-range threads mode (none, threads, or c++11)")
-  endif()
-  set(INTEL_LRT_VALUES none threads c++11)
-  set_property(CACHE INTEL_LRT_MODE PROPERTY STRINGS ${INTEL_LRT_VALUES})
-  validate_option(INTEL_LRT_MODE INTEL_LRT_VALUES)
-  string(TOUPPER ${INTEL_LRT_MODE} INTEL_LRT_MODE)
-  if(INTEL_LRT_MODE STREQUAL "THREADS")
-    if(Threads_FOUND)
-      add_definitions(-DLMP_INTEL_USELRT)
-      list(APPEND LAMMPS_LINK_LIBS ${CMAKE_THREAD_LIBS_INIT})
-    else()
-      message(FATAL_ERROR "Must have working threads library for Long-range thread support")
-    endif()
-  endif()
-  if(INTEL_LRT_MODE STREQUAL "C++11")
-    add_definitions(-DLMP_INTEL_USERLRT -DLMP_INTEL_LRT11)
-  endif()
-
-  if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
-    if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
-      message(FATAL_ERROR "USER-INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
-    endif()
-  else()
-    message(WARNING "USER-INTEL gives best performance with Intel compilers")
-  endif()
-
-  find_package(TBB QUIET)
-  if(TBB_FOUND)
-    list(APPEND LAMMPS_LINK_LIBS ${TBB_MALLOC_LIBRARIES})
-  else()
-    add_definitions(-DLMP_INTEL_NO_TBB)
-    if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
-      message(WARNING "USER-INTEL with Intel compilers should use TBB malloc libraries")
-    endif()
-  endif()
-
-  find_package(MKL QUIET)
-  if(MKL_FOUND)
-    add_definitions(-DLMP_USE_MKL_RNG)
-    list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES})
-  else()
-    message(STATUS "Pair style dpd/intel will be faster with MKL libraries")
-  endif()
-
-  if((NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "64") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "128") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "256"))
-    message(FATAL_ERROR "USER-INTEL only supports memory alignment of 64, 128 or 256 on this platform")
-  endif()
-
-  if(INTEL_ARCH STREQUAL "KNL")
-    if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
-      message(FATAL_ERROR "Must use Intel compiler with USER-INTEL for KNL architecture")
-    endif()
-    set(CMAKE_EXE_LINKER_FLAGS  "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload")
-    set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"")
-    add_compile_options(-xMIC-AVX512 -qoffload -fno-alias -ansi-alias -restrict -qoverride-limits ${MIC_OPTIONS})
-    add_definitions(-DLMP_INTEL_OFFLOAD)
-  else()
-    if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
-      if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xCOMMON-AVX512")
-      else()
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xHost")
-      endif()
-      include(CheckCXXCompilerFlag)
-      foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
-        check_cxx_compiler_flag("${__FLAG}" COMPILER_SUPPORTS${_FLAG})
-        if(COMPILER_SUPPORTS${_FLAG})
-          add_compile_options(${_FLAG})
-        endif()
-      endforeach()
-    else()
-      add_compile_options(-O3 -ffast-math)
-    endif()
-  endif()
-
-  # collect sources
-  set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
-  set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/fix_intel.cpp
-                         ${USER-INTEL_SOURCES_DIR}/fix_nh_intel.cpp
-                         ${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp
-                         ${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp
-                         ${USER-INTEL_SOURCES_DIR}/npair_intel.cpp)
-
-  set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")
-
-  # detect styles which have a USER-INTEL version
-  RegisterStylesExt(${USER-INTEL_SOURCES_DIR} intel USER-INTEL_SOURCES)
-  RegisterNBinStyle(${USER-INTEL_SOURCES_DIR}/nbin_intel.h)
-  RegisterNPairStyle(${USER-INTEL_SOURCES_DIR}/npair_intel.h)
-  RegisterFixStyle(${USER-INTEL_SOURCES_DIR}/fix_intel.h)
-
-  get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES)
-  if(PKG_KSPACE)
-    list(APPEND USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
-    RegisterIntegrateStyle(${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
-  endif()
-
-  list(APPEND LIB_SOURCES ${USER-INTEL_SOURCES})
-  include_directories(${USER-INTEL_SOURCES_DIR})
 endif()
+
+target_compile_definitions(lammps PRIVATE -DLMP_USER_INTEL)
+
+set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)")
+set(INTEL_ARCH_VALUES cpu knl)
+set_property(CACHE INTEL_ARCH PROPERTY STRINGS ${INTEL_ARCH_VALUES})
+validate_option(INTEL_ARCH INTEL_ARCH_VALUES)
+string(TOUPPER ${INTEL_ARCH} INTEL_ARCH)
+
+find_package(Threads QUIET)
+if(Threads_FOUND)
+  set(INTEL_LRT_MODE "threads" CACHE STRING "Long-range threads mode (none, threads, or c++11)")
+else()
+  set(INTEL_LRT_MODE "none" CACHE STRING "Long-range threads mode (none, threads, or c++11)")
+endif()
+set(INTEL_LRT_VALUES none threads c++11)
+set_property(CACHE INTEL_LRT_MODE PROPERTY STRINGS ${INTEL_LRT_VALUES})
+validate_option(INTEL_LRT_MODE INTEL_LRT_VALUES)
+string(TOUPPER ${INTEL_LRT_MODE} INTEL_LRT_MODE)
+if(INTEL_LRT_MODE STREQUAL "THREADS")
+  if(Threads_FOUND)
+    target_compile_definitions(lammps PRIVATE -DLMP_INTEL_USELRT)
+    target_link_libraries(lammps PRIVATE Threads::Threads)
+  else()
+    message(FATAL_ERROR "Must have working threads library for Long-range thread support")
+  endif()
+endif()
+if(INTEL_LRT_MODE STREQUAL "C++11")
+  target_compile_definitions(lammps PRIVATE -DLMP_INTEL_USELRT -DLMP_INTEL_LRT11)
+endif()
+
+if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+  if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
+    message(FATAL_ERROR "USER-INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
+  endif()
+else()
+  message(WARNING "USER-INTEL gives best performance with Intel compilers")
+endif()
+
+find_package(TBB_MALLOC QUIET)
+if(TBB_MALLOC_FOUND)
+  target_link_libraries(lammps PRIVATE TBB::TBB_MALLOC)
+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")
+  endif()
+endif()
+
+find_package(MKL QUIET)
+if(MKL_FOUND)
+  target_compile_definitions(lammps PRIVATE -DLMP_USE_MKL_RNG)
+  target_link_libraries(lammps PRIVATE MKL::MKL)
+else()
+  message(STATUS "Pair style dpd/intel will be faster with MKL libraries")
+endif()
+
+if((NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "64") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "128") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "256"))
+  message(FATAL_ERROR "USER-INTEL only supports memory alignment of 64, 128 or 256 on this platform")
+endif()
+
+if(INTEL_ARCH STREQUAL "KNL")
+  if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+    message(FATAL_ERROR "Must use Intel compiler with USER-INTEL for KNL architecture")
+  endif()
+  set(CMAKE_EXE_LINKER_FLAGS  "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload")
+  set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"")
+  target_compile_options(lammps PRIVATE -xMIC-AVX512 -qoffload -fno-alias -ansi-alias -restrict -qoverride-limits ${MIC_OPTIONS})
+  target_compile_definitions(lammps PRIVATE -DLMP_INTEL_OFFLOAD)
+else()
+  if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+    include(CheckCXXCompilerFlag)
+    foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
+      check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAG})
+      if(COMPILER_SUPPORTS${_FLAG})
+	  target_compile_options(lammps PRIVATE ${_FLAG})
+      endif()
+    endforeach()
+  endif()
+endif()
+
+# collect sources
+set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
+set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/fix_intel.cpp
+                       ${USER-INTEL_SOURCES_DIR}/fix_nh_intel.cpp
+                       ${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp
+                       ${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp
+                       ${USER-INTEL_SOURCES_DIR}/npair_intel.cpp)
+
+set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")
+
+# detect styles which have a USER-INTEL version
+RegisterStylesExt(${USER-INTEL_SOURCES_DIR} intel USER-INTEL_SOURCES)
+RegisterNBinStyle(${USER-INTEL_SOURCES_DIR}/nbin_intel.h)
+RegisterNPairStyle(${USER-INTEL_SOURCES_DIR}/npair_intel.h)
+RegisterFixStyle(${USER-INTEL_SOURCES_DIR}/fix_intel.h)
+
+get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES)
+if(PKG_KSPACE)
+  list(APPEND USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
+  RegisterIntegrateStyle(${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
+endif()
+
+target_sources(lammps PRIVATE ${USER-INTEL_SOURCES})
+target_include_directories(lammps PRIVATE ${USER-INTEL_SOURCES_DIR})

cmake/Modules/Packages/USER-MOLFILE.cmake

@@ -1,14 +1,11 @@
-if(PKG_USER-MOLFILE)
+set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
-  if (CMAKE_VERSION VERSION_LESS "3.10") # due to INTERFACE without a library
+add_library(molfile INTERFACE)
-    message(FATAL_ERROR "For configuring USER-MOLFILE you need CMake 3.10 or later")
+if(NOT BUILD_SHARED_LIBS)
-  endif()
+  install(TARGETS molfile EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-
-  set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
-  add_library(molfile INTERFACE)
-  target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
-  # no need to link with -ldl on windows
-  if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
-    target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
-  endif()
-  list(APPEND LAMMPS_LINK_LIBS molfile)
 endif()
+target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
+# no need to link with -ldl on windows
+if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+  target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
+endif()
+target_link_libraries(lammps PRIVATE molfile)

cmake/Modules/Packages/USER-NETCDF.cmake

@@ -1,6 +1,20 @@
-if(PKG_USER-NETCDF)
+# USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
-  find_package(NetCDF REQUIRED)
+# NetCDF library enables dump style "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
-  include_directories(${NETCDF_INCLUDE_DIRS})
+find_package(NetCDF)
-  list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES})
+if(NETCDF_FOUND)
-  add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
+  find_package(PNetCDF)
-endif()
+else(NETCDF_FOUND)
+  find_package(PNetCDF REQUIRED)
+endif(NETCDF_FOUND)
+
+if(NETCDF_FOUND)
+  target_link_libraries(lammps PRIVATE NetCDF::NetCDF)
+  target_compile_definitions(lammps PRIVATE -DLMP_HAS_NETCDF)
+endif(NETCDF_FOUND)
+
+if(PNETCDF_FOUND)
+  target_link_libraries(lammps PRIVATE PNetCDF::PNetCDF)
+  target_compile_definitions(lammps PRIVATE -DLMP_HAS_PNETCDF)
+endif(PNETCDF_FOUND)
+
+target_compile_definitions(lammps PRIVATE -DNC_64BIT_DATA=0x0020)

cmake/Modules/Packages/USER-OMP.cmake

@@ -1,42 +1,40 @@
-if(PKG_USER-OMP)
+  set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP)
-    set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP)
+  set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
-    set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
+                       ${USER-OMP_SOURCES_DIR}/thr_omp.cpp
-                         ${USER-OMP_SOURCES_DIR}/thr_omp.cpp
+                       ${USER-OMP_SOURCES_DIR}/fix_omp.cpp
-                         ${USER-OMP_SOURCES_DIR}/fix_omp.cpp
+                       ${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp
-                         ${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp
+                       ${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp
-                         ${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp
+                       ${USER-OMP_SOURCES_DIR}/domain_omp.cpp)
-                         ${USER-OMP_SOURCES_DIR}/domain_omp.cpp)
+  target_compile_definitions(lammps PRIVATE -DLMP_USER_OMP)
-    add_definitions(-DLMP_USER_OMP)
+  set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}")
-    set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}")
 
-    # detects styles which have USER-OMP version
+  # detects styles which have USER-OMP version
-    RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
+  RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
-    RegisterFixStyle(${USER-OMP_SOURCES_DIR}/fix_omp.h)
+  RegisterFixStyle(${USER-OMP_SOURCES_DIR}/fix_omp.h)
 
-    get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
+  get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
 
-    # manually add package dependent source files from USER-OMP that do not provide styles
+  # manually add package dependent source files from USER-OMP that do not provide styles
 
-    if(PKG_ASPHERE)
+  if(PKG_ASPHERE)
-      list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_nh_asphere_omp.cpp)
+    list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_nh_asphere_omp.cpp)
-    endif()
+  endif()
 
-    if(PKG_RIGID)
+  if(PKG_RIGID)
-      list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp)
+    list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp)
-    endif()
+  endif()
 
-    if(PKG_USER-REAXC)
+  if(PKG_USER-REAXC)
-      list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/reaxc_bond_orders_omp.cpp
+    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_hydrogen_bonds_omp.cpp
-                                   ${USER-OMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp
+                                 ${USER-OMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp
-                                   ${USER-OMP_SOURCES_DIR}/reaxc_bonds_omp.cpp
+                                 ${USER-OMP_SOURCES_DIR}/reaxc_bonds_omp.cpp
-                                   ${USER-OMP_SOURCES_DIR}/reaxc_init_md_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_torsion_angles_omp.cpp
-                                   ${USER-OMP_SOURCES_DIR}/reaxc_forces_omp.cpp
+                                 ${USER-OMP_SOURCES_DIR}/reaxc_forces_omp.cpp
-                                   ${USER-OMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp
+                                 ${USER-OMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp
-                                   ${USER-OMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp)
+                                 ${USER-OMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp)
-    endif()
+  endif()
 
-    list(APPEND LIB_SOURCES ${USER-OMP_SOURCES})
+  target_sources(lammps PRIVATE ${USER-OMP_SOURCES})
-    include_directories(${USER-OMP_SOURCES_DIR})
+  target_include_directories(lammps PRIVATE ${USER-OMP_SOURCES_DIR})
-endif()

cmake/Modules/Packages/USER-PLUMED.cmake

@@ -1,91 +1,101 @@
-if(PKG_USER-PLUMED)
+set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")
-  set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")
+set(PLUMED_MODE_VALUES static shared runtime)
-  set(PLUMED_MODE_VALUES static shared runtime)
+set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})
-  set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})
+validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
-  validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
+string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
-  string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
 
-  set(PLUMED_LINK_LIBS "")
+set(PLUMED_LINK_LIBS)
-  if(PLUMED_MODE STREQUAL "STATIC")
+if(PLUMED_MODE STREQUAL "STATIC")
-    find_package(LAPACK REQUIRED)
+  find_package(LAPACK REQUIRED)
-    find_package(BLAS REQUIRED)
+  find_package(BLAS REQUIRED)
-    find_package(GSL REQUIRED)
+  find_package(GSL REQUIRED)
-    list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
+  list(APPEND PLUMED_LINK_LIBS ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} GSL::gsl)
-    list(APPEND PLUMED_LINK_LIBS ${LAPACK_LIBRARIES} ${GSL_LIBRARIES})
+  find_package(ZLIB QUIET)
-    find_package(ZLIB QUIET)
+  if(ZLIB_FOUND)
-    if(ZLIB_FOUND)
+    list(APPEND PLUMED_LINK_LIBS ZLIB::ZLIB)
-      list(APPEND PLUMED_LINK_LIBS ${ZLIB_LIBRARIES})
-    endif()
   endif()
-
+  find_package(FFTW3 QUIET)
-  find_package(PkgConfig QUIET)
+  if(FFTW3_FOUND)
-  set(DOWNLOAD_PLUMED_DEFAULT ON)
+    list(APPEND PLUMED_LINK_LIBS FFTW3::FFTW3)
-  if(PKG_CONFIG_FOUND)
-    pkg_check_modules(PLUMED QUIET plumed)
-    if(PLUMED_FOUND)
-      set(DOWNLOAD_PLUMED_DEFAULT OFF)
-    endif()
   endif()
-
-  option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT})
-  if(DOWNLOAD_PLUMED)
-    if(CMAKE_GENERATOR STREQUAL "Ninja")
-      message(FATAL_ERROR "Cannot build downloaded Plumed library with Ninja build tool")
-    endif()
-    if(BUILD_MPI)
-      set(PLUMED_CONFIG_MPI "--enable-mpi")
-      set(PLUMED_CONFIG_CC  ${CMAKE_MPI_C_COMPILER})
-      set(PLUMED_CONFIG_CXX  ${CMAKE_MPI_CXX_COMPILER})
-    else()
-      set(PLUMED_CONFIG_MPI "--disable-mpi")
-      set(PLUMED_CONFIG_CC  ${CMAKE_C_COMPILER})
-      set(PLUMED_CONFIG_CXX  ${CMAKE_CXX_COMPILER})
-    endif()
-    if(BUILD_OMP)
-      set(PLUMED_CONFIG_OMP "--enable-openmp")
-    else()
-      set(PLUMED_CONFIG_OMP "--disable-openmp")
-    endif()
-    message(STATUS "PLUMED download requested - we will build our own")
-    include(ExternalProject)
-    ExternalProject_Add(plumed_build
-      URL https://github.com/plumed/plumed2/releases/download/v2.5.3/plumed-src-2.5.3.tgz
-      URL_MD5 de30d6e7c2dcc0973298e24a6da24286
-      BUILD_IN_SOURCE 1
-      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
-                                               ${CONFIGURE_REQUEST_PIC}
-                                               --enable-modules=all
-                                               ${PLUMED_CONFIG_MPI}
-                                               ${PLUMED_CONFIG_OMP}
-                                               CXX=${PLUMED_CONFIG_CXX}
-                                               CC=${PLUMED_CONFIG_CC}
-    )
-    ExternalProject_get_property(plumed_build INSTALL_DIR)
-    set(PLUMED_INSTALL_DIR ${INSTALL_DIR})
-    list(APPEND LAMMPS_DEPS plumed_build)
-    if(PLUMED_MODE STREQUAL "STATIC")
-      add_definitions(-D__PLUMED_WRAPPER_CXX=1)
-      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.a ${PLUMED_LINK_LIBS} ${CMAKE_DL_LIBS})
-    elseif(PLUMED_MODE STREQUAL "SHARED")
-      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX} ${PLUMED_INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX} ${CMAKE_DL_LIBS})
-    elseif(PLUMED_MODE STREQUAL "RUNTIME")
-      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX})
-      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumedWrapper.a -rdynamic ${CMAKE_DL_LIBS})
-    endif()
-    set(PLUMED_INCLUDE_DIRS "${PLUMED_INSTALL_DIR}/include")
-  else()
-    find_package(PkgConfig REQUIRED)
-    pkg_check_modules(PLUMED REQUIRED plumed)
-    if(PLUMED_MODE STREQUAL "STATIC")
-      add_definitions(-D__PLUMED_WRAPPER_CXX=1)
-      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
-    elseif(PLUMED_MODE STREQUAL "SHARED")
-      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
-    elseif(PLUMED_MODE STREQUAL "RUNTIME")
-      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX})
-      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
-    endif()
-    list(APPEND LAMMPS_LINK_LIBS ${PLUMED_LOAD})
-  endif()
-  include_directories(${PLUMED_INCLUDE_DIRS})
 endif()
+
+find_package(PkgConfig QUIET)
+set(DOWNLOAD_PLUMED_DEFAULT ON)
+if(PKG_CONFIG_FOUND)
+  pkg_check_modules(PLUMED QUIET plumed)
+  if(PLUMED_FOUND)
+    set(DOWNLOAD_PLUMED_DEFAULT OFF)
+  endif()
+endif()
+
+option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT})
+if(DOWNLOAD_PLUMED)
+  if(BUILD_MPI)
+    set(PLUMED_CONFIG_MPI "--enable-mpi")
+    set(PLUMED_CONFIG_CC  ${CMAKE_MPI_C_COMPILER})
+    set(PLUMED_CONFIG_CXX  ${CMAKE_MPI_CXX_COMPILER})
+  else()
+    set(PLUMED_CONFIG_MPI "--disable-mpi")
+    set(PLUMED_CONFIG_CC  ${CMAKE_C_COMPILER})
+    set(PLUMED_CONFIG_CXX  ${CMAKE_CXX_COMPILER})
+  endif()
+  if(BUILD_OMP)
+    set(PLUMED_CONFIG_OMP "--enable-openmp")
+  else()
+    set(PLUMED_CONFIG_OMP "--disable-openmp")
+  endif()
+  message(STATUS "PLUMED download requested - we will build our own")
+  if(PLUMED_MODE STREQUAL "STATIC")
+    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumed.a")
+  elseif(PLUMED_MODE STREQUAL "SHARED")
+    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX};<INSTALL_DIR>/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+  elseif(PLUMED_MODE STREQUAL "RUNTIME")
+    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
+  endif()
+  include(ExternalProject)
+  ExternalProject_Add(plumed_build
+    URL https://github.com/plumed/plumed2/releases/download/v2.6.0/plumed-src-2.6.0.tgz
+    URL_MD5 204d2edae58d9b10ba3ad460cad64191
+    BUILD_IN_SOURCE 1
+    CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
+                                             ${CONFIGURE_REQUEST_PIC}
+                                             --enable-modules=all
+                                             ${PLUMED_CONFIG_MPI}
+                                             ${PLUMED_CONFIG_OMP}
+                                             CXX=${PLUMED_CONFIG_CXX}
+                                             CC=${PLUMED_CONFIG_CC}
+    BUILD_BYPRODUCTS ${PLUMED_BUILD_BYPRODUCTS}
+  )
+  ExternalProject_get_property(plumed_build INSTALL_DIR)
+  add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
+  add_dependencies(LAMMPS::PLUMED plumed_build)
+  if(NOT BUILD_SHARED_LIBS)
+    install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
+  endif()
+  if(PLUMED_MODE STREQUAL "STATIC")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumed.a INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
+  elseif(PLUMED_MODE STREQUAL "SHARED")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}")
+  elseif(PLUMED_MODE STREQUAL "RUNTIME")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumedWrapper.a INTERFACE_LINK_LIBRARIES "${CMAKE_DL_LIBS}")
+  endif()
+  set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
+  file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
+else()
+  find_package(PkgConfig REQUIRED)
+  pkg_check_modules(PLUMED REQUIRED plumed)
+  add_library(LAMMPS::PLUMED INTERFACE IMPORTED)
+  if(PLUMED_MODE STREQUAL "STATIC")
+    include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
+  elseif(PLUMED_MODE STREQUAL "SHARED")
+    include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
+  elseif(PLUMED_MODE STREQUAL "RUNTIME")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+    include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
+  endif()
+  set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")
+  set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_INCLUDE_DIRS}")
+endif()
+target_link_libraries(lammps PRIVATE LAMMPS::PLUMED)

cmake/Modules/Packages/USER-QMMM.cmake

@@ -1,9 +1,12 @@
-if(PKG_USER-QMMM)
+enable_language(C)
-  enable_language(Fortran)
-  enable_language(C)
 
-  message(WARNING "Building QMMM with CMake is still experimental")
+if(NOT BUILD_SHARED_LIBS)
-  find_package(QE REQUIRED)
+  message(WARNING "It is recommended to use BUILD_SHARED_LIBS=yes with USER-QMMM")
-  include_directories(${QE_INCLUDE_DIRS})
-  list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES})
 endif()
+add_library(qmmm STATIC ${LAMMPS_LIB_SOURCE_DIR}/qmmm/libqmmm.c)
+if(NOT BUILD_SHARED_LIBS)
+  install(TARGETS qmmm EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+endif()
+set_target_properties(qmmm PROPERTIES OUTPUT_NAME lammps_qmmm${LAMMPS_MACHINE})
+target_link_libraries(lammps PRIVATE qmmm)
+target_include_directories(qmmm PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/qmmm)

cmake/Modules/Packages/USER-QUIP.cmake

@@ -1,5 +1,3 @@
-if(PKG_USER-QUIP)
+enable_language(Fortran)
-  enable_language(Fortran)
+find_package(QUIP REQUIRED)
-  find_package(QUIP REQUIRED)
+target_link_libraries(lammps PRIVATE QUIP::QUIP ${LAPACK_LIBRARIES})
-  list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES})
-endif()

cmake/Modules/Packages/USER-SCAFACOS.cmake

@@ -1,62 +1,62 @@
-if(PKG_USER-SCAFACOS)
+enable_language(Fortran)
-  enable_language(Fortran)
+enable_language(C)
-  enable_language(C)
 
-  find_package(GSL REQUIRED)
+find_package(GSL REQUIRED)
-  find_package(PkgConfig QUIET)
+find_package(PkgConfig QUIET)
-  set(DOWNLOAD_SCAFACOS_DEFAULT ON)
+find_package(MPI REQUIRED)
-  if(PKG_CONFIG_FOUND)
+set(DOWNLOAD_SCAFACOS_DEFAULT ON)
-    pkg_check_modules(SCAFACOS QUIET scafacos)
+if(PKG_CONFIG_FOUND)
-    if(SCAFACOS_FOUND)
+  pkg_check_modules(SCAFACOS QUIET scafacos)
-      set(DOWNLOAD_SCAFACOS_DEFAULT OFF)
+  if(SCAFACOS_FOUND)
-    endif()
+    set(DOWNLOAD_SCAFACOS_DEFAULT OFF)
   endif()
-  option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
+endif()
-  if(DOWNLOAD_SCAFACOS)
+option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
-    if(CMAKE_GENERATOR STREQUAL "Ninja")
+if(DOWNLOAD_SCAFACOS)
-      message(FATAL_ERROR "Cannot build downloaded ScaFaCoS library with Ninja build tool")
+  message(STATUS "ScaFaCoS download requested - we will build our own")
-    endif()
+  include(ExternalProject)
-    message(STATUS "ScaFaCoS download requested - we will build our own")
+  ExternalProject_Add(scafacos_build
-    include(ExternalProject)
+    URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
-    ExternalProject_Add(scafacos_build
+    URL_MD5 bd46d74e3296bd8a444d731bb10c1738
-      URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
+    CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc
-      URL_MD5 bd46d74e3296bd8a444d731bb10c1738
+                                             --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
-      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc
+                                             --with-internal-fftw --with-internal-pfft
-                                               --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
+                                             --with-internal-pnfft ${CONFIGURE_REQUEST_PIC}
-                                               --with-internal-fftw --with-internal-pfft
+                                             FC=${CMAKE_MPI_Fortran_COMPILER}
-                                               --with-internal-pnfft ${CONFIGURE_REQUEST_PIC}
+                                             CXX=${CMAKE_MPI_CXX_COMPILER}
-                                               FC=${CMAKE_MPI_Fortran_COMPILER}
+                                             CC=${CMAKE_MPI_C_COMPILER}
-                                               CXX=${CMAKE_MPI_CXX_COMPILER}
+                                             F77=
-                                               CC=${CMAKE_MPI_C_COMPILER}
+    BUILD_BYPRODUCTS
-                                               F77=
+      <INSTALL_DIR>/lib/libfcs.a
-    )
+      <INSTALL_DIR>/lib/libfcs_direct.a
-    ExternalProject_get_property(scafacos_build INSTALL_DIR)
+      <INSTALL_DIR>/lib/libfcs_ewald.a
-    set(SCAFACOS_BUILD_DIR ${INSTALL_DIR})
+      <INSTALL_DIR>/lib/libfcs_fmm.a
-    set(SCAFACOS_INCLUDE_DIRS ${SCAFACOS_BUILD_DIR}/include)
+      <INSTALL_DIR>/lib/libfcs_p2nfft.a
-    list(APPEND LAMMPS_DEPS scafacos_build)
+      <INSTALL_DIR>/lib/libfcs_p3m.a
-    # list and order from pkg_config file of ScaFaCoS build
+      <INSTALL_DIR>/lib/libfcs_near.a
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs.a)
+      <INSTALL_DIR>/lib/libfcs_gridsort.a
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_direct.a)
+      <INSTALL_DIR>/lib/libfcs_resort.a
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_ewald.a)
+      <INSTALL_DIR>/lib/libfcs_redist.a
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fmm.a)
+      <INSTALL_DIR>/lib/libfcs_common.a
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p2nfft.a)
+      <INSTALL_DIR>/lib/libfcs_pnfft.a
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p3m.a)
+      <INSTALL_DIR>/lib/libfcs_pfft.a
-    list(APPEND LAMMPS_LINK_LIBS ${GSL_LIBRARIES})
+      <INSTALL_DIR>/lib/libfcs_fftw3_mpi.a
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_near.a)
+      <INSTALL_DIR>/lib/libfcs_fftw3.a
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_gridsort.a)
+  )
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_resort.a)
+  ExternalProject_get_property(scafacos_build INSTALL_DIR)
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_redist.a)
+  file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_common.a)
+  add_library(LAMMPS::SCAFACOS UNKNOWN IMPORTED)
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pnfft.a)
+  set_target_properties(LAMMPS::SCAFACOS PROPERTIES
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pfft.a)
+    IMPORTED_LOCATION "${INSTALL_DIR}/lib/libfcs.a"
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3_mpi.a)
+    INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include"
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3.a)
+    INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/libfcs.a;${INSTALL_DIR}/lib/libfcs_direct.a;${INSTALL_DIR}/lib/libfcs_ewald.a;${INSTALL_DIR}/lib/libfcs_fmm.a;${INSTALL_DIR}/lib/libfcs_p2nfft.a;${INSTALL_DIR}/lib/libfcs_p3m.a;GSL::gsl;${INSTALL_DIR}/lib/libfcs_near.a;${INSTALL_DIR}/lib/libfcs_gridsort.a;${INSTALL_DIR}/lib/libfcs_resort.a;${INSTALL_DIR}/lib/libfcs_redist.a;${INSTALL_DIR}/lib/libfcs_common.a;${INSTALL_DIR}/lib/libfcs_pnfft.a;${INSTALL_DIR}/lib/libfcs_pfft.a;${INSTALL_DIR}/lib/libfcs_fftw3_mpi.a;${INSTALL_DIR}/lib/libfcs_fftw3.a;MPI::MPI_Fortran;MPI::MPI_C")
-    list(APPEND LAMMPS_LINK_LIBS ${MPI_Fortran_LIBRARIES})
+  target_link_libraries(lammps PRIVATE LAMMPS::SCAFACOS)
-    list(APPEND LAMMPS_LINK_LIBS ${MPI_C_LIBRARIES})
+  add_dependencies(LAMMPS::SCAFACOS scafacos_build)
-  else()
+  if(NOT BUILD_SHARED_LIBS)
-    find_package(PkgConfig REQUIRED)
+    install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
-    pkg_check_modules(SCAFACOS REQUIRED scafacos)
+  endif()
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_LDFLAGS})
+else()
-  endif()
+  find_package(PkgConfig REQUIRED)
-  include_directories(${SCAFACOS_INCLUDE_DIRS})
+  pkg_check_modules(SCAFACOS REQUIRED IMPORTED_TARGET scafacos)
+  target_link_libraries(lammps PRIVATE PkgConfig::SCAFACOS)
 endif()

cmake/Modules/Packages/USER-SDPD.cmake

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

cmake/Modules/Packages/USER-SMD.cmake

@@ -1,28 +1,31 @@
-if(PKG_USER-SMD)
+find_package(Eigen3 NO_MODULE)
-  find_package(Eigen3 NO_MODULE)
+if(EIGEN3_FOUND)
-  if(EIGEN3_FOUND)
+  set(DOWNLOAD_EIGEN3_DEFAULT OFF)
-    set(DOWNLOAD_EIGEN3_DEFAULT OFF)
+else()
-  else()
+  set(DOWNLOAD_EIGEN3_DEFAULT ON)
-    set(DOWNLOAD_EIGEN3_DEFAULT ON)
+endif()
-  endif()
+option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT})
-  option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT})
+if(DOWNLOAD_EIGEN3)
-  if(DOWNLOAD_EIGEN3)
+  message(STATUS "Eigen3 download requested - we will build our own")
-    message(STATUS "Eigen3 download requested - we will build our own")
+  include(ExternalProject)
-    include(ExternalProject)
+  ExternalProject_Add(Eigen3_build
-    ExternalProject_Add(Eigen3_build
+    URL http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz
-      URL http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz
+    URL_MD5 f2a417d083fe8ca4b8ed2bc613d20f07
-      URL_MD5 f2a417d083fe8ca4b8ed2bc613d20f07
+    CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
-      CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+  )
-    )
+  ExternalProject_get_property(Eigen3_build SOURCE_DIR)
-    ExternalProject_get_property(Eigen3_build SOURCE_DIR)
+  add_library(LAMMPS::EIGEN3 INTERFACE IMPORTED)
-    set(EIGEN3_INCLUDE_DIR ${SOURCE_DIR})
+  set_target_properties(LAMMPS::EIGEN3 PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}")
-    list(APPEND LAMMPS_DEPS Eigen3_build)
+  target_link_libraries(lammps PRIVATE LAMMPS::EIGEN3)
-  else()
+  add_dependencies(LAMMPS::EIGEN3 Eigen3_build)
-    find_package(Eigen3 NO_MODULE)
+  if(NOT BUILD_SHARED_LIBS)
-    mark_as_advanced(Eigen3_DIR)
+    install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
-    if(NOT EIGEN3_FOUND)
+  endif()
-      message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_EIGEN3=ON to download it")
+else()
-    endif()
+  find_package(Eigen3 NO_MODULE)
-  endif()
+  mark_as_advanced(Eigen3_DIR)
-  include_directories(${EIGEN3_INCLUDE_DIR})
+  if(NOT EIGEN3_FOUND)
+    message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_EIGEN3=ON to download it")
+  endif()
+  target_link_libraries(lammps PRIVATE Eigen3::Eigen)
 endif()

cmake/Modules/Packages/USER-VTK.cmake

@@ -1,6 +1,4 @@
-if(PKG_USER-VTK)
+find_package(VTK REQUIRED NO_MODULE)
-  find_package(VTK REQUIRED NO_MODULE)
+include(${VTK_USE_FILE})
-  include(${VTK_USE_FILE})
+target_compile_definitions(lammps PRIVATE -DLAMMPS_VTK)
-  add_definitions(-DLAMMPS_VTK)
+target_link_libraries(lammps PRIVATE ${VTK_LIBRARIES})
-  list(APPEND LAMMPS_LINK_LIBS ${VTK_LIBRARIES})
-endif()

cmake/Modules/Packages/VORONOI.cmake

@@ -1,45 +1,47 @@
-if(PKG_VORONOI)
+find_package(VORO)
-  find_package(VORO)
+if(VORO_FOUND)
-  if(VORO_FOUND)
+  set(DOWNLOAD_VORO_DEFAULT OFF)
-    set(DOWNLOAD_VORO_DEFAULT OFF)
+else()
-  else()
+  set(DOWNLOAD_VORO_DEFAULT ON)
-    set(DOWNLOAD_VORO_DEFAULT ON)
+endif()
-  endif()
+option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT})
-  option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT})
+if(DOWNLOAD_VORO)
-  if(DOWNLOAD_VORO)
+  message(STATUS "Voro++ download requested - we will build our own")
-    if(CMAKE_GENERATOR STREQUAL "Ninja")
+  include(ExternalProject)
-      message(FATAL_ERROR "Cannot build downloaded Voro++ library with Ninja build tool")
+
-    endif()
+  if(BUILD_SHARED_LIBS)
-    message(STATUS "Voro++ download requested - we will build our own")
+    set(VORO_BUILD_CFLAGS "${CMAKE_SHARED_LIBRARY_CXX_FLAGS} ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
-    include(ExternalProject)
+  else()
-
+    set(VORO_BUILD_CFLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
-    if(BUILD_SHARED_LIBS)
+  endif()
-      set(VORO_BUILD_CFLAGS "${CMAKE_SHARED_LIBRARY_CXX_FLAGS} ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
+  if(APPLE)
-    else()
+    get_filename_component(VORO_CXX ${CMAKE_CXX_COMPILER} NAME_WE)
-      set(VORO_BUILD_CFLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
+    set(VORO_BUILD_OPTIONS CXX=${VORO_CXX} CFLAGS=${VORO_BUILD_CFLAGS})
-    endif()
+  else()
-    if(APPLE)
+    set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
-      get_filename_component(VORO_CXX ${CMAKE_CXX_COMPILER} NAME_WE)
+  endif()
-      set(VORO_BUILD_OPTIONS CXX=${VORO_CXX} CFLAGS=${VORO_BUILD_CFLAGS})
+
-    else()
+  ExternalProject_Add(voro_build
-      set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
+    URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
-    endif()
+    URL_MD5 2338b824c3b7b25590e18e8df5d68af9
-
+    CONFIGURE_COMMAND "" BUILD_COMMAND make ${VORO_BUILD_OPTIONS} BUILD_IN_SOURCE 1 INSTALL_COMMAND ""
-    ExternalProject_Add(voro_build
+    BUILD_BYPRODUCTS <SOURCE_DIR>/src/libvoro++.a
-      URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
+    )
-      URL_MD5 2338b824c3b7b25590e18e8df5d68af9
+  ExternalProject_get_property(voro_build SOURCE_DIR)
-      CONFIGURE_COMMAND "" BUILD_COMMAND make ${VORO_BUILD_OPTIONS} BUILD_IN_SOURCE 1 INSTALL_COMMAND ""
+  file(MAKE_DIRECTORY ${SOURCE_DIR}/src)
-      )
+  add_library(LAMMPS::VORO UNKNOWN IMPORTED)
-    ExternalProject_get_property(voro_build SOURCE_DIR)
+  set_target_properties(LAMMPS::VORO PROPERTIES
-    set(VORO_LIBRARIES ${SOURCE_DIR}/src/libvoro++.a)
+    IMPORTED_LOCATION "${SOURCE_DIR}/src/libvoro++.a"
-    set(VORO_INCLUDE_DIRS ${SOURCE_DIR}/src)
+    INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/src")
-    list(APPEND LAMMPS_DEPS voro_build)
+  target_link_libraries(lammps PRIVATE LAMMPS::VORO)
-  else()
+  add_dependencies(LAMMPS::VORO voro_build)
-    find_package(VORO)
+  if(NOT BUILD_SHARED_LIBS)
-    if(NOT VORO_FOUND)
+    install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
-      message(FATAL_ERROR "Voro++ library not found. Help CMake to find it by setting VORO_LIBRARY and VORO_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
+  endif()
-    endif()
+else()
-  endif()
+  find_package(VORO)
-  include_directories(${VORO_INCLUDE_DIRS})
+  if(NOT VORO_FOUND)
-  list(APPEND LAMMPS_LINK_LIBS ${VORO_LIBRARIES})
+    message(FATAL_ERROR "Voro++ library not found. Help CMake to find it by setting VORO_LIBRARY and VORO_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
+  endif()
+  target_link_libraries(lammps PRIVATE VORO::VORO)
 endif()

cmake/Modules/Testing.cmake

@@ -2,7 +2,7 @@
 # Testing
 ###############################################################################
 option(ENABLE_TESTING "Enable testing" OFF)
-if(ENABLE_TESTING AND BUILD_EXE)
+if(ENABLE_TESTING)
   enable_testing()
   option(LAMMPS_TESTING_SOURCE_DIR "Location of lammps-testing source directory" "")
   option(LAMMPS_TESTING_GIT_TAG    "Git tag of lammps-testing" "master")
@@ -28,7 +28,7 @@ if(ENABLE_TESTING AND BUILD_EXE)
                     "https://github.com/lammps/lammps-testing in LAMMPS_TESTING_SOURCE_DIR")
   endif()
 
-  add_test(ShowHelp ${CMAKE_BINARY_DIR}/${LAMMPS_BINARY} -help)
+  add_test(NAME ShowHelp COMMAND $<TARGET_FILE:lmp> -help)
 
   if(EXISTS ${LAMMPS_TESTING_SOURCE_DIR})
     message(STATUS "Running test discovery...")
@@ -42,8 +42,7 @@ if(ENABLE_TESTING AND BUILD_EXE)
       string(REPLACE "-" "_" TEST_NAME ${TEST_NAME})
       string(REPLACE "+" "_" TEST_NAME ${TEST_NAME})
       set(TEST_NAME "test_core_${TEST_NAME}_serial")
-      add_test(${TEST_NAME} ${CMAKE_BINARY_DIR}/${LAMMPS_BINARY} -in ${SCRIPT_NAME})
+      add_test(NAME ${TEST_NAME} COMMAND $<TARGET_FILE:lmp> -in ${SCRIPT_NAME} WORKING_DIRECTORY ${PARENT_DIR})
-      set_tests_properties(${TEST_NAME} PROPERTIES WORKING_DIRECTORY ${PARENT_DIR})
     endforeach()
     list(LENGTH TEST_SCRIPTS NUM_TESTS)
 

cmake/pkgconfig/liblammps.pc.in

@@ -18,12 +18,6 @@
 # myapp_CFLAGS = $(LAMMPS_CFLAGS)
 # myapp_LDADD = $(LAMMPS_LIBS)
 
-# Use this in CMake:
-# CMakeLists.txt:
-# find_package(PkgConfig)
-# pkg_check_modules(LAMMPS IMPORTED_TARGET lammps)
-# target_link_libraries(<lib> PkgConfig::LAMMPS)
-
 prefix=@CMAKE_INSTALL_PREFIX@
 libdir=@CMAKE_INSTALL_FULL_LIBDIR@
 includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
@@ -31,8 +25,8 @@ includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
 Name: liblammps@LAMMPS_MACHINE@
 Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library
 URL: http://lammps.sandia.gov
-Version: @LAMMPS_VERSION@
+Version: @PROJECT_VERSION@
 Requires:
-Libs: -L${libdir} -llammps@LAMMPS_LIB_SUFFIX@
+Libs: -L${libdir} -llammps@LAMMPS_MACHINE@
 Libs.private: -lm
 Cflags: -I${includedir} @LAMMPS_API_DEFINES@

cmake/presets/all_off.cmake

@@ -7,11 +7,11 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
         SRD VORONOI
         USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
         USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
-        USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
+        USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD
         USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
         USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
-        USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
+        USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
-        USER-TALLY USER-UEF USER-VTK USER-YAFF)
+        USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

cmake/presets/all_on.cmake

@@ -9,11 +9,11 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
         SRD VORONOI
         USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
         USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
-        USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
+        USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD
         USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
         USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
-        USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
+        USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
-        USER-TALLY USER-UEF USER-VTK USER-YAFF)
+        USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)

cmake/presets/clang.cmake

@@ -2,7 +2,7 @@
 
 set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
-set(CMAKE_CXX_FLAGS "-Wall -Wextra -g -O2 -DNDEBG" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS "-Wall -Wextra -g -O2 -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)
@@ -13,5 +13,5 @@ set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
 set(OpenMP_CXX "clang++" CACHE STRING "" FORCE)
 set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
 set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
-set(OpenMP_omp_LIBRARY "/usr/lib64/libomp.so" CACHE PATH "" FORCE)
+set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)
 

cmake/presets/hip.cmake

@@ -0,0 +1,12 @@
+# preset that will enable hipcc plus gcc 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_CXX_FLAGS "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+unset(HAVE_OMP_H_INCLUDE CACHE)
+
+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)
+

cmake/presets/intel.cmake

@@ -0,0 +1,16 @@
+# preset that will enable clang/clang++ with support for MPI and OpenMP (on Linux boxes)
+
+set(CMAKE_CXX_COMPILER "icpc" CACHE STRING "" FORCE)
+set(CMAKE_C_COMPILER "icc" CACHE STRING "" FORCE)
+set(MPI_CXX "icpc" CACHE STRING "" FORCE)
+set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
+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)
+set(OpenMP_CXX "icpc" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-qopenmp" CACHE STRING "" FORCE)
+set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
+set(OpenMP_omp_LIBRARY "libiomp5.so" CACHE PATH "" FORCE)
+

cmake/presets/kokkos-cuda.cmake

@@ -0,0 +1,11 @@
+# preset that enables KOKKOS and selects CUDA compilation with OpenMP
+# enabled as well. This preselects CC 5.0 as default GPU arch, since
+# that is compatible with all higher CC, but not the default CC 3.5
+set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
+set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
+set(Kokkos_ENABLE_OPENMP ON CACHE BOOL "" FORCE)
+set(Kokkos_ENABLE_CUDA   ON CACHE BOOL "" FORCE)
+set(Kokkos_ARCH_MAXWELL50 on CACHE BOOL "" FORCE)
+set(BUILD_OMP ON CACHE BOOL "" FORCE)
+get_filename_component(NVCC_WRAPPER_CMD ${CMAKE_CURRENT_SOURCE_DIR}/../lib/kokkos/bin/nvcc_wrapper ABSOLUTE)
+set(CMAKE_CXX_COMPILER ${NVCC_WRAPPER_CMD} CACHE FILEPATH "" FORCE)

cmake/presets/kokkos-openmp.cmake

@@ -0,0 +1,6 @@
+# preset that enables KOKKOS and selects OpenMP (only) compilation
+set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
+set(Kokkos_ENABLE_SERIAL ON  CACHE BOOL "" FORCE)
+set(Kokkos_ENABLE_OPENMP ON  CACHE BOOL "" FORCE)
+set(Kokkos_ENABLE_CUDA   OFF CACHE BOOL "" FORCE)
+set(BUILD_OMP ON CACHE BOOL "" FORCE)

cmake/presets/kokkos-serial.cmake

@@ -0,0 +1,5 @@
+# preset that enables KOKKOS and selects serial compilation only
+set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
+set(Kokkos_ENABLE_SERIAL ON  CACHE BOOL "" FORCE)
+set(Kokkos_ENABLE_OPENMP OFF CACHE BOOL "" FORCE)
+set(Kokkos_ENABLE_CUDA   OFF CACHE BOOL "" FORCE)

cmake/presets/mingw-cross.cmake

@@ -1,17 +1,29 @@
 set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-                 GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI POEMS QEQ
+                 GRANULAR KSPACE LATTE MANYBODY MC MISC MOLECULE OPT PERI
-                 REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI USER-ATC USER-AWPMD
+                 POEMS QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
-                 USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
+                 USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
-                 USER-DPD USER-DRUDE USER-EFF USER-FEP USER-INTEL USER-MANIFOLD
+                 USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
-                 USER-MEAMC USER-MESO USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE
+                 USER-FEP USER-INTEL USER-MANIFOLD USER-MEAMC USER-MESODPD
-                 USER-OMP USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SDPD
+                 USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE USER-OMP
-                 USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-YAFF)
+                 USER-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC
+                 USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
+                 USER-YAFF)
 
 foreach(PKG ${WIN_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)
 endforeach()
 
+# 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)
+endif()
+
 set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
 set(LAMMPS_MEMALIGN "0" CACHE STRING "" FORCE)
+set(CMAKE_TUNE_FLAGS "-Wno-missing-include-dirs" CACHE STRING "" FORCE)
+set(CMAKE_EXE_LINKER_FLAGS "-Wl,--enable-stdcall-fixup" CACHE STRING "" FORCE)
+set(CMAKE_SHARED_LINKER_FLAGS "-Wl,--enable-stdcall-fixup" CACHE STRING "" FORCE)
+set(BUILD_TOOLS ON CACHE BOOL "" FORCE)
 set(CMAKE_INSTALL_PREFIX "${CMAKE_CURRENT_BINARY_DIR}/lammps-installer")

cmake/presets/most.cmake

@@ -2,14 +2,16 @@
 # external libraries. Compared to all_on.cmake some more unusual packages
 # are removed. The resulting binary should be able to run most inputs.
 
-set(ALL_PACKAGES ASPHERE CLASS2 COLLOID CORESHELL DIPOLE
+set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL
-        GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI
+        DIPOLE GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI
-        PYTHON QEQ REPLICA RIGID SHOCK SNAP SRD VORONOI
+        POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
-        USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD
+        USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
-        USER-DRUDE USER-FEP USER-MEAMC USER-MESO
+        USER-DPD USER-DRUDE USER-FEP USER-MEAMC USER-MESODPD
-        USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REAXC
+        USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION
-        USER-SPH USER-SMD USER-UEF USER-YAFF)
+        USER-REAXC USER-SPH USER-SMD USER-UEF USER-YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)
 endforeach()
+
+set(BUILD_TOOLS ON CACHE BOOL "" FORCE)

doc/.gitignore

@@ -1,6 +1,8 @@
 /old
 /html
+/html-offline
 /latex
+/mathjax
 /spelling
 /LAMMPS.epub
 /LAMMPS.mobi

doc/Makefile

@@ -3,8 +3,8 @@
 SHELL         = /bin/bash
 BUILDDIR      = ${CURDIR}
 RSTDIR        = $(BUILDDIR)/src
-TXTDIR        = $(BUILDDIR)/txt
 VENV          = $(BUILDDIR)/docenv
+MATHJAX       = $(BUILDDIR)/mathjax
 TXT2RST       = $(VENV)/bin/txt2rst
 ANCHORCHECK   = $(VENV)/bin/rst_anchor_check
 
@@ -12,6 +12,7 @@ PYTHON        = $(shell which python3)
 VIRTUALENV     = virtualenv
 HAS_PYTHON3    = NO
 HAS_VIRTUALENV = NO
+HAS_PDFLATEX   = NO
 
 ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 0)
 HAS_PYTHON3 = YES
@@ -27,74 +28,77 @@ VIRTUALENV     = virtualenv
 HAS_VIRTUALENV = YES
 endif
 
-SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
+ifeq ($(shell which pdflatex >/dev/null 2>&1; echo $$?), 0)
-SOURCES=$(filter-out $(wildcard $(TXTDIR)/lammps_commands*.txt) $(TXTDIR)/lammps_support.txt $(TXTDIR)/lammps_tutorials.txt,$(wildcard $(TXTDIR)/*.txt))
+HAS_PDFLATEX = YES
-OBJECTS=$(SOURCES:$(TXTDIR)/%.txt=$(RSTDIR)/%.rst)
+endif
 
-.PHONY: help clean-all clean epub mobi rst html pdf venv spelling anchor_check
+
+SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
+
+.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check
 
 # ------------------------------------------
 
 help:
 	@echo "Please use \`make <target>' where <target> is one of"
-	@echo "  html       create HTML doc pages in html dir"
+	@echo "  html          create HTML doc pages in html dir"
-	@echo "  pdf        create Developer.pdf and Manual.pdf in this dir"
+	@echo "  pdf           create Developer.pdf and Manual.pdf in this dir"
-	@echo "  fetch      fetch HTML and PDF files from LAMMPS web site"
+	@echo "  fetch         fetch HTML and PDF files from LAMMPS web site"
-	@echo "  epub       create ePUB format manual for e-book readers"
+	@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 "  mobi          convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
 	@echo "                      (requires ebook-convert tool from calibre)"
-	@echo "  clean      remove all intermediate RST files"
+	@echo "  clean         remove all intermediate RST files"
-	@echo "  clean-all  reset the entire build environment"
+	@echo "  clean-all     reset the entire build environment"
 	@echo "  anchor_check  scan for duplicate anchor labels"
-	@echo "  spelling   spell-check the manual"
+	@echo "  style_check   check for complete and consistent style lists"
+	@echo "  package_check check for complete and consistent package lists"
+	@echo "  spelling      spell-check the manual"
 
 # ------------------------------------------
 
 clean-all: clean
-	rm -rf $(BUILDDIR)/docenv $(BUILDDIR)/doctrees
+	rm -rf $(BUILDDIR)/docenv $(BUILDDIR)/doctrees $(BUILDDIR)/mathjax Manual.pdf Developer.pdf
 
-clean:
+clean: clean-spelling
 	rm -rf html epub latex
-	rm -rf spelling
 
 clean-spelling:
 	rm -rf spelling
 
-rst: clean $(OBJECTS) $(ANCHORCHECK)
+html: $(ANCHORCHECK) $(MATHJAX)
-
-html: $(OBJECTS) $(ANCHORCHECK)
 	@(\
 		. $(VENV)/bin/activate ;\
 		sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
 		echo "############################################" ;\
 		rst_anchor_check src/*.rst ;\
+		python utils/check-packages.py -s ../src -d src ;\
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
+		python utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)
-	-rm html/searchindex.js
 	@rm -rf html/_sources
 	@rm -rf html/PDF
 	@rm -rf html/USER
+	@rm -rf html/JPG
 	@cp -r src/PDF html/PDF
-	@cp -r src/USER html/USER
+	@mkdir -p html/JPG
+	@cp `grep -A2 '\.\. .*\(image\|figure\)::' src/*.rst | grep ':target:' | sed -e 's,.*:target: JPG/,src/JPG/,' | sort | uniq` html/JPG/
 	@rm -rf html/PDF/.[sg]*
-	@rm -rf html/USER/.[sg]*
+	@mkdir -p html/_static/mathjax
-	@rm -rf html/USER/*/.[sg]*
+	@cp -r $(MATHJAX)/es5 html/_static/mathjax/
-	@rm -rf html/USER/*/*.[sg]*
 	@echo "Build finished. The HTML pages are in doc/html."
 
-spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt
+spelling: $(VENV) utils/sphinx-config/false_positives.txt
 	@(\
 		. $(VENV)/bin/activate ;\
-		pip install sphinxcontrib-spelling ;\
+		cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ; env PYTHONWARNINGS= \
-		cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ;\
 		sphinx-build -b spelling -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) spelling ;\
 		deactivate ;\
 	)
 	@echo "Spell check finished."
 
-epub: $(OBJECTS)
+epub: $(VENV)
 	@mkdir -p epub/JPG
 	@rm -f LAMMPS.epub
 	@cp src/JPG/lammps-logo.png epub/
@@ -113,7 +117,8 @@ mobi: epub
 	@ebook-convert LAMMPS.epub LAMMPS.mobi
 	@echo "Conversion finished. The MOBI manual file is created."
 
-pdf: $(OBJECTS) $(ANCHORCHECK)
+pdf: $(ANCHORCHECK)
+	@if [ "$(HAS_PDFLATEX)" == "NO" ] ; then echo "PDFLaTeX was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
 	@(\
 		cd src/Developer; \
 		pdflatex developer; \
@@ -122,33 +127,33 @@ pdf: $(OBJECTS) $(ANCHORCHECK)
 		cd ../../; \
 	)
 	@(\
-                . $(VENV)/bin/activate ;\
+		. $(VENV)/bin/activate ;\
-                sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
+		sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
-                echo "############################################" ;\
+		echo "############################################" ;\
-                rst_anchor_check src/*.rst ;\
+		rst_anchor_check src/*.rst ;\
-                echo "############################################" ;\
+		python utils/check-packages.py -s ../src -d src ;\
-                deactivate ;\
+		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
+		python utils/check-styles.py -s ../src -d src ;\
+		echo "############################################" ;\
+		deactivate ;\
 	)
 	@cd latex && \
-          sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \
+		sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \
-	  mv temp Makefile && \
+		mv temp Makefile && \
-	  sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \
+		sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \
-	  mv tmp.tex LAMMPS.tex && \
+		mv tmp.tex LAMMPS.tex && \
-	  sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
+		sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
-	  mv tmp.tex LAMMPS.tex && \
+		mv tmp.tex LAMMPS.tex && \
-	  make && \
+		make && \
-	  make && \
+		make && \
-	  mv LAMMPS.pdf ../Manual.pdf && \
+		make && \
-	  cd ../;
+		mv LAMMPS.pdf ../Manual.pdf && \
+		cd ../;
 	@rm -rf latex/_sources
 	@rm -rf latex/PDF
 	@rm -rf latex/USER
 	@cp -r src/PDF latex/PDF
-	@cp -r src/USER latex/USER
 	@rm -rf latex/PDF/.[sg]*
-	@rm -rf latex/USER/.[sg]*
-	@rm -rf latex/USER/*/.[sg]*
-	@rm -rf latex/USER/*/*.[sg]*
 	@echo "Build finished. Manual.pdf and Developer.pdf are in this directory."
 
 fetch:
@@ -162,30 +167,42 @@ fetch:
 anchor_check : $(ANCHORCHECK)
 	@(\
 		. $(VENV)/bin/activate ;\
-		rst_anchor_check src/*.txt ;\
+		rst_anchor_check src/*.rst ;\
+		deactivate ;\
+	)
+
+style_check : $(VENV)
+	@(\
+		. $(VENV)/bin/activate ;\
+		python utils/check-styles.py -s ../src -d src ;\
+		deactivate ;\
+	)
+
+package_check : $(VENV)
+	@(\
+		. $(VENV)/bin/activate ;\
+		python utils/check-packages.py -s ../src -d src ;\
 		deactivate ;\
 	)
 
 # ------------------------------------------
 
-$(RSTDIR)/%.rst : $(TXTDIR)/%.txt $(TXT2RST)
-	@(\
-		mkdir -p $(RSTDIR) ; \
-		. $(VENV)/bin/activate ;\
-		txt2rst -v $< > $@ ;\
-		deactivate ;\
-	)
-
 $(VENV):
 	@if [ "$(HAS_PYTHON3)" == "NO" ] ; then echo "Python3 was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
 	@if [ "$(HAS_VIRTUALENV)" == "NO" ] ; then echo "virtualenv was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
 	@( \
 		$(VIRTUALENV) -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
+		pip install --upgrade pip; \
 		pip install Sphinx; \
+		pip install sphinxcontrib-spelling ;\
+		pip install breathe; \
 		deactivate;\
 	)
 
+$(MATHJAX):
+	@git clone --depth 1 https://github.com/mathjax/MathJax.git mathjax
+
 $(TXT2RST) $(ANCHORCHECK): $(VENV)
 	@( \
 		. $(VENV)/bin/activate; \

doc/README

@@ -93,12 +93,18 @@ support for PDFLaTeX. Also the following LaTeX packages need
 to be installed (e.g. from texlive):
 - amsmath
 - babel
+- capt-of
 - cmap
 - fncychap
+- framed
 - geometry
 - hyperref
 - hypcap
+- needspace
 - times
+- tabulary
+- upquote
+- wrapfig
 ----------------
 
 Installing prerequisites for epub build

doc/github-development-workflow.md

@@ -104,14 +104,17 @@ Here are some items to check:
   * every new command or style should have documentation. The names of
   source files (c++ and manual) should follow the name of the style.
   (example: `src/fix_nve.cpp`, `src/fix_nve.h` for `fix nve` command,
-  implementing the class `FixNVE`, documented in `doc/src/fix_nve.txt`)
+  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_*.txt`, `doc/src/{fixes,computes,pairs,bonds,...}.txt`
+  `doc/src/Commands_*.rst`, `doc/src/{fixes,computes,pairs,bonds,...}.rst`
-  and `doc/src/lammps.book`
   * 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
@@ -136,7 +139,7 @@ Here are some items to check:
   * Code should follow the C++-98 standard. C++-11 is only accepted
   in individual special purpose packages
   * indentation is 2 spaces per level
-  * there should be NO tabs and no trailing whitespace
+  * 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.

doc/include-file-conventions.md

@@ -49,22 +49,15 @@ include files provided with LAMMPS are included with double quotes
 
 For headers declaring functions of the C-library, the corresponding
 C++ versions should be included (examples: `#include <cstdlib>` or
-`#include <cctypes>`).  However, these includes are limited to those defined
+`#include <cctypes>` instead of `#include <stdlib.h>` or
-in the C++98 standard.  Some files thus must use the older style until
+`#include<ctypes.h>` ).
-the minimum C++ standard requirement of LAMMPS is lifted to C++11 or
-even beyond (examples: `#include <stdint.h>` versus `#include <cstdint>`
-or `#include <inttypes.h>` versus `#include <cinttypes>`).
 
 ### C++ Standard Compliance
 
-LAMMPS core files currently correspond to the C++98 standard. Files
+LAMMPS core files use standard conforming C++ compatible with the
-requiring C++11 or later are only permitted in (optional) packages
+C++11 standard, unless explicitly noted.  Also, LAMMPS uses the C-style
-and particularly packages that are not part of the list of commonly
+stdio library for I/O instead of iostreams.  Since using both at the
-used packages such as MOLECULE, KSPACE, MANYBODY, or RIGID.
+same time can cause problems, iostreams should be avoided where possible.
-
-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
 

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "20 November 2019" "2019-11-20"
+.TH LAMMPS "15 April 2020" "2020-04-15"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.
@@ -11,13 +11,18 @@ or
 
 mpirun \-np 2
 .B lmp
-<input file> [OPTIONS] ...
+\-in <input file> [OPTIONS] ...
 
 or
 
 .B lmp
 \-r2data file.restart file.data
 
+or
+
+.B lmp
+\-h
+
 .SH DESCRIPTION
 .B LAMMPS
 is a classical molecular dynamics code, and an acronym for \fBL\fRarge-scale
@@ -249,7 +254,7 @@ the chapter on errors in the
 manual gives some additional information about error messages, if possible.
 
 .SH COPYRIGHT
-© 2003--2019 Sandia Corporation
+© 2003--2020 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

doc/msi2lmp.1

@@ -31,7 +31,7 @@ of benzene, you have to provide the files 'benzene.car' and 'benzene.mdf'
 in the current working directory.
 .B msi2lmp
 will then read and process those files according to its remaining settings.
-All other settins are optional and have defaults as listed.
+All other settings are optional and have defaults as listed.
 .TP
 \fB\-c <I,1,II,2,O,0>\fR, \fB\-class <I,1,II,2,O,0>\fR
 The \-c or \-class option selects the force field class, i.e which pair

doc/src/.gitignore

@@ -1,2 +1 @@
-Eqs
+/false_positives.txt
-JPG

doc/src/2001/README.html

@@ -10,7 +10,7 @@ LAMMPS</H2>
 LAMMPS = Large-scale Atomic/Molecular Massively Parallel Simulator</P>
 <P>
 This is the documentation for the LAMMPS 2001 version, written in F90,
-which has been superceded by more current versions.  See the <A
+which has been superseded by more current versions.  See the <A
 HREF="http://www.cs.sandia.gov/~sjplimp/lammps.html">LAMMPS WWW
 Site</A> for more information.
 <P>

doc/src/2001/basics.html

@@ -47,7 +47,7 @@ directories: </P>
 <P>
 The src directory contains the F90 and C source files for LAMMPS as 
 well as several sample Makefiles for different machines. To make LAMMPS 
-for a specfic machine, you simply type</P>
+for a specific machine, you simply type</P>
 <P>
 make machine</P>
 <P>

doc/src/2001/input_commands.html

@@ -1079,7 +1079,7 @@ for style aveforce, average force on the group of fixed atoms is computed,
   to new total value -> has effect of applying same force to entire group
   of atoms
 thermostatting constraints (rescale, hoover/drag, langevin) cannot be used in
-  conjuction with global "temp control", since they conflict and will
+  conjunction with global "temp control", since they conflict and will
   cause atom velocities to be reset twice
 thermostatting constraints (rescale, hoover/drag, langevin) cannot be used
   when performing a minimization
@@ -1089,7 +1089,7 @@ meaning of rescale and Langevin thermostatting coefficients is same as in
   "temp control" command
 for rescale style, it can be used as a coarse temperature rescaler,
   for example "rescale 200.0 300.0 100 10.0 1.0" will ramp the temperature
-  up during the simulation, resetting it to the target temperatue as needed
+  up during the simulation, resetting it to the target temperature as needed
 for rescale style, it can be used to create an instantaneous
   drag force that slowly rescales the temperature without oscillation,
   for example "rescale 300.0 300.0 1 0.0 0.0001" will force (or keep) 
@@ -1952,7 +1952,7 @@ for rescale style, the amount of rescaling is contfolled by the fractional
   to halfway between the current and target temperature
 for rescale style, it can be used as a coarse temperature rescaler,
   for example "rescale 200.0 300.0 100 10.0 1.0" will ramp the temperature
-  up during the simulation, resetting it to the target temperatue as needed
+  up during the simulation, resetting it to the target temperature as needed
 for rescale style, it can be used to create an instantaneous
   drag force that slowly rescales the temperature without oscillation,
   for example "rescale 300.0 300.0 1 0.0 0.0001" will force (or keep) 

doc/src/99/README.html

@@ -10,7 +10,7 @@ LAMMPS</H2>
 LAMMPS = Large-scale Atomic/Molecular Massively Parallel Simulator</P>
 <P>
 This is the documentation for the LAMMPS 99 version, written in F77,
-which has been superceded by more current versions.  See the <A
+which has been superseded by more current versions.  See the <A
 HREF="http://www.cs.sandia.gov/~sjplimp/lammps.html">LAMMPS WWW
 Site</A> for more information.
 <P>

doc/src/99/basics.html

@@ -45,7 +45,7 @@ directories: </P>
 <P>
 The src directory contains the F77 and C source files for LAMMPS as 
 well as several sample Makefiles for different machines. To make LAMMPS 
-for a specfic machine, you simply type</P>
+for a specific machine, you simply type</P>
 <P>
 make machine</P>
 <P>

doc/src/99/input_commands.html

@@ -430,7 +430,7 @@ accuracy criterion effectively determines how many k-space vectors are used
 for PPPM, accuracy criterion determines mesh spacing (see "particle mesh"
   command)
 for PPPM, must be running on power-of-2 number of processors for FFTs
-must use periodic boundary conditions in conjuction with Ewald and PPPM
+must use periodic boundary conditions in conjunction with Ewald and PPPM
 cannot use any styles other than none with nonbond style = lj/shift or
   nonbond style = soft
 Coulomb style = smooth should be used with nonbond style = lj/switch,
@@ -772,7 +772,7 @@ for style aveforce, average force on the group of fixed atoms is computed,
   to new total value -> has effect of applying same force to entire group
   of atoms
 thermostatting constraints (rescale, langevin, nose/hoover) cannot be used in
-  conjuction with global "temp control", since they conflict and will
+  conjunction with global "temp control", since they conflict and will
   cause atom velocities to be reset twice
 if multiple Langevin constraints are specified the Marsaglia RNG will
   only use the last RNG seed specified for initialization

doc/src/Build.rst

@@ -1,13 +1,14 @@
 Build LAMMPS
 ************
 
-LAMMPS can be built as an executable or library from source code via
+LAMMPS is built as a library and an executable from source code using
-either traditional makefiles (which may require manual editing)
+either traditional makefiles for use with GNU make (which may require
-for use with GNU make or gmake, or a build environment generated by CMake
+manual editing), or using a build environment generated by CMake (Unix
-(Unix Makefiles, Xcode, Visual Studio, KDevelop or more).  As an
+Makefiles, Ninja, Xcode, Visual Studio, KDevelop, CodeBlocks and more).
-alternative you can download a package with pre-built executables
-as described on the :doc:`Install <Install>` doc page.
 
+As an alternative you can download a package with pre-built executables
+or automated build trees as described on the :doc:`Install <Install>`
+doc page.
 
 .. toctree::
    :maxdepth: 1
@@ -21,8 +22,3 @@ as described on the :doc:`Install <Install>` doc page.
    Build_extras
    Build_windows
    Build_development
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_basics.rst

@@ -6,159 +6,203 @@ CMake and make:
 
 * :ref:`Serial vs parallel build <serial>`
 * :ref:`Choice of compiler and compile/link options <compile>`
-* :ref:`Build LAMMPS as an executable or a library <exe>`
+* :ref:`Build the LAMMPS executable and library <exe>`
+* :ref:`Including and removing debug support <debug>`
 * :ref:`Build the LAMMPS documentation <doc>`
 * :ref:`Install LAMMPS after a build <install>`
 
-
 ----------
 
-
 .. _serial:
 
 Serial vs parallel build
--------------------------------------
+------------------------
 
-LAMMPS can be built to run in parallel using the ubiquitous `MPI (message-passing interface) <https://en.wikipedia.org/wiki/Message_Passing_Interface>`_
+LAMMPS is written to use the ubiquitous `MPI (Message Passing Interface)
-library.  Or it can built to run on a single processor (serial)
+<https://en.wikipedia.org/wiki/Message_Passing_Interface>`_ library API
-without MPI.  It can also be built with support for OpenMP threading
+for distributed memory parallel computation.  You need to have such a
-(see more discussion below).
+library installed for building and running LAMMPS in parallel using a
+domain decomposition parallelization.  It is compatible with the MPI
+standard version 2.x and later.  LAMMPS can also be built into a
+"serial" executable for use with a single processor using the bundled
+MPI STUBS library.
 
-**CMake variables**\ :
+Independent of the distributed memory MPI parallelization, parts of
+LAMMPS are also written with support for shared memory parallelization
+using the `OpenMP <https://en.wikipedia.org/wiki/OpenMP>`_ threading
+standard. A more detailed discussion of that is below.
 
+**CMake build**\ :
 
-.. parsed-literal::
+.. code-block:: bash
 
    -D BUILD_MPI=value        # yes or no, default is yes if CMake finds MPI, else no
-   -D BUILD_OMP=value        # yes or no (default)
+   -D BUILD_OMP=value        # yes or no, default is yes if a compatible compiler is detected
    -D LAMMPS_MACHINE=name    # name = mpi, serial, mybox, titan, laptop, etc
                              # no default value
 
-The executable created by CMake (after running make) is lmp\_name.  If
+The executable created by CMake (after running make) is named ``lmp`` unless
-the LAMMPS\_MACHINE variable is not specified, the executable is just
+the ``LAMMPS_MACHINE`` option is set.  When setting ``LAMMPS_MACHINE=name``
-lmp.  Using BUILD\_MPI=no will produce a serial executable.
+the executable will be called ``lmp_name``.  Using ``BUILD_MPI=no`` will
+enforce building a serial executable using the MPI STUBS library.
 
 **Traditional make**\ :
 
+The build with traditional makefiles has to be done inside the source folder ``src``.
 
-.. parsed-literal::
+.. code-block:: bash
 
-   cd lammps/src
    make mpi                # parallel build, produces lmp_mpi using Makefile.mpi
    make serial             # serial build, produces lmp_serial using Makefile/serial
-   make mybox          # uses Makefile.mybox to produce lmp_mybox
+   make mybox              # uses Makefile.mybox to produce lmp_mybox
 
-Serial build (see src/MAKE/Makefile.serial):
+Any ``make machine`` command will look up the make settings from a file
+``Makefile.machine`` in the folder ``src/MAKE`` or one of its
+sub-directories ``MINE``, ``MACHINES``, or ``OPTIONS``, create a folder
+``Obj_machine`` with all objects and generated files and an executable
+called ``lmp_machine``\ .  The standard parallel build with ``make mpi``
+assumes a standard MPI installation with MPI compiler wrappers where all
+necessary compiler and linker flags to get access and link with the
+suitable MPI headers and libraries are set by the wrapper programs.  For
+other cases or the serial build, you have to adjust the make file
+variables ``MPI_INC``, ``MPI_PATH``, ``MPI_LIB`` as well as ``CC`` and
+``LINK``\ .  To enable OpenMP threading usually a compiler specific flag
+needs to be added to the compile and link commands.  For the GNU
+compilers, this is ``-fopenmp``\ , which can be added to the ``CC`` and
+``LINK`` makefile variables.
 
+For the serial build the following make variables are set (see src/MAKE/Makefile.serial):
 
-.. parsed-literal::
+.. code-block:: make
 
+   CC =            g++
+   LINK =          g++
    MPI_INC =       -I../STUBS
    MPI_PATH =      -L../STUBS
    MPI_LIB =       -lmpi_stubs
 
-For a parallel build, if MPI is installed on your system in the usual
+You also need to build the STUBS library for your platform before making
-place (e.g. under /usr/local), you do not need to specify the 3
+LAMMPS itself.  A ``make serial`` build does this for you automatically,
-variables MPI\_INC, MPI\_PATH, MPI\_LIB.  The MPI wrapper on the compiler
+otherwise, type ``make mpi-stubs`` from the src directory, or ``make``
-(e.g. mpicxx, mpiCC) knows where to find the needed include and
+from the ``src/STUBS`` dir.  If the build fails, you may need to edit
-library files.  Failing this, these 3 variables can be used to specify
+the ``STUBS/Makefile`` for your platform.  The stubs library does not
-where the mpi.h file (MPI\_INC), and the MPI library files (MPI\_PATH)
+provide MPI/IO functions required by some LAMMPS packages,
-are found, and the name of the library files (MPI\_LIB).
+e.g. ``MPIIO`` or ``USER-LB``, and thus is not compatible with those
+packages.
 
-For a serial build, you need to specify the 3 variables, as shown
+.. note::
-above.
 
-For a serial LAMMPS build, use the dummy MPI library provided in
+   The file ``src/STUBS/mpi.c`` provides a CPU timer function called
-src/STUBS.  You also need to build the STUBS library for your platform
+   ``MPI_Wtime()`` that calls ``gettimeofday()``.  If your operating system
-before making LAMMPS itself.  A "make serial" build does this for.
+   does not support ``gettimeofday()``, you will need to insert code to
-Otherwise, type "make mpi-stubs" from the src directory, or "make"
+   call another timer.  Note that the ANSI-standard function ``clock()``
-from the src/STUBS dir.  If the build fails, you will need to edit the
+   rolls over after an hour or so, and is therefore insufficient for
-STUBS/Makefile for your platform.
+   timing long LAMMPS simulations.
 
-The file STUBS/mpi.c provides a CPU timer function called MPI\_Wtime()
+**MPI and OpenMP support info**\ :
-that calls gettimeofday() .  If your system doesn't support
-gettimeofday() , you'll need to insert code to call another timer.
-Note that the ANSI-standard function clock() rolls over after an hour
-or so, and is therefore insufficient for timing long LAMMPS
-simulations.
 
-**CMake and make info**\ :
+If you are installing MPI yourself to build a parallel LAMMPS
+executable, we recommend either MPICH or OpenMPI which are regularly
+used and tested with LAMMPS by the LAMMPS developers.  MPICH can be
+downloaded from the `MPICH home page <https://www.mpich.org>`_ and
+OpenMPI can be downloaded correspondingly from the `OpenMPI home page
+<https://www.open-mpi.org>`_.  Other MPI packages should also work.  No
+specific vendor provided and standard compliant MPI library is currently
+known to be incompatible with LAMMPS.  If you are running on a large
+parallel machine, your system admins or the vendor should have already
+installed a version of MPI, which is likely to be faster than a
+self-installed MPICH or OpenMPI, so you should study the provided
+documentation to find out how to build and link with it.
 
-If you are installing MPI yourself, we recommend MPICH2 from Argonne
+The majority of OpenMP (threading) support in LAMMPS is provided by the
-National Laboratory or OpenMPI.  MPICH can be downloaded from the
+``USER-OMP`` package; see the :doc:`Speed omp <Speed_omp>` doc page for
-`Argonne MPI site <http://www.mcs.anl.gov/research/projects/mpich2/>`_.
+details. The ``USER-INTEL`` package also includes OpenMP threading (it
-OpenMPI can be downloaded from the `OpenMPI site <http://www.open-mpi.org>`_.  Other MPI packages should also work.
+is compatible with ``USER-OMP`` and will usually fall back on styles
-If you are running on a large parallel machine, your system admins or
+from that package, if a ``USER-INTEL`` does not exist) and adds
-the vendor should have already installed a version of MPI, which is
+vectorization support when compiled with compatible compilers, in
-likely to be faster than a self-installed MPICH or OpenMPI, so find
+particular the Intel compilers on top of OpenMP. Also, the ``KOKKOS``
-out how to build and link with it.
+package can be compiled to include OpenMP threading.
 
-The majority of OpenMP (threading) support in LAMMPS is provided by
+In addition, there are a few commands in LAMMPS that have native OpenMP
-the USER-OMP package; see the :doc:`Speed omp <Speed_omp>` doc page for
+support included as well.  These are commands in the ``MPIIO``,
-details. The USER-INTEL package also provides OpenMP support (it is
+``SNAP``, ``USER-DIFFRACTION``, and ``USER-DPD`` packages.  In addition
-compatible with USER-OMP) and adds vectorization support when compiled
+some packages support OpenMP threading indirectly through the libraries
-with the Intel compilers on top of that. Also, the KOKKOS package can
+they interface to: e.g. ``LATTE``, ``KSPACE``, and ``USER-COLVARS``.
-be compiled for using OpenMP threading.
+See the :doc:`Packages details <Packages_details>` doc page for more
+info on these packages and the doc pages for their respective commands
+for OpenMP threading info.
 
-However, there are a few commands in LAMMPS that have native OpenMP
+For CMake, if you use ``BUILD_OMP=yes``, you can use these packages
-support.  These are commands in the MPIIO, SNAP, USER-DIFFRACTION, and
+and turn on their native OpenMP support and turn on their native OpenMP
-USER-DPD packages.  In addition some packages support OpenMP threading
+support at run time, by setting the ``OMP_NUM_THREADS`` environment
-indirectly through the libraries they interface to: e.g. LATTE and
-USER-COLVARS.  See the :doc:`Packages details <Packages_details>` doc
-page for more info on these packages and the doc pages for their
-respective commands for OpenMP threading info.
-
-For CMake, if you use BUILD\_OMP=yes, you can use these packages and
-turn on their native OpenMP support and turn on their native OpenMP
-support at run time, by setting the OMP\_NUM\_THREADS environment
 variable before you launch LAMMPS.
 
-For building via conventional make, the CCFLAGS and LINKFLAGS
+For building via conventional make, the ``CCFLAGS`` and ``LINKFLAGS``
 variables in Makefile.machine need to include the compiler flag that
-enables OpenMP. For GNU compilers it is -fopenmp.  For (recent) Intel
+enables OpenMP. For GNU compilers it is ``-fopenmp``\ .  For (recent) Intel
-compilers it is -qopenmp.  If you are using a different compiler,
+compilers it is ``-qopenmp``\ .  If you are using a different compiler,
 please refer to its documentation.
 
 .. _default-none-issues:
 
-**OpenMP Compiler compatibility info**\ : 
+**OpenMP Compiler compatibility info**\ :
-
-Some compilers do not fully support the 'default(none)' directive
-and others (e.g. GCC version 9 and beyond) may implement OpenMP 4.0
-semantics, which are incompatible with the OpenMP 3.1 directives used
-in LAMMPS (for maximal compatibility with compiler versions in use).
-In those case, all 'default(none)' directives (which aid in detecting
-incorrect and unwanted sharing) can be replaced with 'default(shared)'
-while dropping all 'shared()' directives. The script
-'src/USER-OMP/hack\_openmp\_for\_pgi\_gcc9.sh' can be used to automate
-this conversion.
 
+Some compilers do not fully support the ``default(none)`` directive
+and others (e.g. GCC version 9 and beyond, Clang version 10 and later)
+may implement strict OpenMP 4.0 and later semantics, which are incompatible
+with the OpenMP 3.1 semantics used in LAMMPS for maximal compatibility
+with compiler versions in use.  If compilation with OpenMP enabled fails
+because of your compiler requiring strict OpenMP 4.0 semantic, you can
+change the behavior by adding ``-D LAMMPS_OMP_COMPAT=4`` to the ``LMP_INC``
+variable in your makefile, or add it to the command line while configuring
+with CMake. CMake will detect the suitable setting for the GNU, Clang,
+and Intel compilers.
 
 ----------
 
-
 .. _compile:
 
 Choice of compiler and compile/link options
 ---------------------------------------------------------
 
-The choice of compiler and compiler flags can be important for
+The choice of compiler and compiler flags can be important for maximum
-performance.  Vendor compilers can produce faster code than
+performance.  Vendor provided compilers for a specific hardware can
-open-source compilers like GNU.  On boxes with Intel CPUs, we suggest
+produce faster code than open-source compilers like the GNU compilers.
-trying the `Intel C++ compiler <intel_>`_.
+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
+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
+high degrees of vectorization.  This may change over time as equivalent
+vectorization directives are included into OpenMP standard revisions and
+other compilers adopt them.
 
 .. _intel: https://software.intel.com/en-us/intel-compilers
 
+On parallel clusters or supercomputers which use "environment modules"
+for their compile/link environments, you can often access different
+compilers by simply loading the appropriate module before building
+LAMMPS.
 
+**CMake build**\ :
 
-On parallel clusters or supercomputers which use "modules" for their
+By default CMake will use a compiler it finds according to internal
-compile/link environments, you can often access different compilers by
+preferences and it will add optimization flags appropriate to that
-simply loading the appropriate module before building LAMMPS.
+compiler and any :doc:`accelerator packages <Speed_packages>` you have
+included in the build.
 
-**CMake variables**\ :
+You can tell CMake to look for a specific compiler with setting CMake
+variable during configuration.  For a few common choices, there are also
+presets in the ``cmake/presets`` folder.  For convenience, there is a
+``CMAKE_TUNE_FLAGS`` variable that can be set to apply global compiler
+options.  More on that below, but you can also specify the corresponding
+``CMAKE_*_FLAGS`` variables individually if you want to experiment with
+alternate optimization flags.  You should specify all 3 compilers, so
+that the (few) LAMMPS source files written in C or Fortran are built
+with a compiler consistent with the one used for the C++ files:
 
-
+.. code-block:: bash
-.. parsed-literal::
 
    -D CMAKE_CXX_COMPILER=name            # name of C++ compiler
    -D CMAKE_C_COMPILER=name              # name of C compiler
@@ -168,77 +212,96 @@ simply loading the appropriate module before building LAMMPS.
    -D CMAKE_C_FLAGS=string               # flags to use with C compiler
    -D CMAKE_Fortran_FLAGS=string         # flags to use with Fortran compiler
 
-By default CMake will use a compiler it finds and it will add
+A few example command lines are:
-optimization flags appropriate to that compiler and any :doc:`accelerator packages <Speed_packages>` you have included in the build.
 
-You can tell CMake to look for a specific compiler with these variable
+.. code-block:: bash
-settings.  Likewise you can specify the FLAGS variables if you want to
-experiment with alternate optimization flags.  You should specify all
-3 compilers, so that the small number of LAMMPS source files written
-in C or Fortran are built with a compiler consistent with the one used
-for all the C++ files:
 
-
+   # Building with GNU Compilers:
-.. parsed-literal::
-
-   Building with GNU Compilers:
    cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
-   Building with Intel Compilers:
+   # Building with Intel Compilers:
    cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
-   Building with LLVM/Clang Compilers:
+   # Building with LLVM/Clang Compilers:
    cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
 
+For compiling with the Clang/LLVM compilers a CMake preset is provided that
+can be loaded with `-C ../cmake/presets/clang.cmake`.  Similarly,
+`-C ../cmake/presets/intel.cmake` should switch the 
+
+In addition you can set ``CMAKE_TUNE_FLAGS`` to specifically add
+compiler flags to tune for optimal performance on given hosts. By
+default these are initialized to some compiler specific flags, to
+optimize the LAMMPS executable with optimizations and instructions
+available on the host where LAMMPS is compiled. For example, for Intel
+compilers this would be ``-xHost`` and for GNU compilers this would be
+``-march=native``. To turn these flags off, do ``-D CMAKE_TUNE_FLAGS=``.
+
 .. note::
 
-   When the cmake command completes, it prints info to the screen
+   When the cmake command completes, it prints a summary to the screen
-   as to which compilers it is using, and what flags will be used in the
+   which compilers it is using and what flags and settings will be used
-   compilation.  Note that if the top-level compiler is mpicxx, it is
+   for the  compilation.  Note that if the top-level compiler is mpicxx,
-   simply a wrapper on a real compiler.  The underlying compiler info is
+   it is simply a wrapper on a real compiler.  The underlying compiler
-   what will be listed in the CMake output.  You should check to insure
+   info is what CMake will try to determine and report.  You should check
-   you are using the compiler and optimization flags are the ones you
+   to confirm you are using the compiler and optimization flags you want.
-   want.
 
-**Makefile.machine settings**\ :
+**Makefile.machine settings for traditional make**\ :
 
-Parallel build (see src/MAKE/Makefile.mpi):
+The "compiler/linker settings" section of a Makefile.machine lists
+compiler and linker settings for your C++ compiler, including
+optimization flags.  For a parallel build it is recommended to use
+``mpicxx`` or ``mpiCC``, since these compiler wrappers will include a
+variety of settings appropriate for your MPI installation and thus
+avoiding the guesswork of finding the right flags.
 
+Parallel build (see ``src/MAKE/Makefile.mpi``):
 
-.. parsed-literal::
+.. code-block:: bash
 
    CC =            mpicxx
    CCFLAGS =       -g -O3
    LINK =          mpicxx
    LINKFLAGS =     -g -O
 
-Serial build (see src/MAKE/Makefile.serial):
+Serial build with GNU gcc (see ``src/MAKE/Makefile.serial``):
 
-
+.. code-block:: make
-.. parsed-literal::
 
    CC =            g++
    CCFLAGS =       -g -O3
    LINK =          g++
    LINKFLAGS =     -g -O
 
-The "compiler/linker settings" section of a Makefile.machine lists
-compiler and linker settings for your C++ compiler, including
-optimization flags.  You should always use mpicxx or mpiCC for
-a parallel build, since these compiler wrappers will include
-a variety of settings appropriate for your MPI installation.
 
 .. note::
 
-   If you build LAMMPS with any :doc:`accelerator packages <Speed_packages>` included, they have specific
+   If compilation stops with a message like the following:
-   optimization flags that are either required or recommended for optimal
-   performance.  You need to include these in the CCFLAGS and LINKFLAGS
-   settings above.  For details, see the individual package doc pages
-   listed on the :doc:`Speed packages <Speed_packages>` doc page.  Or
-   examine these files in the src/MAKE/OPTIONS directory.  They
-   correspond to each of the 5 accelerator packages and their hardware
-   variants:
 
+   .. code-block::
 
-.. parsed-literal::
+      g++ -g -O3  -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64    -I../STUBS     -c ../main.cpp
+      In file included from ../pointers.h:24:0,
+                 from ../input.h:17,
+                 from ../main.cpp:16:
+      ../lmptype.h:34:2: error: #error LAMMPS requires a C++11 (or later) compliant compiler. Enable C++11 compatibility or upgrade the compiler.
+
+   then you have either an unsupported (old) compiler or you have to
+   turn on C++11 mode.  The latter applies to GCC 4.8.x shipped with
+   RHEL 7.x and CentOS 7.x.  For those compilers, you need to add the
+   ``-std=c++11`` flag.  Otherwise, you would have to install a newer
+   compiler that supports C++11; either as a binary package or through
+   compiling from source.
+
+If you build LAMMPS with any :doc:`accelerator packages
+<Speed_packages>` included, there may be specific optimization flags
+that are either required or recommended to enable required features and
+to achieve optimal performance.  You need to include these in the
+CCFLAGS and LINKFLAGS settings above.  For details, see the individual
+package doc pages listed on the :doc:`Speed packages <Speed_packages>`
+doc page.  Or examine these files in the src/MAKE/OPTIONS directory.
+They correspond to each of the 5 accelerator packages and their hardware
+variants:
+
+.. code-block:: bash
 
    Makefile.opt                   # OPT package
    Makefile.omp                   # USER-OMP package
@@ -249,129 +312,198 @@ a variety of settings appropriate for your MPI installation.
    Makefile.kokkos_omp            # KOKKOS package for CPUs (OpenMP)
    Makefile.kokkos_phi            # KOKKOS package for KNLs (OpenMP)
 
-
 ----------
 
-
 .. _exe:
 
-Build LAMMPS as an executable or a library
+Build the LAMMPS executable and library
-----------------------------------------------------
+---------------------------------------
 
-LAMMPS can be built as either an executable or as a static or shared
+LAMMPS is always built as a library of C++ classes plus an executable.
-library.  The LAMMPS library can be called from another application or
+The executable is a simple ``main()`` function that sets up MPI and then
-a scripting language.  See the :doc:`Howto couple <Howto_couple>` doc
+creates a LAMMPS class instance from the LAMMPS library, which
+will then process commands provided via a file or from the console
+input.  The LAMMPS library can also be called from another application
+or a scripting language.  See the :doc:`Howto couple <Howto_couple>` doc
 page for more info on coupling LAMMPS to other codes.  See the
 :doc:`Python <Python_head>` doc page for more info on wrapping and
 running LAMMPS from Python via its library interface.
 
-**CMake variables**\ :
+**CMake build**\ :
 
+For CMake builds, you can select through setting CMake variables between
+building a shared or a static LAMMPS library and what kind of suffix is
+added to them (in case you want to concurrently install multiple variants
+of binaries with different settings). If none are set, defaults are applied.
 
-.. parsed-literal::
+.. code-block:: bash
 
-   -D BUILD_EXE=value           # yes (default) or no
-   -D BUILD_LIB=value           # yes or no (default)
    -D BUILD_SHARED_LIBS=value   # yes or no (default)
-   -D LAMMPS_LIB_SUFFIX=name    # name = mpi, serial, mybox, titan, laptop, etc
+   -D LAMMPS_MACHINE=name       # name = mpi, serial, mybox, titan, laptop, etc
                                 # no default value
 
-Setting BUILD\_EXE=no will not produce an executable.  Setting
+The compilation will always produce a LAMMPS library and an executable
-BUILD\_LIB=yes will produce a static library named liblammps.a.
+linked to it.  By default this will be a static library named
-Setting both BUILD\_LIB=yes and BUILD\_SHARED\_LIBS=yes will produce a
+``liblammps.a`` and an executable named ``lmp`` Setting
-shared library named liblammps.so. If LAMMPS\_LIB\_SUFFIX is set the generated
+``BUILD_SHARED_LIBS=yes`` will instead produce a shared library called
-libraries will be named liblammps\_name.a or liblammps\_name.so instead.
+``liblammps.so`` (or ``liblammps.dylib`` or ``liblammps.dll`` depending
+on the platform) If ``LAMMPS_MACHINE=name`` is set in addition, the name
+of the generated libraries will be changed to either
+``liblammps_name.a`` or ``liblammps_name.so``\ , respectively and the
+executable will be called ``lmp_name``.
 
 **Traditional make**\ :
 
+With the traditional makefile based build process, the choice of
+the generated executable or library depends on the "mode" setting.
+Several options are available and ``mode=static`` is the default.
 
-.. parsed-literal::
+.. code-block:: bash
 
-   cd lammps/src
    make machine               # build LAMMPS executable lmp_machine
-   make mode=lib machine      # build LAMMPS static lib liblammps_machine.a
+   make mode=static machine   # same as "make machine"
-   make mode=shlib machine    # build LAMMPS shared lib liblammps_machine.so
+   make mode=shared machine   # build LAMMPS shared lib liblammps_machine.so instead
 
-The two library builds also create generic soft links, named
+The "static" build will generate a static library called
-liblammps.a and liblammps.so, which point to the liblammps\_machine
+``liblammps_machine.a`` and an executable named ``lmp_machine``\ , while
-files.
+the "shared" build will generate a shared library
+``liblammps_machine.so`` instead and ``lmp_machine`` will be linked to
+it.  The build step will also create generic soft links, named
+``liblammps.a`` and ``liblammps.so``\ , which point to the specific
+``liblammps_machine.a/so`` files.
 
 **CMake and make info**\ :
 
-Note that for a shared library to be usable by a calling program, all
+Note that for creating a shared library, all the libraries it depends on
-the auxiliary libraries it depends on must also exist as shared
+must be compiled to be compatible with shared libraries.  This should be
-libraries.  This will be the case for libraries included with LAMMPS,
+the case for libraries included with LAMMPS, such as the dummy MPI
-such as the dummy MPI library in src/STUBS or any package libraries in
+library in ``src/STUBS`` or any package libraries in the ``lib``
-the lib/packages directory, since they are always built as shared
+directory, since they are always built in a shared library compatible
-libraries using the -fPIC switch.  However, if a library like MPI or
+way using the ``-fPIC`` compiler switch.  However, if an auxiliary
-FFTW does not exist as a shared library, the shared library build will
+library (like MPI or FFTW) does not exist as a compatible format, the
-generate an error.  This means you will need to install a shared
+shared library linking step may generate an error.  This means you will
-library version of the auxiliary library.  The build instructions for
+need to install a compatible version of the auxiliary library.  The
-the library should tell you how to do this.
+build instructions for that library should tell you how to do this.
 
-As an example, here is how to build and install the `MPICH library <mpich_>`_, a popular open-source version of MPI, distributed by
+As an example, here is how to build and install the `MPICH library
-Argonne National Lab, as a shared library in the default
+<mpich_>`_, a popular open-source version of MPI, as a shared library
-/usr/local/lib location:
+in the default /usr/local/lib location:
 
-.. _mpich: http://www-unix.mcs.anl.gov/mpi
+.. _mpich: https://www.mpich.org
 
-
+.. code-block:: bash
-
-
-.. parsed-literal::
 
    ./configure --enable-shared
    make
    make install
 
-You may need to use "sudo make install" in place of the last line if
+You may need to use ``sudo make install`` in place of the last line if
-you do not have write privileges for /usr/local/lib.  The end result
+you do not have write privileges for ``/usr/local/lib`` or use the
-should be the file /usr/local/lib/libmpich.so.
+``--prefix`` configuration option to select an installation folder,
+where you do have write access.  The end result should be the file
+``/usr/local/lib/libmpich.so``.  On many Linux installations the folder
+``${HOME}/.local`` is an alternative to using ``/usr/local`` and does
+not require superuser or sudo access.  In that case the configuration
+step becomes:
 
+.. code-block:: bash
+
+  ./configure --enable-shared --prefix=${HOME}/.local
+
+Avoiding to use "sudo" for custom software installation (i.e. from source
+and not through a package manager tool provided by the OS) is generally
+recommended to ensure the integrity of the system software installation.
 
 ----------
 
+.. _debug:
+
+Excluding or removing debug support
+-----------------------------------
+
+By default the compilation settings will include the *-g* flag which
+instructs the compiler to include debug information (e.g. which line of
+source code a particular instruction correspond to).  This can be
+extremely useful in case LAMMPS crashes and can help to provide crucial
+information in :doc:`tracking down the origin of a crash <Errors_debug>`
+and help the LAMMPS developers fix bugs in the source code.  However,
+this increases the storage requirements for object files, libraries, and
+the executable 3-5 fold.
+
+If this is a concern, you can change the compilation settings or remove
+the debug information from the LAMMPS executable:
+
+- **Traditional make**: edit your ``Makefile.<machine>`` to remove the
+  *-g* flag from the ``CCFLAGS`` and ``LINKFLAGS`` definitions
+- **CMake**: use ``-D CMAKE_BUILD_TYPE=Release`` or explicitly reset
+  the applicable compiler flags (best done using the text mode or
+  graphical user interface).
+- **Remove debug info**: If you are only concerned about the executable
+  being too large, you can use the ``strip`` tool (e.g. ``strip
+  lmp_serial``) to remove the debug information from the executable file.
+  Do not strip libraries or object files, as that will render them unusable.
+
+----------
 
 .. _doc:
 
 Build the LAMMPS documentation
 ----------------------------------------
 
-**CMake variable**\ :
+The LAMMPS manual is written in `reStructuredText <rst_>`_ format which
+can be translated to different output format using the `Sphinx <sphinx_>`_
+document generator tool.  Currently the translation to HTML and PDF (via
+LaTeX) are supported.  For that to work a Python 3 interpreter and
+internet access is required.  For the documentation build a python
+based virtual environment is set up in the folder doc/docenv and various
+python packages are installed into that virtual environment via the pip
+tool.  The actual translation is then done via make commands.
 
+.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
+.. _sphinx: https://sphinx-doc.org
 
-.. parsed-literal::
+**Documentation make option**\ :
 
-   -D BUILD_DOC=value       # yes or no (default)
+The following make commands can be issued in the doc folder of the
+LAMMPS source distribution.
 
-This will create the HTML doc pages within the CMake build directory.
+.. code-block:: bash
-The reason to do this is if you want to "install" LAMMPS on a system
-after the CMake build via "make install", and include the doc pages in
-the install.
 
-**Traditional make**\ :
+  make html          # create HTML doc pages in html directory
+  make pdf           # create Developer.pdf and Manual.pdf in this directory
+  make fetch         # fetch HTML and PDF files from LAMMPS web site
+  make clean         # remove all intermediate files
+  make clean-all     # reset the entire doc build environment
+  make anchor_check  # scan for duplicate anchor labels
+  make style_check   # check for complete and consistent style lists
+  make package_check # check for complete and consistent package lists
+  make spelling      # spell-check the manual
 
-
+Thus "make html" will create a "doc/html" directory with the HTML format
-.. parsed-literal::
+manual pages so that you can browse them with a web browser locally on
-
+your system.
-   cd lammps/doc
-   make html       # html doc pages
-   make pdf        # single Manual.pdf file
-
-This will create a lammps/doc/html dir with the HTML doc pages so that
-you can browse them locally on your system.  Type "make" from the
-lammps/doc dir to see other options.
 
 .. note::
 
    You can also download a tarball of the documentation for the
    current LAMMPS version (HTML and PDF files), from the website
-   `download page <http://lammps.sandia.gov/download.html>`_.
+   `download page <https://lammps.sandia.gov/download.html>`_.
 
+**CMake build option**\ :
+
+It is also possible to create the HTML version of the manual within
+the :doc:`CMake build directory <Build_cmake>`.  The reason for this
+option is to include the installation of the HTML manual pages into
+the "install" step when installing LAMMPS after the CMake build via
+``make install``.  The documentation build is included in the default
+build target, but can also be requested independently with ``make doc``.
+
+.. code-block:: bash
+
+   -D BUILD_DOC=value       # yes or no (default)
 
 ----------
 
-
 .. _tools:
 
 Build LAMMPS tools
@@ -380,19 +512,18 @@ Build LAMMPS tools
 Some tools described in :doc:`Auxiliary tools <Tools>` can be built directly
 using CMake or Make.
 
-**CMake variable**\ :
+**CMake build3**\ :
 
-
+.. code-block:: bash
-.. parsed-literal::
 
    -D BUILD_TOOLS=value       # yes or no (default)
 
-The generated binaries will also become part of the LAMMPS installation (see below)
+The generated binaries will also become part of the LAMMPS installation
+(see below).
 
 **Traditional make**\ :
 
-
+.. code-block:: bash
-.. parsed-literal::
 
    cd lammps/tools
    make all              # build all binaries of tools
@@ -401,10 +532,8 @@ The generated binaries will also become part of the LAMMPS installation (see bel
    make micelle2d        # build only micelle2d tool
    make thermo_extract   # build only thermo_extract tool
 
-
 ----------
 
-
 .. _install:
 
 Install LAMMPS after a build
@@ -416,10 +545,9 @@ a globally visible place on your system, for others to access.  Note
 that you may need super-user privileges (e.g. sudo) if the directory
 you want to copy files to is protected.
 
-**CMake variable**\ :
+**CMake build**\ :
 
-
+.. code-block:: bash
-.. parsed-literal::
 
    cmake -D CMAKE_INSTALL_PREFIX=path [options ...] ../cmake
    make                        # perform make after CMake command
@@ -427,11 +555,6 @@ you want to copy files to is protected.
 
 **Traditional make**\ :
 
-There is no "install" option in the src/Makefile for LAMMPS.  If you
+There is no "install" option in the ``src/Makefile`` for LAMMPS.  If
-wish to do this you will need to first build LAMMPS, then manually
+you wish to do this you will need to first build LAMMPS, then manually
 copy the desired LAMMPS files to the appropriate system directories.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_cmake.rst

@@ -1,222 +1,162 @@
 Build LAMMPS with CMake
 =======================
 
-This page is a short summary of how to use CMake to build LAMMPS.
+This page describes how to use `CMake <https://cmake.org>`_ in general
-Details on CMake variables that enable specific LAMMPS build options
+to build LAMMPS.  Details for specific compile time settings and options
-are given on the pages linked to from the :doc:`Build <Build>` doc page.
+to enable and configure add-on packages are discussed with those
+packages.  Links to those pages on the :doc:`Build overview <Build>`
+page.
 
-Richard Berger (Temple U) has also written a `more comprehensive guide <https://github.com/lammps/lammps/blob/master/cmake/README.md>`_
+The following text assumes some familiarity with CMake and focuses on
-for how to use CMake to build LAMMPS.  If you are new to CMake it is a
+using the command line tool ``cmake`` and what settings are supported
-good place to start.
+for building LAMMPS.  A more detailed tutorial on how to use ``cmake``
+itself, the text mode or graphical user interface, change the generated
+output files for different build tools and development environments is
+on a :doc:`separate page <Howto_cmake>`.
+
+.. note::
+
+   LAMMPS currently requires that CMake version 3.10 or later is available;
+   version 3.12 or later is preferred.
+
+.. warning::
+
+   You must not mix the :doc:`traditional make based <Build_make>`
+   LAMMPS build procedure with using CMake.  Thus no packages may be
+   installed or a build been previously attempted in the LAMMPS source
+   directory by using ``make <machine>``.  CMake will detect if this is
+   the case and generate an error.  To remove conflicting files from the
+   ``src`` you can use the command ``make no-all purge`` which will
+   un-install all packages and delete all auto-generated files.
 
 
-----------
+Advantages of using CMake
+^^^^^^^^^^^^^^^^^^^^^^^^^
 
+CMake is an alternative to compiling LAMMPS in the traditional way
+through :doc:`(manually customized) makefiles <Build_make>` and a recent
+addition to LAMMPS thanks to the efforts of Christoph Junghans (LANL)
+and Richard Berger (Temple U).  Using CMake has multiple advantages that
+are specifically helpful for people with limited experience in compiling
+software or for people that want to modify or extend LAMMPS.
+
+- CMake can detect available hardware, tools, features, and libraries
+  and adapt the LAMMPS default build configuration accordingly.
+- CMake can generate files for different build tools and integrated
+  development environments (IDE).
+- CMake supports customization of settings with a text mode or graphical
+  user interface. No knowledge of file formats or and complex command
+  line syntax required.
+- All enabled components are compiled in a single build operation.
+- Automated dependency tracking for all files and configuration options.
+- Support for true out-of-source compilation. Multiple configurations
+  and settings with different choices of LAMMPS packages, settings, or
+  compilers can be configured and built concurrently from the same
+  source tree.
+- Simplified packaging of LAMMPS for Linux distributions, environment
+  modules, or automated build tools like `Homebrew <https://brew.sh/>`_.
+- Integration of automated regression testing (the LAMMPS side for that
+  is still under development).
+
+.. _cmake_build:
+
+Getting started
+^^^^^^^^^^^^^^^
 
 Building LAMMPS with CMake is a two-step process.  First you use CMake
-to create a build environment in a new directory.  On Linux systems,
+to generate a build environment in a new directory.  For that purpose
-this will be based on makefiles for use with make.  Then you use the
+you can use either the command-line utility ``cmake`` (or ``cmake3``),
-make command to build LAMMPS, which uses the created
+the text-mode UI utility ``ccmake`` (or ``ccmake3``) or the graphical
-Makefile(s). Example:
+utility ``cmake-gui``, or use them interchangeably.  The second step is
+then the compilation and linking of all objects, libraries, and
+executables. Here is a minimal example using the command line version of
+CMake to build LAMMPS with no add-on packages enabled and no
+customization:
 
+.. code-block:: bash
 
-.. parsed-literal::
+   cd lammps                # change to the LAMMPS distribution directory
+   mkdir build; cd build    # create and use a build directory
+   cmake ../cmake           # configuration reading CMake scripts from ../cmake
+   cmake --build .          # compilation (or type "make")
 
-   cd lammps                        # change to the LAMMPS distribution directory
+This will create and change into a folder called ``build``, then run the
-   mkdir build; cd build            # create a new directory (folder) for build
+configuration step to generate build files for the default build command
-   cmake [options ...] ../cmake     # configuration with (command-line) cmake
+and then launch that build command to compile LAMMPS.  During the
-   make                             # compilation
+configuration step CMake will try to detect whether support for MPI,
+OpenMP, FFTW, gzip, JPEG, PNG, and ffmpeg are available and enable the
+corresponding configuration settings.  The progress of this
+configuration can be followed on the screen and a summary of selected
+options and settings will be printed at the end.  The ``cmake --build
+.`` command will launch the compilation, which, if successful, will
+ultimately produce a library ``liblammps.a`` and the LAMMPS executable
+``lmp`` inside the ``build`` folder.
 
-The cmake command will detect available features, enable selected
+Compilation can take a long time, since LAMMPS is a large project with
-packages and options, and will generate the build environment.  By default
+many features. If your machine has multiple CPU cores (most do these
-this build environment will be created for "Unix Makefiles" on most
+days), you can speed this up by compiling sources in parallel with
-platforms and particularly on Linux.  However, alternate build tools
+``make -j N`` (with N being the maximum number of concurrently executed
-(e.g. Ninja) and support files for Integrated Development Environments
+tasks).  Also installation of the `ccache <https://ccache.dev/>`_ (=
-(IDE) like Eclipse, CodeBlocks, or Kate can be generated, too. This is
+Compiler Cache) software may speed up repeated compilation even more,
-selected via the "-G" command line flag. For the rest of the documentation
+e.g. during code development.
-we will assume that the build environment is generated for makefiles
-and thus the make command will be used to compile and link LAMMPS as
-indicated above, producing (by default) an executable called "lmp" and
-a library called "liblammps.a" in the "build" folder.  When generating
-a build environment for the "Ninja" build tool, the build command would
-be "ninja" instead of "make".
 
-If your machine has multiple CPU cores (most do these days), using a
+After the initial build, whenever you edit LAMMPS source files, enable
-command like "make -jN" (with N being the number of available local
+or disable packages, change compiler flags or build options, you must
-CPU cores) can be much faster.  If you plan to do development on
+re-compile and relink the LAMMPS executable with ``cmake --build .`` (or
-LAMMPS or need to re-compile LAMMPS repeatedly, installation of the
+``make``).  If the compilation fails for some reason, try running
-ccache (= Compiler Cache) software may speed up repeated compilation
+``cmake .`` and then compile again. The included dependency tracking
-even more.
+should make certain that only the necessary subset of files are
+re-compiled.  You can also delete compiled objects, libraries and
+executables with ``cmake --build . clean`` (or ``make clean``).
 
 After compilation, you may optionally install the LAMMPS executable into
 your system with:
 
+.. code-block:: bash
 
-.. parsed-literal::
+   make install    # optional, copy compiled files into installation location
 
-   make install    # optional, copy LAMMPS executable & library elsewhere
+This will install the LAMMPS executable and library, some tools (if
+configured) and additional files like LAMMPS API headers, manpages,
+potential and force field files.  The location of the installation tree
+defaults to ``${HOME}/.local``.
 
-This will install the lammps executable and library (if requested), some
+.. _cmake_options:
-tools (if configured) and additional files like library API headers,
+
-manpages, potential and force field files. The location of the installation
+Configuration and build options
-tree is set by the CMake variable "CMAKE\_INSTALL\_PREFIX" which defaults
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-to ${HOME}/.local
+
+The CMake commands have one mandatory argument: a folder containing a
+file called ``CMakeLists.txt`` (for LAMMPS it is located in the
+``cmake`` folder) or a build folder containing a file called
+``CMakeCache.txt``, which is generated at the end of the CMake
+configuration step.  The cache file contains all current CMake settings.
+
+To modify settings, enable or disable features, you need to set *variables*
+with either the *-D* command line flag (``-D VARIABLE1_NAME=value``) or
+change them in the text mode of graphical user interface.  The *-D* flag
+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
+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.
+
+Generating files for alternate build tools (e.g. Ninja) and project files
+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``.
 
 
-----------
+Installing CMake
-
+^^^^^^^^^^^^^^^^
-
-There are 3 variants of CMake: a command-line version (cmake), a text mode
-UI version (ccmake), and a graphical GUI version (cmake-GUI).  You can use
-any of them interchangeably to configure and create the LAMMPS build
-environment.  On Linux all the versions produce a Makefile as their
-output.  See more details on each below.
-
-You can specify a variety of options with any of the 3 versions, which
-affect how the build is performed and what is included in the LAMMPS
-executable.  Links to pages explaining all the options are listed on
-the :doc:`Build <Build>` doc page.
-
-You must perform the CMake build system generation and compilation in
-a new directory you create.  It can be anywhere on your local machine.
-In these Build pages we assume that you are building in a directory
-called "lammps/build".  You can perform separate builds independently
-with different options, so long as you perform each of them in a
-separate directory you create.  All the auxiliary files created by one
-build process (executable, object files, log files, etc) are stored in
-this directory or sub-directories within it that CMake creates.
-
-.. note::
-
-   To perform a CMake build, no packages can be installed or a
-   build been previously attempted in the LAMMPS src directory by using
-   "make" commands to :doc:`perform a conventional LAMMPS build <Build_make>`.  CMake detects if this is the case and
-   generates an error, telling you to type "make no-all purge" in the src
-   directory to un-install all packages.  The purge removes all the \*.h
-   files auto-generated by make.
-
-You must have CMake version 2.8 or later on your system to build
-LAMMPS.  A handful of LAMMPS packages (KOKKOS, LATTE, MSCG) require a
-later version.  CMake will print a message telling you if a later
-version is required.  Installation instructions for CMake are below.
-
-After the initial build, if you edit LAMMPS source files, or add your
-own new files to the source directory, you can just re-type make from
-your build directory and it will re-compile only the files that have
-changed.  If you want to change CMake options you can run cmake (or
-ccmake or cmake-gui) again from the same build directory and alter
-various options; see details below.  Or you can remove the entire build
-folder, recreate the directory and start over.
-
-
-----------
-
-
-**Command-line version of CMake**\ :
-
-
-.. parsed-literal::
-
-   cmake [options ...] /path/to/lammps/cmake  # build from any dir
-   cmake [options ...] ../cmake               # build from lammps/build
-
-The cmake command takes one required argument, which is the LAMMPS
-cmake directory which contains the CMakeLists.txt file.
-
-The argument can be preceeded or followed by various CMake
-command-line options.  Several useful ones are:
-
-
-.. parsed-literal::
-
-   -D CMAKE_INSTALL_PREFIX=path  # where to install LAMMPS executable/lib if desired
-   -D CMAKE_BUILD_TYPE=type      # type = RelWithDebInfo (default), Release, MinSizeRel, or Debug
-   -G output                     # style of output CMake generates
-   -DVARIABLE=value              # setting for a LAMMPS feature to enable
-   -D VARIABLE=value             # ditto, but cannot come after CMakeLists.txt dir
-   -C path/to/preset/file        # load some CMake settings before configuring
-
-All the LAMMPS-specific -D variables that a LAMMPS build supports are
-described on the pages linked to from the :doc:`Build <Build>` doc page.
-All of these variable names are upper-case and their values are
-lower-case, e.g. -D LAMMPS\_SIZES=smallbig.  For boolean values, any of
-these forms can be used: yes/no, on/off, 1/0.
-
-On Unix/Linux machines, CMake generates a Makefile by default to
-perform the LAMMPS build.  Alternate forms of build info can be
-generated via the -G switch, e.g. Visual Studio on a Windows machine,
-Xcode on MacOS, or KDevelop on Linux.  Type "cmake --help" to see the
-"Generator" styles of output your system supports.
-
-.. note::
-
-   When CMake runs, it prints configuration info to the screen.
-   You should review this to verify all the features you requested were
-   enabled, including packages.  You can also see what compilers and
-   compile options will be used for the build.  Any errors in CMake
-   variable syntax will also be flagged, e.g. mis-typed variable names or
-   variable values.
-
-CMake creates a CMakeCache.txt file when it runs.  This stores all the
-settings, so that when running CMake again you can use the current
-folder '.' instead of the path to the LAMMPS cmake folder as the
-required argument to the CMake command. Either way the existing
-settings will be inherited unless the CMakeCache.txt file is removed.
-
-If you later want to change a setting you can rerun cmake in the build
-directory with different setting. Please note that some automatically
-detected variables will not change their value when you rerun cmake.
-In these cases it is usually better to first remove all the
-files/directories in the build directory, or start with a fresh build
-directory.
-
-
-----------
-
-
-**Curses version (terminal-style menu) of CMake**\ :
-
-
-.. parsed-literal::
-
-   ccmake ../cmake
-
-You initiate the configuration and build environment generation steps
-separately. For the first you have to type **c**\ , for the second you
-have to type **g**\ . You may need to type **c** multiple times, and may be
-required to edit some of the entries of CMake configuration variables
-in between.  Please see the `ccmake manual <https://cmake.org/cmake/help/latest/manual/ccmake.1.html>`_ for
-more information.
-
-
-----------
-
-
-**GUI version of CMake**\ :
-
-
-.. parsed-literal::
-
-   cmake-gui ../cmake
-
-You initiate the configuration and build environment generation steps
-separately. For the first you have to click on the **Configure** button,
-for the second you have to click on the **Generate** button.  You may
-need to click on **Configure** multiple times, and may be required to
-edit some of the entries of CMake configuration variables in between.
-Please see the `cmake-gui manual <https://cmake.org/cmake/help/latest/manual/cmake-gui.1.html>`_
-for more information.
-
-
-----------
-
-
-**Installing CMake**
 
 Check if your machine already has CMake installed:
 
-
+.. code-block:: bash
-.. parsed-literal::
 
    which cmake             # do you have it?
    which cmake3            # version 3 may have this name
@@ -225,21 +165,16 @@ Check if your machine already has CMake installed:
 On clusters or supercomputers which use environment modules to manage
 software packages, do this:
 
+.. code-block:: bash
 
-.. parsed-literal::
+   module list            # is a module for cmake already loaded?
+   module avail           # is a module for cmake available?
+   module load cmake      # load cmake module with appropriate name
 
-   module list            # is a cmake module already loaded?
+Most Linux distributions offer pre-compiled cmake packages through their
-   module avail           # is a cmake module available?
+package management system. If you do not have CMake or a recent enough
-   module load cmake3     # load cmake module with appropriate name
+version (Note: for CentOS 7.x you need to enable the EPEL repository),
-
+you can download the latest version from `https://cmake.org/download/
-Most Linux distributions offer pre-compiled cmake packages through
+<https://cmake.org/download/>`_.  Instructions on how to install it on
-their package management system. If you do not have CMake or a new
+various platforms can be found `on this page
-enough version, you can download the latest version at
+<https://cmake.org/install/>`_.
-`https://cmake.org/download/ <https://cmake.org/download/>`_.
-Instructions on how to install it on various platforms can be found
-`on this page <https://cmake.org/install/>`_.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_development.rst

@@ -1,63 +1,60 @@
 Development build options (CMake only)
 ======================================
 
-The CMake build of LAMMPS has a few extra options which are useful during
+The CMake build procedure of LAMMPS offers a few extra options which are
-development,  testing or debugging.
+useful during development, testing or debugging.
-
 
 ----------
 
-
 .. _compilation:
 
 Verify compilation flags
-------------------------------------------
+------------------------
 
 Sometimes it is necessary to verify the complete sequence of compilation flags
 generated by the CMake build. To enable a more verbose output during
 compilation you can use the following option.
 
-
+.. code-block:: bash
-.. parsed-literal::
 
    -D CMAKE_VERBOSE_MAKEFILE=value    # value = no (default) or yes
 
 Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1:
 
-
+.. code-block:: bash
-.. parsed-literal::
 
    make VERBOSE=1
 
-
 ----------
 
-
 .. _sanitizer:
 
 Address, Undefined Behavior, and Thread Sanitizer Support
--------------------------------------------------------------------------
+---------------------------------------------------------
 
-Compilers such as GCC and Clang support generating binaries which use different
+Compilers such as GCC and Clang support generating instrumented binaries
-sanitizers to detect problems in code during run-time. They can detect `memory leaks <https://clang.llvm.org/docs/AddressSanitizer.html>`_,
+which use different sanitizer libraries to detect problems in code
-code that runs into `undefined behavior <https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html>`_ of the
+during run-time. They can detect issues like:
-language and `data races <https://clang.llvm.org/docs/ThreadSanitizer.html>`_ in threaded code.
 
-The following settings allow you enable these features if your compiler supports
+ - `memory leaks <https://clang.llvm.org/docs/AddressSanitizer.html>`_
-it. Please note that they come with a performance hit. However, they are
+ - `undefined behavior <https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html>`_
-usually faster than using tools like Valgrind.
+ - `data races <https://clang.llvm.org/docs/ThreadSanitizer.html>`_
 
+Please note that this kind of instrumentation usually comes with a small
+performance hit (much less than using tools like `Valgrind
+<https://valgrind.org>`_).  The to enable these features additional
+compiler flags need to be added to the compilation and linking stages.
+This is most easily done through setting the ``CMAKE_TUNE_FLAGS``
+variable during configuration. Examples:
 
-.. parsed-literal::
+.. code-block:: bash
-
-   -D ENABLE_SANITIZE_ADDRESS=value    # enable Address Sanitizer, value = no (default) or yes
-   -D ENABLE_SANITIZE_UNDEFINED=value  # enable Undefined Behaviour Sanitizer, value = no (default) or yes
-   -D ENABLE_SANITIZE_THREAD=value     # enable Thread Sanitizer, value = no (default) or yes
 
+   -D CMAKE_TUNE_FLAGS=-fsanitize=address    # enable address sanitizer / memory leak checker
+   -D CMAKE_TUNE_FLAGS=-fsanitize=undefined  # enable undefined behavior sanitizer
+   -D CMAKE_TUNE_FLAGS=-fsanitize=thread     # enable thread sanitizer
 
 ----------
 
-
 .. _testing:
 
 Code Coverage and Testing
@@ -71,50 +68,42 @@ developers can run the tests directly on their workstation.
 
    this is incomplete and only represents a small subset of tests that we run
 
-
+.. code-block:: bash
-.. parsed-literal::
 
    -D ENABLE_TESTING=value               # enable simple run tests of LAMMPS, value = no (default) or yes
    -D LAMMPS_TESTING_SOURCE_DIR=path     # path to lammps-testing repository (option if in custom location)
    -D LAMMPS_TESTING_GIT_TAG=value       # version of lammps-testing repository that should be used, value = master (default) or custom git commit or tag
 
-If you enable testing in the CMake build it will create an additional target called "test". You can run them with:
+If you enable testing in the CMake build it will create an additional
+target called "test". You can run them with:
 
+.. code-block:: bash
 
-.. parsed-literal::
+   cmake --build . test
-
-   make test
 
 The test cases used come from the lammps-testing repository. They are
-derivatives of the examples folder with some modifications to make the run
+derivatives of the examples folder with some modifications to make the
-faster.
+run faster.
 
-You can also collect code coverage metrics while running the tests by enabling
+You can also collect code coverage metrics while running the tests by
-coverage support during building.
+enabling coverage support during building.
 
-
+.. code-block:: bash
-.. parsed-literal::
 
    -D ENABLE_COVERAGE=value  # enable coverage measurements, value = no (default) or yes
 
-This will also add the following targets to generate coverage reports after running the LAMMPS executable:
+This will also add the following targets to generate coverage reports
+after running the LAMMPS executable:
 
-
+.. code-block:: bash
-.. parsed-literal::
 
    make test               # run tests first!
    make gen_coverage_html  # generate coverage report in HTML format
    make gen_coverage_xml   # generate coverage report in XML format
 
-These reports require GCOVR to be installed. The easiest way to do this to install it via pip:
+These reports require GCOVR to be installed. The easiest way to do this
+to install it via pip:
 
-
+.. code-block:: bash
-.. parsed-literal::
 
    pip install git+https://github.com/gcovr/gcovr.git
-
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_link.rst

@@ -1,91 +1,259 @@
 Link LAMMPS as a library to another code
 ========================================
 
-LAMMPS can be used as a library by another application, including
+LAMMPS is designed as a library of C++ objects and can thus be
-Python scripts.  The files src/library.cpp and library.h define the
+integrated into other applications including Python scripts.
-C-style API for using LAMMPS as a library.  See the :doc:`Howto library <Howto_library>` doc page for a description of the
+The files ``src/library.cpp`` and ``src/library.h`` define a
-interface and how to extend it for your needs.
+C-style API for using LAMMPS as a library.  See the :doc:`Howto
+library <Howto_library>` doc page for a description of the interface
+and how to extend it for your needs.
 
 The :doc:`Build basics <Build_basics>` doc page explains how to build
-LAMMPS as either a shared or static library.  This results in one of
+LAMMPS as either a shared or static library.  This results in a file
-these 2 files:
+in the compilation folder called ``liblammps.a`` or ``liblammps_<name>.a``
+in case of building a static library.  In case of a shared library
+the name is the same only that the suffix is going to be either ``.so``
+or ``.dylib`` or ``.dll`` instead of ``.a`` depending on the OS.
+In some cases the ``.so`` file may be a symbolic link to a file with
+the suffix ``.so.0`` (or some other number).
 
-liblammps.so      # shared library
+.. note::
-liblammps.a       # static library
 
+   Care should be taken to use the same MPI library for the calling code
+   and the LAMMPS library.  The ``library.h`` file includes ``mpi.h``
+   and uses definitions from it so those need to be available and
+   consistent.  When LAMMPS is compiled with the included STUBS MPI
+   library, then its ``mpi.h`` file needs to be included.  While it is
+   technically possible to use a full MPI library in the calling code
+   and link to a serial LAMMPS library compiled with MPI STUBS, it is
+   recommended to use the *same* MPI library for both, and then use
+   ``MPI_Comm_split()`` in the calling code to pass a suitable
+   communicator with a subset of MPI ranks to the function creating the
+   LAMMPS instance.
 
 ----------
 
-
 **Link with LAMMPS as a static library**\ :
 
-The calling application can link to LAMMPS as a static library with a
+The calling application can link to LAMMPS as a static library with
-link command like this:
+compilation and link commands as in the examples shown below.  These
+are examples for a code written in C in the file *caller.c*.
+The benefit of linking to a static library is, that the resulting
+executable is independent of that library since all required
+executable code from the library is copied into the calling executable.
 
-g++ caller.o -L/home/sjplimp/lammps/src -llammps -o caller
+*CMake build*\ :
 
-The -L argument is the path to where the liblammps.a file is.  The
+This assumes that LAMMPS has been configured without setting a
--llammps argument is shorthand for the file liblammps.a.
+``LAMMPS_MACHINE`` name, installed with "make install", and the
+``PKG_CONFIG_PATH`` environment variable has been updated to include the
+``liblammps.pc`` file installed into the configured destination folder.
+The commands to compile and link a coupled executable are then:
 
+.. code-block:: bash
+
+   mpicc -c -O $(pkgconf liblammps --cflags) caller.c
+   mpicxx -o caller caller.o -$(pkgconf liblammps --libs)
+
+*Traditional make*\ :
+
+This assumes that LAMMPS has been compiled in the folder
+``${HOME}/lammps/src`` with "make mpi". The commands to compile and link
+a coupled executable are then:
+
+.. code-block:: bash
+
+   mpicc -c -O -I${HOME}/lammps/src caller.c
+   mpicxx -o caller caller.o -L${HOME}/lammps/src -llammps_mpi
+
+The *-I* argument is the path to the location of the ``library.h``
+header file containing the interface to the LAMMPS C-style library
+interface.  The *-L* argument is the path to where the ``liblammps_mpi.a``
+file is located.  The *-llammps_mpi* argument is shorthand for telling the
+compiler to link the file ``liblammps_mpi.a``.  If LAMMPS has been
+built as a shared library, then the linker will use ``liblammps_mpi.so``
+instead.  If both files are available, the linker will usually prefer
+the shared library.  In case of a shared library, you may need to update
+the ``LD_LIBRARY_PATH`` environment variable or running the ``caller``
+executable will fail since it cannot find the shared library at runtime.
+
+However, it is only as simple as shown above for the case of a plain
+LAMMPS library without any optional packages that depend on libraries
+(bundled or external) or when using a shared library.  Otherwise, you
+need to include all flags, libraries, and paths for the coupled
+executable, that are also required to link the LAMMPS executable.
+
+*CMake build*\ :
+
+When using CMake, additional libraries with sources in the lib folder
+are built, but not included in ``liblammps.a`` and (currently) not
+installed with "make install" and not included in the *pkgconfig*
+configuration file.  They can be found in the top level build folder,
+but you have to determine the necessary link flags manually.  It is
+therefore recommended to either use the traditional make procedure to
+build and link with a static library or build and link with a shared
+library instead.
+
+.. TODO: this needs to be updated to reflect that latest CMake changes after they are complete.
+
+*Traditional make*\ :
+
+After you have compiled a static LAMMPS library using the conventional
+build system for example with "make mode=static serial". And you also
+have installed the ``POEMS`` package after building its bundled library
+in ``lib/poems``. Then the commands to build and link the coupled executable
+change to:
+
+.. code-block:: bash
+
+   gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
+   g++ -o caller caller.o -L${HOME}/lammps/lib/poems \
+     -L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src -llammps_serial -lpoems -lmpi_stubs
+
+Note, that you need to link with "g++" instead of "gcc", since the
+LAMMPS library is C++ code.  You can display the currently applied
+settings for building LAMMPS for the "serial" machine target by using
+the command:
+
+.. code-block:: bash
+
+   make mode=print serial
+
+Which should output something like:
+
+.. code-block:: bash
+
+   # Compiler: 
+   CXX=g++
+   # Linker: 
+   LD=g++
+   # Compilation: 
+   CXXFLAGS=-g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -I${HOME}/compile/lammps/lib/poems -I${HOME}/compile/lammps/src/STUBS
+   # Linking: 
+   LDFLAGS=-g -O
+   # Libraries: 
+   LDLIBS=-L${HOME}/compile/lammps/src -llammps_serial -L${HOME}/compile/lammps/lib/poems -L${HOME}/compile/lammps/src/STUBS -lpoems -lmpi_stubs
+
+From this you can gather the necessary paths and flags.  With
+makefiles for other *machine* configurations you need to do the
+equivalent and replace "serial" with the corresponding *machine* name
+of the makefile.
 
 ----------
 
-
 **Link with LAMMPS as a shared library**\ :
 
-If you wish to link to liblammps.so, the operating system finds shared
+When linking to LAMMPS built as a shared library, the situation becomes
-libraries to load at run-time using the environment variable
+much simpler, as all dependent libraries and objects are either included
-LD\_LIBRARY\_PATH.  To enable this you can do one of two things:
+in the shared library or registered as a dependent library in the shared
+library file.  Thus those libraries need not to be specified when
+linking the calling executable.  Only the *-I* flags are needed.  So the
+example case from above of the serial version static LAMMPS library with
+the POEMS package installed becomes:
 
-(1) Copy the liblammps.so file to a location the system can find it,
+*CMake build*\ :
-such as /usr/local/lib.  I.e. a directory already listed in your
-LD\_LIBRARY\_PATH variable.  You can type
 
+The commands with a shared LAMMPS library compiled with the CMake
+build process are the same as for the static library.
 
-.. parsed-literal::
+.. code-block:: bash
+
+   mpicc -c -O $(pkgconf liblammps --cflags) caller.c
+   mpicxx -o caller caller.o -$(pkgconf --libs)
+
+*Traditional make*\ :
+
+The commands with a shared LAMMPS library compiled with the
+traditional make build using "make mode=shared serial" becomes:
+
+.. code-block:: bash
+
+   gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
+   g++ -o caller caller.o -L${HOME}/lammps/src -llammps_serial
+
+*Locating liblammps.so at runtime*\ :
+
+However, now the ``liblammps.so`` file is required at runtime and needs
+to be in a folder, where the shared linker program of the operating
+system can find it.  This would be either a folder like ``/usr/local/lib64``
+or ``${HOME}/.local/lib64`` or a folder pointed to by the ``LD_LIBRARY_PATH``
+environment variable. You can type
+
+.. code-block:: bash
 
    printenv LD_LIBRARY_PATH
 
 to see what directories are in that list.
 
-(2) Add the LAMMPS src directory (or the directory you perform CMake
+Or you can add the LAMMPS src directory (or the directory you performed
-build in) to your LD\_LIBRARY\_PATH, so that the current version of the
+a CMake style build in) to your ``LD_LIBRARY_PATH``, so that the current
-shared library is always available to programs that use it.
+version of the shared library is always available to programs that use it.
 
-For the csh or tcsh shells, you would add something like this to your
+For the Bourne or Korn shells (/bin/sh, /bin/ksh, /bin/bash etc.), you
-~/.cshrc file:
+would add something like this to your ``${HOME}/.profile`` file:
 
+.. code-block:: bash
 
-.. parsed-literal::
+   LD_LIBRARY_PATH ${LD_LIBRARY_PATH-/usr/lib64}:${HOME}/lammps/src
+   export LD_LIBRARY_PATH
 
-   setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
+For the csh or tcsh shells, you would equivalently add something like this
+to your ``${HOME}/.cshrc`` file:
 
+.. code-block:: csh
+
+   setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${HOME}/lammps/src
+
+You can verify whether all required shared libraries are found with the
+``ldd`` tool.  Example:
+
+.. code-block:: bash
+
+   $ LD_LIBRARY_PATH=/home/user/lammps/src ldd caller
+        linux-vdso.so.1 (0x00007ffe729e0000)
+        liblammps.so => /home/user/lammps/src/liblammps.so (0x00007fc91bb9e000)
+        libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fc91b984000)
+        libm.so.6 => /lib64/libm.so.6 (0x00007fc91b83e000)
+        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fc91b824000)
+        libc.so.6 => /lib64/libc.so.6 (0x00007fc91b65b000)
+        /lib64/ld-linux-x86-64.so.2 (0x00007fc91c094000)
+
+If a required library is missing, you would get a 'not found' entry:
+
+.. code-block:: bash
+
+   $  ldd caller
+        linux-vdso.so.1 (0x00007ffd672fe000)
+        liblammps.so => not found
+        libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fb7c7e86000)
+        libm.so.6 => /usr/lib64/libm.so.6 (0x00007fb7c7d40000)
+        libgcc_s.so.1 => /usr/lib64/libgcc_s.so.1 (0x00007fb7c7d26000)
+        libc.so.6 => /usr/lib64/libc.so.6 (0x00007fb7c7b5d000)
+        /lib64/ld-linux-x86-64.so.2 (0x00007fb7c80a2000)
 
 ----------
 
-
 **Calling the LAMMPS library**\ :
 
 Either flavor of library (static or shared) allows one or more LAMMPS
-objects to be instantiated from the calling program.
+objects to be instantiated from the calling program. When used from a
+C++ program, most of the symbols and functions in LAMMPS are wrapped
+in a ``LAMMPS_NS`` namespace; you can safely use any of its classes and
+methods from within the calling code, as needed, and you will not incur
+conflicts with functions and variables in your code that share the name.
+This, however, does not extend to all additional libraries bundled with
+LAMMPS in the lib folder and some of the low-level code of some packages.
 
-When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS\_NS
+To be compatible with C, Fortran, Python programs, the library has a simple
-namespace; you can safely use any of its classes and methods from
+C-style interface, provided in ``src/library.cpp`` and ``src/library.h``.
-within the calling code, as needed.
-
-When used from a C or Fortran program, the library has a simple
-C-style interface, provided in src/library.cpp and src/library.h.
 
 See the :doc:`Python library <Python_library>` doc page for a
 description of the Python interface to LAMMPS, which wraps the C-style
-interface.
+interface from a shared library through the `ctypes python module <ctypes_>`_.
 
-See the sample codes in examples/COUPLE/simple for examples of C++ and
+See the sample codes in ``examples/COUPLE/simple`` for examples of C++ and
 C and Fortran codes that invoke LAMMPS through its library interface.
 Other examples in the COUPLE directory use coupling ideas discussed on
 the :doc:`Howto couple <Howto_couple>` doc page.
 
-
+.. _ctypes: https://docs.python.org/3/library/ctypes.html
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_make.rst

@@ -2,71 +2,109 @@ Build LAMMPS with make
 ======================
 
 Building LAMMPS with traditional makefiles requires that you have a
-Makefile."machine" file appropriate for your system in the src/MAKE,
+``Makefile.<machine>`` file appropriate for your system in either the
-src/MAKE/MACHINES, src/MAKE/OPTIONS, or src/MAKE/MINE directory (see
+``src/MAKE``, ``src/MAKE/MACHINES``, ``src/MAKE/OPTIONS``, or
-below).  It can include various options for customizing your LAMMPS
+``src/MAKE/MINE`` directory (see below).  It can include various options
-build with a number of global compilation options and features.
+for customizing your LAMMPS build with a number of global compilation
+options and features.
 
-To include LAMMPS packages (i.e. optional commands and styles) you
+Requirements
-must install them first, as discussed on the :doc:`Build package <Build_package>` doc page.  If the packages require
+^^^^^^^^^^^^
-provided or external libraries, you must build those libraries before
-building LAMMPS.  Building :doc:`LAMMPS with CMake <Build_cmake>` can
-automate all of this for many types of machines, especially
-workstations, desktops and laptops, so we suggest you try it first.
 
-These commands perform a default LAMMPS build, producing the LAMMPS
+Those makefiles are written for and tested with GNU make and may not
-executable lmp\_serial or lmp\_mpi in lammps/src:
+be compatible with other make programs.  In most cases, if the "make"
+program is not GNU make, then there will be a GNU make program
+available under the name "gmake".  If GNU make or a compatible make is
+not available, you may have to first install it or switch to building
+with :doc:`CMake <Build_cmake>`.  The makefiles of the traditional
+make based build process and the scripts they are calling expect a few
+additional tools to be available and functioning.
 
+  * a working C/C++ compiler toolchain supporting the C++11 standard; on
+    Linux these are often the GNU compilers. Some older compilers
+    require adding flags like ``-std=c++11`` to enable the C++11 mode.
+  * a Bourne shell compatible "Unix" shell program (often this is ``bash``)
+  * a few shell utilities: ``ls``, ``mv``, ``ln``, ``rm``, ``grep``, ``sed``, ``tr``, ``cat``, ``touch``, ``diff``, ``dirname``
+  * python (optional, required for ``make lib-<pkg>`` in the src folder).
+    python scripts are currently tested with python 2.7 and 3.6. The procedure
+    for :doc:`building the documentation <Manual_build>` requires python 3.
 
-.. parsed-literal::
+Getting started
+^^^^^^^^^^^^^^^
 
-   cd lammps/src
+To include LAMMPS packages (i.e. optional commands and styles) you must
-   make serial     # build a serial LAMMPS executable
+enable (or "install") them first, as discussed on the :doc:`Build
+package <Build_package>` doc page.  If a packages requires (provided or
+external) libraries, you must configure and build those libraries
+**before** building LAMMPS itself and especially **before** enabling
+such a package with ``make yes-<package>``.  Building :doc:`LAMMPS with
+CMake <Build_cmake>` can automate much of this for many types of
+machines, especially workstations, desktops, and laptops, so we suggest
+you try it first when building LAMMPS in those cases.
+
+The commands below perform a default LAMMPS build, producing the LAMMPS
+executable ``lmp_serial`` and ``lmp_mpi`` in ``lammps/src``:
+
+.. code-block:: bash
+
+   cd lammps/src   # change to main LAMMPS source folder
+   make serial     # build a serial LAMMPS executable using GNU g++
    make mpi        # build a parallel LAMMPS executable with MPI
    make            # see a variety of make options
 
-This initial compilation can take a long time, since LAMMPS is a large
+Compilation can take a long time, since LAMMPS is a large project with
-project with many features. If your machine has multiple CPU cores
+many features. If your machine has multiple CPU cores (most do these
-(most do these days), using a command like "make -jN mpi" (with N =
+days), you can speed this up by compiling sources in parallel with
-the number of available CPU cores) can be much faster.  If you plan to
+``make -j N`` (with N being the maximum number of concurrently executed
-do development on LAMMPS or need to re-compile LAMMPS repeatedly, the
+tasks).  Also installation of the `ccache <https://ccache.dev/>`_ (=
-installation of the ccache (= Compiler Cache) software may speed up
+Compiler Cache) software may speed up repeated compilation even more,
-compilation even more.
+e.g. during code development.
 
 After the initial build, whenever you edit LAMMPS source files, or add
 or remove new files to the source directory (e.g. by installing or
 uninstalling packages), you must re-compile and relink the LAMMPS
-executable with the same "make" command.  This makefiles dependencies
+executable with the same ``make <machine>`` command.  The makefile's
-should insure that only the subset of files that need to be are
+dependency tracking should insure that only the necessary subset of
-re-compiled.
+files are re-compiled.  If you change settings in the makefile, you have
+to recompile *everything*.  To delete all objects you can use ``make
+clean-<machine>``.
 
 .. note::
 
-   When you build LAMMPS for the first time, a long list of \*.d
+   Before the actual compilation starts, LAMMPS will perform several
-   files will be printed out rapidly.  This is not an error; it is the
+   steps to collect information from the configuration and setup that
-   Makefile doing its normal creation of dependencies.
+   is then embedded into the executable.  When you build LAMMPS for
+   the first time, it will also compile a tool to quickly assemble
+   a list of dependencies, that are required for the make program to
+   correctly detect which parts need to be recompiled after changes
+   were made to the sources.
 
+Customized builds and alternate makefiles
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-----------
+The ``src/MAKE`` directory tree contains the ``Makefile.<machine>``
+files included in the LAMMPS distribution.  Typing ``make example`` uses
+``Makefile.example`` from one of those folders, if available.  Thus the
+``make serial`` and ``make mpi`` lines above use
+``src/MAKE/Makefile.serial`` and ``src/MAKE/Makefile.mpi``,
+respectively.  Other makefiles are in these directories:
 
-
+.. code-block:: bash
-The lammps/src/MAKE tree contains all the Makefile.machine files
-included in the LAMMPS distribution.  Typing "make machine" uses
-Makefile.machine.  Thus the "make serial" or "make mpi" lines above
-use Makefile.serial and Makefile.mpi.  Others are in these dirs:
-
-
-.. parsed-literal::
 
    OPTIONS      # Makefiles which enable specific options
    MACHINES     # Makefiles for specific machines
    MINE         # customized Makefiles you create (you may need to create this folder)
 
-Typing "make" lists all the available Makefile.machine files.  A file
+Simply typing ``make`` lists all the available ``Makefile.<machine>``
-with the same name can appear in multiple folders (not a good idea).
+files with a single line description toward the end of the output.  A
-The order the dirs are searched is as follows: src/MAKE/MINE,
+file with the same name can appear in multiple folders (not a good
-src/MAKE, src/MAKE/OPTIONS, src/MAKE/MACHINES.  This gives preference
+idea).  The order the directories are searched is as follows:
-to a customized file you put in src/MAKE/MINE.
+``src/MAKE/MINE``, ``src/MAKE``, ``src/MAKE/OPTIONS``,
+``src/MAKE/MACHINES``.  This gives preference to a customized file you
+put in ``src/MAKE/MINE``.  If you create your own custom makefile under
+a new name, please edit the first line with the description and machine
+name, so you will not confuse yourself, when looking at the machine
+summary.
 
 Makefiles you may wish to try include these (some require a package
 first be installed).  Many of these include specific compiler flags
@@ -75,8 +113,7 @@ customized machine Makefile are contributed by users.  Since both
 compilers, OS configurations, and LAMMPS itself keep changing, their
 settings may become outdated:
 
-
+.. code-block:: bash
-.. parsed-literal::
 
    make mac             # build serial LAMMPS on a Mac
    make mac_mpi         # build parallel LAMMPS on a Mac
@@ -87,8 +124,3 @@ settings may become outdated:
    make kokkos_omp      # build with the KOKKOS package for OpenMP
    make kokkos_cuda_mpi # build with the KOKKOS package for GPUs
    make kokkos_phi      # build with the KOKKOS package for KNLs
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_package.rst

@@ -14,10 +14,13 @@ package.  In general there is no need to include a package if you
 never plan to use its features.
 
 If you get a run-time error that a LAMMPS command or style is
-"Unknown", it is often because the command is contained in a package,
+"unknown", it is often because the command is contained in a package,
-and your build did not include that package.  Running LAMMPS with the
+and your build did not include that package.  If the command or style
-:doc:`-h command-line switch <Run_options>` will print all the included
+*is* available in a package included in the LAMMPS distribution,
-packages and commands for that executable.
+the error message will indicate which package would be needed.
+Running LAMMPS with the :doc:`-h command-line switch <Run_options>`
+will print *all* optional commands and packages that were enabled
+when building that executable.
 
 For the majority of packages, if you follow the single step below to
 include it, you can then build LAMMPS exactly the same as you would
@@ -42,17 +45,15 @@ packages:
 The mechanism for including packages is simple but different for CMake
 versus make.
 
-**CMake variables**\ :
+**CMake build**\ :
 
-
+.. code-block:: csh
-.. parsed-literal::
 
    -D PKG_NAME=value          # yes or no (default)
 
 Examples:
 
-
+.. code-block:: csh
-.. parsed-literal::
 
    -D PKG_MANYBODY=yes
    -D PKG_USER-INTEL=yes
@@ -73,8 +74,7 @@ once with CMake.
 
 **Traditional make**\ :
 
-
+.. code-block:: bash
-.. parsed-literal::
 
    cd lammps/src
    make ps                    # check which packages are currently installed
@@ -84,8 +84,7 @@ once with CMake.
 
 Examples:
 
-
+.. code-block:: bash
-.. parsed-literal::
 
    make no-rigid
    make yes-user-intel
@@ -119,7 +118,7 @@ are already included.  Likewise, if a package is excluded, other files
 dependent on that package are also excluded.
 
 When you download a LAMMPS tarball or download LAMMPS source files
-from the Git or SVN repositories, no packages are pre-installed in the
+from the git repository, no packages are pre-installed in the
 src directory.
 
 .. note::
@@ -129,16 +128,17 @@ src directory.
    That is no longer the case, so that CMake will build as-is without the
    need to un-install those packages.
 
-
 ----------
 
+.. _cmake_presets:
 
 **CMake shortcuts for installing many packages**\ :
 
 Instead of specifying all the CMake options via the command-line,
-CMake allows initializing the variable cache using script files. These
+CMake allows initializing its settings cache using script files.
-are regular CMake files which can manipulate and set variables, and
+These are regular CMake files which can manipulate and set CMake
-can also contain control flow constructs.
+variables (which represent selected options), and can also contain
+control flow constructs for more complex operations.
 
 LAMMPS includes several of these files to define configuration
 "presets", similar to the options that exist for the Make based
@@ -146,33 +146,27 @@ system. Using these files you can enable/disable portions of the
 available packages in LAMMPS. If you need a custom preset you can take
 one of them as a starting point and customize it to your needs.
 
-+-------------------------------------------------------------+-----------------------------------------------------------+
+.. code-block:: bash
-| cmake -C ../cmake/presets/all\_on.cmake  [OPTIONS] ../cmake | enable all packages                                       |
+
-+-------------------------------------------------------------+-----------------------------------------------------------+
+    cmake -C ../cmake/presets/minimal.cmake [OPTIONS] ../cmake  # enable just a few core packages
-| cmake -C ../cmake/presets/all\_off.cmake [OPTIONS] ../cmake | disable all packages                                      |
+    cmake -C ../cmake/presets/most.cmake    [OPTIONS] ../cmake  # enable most packages
-+-------------------------------------------------------------+-----------------------------------------------------------+
+    cmake -C ../cmake/presets/nolib.cmake   [OPTIONS] ../cmake  # disable packages that do require extra libraries or tools
-| cmake -C ../cmake/presets/minimal.cmake [OPTIONS] ../cmake  | enable just a few core packages                           |
+    cmake -C ../cmake/presets/clang.cmake   [OPTIONS] ../cmake  # change settings to use the Clang compilers by default
-+-------------------------------------------------------------+-----------------------------------------------------------+
+    cmake -C ../cmake/presets/intel.cmake   [OPTIONS] ../cmake  # change settings to use the Intel compilers by default
-| cmake -C ../cmake/presets/most.cmake    [OPTIONS] ../cmake  | enable most common packages                               |
+    cmake -C ../cmake/presets/all_on.cmake  [OPTIONS] ../cmake  # enable all packages
-+-------------------------------------------------------------+-----------------------------------------------------------+
+    cmake -C ../cmake/presets/all_off.cmake [OPTIONS] ../cmake  # disable all packages
-| cmake -C ../cmake/presets/nolib.cmake   [OPTIONS] ../cmake  | disable packages that do require extra libraries or tools |
+    mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake  #  compile with MinGW cross compilers
-+-------------------------------------------------------------+-----------------------------------------------------------+
-| cmake -C ../cmake/presets/clang.cmake   [OPTIONS] ../cmake  | change settings to use the Clang compilers by default     |
-+-------------------------------------------------------------+-----------------------------------------------------------+
-| cmake -C ../cmake/presets/mingw.cmake [OPTIONS] ../cmake    | enable all packages compatible with MinGW compilers       |
-+-------------------------------------------------------------+-----------------------------------------------------------+
 
 .. note::
 
-   Running cmake this way manipulates the variable cache in your
+   Running cmake this way manipulates the CMake settings cache in your
    current build directory. You can combine multiple presets and options
    in a single cmake run, or change settings incrementally by running
    cmake with new flags.
 
 **Example:**
 
-
+.. code-block:: bash
-.. parsed-literal::
 
    # build LAMMPS with most commonly used packages, but then remove
    # those requiring additional library or tools, but still enable
@@ -188,49 +182,40 @@ one of them as a starting point and customize it to your needs.
    # but leaving all other settings untouched. You can run:
    cmake -C ../cmake/presets/no_all.cmake .
 
-
 ----------
 
-
 **Make shortcuts for installing many packages**\ :
 
 The following commands are useful for managing package source files
 and their installation when building LAMMPS via traditional make.
-Just type "make" in lammps/src to see a one-line summary.
+Just type ``make`` in lammps/src to see a one-line summary.
 
 These commands install/un-install sets of packages:
 
-+-----------------------------------+-----------------------------------------------------+
+.. code-block:: bash
-| make yes-all                      | install all packages                                |
-+-----------------------------------+-----------------------------------------------------+
-| make no-all                       | un-install all packages                             |
-+-----------------------------------+-----------------------------------------------------+
-| make yes-standard or make yes-std | install standard packages                           |
-+-----------------------------------+-----------------------------------------------------+
-| make no-standard or make no-std   | un-install standard packages                        |
-+-----------------------------------+-----------------------------------------------------+
-| make yes-user                     | install user packages                               |
-+-----------------------------------+-----------------------------------------------------+
-| make no-user                      | un-install user packages                            |
-+-----------------------------------+-----------------------------------------------------+
-| make yes-lib                      | install packages that require extra libraries       |
-+-----------------------------------+-----------------------------------------------------+
-| make no-lib                       | un-install packages that require extra libraries    |
-+-----------------------------------+-----------------------------------------------------+
-| make yes-ext                      | install packages that require external libraries    |
-+-----------------------------------+-----------------------------------------------------+
-| make no-ext                       | un-install packages that require external libraries |
-+-----------------------------------+-----------------------------------------------------+
 
-which install/un-install various sets of packages.  Typing "make
+    make yes-all                        # install all packages
-package" will list all the these commands.
+    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-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
+    make no-ext                         # uninstall packages that require external libraries
+
+which install/un-install various sets of packages.  Typing ``make
+package`` will list all the these commands.
 
 .. note::
 
-   Installing or un-installing a package works by simply copying
+   Installing or un-installing a package for the make based build process
-   files back and forth between the main src directory and
+   works by simply copying files back and forth between the main source
-   sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC),
+   directory src and the sub-directories with the package name (e.g.
-   so that the files are included or excluded when LAMMPS is built.
+   src/KSPACE, src/USER-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
@@ -238,28 +223,23 @@ need to use these commands unless you are editing LAMMPS files or are
 :doc:`installing a patch <Install_patch>` downloaded from the LAMMPS web
 site.
 
-Type "make package-status" or "make ps" to show which packages are
+Type ``make package-status`` or ``make ps`` to show which packages are
 currently installed.  For those that are installed, it will list any
 files that are different in the src directory and package
 sub-directory.
 
-Type "make package-installed" or "make pi" to show which packages are
+Type ``make package-installed`` or ``make pi`` to show which packages are
 currently installed, without listing the status of packages that are
 not installed.
 
-Type "make package-update" or "make pu" to overwrite src files with
+Type ``make package-update`` or ``make pu`` to overwrite src files with
 files from the package sub-directories if the package is installed.
 It should be used after a :doc:`patch has been applied <Install_patch>`,
 since patches only update the files in the package sub-directory, but
 not the src files.
 
-Type "make package-overwrite" to overwrite files in the package
+Type ``make package-overwrite`` to overwrite files in the package
 sub-directories with src files.
 
-Type "make package-diff" to list all differences between pairs of
+Type ``make package-diff`` to list all differences between pairs of
-files in both the src dir and a package dir.
+files in both the source directory and the package directory.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_settings.rst

@@ -4,77 +4,49 @@ Optional build settings
 LAMMPS can be built with several optional settings.  Each sub-section
 explain how to do this for building both with CMake and make.
 
-| :ref:`C++11 standard compliance test <cxx11>` when building all of LAMMPS
+* :ref:`C++11 standard compliance <cxx11>` when building all of LAMMPS
-| :ref:`FFT library <fft>` for use with the :doc:`kspace\_style pppm <kspace_style>` command
+* :ref:`FFT library <fft>` for use with the :doc:`kspace_style pppm <kspace_style>` command
-| :ref:`Size of LAMMPS data types <size>`
+* :ref:`Size of LAMMPS data types <size>`
-| :ref:`Read or write compressed files <gzip>`
+* :ref:`Read or write compressed files <gzip>`
-| :ref:`Output of JPG and PNG files <graphics>` via the :doc:`dump image <dump_image>` command
+* :ref:`Output of JPG and PNG files <graphics>` via the :doc:`dump image <dump_image>` command
-| :ref:`Output of movie files <graphics>` via the :doc:`dump\_movie <dump_image>` command
+* :ref:`Output of movie files <graphics>` via the :doc:`dump_movie <dump_image>` command
-| :ref:`Memory allocation alignment <align>`
+* :ref:`Memory allocation alignment <align>`
-| :ref:`Workaround for long long integers <longlong>`
+* :ref:`Workaround for long long integers <longlong>`
-| :ref:`Error handling exceptions <exceptions>` when using LAMMPS as a library 
+* :ref:`Error handling exceptions <exceptions>` when using LAMMPS as a library
-| 
-
 
 ----------
 
-
 .. _cxx11:
 
-C++11 standard compliance test
+C++11 standard compliance
 ------------------------------------------
 
-The LAMMPS developers plan to transition to make the C++11 standard the
+A C++11 standard compatible compiler is a requirement for compiling LAMMPS.
-minimum requirement for compiling LAMMPS.  Currently this only applies to
+LAMMPS version 3 March 2020 is the last version compatible with the previous
-some packages like KOKKOS while the rest aims to be compatible with the C++98
+C++98 standard for the core code and most packages. Most currently used
-standard.  Most currently used compilers are compatible with C++11; some need
+C++ compilers are compatible with C++11, but some older ones may need extra
-to set extra flags to switch.  To determine the impact of requiring C++11,
+flags to enable C++11 compliance.  Example for GNU c++ 4.8.x:
-we have added a simple compliance test to the source code, that will cause
-the compilation to abort, if C++11 compliance is not available or enabled.
-To bypass this check, you need to change a setting in the makefile or
-when calling CMake.
 
-**CMake variable**\ :
+.. code-block:: make
-
-
-.. parsed-literal::
-
-   -D DISABLE_CXX11_REQUIREMENT=yes
-
-You can set additional C++ compiler flags (beyond those selected by CMake)
-through the CMAKE\_CXX\_FLAGS variable. Example for CentOS 7:
-
-
-.. parsed-literal::
-
-   -D CMAKE_CXX_FLAGS="-O3 -g -fopenmp -DNDEBUG -std=c++11"
-
-**Makefile.machine setting**\ :
-
-
-.. parsed-literal::
-
-   LMP_INC = -DLAMMPS_CXX98
 
+   CCFLAGS = -g -O3 -std=c++11
 
 ----------
 
-
 .. _fft:
 
 FFT library
 ---------------------
 
 When the KSPACE package is included in a LAMMPS build, the
-:doc:`kspace\_style pppm <kspace_style>` command performs 3d FFTs which
+:doc:`kspace_style pppm <kspace_style>` command performs 3d FFTs which
 require use of an FFT library to compute 1d FFTs.  The KISS FFT
 library is included with LAMMPS but other libraries can be faster.
 LAMMPS can use them if they are available on your system.
 
 **CMake variables**\ :
 
-
+.. code-block:: bash
-.. parsed-literal::
 
    -D FFT=value              # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
    -D FFT_SINGLE=value       # yes or no (default), no = double precision
@@ -86,70 +58,83 @@ LAMMPS can use them if they are available on your system.
    an exception to the rule that all CMake variables can be specified
    with lower-case values.
 
-Usually these settings are all that is needed.  If CMake cannot find
+Usually these settings are all that is needed.  If FFTW3 is selected,
-the FFT library, you can set these variables:
+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 the FFT library, you can set these variables
+to assist:
 
-
+.. code-block:: bash
-.. parsed-literal::
 
    -D FFTW3_INCLUDE_DIRS=path  # path to FFTW3 include files
    -D FFTW3_LIBRARIES=path     # path to FFTW3 libraries
+   -D FFT_FFTW_THREADS=on      # enable using threaded FFTW3 libraries
    -D MKL_INCLUDE_DIRS=path    # ditto for Intel MKL library
+   -D FFT_MKL_THREADS=on       # enable using threaded FFTs with MKL libraries
    -D MKL_LIBRARIES=path
 
 **Makefile.machine settings**\ :
 
-
+.. code-block:: make
-.. parsed-literal::
 
    FFT_INC = -DFFT_FFTW3         # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
                                  # default is KISS if not specified
    FFT_INC = -DFFT_SINGLE        # do not specify for double precision
+   FFT_INC = -DFFT_FFTW_THREADS  # enable using threaded FFTW3 libraries
+   FFT_INC = -DFFT_MKL_THREADS   # enable using threaded FFTs with MKL libraries
    FFT_INC = -DFFT_PACK_ARRAY    # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
 
-# default is FFT\_PACK\_ARRAY if not specified
+# default is FFT_PACK_ARRAY if not specified
 
-
+.. code-block:: make
-.. parsed-literal::
 
    FFT_INC =       -I/usr/local/include
    FFT_PATH =      -L/usr/local/lib
    FFT_LIB =       -lfftw3             # FFTW3 double precision
+   FFT_LIB =       -lfftw3 -lfftw3_omp # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
    FFT_LIB =       -lfftw3 -lfftw3f    # FFTW3 single precision
-   FFT_LIB =       -lmkl_intel_lp64 -lmkl_sequential -lmkl_core  # MKL with Intel compiler
+   FFT_LIB =       -lmkl_intel_lp64 -lmkl_sequential -lmkl_core   # MKL with Intel compiler, serial interface
-   FFT_LIB =       -lmkl_gf_lp64 -lmkl_sequential -lmkl_core     # MKL with GNU compier
+   FFT_LIB =       -lmkl_gf_lp64 -lmkl_sequential -lmkl_core      # MKL with GNU compiler, serial interface
+   FFT_LIB =       -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core # MKL with Intel compiler, threaded interface
+   FFT_LIB =       -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core      # MKL with GNU compiler, threaded interface
+   FFT_LIB =       -lmkl_rt            # MKL with automatic runtime selection of interface libs
 
-As with CMake, you do not need to set paths in FFT\_INC or FFT\_PATH, if
+As with CMake, you do not need to set paths in ``FFT_INC`` or ``FFT_PATH``, if
-make can find the FFT header and library files.  You must specify
+the compiler can find the FFT header and library files in its default search path.
-FFT\_LIB with the appropriate FFT libraries to include in the link.
+You must specify ``FFT_LIB`` with the appropriate FFT libraries to include in the link.
 
 **CMake and make info**\ :
 
 The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS
-distribution.  It is portable across all platforms.  Depending on the
+distribution.  It is portable across all platforms.  Depending on the size
-size of the FFTs and the number of processors used, the other
+of the FFTs and the number of processors used, the other libraries listed
-libraries listed here can be faster.
+here can be faster.
 
 However, note that long-range Coulombics are only a portion of the
 per-timestep CPU cost, FFTs are only a portion of long-range
 Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
 communication can be costly).  A breakdown of these timings is printed
-to the screen at the end of a run using the :doc:`kspace\_style pppm <kspace_style>` command.  The :doc:`Run output <Run_output>`
+to the screen at the end of a run when using the
-doc page gives more details.
+:doc:`kspace_style pppm <kspace_style>` command. The :doc:`Run output <Run_output>`
+doc page gives more details.  A more detailed (and time consuming)
+report of the FFT performance is generated with the
+:doc:`kspace_modify fftbench yes <kspace_modify>` command.
 
 FFTW is a fast, portable FFT library that should also work on any
 platform and can be faster than the KISS FFT library.  You can
 download it from `www.fftw.org <http://www.fftw.org>`_.  LAMMPS requires
 version 3.X; the legacy version 2.1.X is no longer supported.
 
-Building FFTW for your box should be as simple as ./configure; make;
+Building FFTW for your box should be as simple as ``./configure; make;
-make install.  The install command typically requires root privileges
+make install``\ .  The install command typically requires root privileges
 (e.g. invoke it via sudo), unless you specify a local directory with
-the "--prefix" option of configure.  Type "./configure --help" to see
+the "--prefix" option of configure.  Type ``./configure --help`` to see
 various options.
 
 The Intel MKL math library is part of the Intel compiler suite.  It
-can be used with the Intel or GNU compiler (see FFT\_LIB setting above).
+can be used with the Intel or GNU compiler (see the ``FFT_LIB`` setting
+above).
 
 Performing 3d FFTs in parallel can be time consuming due to data
 access and required communication.  This cost can be reduced by
@@ -158,33 +143,30 @@ precision means the real and imaginary parts of a complex datum are
 4-byte floats.  Double precision means they are 8-byte doubles.  Note
 that Fourier transform and related PPPM operations are somewhat less
 sensitive to floating point truncation errors and thus the resulting
-error is less than the difference in precision. Using the -DFFT\_SINGLE
+error is less than the difference in precision. Using the ``-DFFT_SINGLE``
 setting trades off a little accuracy for reduced memory use and
 parallel communication costs for transposing 3d FFT data.
 
-When using -DFFT\_SINGLE with FFTW3 you may need to build the FFTW
+When using ``-DFFT_SINGLE`` with FFTW3 you may need to build the FFTW
 library a second time with support for single-precision.
 
 For FFTW3, do the following, which should produce the additional
-library libfftw3f.a
+library ``libfftw3f.a`` or ``libfftw3f.so``\ .
 
-
+.. code-block:: bash
-.. parsed-literal::
 
    make clean
    ./configure --enable-single; make; make install
 
 Performing 3d FFTs requires communication to transpose the 3d FFT
 grid.  The data packing/unpacking for this can be done in one of 3
-modes (ARRAY, POINTER, MEMCPY) as set by the FFT\_PACK syntax above.
+modes (ARRAY, POINTER, MEMCPY) as set by the FFT_PACK syntax above.
 Depending on the machine, the size of the FFT grid, the number of
 processors used, one option may be slightly faster.  The default is
 ARRAY mode.
 
-
 ----------
 
-
 .. _size:
 
 Size of LAMMPS data types
@@ -196,19 +178,18 @@ adequate.
 
 **CMake variable**\ :
 
-
+.. code-block:: bash
-.. parsed-literal::
 
    -D LAMMPS_SIZES=value   # smallbig (default) or bigbig or smallsmall
 
 **Makefile.machine setting**\ :
 
-
+.. code-block:: make
-.. parsed-literal::
 
    LMP_INC = -DLAMMPS_SMALLBIG    # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL
 
-# default is LAMMPS\_SMALLBIG if not specified
+The default setting is ``-DLAMMPS_SMALLBIG`` if nothing is specified
+
 **CMake and make info**\ :
 
 The default "smallbig" setting allows for simulations with:
@@ -235,7 +216,7 @@ support 8-byte integers.  It allows for:
 
 Atom IDs are not required for atomic systems which do not store bond
 topology information, though IDs are enabled by default.  The
-:doc:`atom\_modify id no <atom_modify>` command will turn them off.  Atom
+:doc:`atom_modify id no <atom_modify>` command will turn them off.  Atom
 IDs are required for molecular systems with bond topology (bonds,
 angles, dihedrals, etc).  Thus if you model a molecular system with
 more than 2 billion atoms, you need the "bigbig" setting.
@@ -256,12 +237,10 @@ than crashing randomly or corrupting data.
 Also note that the GPU package requires its lib/gpu library to be
 compiled with the same size setting, or the link will fail.  A CMake
 build does this automatically.  When building with make, the setting
-in whichever lib/gpu/Makefile is used must be the same as above.
+in whichever ``lib/gpu/Makefile`` is used must be the same as above.
-
 
 ----------
 
-
 .. _graphics:
 
 Output of JPG, PNG, and movie files
@@ -274,22 +253,20 @@ following settings:
 
 **CMake variables**\ :
 
-
+.. code-block:: bash
-.. parsed-literal::
 
    -D WITH_JPEG=value      # yes or no
-                             # default = yes if CMake finds JPEG files, else no
+                           # default = yes if CMake finds JPEG files, else no
    -D WITH_PNG=value       # yes or no
-                             # default = yes if CMake finds PNG and ZLIB files, else no
+                           # default = yes if CMake finds PNG and ZLIB files, else no
    -D WITH_FFMPEG=value    # yes or no
-                             # default = yes if CMake can find ffmpeg, else no
+                           # default = yes if CMake can find ffmpeg, else no
 
 Usually these settings are all that is needed.  If CMake cannot find
 the graphics header, library, executable files, you can set these
 variables:
 
-
+.. code-block:: bash
-.. parsed-literal::
 
    -D JPEG_INCLUDE_DIR=path    # path to jpeglib.h header file
    -D JPEG_LIBRARIES=path      # path to libjpeg.a (.so) file
@@ -301,8 +278,7 @@ variables:
 
 **Makefile.machine settings**\ :
 
-
+.. code-block:: make
-.. parsed-literal::
 
    LMP_INC = -DLAMMPS_JPEG
    LMP_INC = -DLAMMPS_PNG
@@ -312,28 +288,27 @@ variables:
    JPG_PATH = -L/usr/lib            # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them
    JPG_LIB = -ljpeg -lpng -lz       # library names
 
-As with CMake, you do not need to set JPG\_INC or JPG\_PATH, if make can
+As with CMake, you do not need to set ``JPG_INC`` or ``JPG_PATH``,
-find the graphics header and library files.  You must specify JPG\_LIB
+if make can find the graphics header and library files.  You must
+specify ``JPG_LIB``
 with a list of graphics libraries to include in the link.  You must
 insure ffmpeg is in a directory where LAMMPS can find it at runtime,
-i.e. a dir in your PATH environment variable.
+that is a directory in your PATH environment variable.
 
 **CMake and make info**\ :
 
-Using ffmpeg to output movie files requires that your machine
+Using ``ffmpeg`` to output movie files requires that your machine
 supports the "popen" function in the standard runtime library.
 
 .. note::
 
    On some clusters with high-speed networks, using the fork()
-   library calls (required by popen()) can interfere with the fast
+   library call (required by popen()) can interfere with the fast
    communication library and lead to simulations using ffmpeg to hang or
    crash.
 
-
 ----------
 
-
 .. _gzip:
 
 Read or write compressed files
@@ -341,12 +316,11 @@ 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>`.
+:doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
 
 **CMake variables**\ :
 
-
+.. code-block:: bash
-.. parsed-literal::
 
    -D WITH_GZIP=value       # yes or no
                             # default is yes if CMake can find gzip, else no
@@ -354,8 +328,7 @@ gzip compression by several LAMMPS commands, including
 
 **Makefile.machine setting**\ :
 
-
+.. code-block:: make
-.. parsed-literal::
 
    LMP_INC = -DLAMMPS_GZIP
 
@@ -368,22 +341,20 @@ found by LAMMPS during a run.
 .. note::
 
    On some clusters with high-speed networks, using the fork()
-   library calls (required by popen()) can interfere with the fast
+   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 :ref:`COMPRESS package <PKG-COMPRESS>` enables.
 
-
 ----------
 
-
 .. _align:
 
 Memory allocation alignment
 ---------------------------------------
 
-This setting enables the use of the posix\_memalign() call instead of
+This setting enables the use of the posix_memalign() call instead of
 malloc() when LAMMPS allocates large chunks or memory.  This can make
 vector instructions on CPUs more efficient, if dynamically allocated
 memory is aligned on larger-than-default byte boundaries.
@@ -394,33 +365,29 @@ aligned on 64-byte boundaries.
 
 **CMake variable**\ :
 
-
+.. code-block:: bash
-.. parsed-literal::
 
    -D LAMMPS_MEMALIGN=value            # 0, 8, 16, 32, 64 (default)
 
-Use a LAMMPS\_MEMALIGN value of 0 to disable using posix\_memalign()
+Use a ``LAMMPS_MEMALIGN`` value of 0 to disable using posix_memalign()
 and revert to using the malloc() C-library function instead.  When
 compiling LAMMPS for Windows systems, malloc() will always be used
 and this setting ignored.
 
 **Makefile.machine setting**\ :
 
-
+.. code-block:: make
-.. parsed-literal::
 
    LMP_INC = -DLAMMPS_MEMALIGN=value   # 8, 16, 32, 64
 
-Do not set -DLAMMPS\_MEMALIGN, if you want to have memory allocated
+Do not set ``-DLAMMPS_MEMALIGN``, if you want to have memory allocated
-with the malloc() function call instead. -DLAMMPS\_MEMALIGN **cannot**
+with the malloc() function call instead. ``-DLAMMPS_MEMALIGN`` **cannot**
 be used on Windows, as it does use different function calls for
 allocating aligned memory, that are not compatible with how LAMMPS
 manages its dynamical memory.
 
-
 ----------
 
-
 .. _longlong:
 
 Workaround for long long integers
@@ -433,47 +400,37 @@ those systems:
 
 **CMake variable**\ :
 
-
+.. code-block:: bash
-.. parsed-literal::
 
    -D LAMMPS_LONGLONG_TO_LONG=value     # yes or no (default)
 
 **Makefile.machine setting**\ :
 
-
+.. code-block:: make
-.. parsed-literal::
 
    LMP_INC = -DLAMMPS_LONGLONG_TO_LONG
 
-
 ----------
 
-
 .. _exceptions:
 
 Exception handling when using LAMMPS as a library
 ------------------------------------------------------------------
 
 This setting is useful when external codes drive LAMMPS as a library.
-With this option enabled LAMMPS errors do not kill the caller.
+With this option enabled, LAMMPS errors do not kill the calling code.
 Instead, the call stack is unwound and control returns to the caller,
-e.g. to Python.
+e.g. to Python. Of course the calling code has to be set up to
+*catch* exceptions from within LAMMPS.
 
 **CMake variable**\ :
 
-
+.. code-block:: bash
-.. parsed-literal::
 
    -D LAMMPS_EXCEPTIONS=value        # yes or no (default)
 
 **Makefile.machine setting**\ :
 
-
+.. code-block:: make
-.. parsed-literal::
 
    LMP_INC = -DLAMMPS_EXCEPTIONS
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_windows.rst

@@ -6,10 +6,8 @@ Notes for building LAMMPS on Windows
 * :ref:`Using GNU GCC ported to Windows <gnu>`
 * :ref:`Using a cross-compiler <cross>`
 
-
 ----------
 
-
 .. _generic:
 
 General remarks
@@ -17,9 +15,9 @@ General remarks
 
 LAMMPS is developed and tested primarily on Linux machines.  The vast
 majority of HPC clusters and supercomputers today runs on Linux as well.
-Thus portability to other platforms is desired, but not always achieved.
+While portability to other platforms is desired, it is not always achieved.
 The LAMMPS developers strongly rely on LAMMPS users giving feedback and
-providing assistance in resolving portability issues. This particularly
+providing assistance in resolving portability issues. This is particularly
 true for compiling LAMMPS on Windows, since this platform has significant
 differences with some low-level functionality.
 
@@ -31,18 +29,20 @@ Running Linux on Windows
 So before trying to build LAMMPS on Windows, please consider if using
 the pre-compiled Windows binary packages are sufficient for your needs
 (as an aside, those packages themselves are build on a Linux machine
-using cross-compilers).  If it is necessary for your to compile LAMMPS
+using cross-compilers).  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 run a Linux virtual machine,
+consider using a virtual machine software and compile and run LAMMPS in
-or - if have a recently updated Windows 10 installation - consider using
+a Linux virtual machine, or - if you have a recently updated Windows 10
-the Windows subsystem for Linux, which allows to run a bash shell from
+installation - consider using the Windows subsystem for Linux.  This
-Ubuntu and from there on, you can pretty much use that shell like you
+optional Windows feature allows you to run the bash shell from Ubuntu
-are running on an Ubuntu Linux machine (e.g. installing software via
+from within Windows and from there on, you can pretty much use that
-apt-get). For more details on that, please see :doc:`this tutorial <Howto_bash>`
+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_bash>`
 
 .. _gnu:
 
-Using GNU GCC ported to Windows
+Using a GNU GCC ported to Windows
 -----------------------------------------
 
 One option for compiling LAMMPS on Windows natively, that has been known
@@ -55,8 +55,8 @@ and the corresponding new code. A machine makefile for using cygwin for
 the old build system is provided. Using CMake for this mode of compilation
 is untested and not likely to work.
 
-When compiling for Windows do **not** set the -DLAMMPS\_MEMALIGN define
+When compiling for Windows do **not** set the -DLAMMPS_MEMALIGN define
-in the LMP\_INC makefile variable and add -lwsock32 -lpsapi to the linker
+in the LMP_INC makefile variable and add -lwsock32 -lpsapi to the linker
 flags in LIB makefile variable. Try adding -static-libgcc or -static or
 both to the linker flags when your resulting LAMMPS Windows executable
 complains about missing .dll files. The CMake configuration should set
@@ -83,13 +83,19 @@ traditional build system, but CMake has also been successfully tested
 using the mingw32-cmake and mingw64-cmake wrappers that are bundled
 with the cross-compiler environment on Fedora machines. A CMake preset
 selecting all packages compatible with this cross-compilation build
-is provided. You likely need to disable the GPU package unless you
+is provided.  The GPU package can only be compiled with OpenCL support
-download and install the contents of the pre-compiled `OpenCL ICD loader library <https://download.lammps.org/thirdparty/opencl-win-devel.tar.gz>`_
+and you need to download and install the pre-compiled
-into your MinGW64 cross-compiler environment. The cross-compilation
+`OpenCL ICD loader library <https://download.lammps.org/thirdparty/opencl-win-devel.tar.gz>`_
-currently will only produce non-MPI serial binaries.
+into your MinGW64 cross-compiler environment.  With CMake this will be
+done transparently.  To compile with MPI support, a pre-compiled
+library and the corresponding header files are required.  There is
+`one package for 32-bit Windows <https://download.lammps.org/thirdparty/mpich2-win32-devel.tar.gz>`_
+and `a second package for 64-bit Windows <https://download.lammps.org/thirdparty/mpich2-win64-devel.tar.gz>`_.
+When building with CMake, the matching package will be downloaded
+automatically, but MPI support has to be explicitly enabled with ``-DBUILD_MPI=on``.
 
-Please keep in mind, though, that this only applies to compiling LAMMPS.
+Please keep in mind, though, that this only applies to **compiling** LAMMPS.
-Whether the resulting binaries do work correctly is no tested by the
+Whether the resulting binaries do work correctly is not tested by the
 LAMMPS developers.  We instead rely on the feedback of the users
 of these pre-compiled LAMMPS packages for Windows.  We will try to resolve
 issues to the best of our abilities if we become aware of them. However
@@ -104,8 +110,3 @@ Support for the Visual C++ compilers is currently not available. The
 CMake build system is capable of creating suitable a Visual Studio
 style build environment, but the LAMMPS code itself is not fully ported
 to support Visual C++. Volunteers to take on this task are welcome.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Commands.rst

@@ -4,7 +4,6 @@ Commands
 These pages describe how a LAMMPS input script is formatted and the
 commands in it are used to define a LAMMPS simulation.
 
-
 .. toctree::
    :maxdepth: 1
 
@@ -27,8 +26,3 @@ commands in it are used to define a LAMMPS simulation.
    :maxdepth: 1
 
    Commands_removed
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Commands_all.rst

@@ -1,59 +1,139 @@
-+----------------------------------------+------------------------------------+------------------------------------------+
+.. table_from_list::
-| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>`   | :doc:`Compute styles <Commands_compute>` |
+   :columns: 3
-+----------------------------------------+------------------------------------+------------------------------------------+
+
-| :doc:`Pair styles <Commands_pair>`     | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>`              |
+   * :doc:`General commands <Commands_all>`
-+----------------------------------------+------------------------------------+------------------------------------------+
+   * :doc:`Fix styles <Commands_fix>`
-| :ref:`Dihedral styles <dihedral>`      | :ref:`Improper styles <improper>`  | :doc:`KSpace styles <Commands_kspace>`   |
+   * :doc:`Compute styles <Commands_compute>`
-+----------------------------------------+------------------------------------+------------------------------------------+
+   * :doc:`Pair styles <Commands_pair>`
+   * :ref:`Bond styles <bond>`
+   * :ref:`Angle styles <angle>`
+   * :ref:`Dihedral styles <dihedral>`
+   * :ref:`Improper styles <improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
 
 General commands
 ================
 
 An alphabetic list of all general LAMMPS commands.
 
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
+.. table_from_list::
-| :doc:`angle\_coeff <angle_coeff>`       | :doc:`angle\_style <angle_style>`       | :doc:`atom\_modify <atom_modify>`       | :doc:`atom\_style <atom_style>`         | :doc:`balance <balance>`                    | :doc:`bond\_coeff <bond_coeff>`         |
+   :columns: 5
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`bond\_style <bond_style>`         | :doc:`bond\_write <bond_write>`         | :doc:`boundary <boundary>`              | :doc:`box <box>`                        | :doc:`change\_box <change_box>`             | :doc:`clear <clear>`                    |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`comm\_modify <comm_modify>`       | :doc:`comm\_style <comm_style>`         | :doc:`compute <compute>`                | :doc:`compute\_modify <compute_modify>` | :doc:`create\_atoms <create_atoms>`         | :doc:`create\_bonds <create_bonds>`     |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`create\_box <create_box>`         | :doc:`delete\_atoms <delete_atoms>`     | :doc:`delete\_bonds <delete_bonds>`     | :doc:`dielectric <dielectric>`          | :doc:`dihedral\_coeff <dihedral_coeff>`     | :doc:`dihedral\_style <dihedral_style>` |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`dimension <dimension>`            | :doc:`displace\_atoms <displace_atoms>` | :doc:`dump <dump>`                      | :doc:`dump adios <dump_adios>`          | :doc:`dump image <dump_image>`              | :doc:`dump movie <dump_image>`          |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`dump netcdf <dump_netcdf>`        | :doc:`dump netcdf/mpiio <dump_netcdf>`  | :doc:`dump vtk <dump_vtk>`              | :doc:`dump\_modify <dump_modify>`       | :doc:`dynamical\_matrix <dynamical_matrix>` | :doc:`echo <echo>`                      |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`fix <fix>`                        | :doc:`fix\_modify <fix_modify>`         | :doc:`group <group>`                    | :doc:`group2ndx <group2ndx>`            | :doc:`hyper <hyper>`                        | :doc:`if <if>`                          |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`info <info>`                      | :doc:`improper\_coeff <improper_coeff>` | :doc:`improper\_style <improper_style>` | :doc:`include <include>`                | :doc:`jump <jump>`                          | :doc:`kim\_init <kim_commands>`         |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`kim\_interactions <kim_commands>` | :doc:`kim\_query <kim_commands>`        | :doc:`kspace\_modify <kspace_modify>`   | :doc:`kspace\_style <kspace_style>`     | :doc:`label <label>`                        | :doc:`lattice <lattice>`                |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`log <log>`                        | :doc:`mass <mass>`                      | :doc:`message <message>`                | :doc:`minimize <minimize>`              | :doc:`min\_modify <min_modify>`             | :doc:`min\_style <min_style>`           |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`min\_style spin <min_spin>`       | :doc:`molecule <molecule>`              | :doc:`ndx2group <group2ndx>`            | :doc:`neb <neb>`                        | :doc:`neb/spin <neb_spin>`                  | :doc:`neigh\_modify <neigh_modify>`     |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`neighbor <neighbor>`              | :doc:`newton <newton>`                  | :doc:`next <next>`                      | :doc:`package <package>`                | :doc:`pair\_coeff <pair_coeff>`             | :doc:`pair\_modify <pair_modify>`       |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`pair\_style <pair_style>`         | :doc:`pair\_write <pair_write>`         | :doc:`partition <partition>`            | :doc:`prd <prd>`                        | :doc:`print <print>`                        | :doc:`processors <processors>`          |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`python <python>`                  | :doc:`quit <quit>`                      | :doc:`read\_data <read_data>`           | :doc:`read\_dump <read_dump>`           | :doc:`read\_restart <read_restart>`         | :doc:`region <region>`                  |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`replicate <replicate>`            | :doc:`rerun <rerun>`                    | :doc:`reset\_ids <reset_ids>`           | :doc:`reset\_timestep <reset_timestep>` | :doc:`restart <restart>`                    | :doc:`run <run>`                        |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`run\_style <run_style>`           | :doc:`server <server>`                  | :doc:`set <set>`                        | :doc:`shell <shell>`                    | :doc:`special\_bonds <special_bonds>`       | :doc:`suffix <suffix>`                  |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`tad <tad>`                        | :doc:`temper <temper>`                  | :doc:`temper/grem <temper_grem>`        | :doc:`temper/npt <temper_npt>`          | :doc:`thermo <thermo>`                      | :doc:`thermo\_modify <thermo_modify>`   |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`thermo\_style <thermo_style>`     | :doc:`third\_order <third_order>`       | :doc:`timer <timer>`                    | :doc:`timestep <timestep>`              | :doc:`uncompute <uncompute>`                | :doc:`undump <undump>`                  |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`unfix <unfix>`                    | :doc:`units <units>`                    | :doc:`variable <variable>`              | :doc:`velocity <velocity>`              | :doc:`write\_coeff <write_coeff>`           | :doc:`write\_data <write_data>`         |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
-| :doc:`write\_dump <write_dump>`         | :doc:`write\_restart <write_restart>`   |                                         |                                         |                                             |                                         |
-+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
 
-
+   * :doc:`angle_coeff <angle_coeff>`
-.. _lws: http://lammps.sandia.gov
+   * :doc:`angle_style <angle_style>`
-.. _ld: Manual.html
+   * :doc:`atom_modify <atom_modify>`
-.. _lc: Commands_all.html
+   * :doc:`atom_style <atom_style>`
+   * :doc:`balance <balance>`
+   * :doc:`bond_coeff <bond_coeff>`
+   * :doc:`bond_style <bond_style>`
+   * :doc:`bond_write <bond_write>`
+   * :doc:`boundary <boundary>`
+   * :doc:`box <box>`
+   * :doc:`change_box <change_box>`
+   * :doc:`clear <clear>`
+   * :doc:`comm_modify <comm_modify>`
+   * :doc:`comm_style <comm_style>`
+   * :doc:`compute <compute>`
+   * :doc:`compute_modify <compute_modify>`
+   * :doc:`create_atoms <create_atoms>`
+   * :doc:`create_bonds <create_bonds>`
+   * :doc:`create_box <create_box>`
+   * :doc:`delete_atoms <delete_atoms>`
+   * :doc:`delete_bonds <delete_bonds>`
+   * :doc:`dielectric <dielectric>`
+   * :doc:`dihedral_coeff <dihedral_coeff>`
+   * :doc:`dihedral_style <dihedral_style>`
+   * :doc:`dimension <dimension>`
+   * :doc:`displace_atoms <displace_atoms>`
+   * :doc:`dump <dump>`
+   * :doc:`dump atom/adios <dump_adios>`
+   * :doc:`dump custom/adios <dump_adios>`
+   * :doc:`dump image <dump_image>`
+   * :doc:`dump movie <dump_image>`
+   * :doc:`dump netcdf <dump_netcdf>`
+   * :doc:`dump netcdf/mpiio <dump_netcdf>`
+   * :doc:`dump vtk <dump_vtk>`
+   * :doc:`dump_modify <dump_modify>`
+   * :doc:`dynamical_matrix <dynamical_matrix>`
+   * :doc:`echo <echo>`
+   * :doc:`fix <fix>`
+   * :doc:`fix_modify <fix_modify>`
+   * :doc:`group <group>`
+   * :doc:`group2ndx <group2ndx>`
+   * :doc:`hyper <hyper>`
+   * :doc:`if <if>`
+   * :doc:`improper_coeff <improper_coeff>`
+   * :doc:`improper_style <improper_style>`
+   * :doc:`include <include>`
+   * :doc:`info <info>`
+   * :doc:`jump <jump>`
+   * :doc:`kim_init <kim_commands>`
+   * :doc:`kim_interactions <kim_commands>`
+   * :doc:`kim_param <kim_commands>`
+   * :doc:`kim_property <kim_commands>`
+   * :doc:`kim_query <kim_commands>`
+   * :doc:`kspace_modify <kspace_modify>`
+   * :doc:`kspace_style <kspace_style>`
+   * :doc:`label <label>`
+   * :doc:`lattice <lattice>`
+   * :doc:`log <log>`
+   * :doc:`mass <mass>`
+   * :doc:`message <message>`
+   * :doc:`minimize <minimize>`
+   * :doc:`min_modify <min_modify>`
+   * :doc:`min_style <min_style>`
+   * :doc:`min_style spin <min_spin>`
+   * :doc:`molecule <molecule>`
+   * :doc:`ndx2group <group2ndx>`
+   * :doc:`neb <neb>`
+   * :doc:`neb/spin <neb_spin>`
+   * :doc:`neigh_modify <neigh_modify>`
+   * :doc:`neighbor <neighbor>`
+   * :doc:`newton <newton>`
+   * :doc:`next <next>`
+   * :doc:`package <package>`
+   * :doc:`pair_coeff <pair_coeff>`
+   * :doc:`pair_modify <pair_modify>`
+   * :doc:`pair_write <pair_write>`
+   * :doc:`partition <partition>`
+   * :doc:`prd <prd>`
+   * :doc:`print <print>`
+   * :doc:`processors <processors>`
+   * :doc:`python <python>`
+   * :doc:`quit <quit>`
+   * :doc:`read_data <read_data>`
+   * :doc:`read_dump <read_dump>`
+   * :doc:`read_restart <read_restart>`
+   * :doc:`region <region>`
+   * :doc:`replicate <replicate>`
+   * :doc:`rerun <rerun>`
+   * :doc:`reset_ids <reset_ids>`
+   * :doc:`reset_timestep <reset_timestep>`
+   * :doc:`restart <restart>`
+   * :doc:`run <run>`
+   * :doc:`run_style <run_style>`
+   * :doc:`server <server>`
+   * :doc:`set <set>`
+   * :doc:`shell <shell>`
+   * :doc:`special_bonds <special_bonds>`
+   * :doc:`suffix <suffix>`
+   * :doc:`tad <tad>`
+   * :doc:`temper <temper>`
+   * :doc:`temper/grem <temper_grem>`
+   * :doc:`temper/npt <temper_npt>`
+   * :doc:`thermo <thermo>`
+   * :doc:`thermo_modify <thermo_modify>`
+   * :doc:`thermo_style <thermo_style>`
+   * :doc:`third_order <third_order>`
+   * :doc:`timer <timer>`
+   * :doc:`timestep <timestep>`
+   * :doc:`uncompute <uncompute>`
+   * :doc:`undump <undump>`
+   * :doc:`unfix <unfix>`
+   * :doc:`units <units>`
+   * :doc:`variable <variable>`
+   * :doc:`velocity <velocity>`
+   * :doc:`write_coeff <write_coeff>`
+   * :doc:`write_data <write_data>`
+   * :doc:`write_dump <write_dump>`
+   * :doc:`write_restart <write_restart>`

doc/src/Commands_bond.rst

@@ -1,112 +1,159 @@
+.. table_from_list::
+   :columns: 3
+
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :ref:`Bond styles <bond>`
+   * :ref:`Angle styles <angle>`
+   * :ref:`Dihedral styles <dihedral>`
+   * :ref:`Improper styles <improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
+
 .. _bond:
 
-Bond\_style potentials
+Bond_style potentials
-=================================
+=====================
 
-All LAMMPS :doc:`bond\_style <bond_style>` commands.  Some styles have
+All LAMMPS :doc:`bond_style <bond_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
 parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.
 
-+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
+.. table_from_list::
-| :doc:`none <bond_none>`               | :doc:`zero <bond_zero>`                         | :doc:`hybrid <bond_hybrid>`                             |                                 |
+   :columns: 4
-+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
-|                                       |                                                 |                                                         |                                 |
-+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
-| :doc:`class2 (ko) <bond_class2>`      | :doc:`fene (iko) <bond_fene>`                   | :doc:`fene/expand (o) <bond_fene_expand>`               | :doc:`gromos (o) <bond_gromos>` |
-+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
-| :doc:`harmonic (iko) <bond_harmonic>` | :doc:`harmonic/shift (o) <bond_harmonic_shift>` | :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>` | :doc:`mm3 <bond_mm3>`           |
-+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
-| :doc:`morse (o) <bond_morse>`         | :doc:`nonlinear (o) <bond_nonlinear>`           | :doc:`oxdna/fene <bond_oxdna>`                          | :doc:`oxdna2/fene <bond_oxdna>` |
-+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
-| :doc:`quartic (o) <bond_quartic>`     | :doc:`table (o) <bond_table>`                   |                                                         |                                 |
-+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
-
-
-----------
 
+   * :doc:`none <bond_none>`
+   * :doc:`zero <bond_zero>`
+   * :doc:`hybrid <bond_hybrid>`
+   *
+   *
+   *
+   *
+   *
+   * :doc:`class2 (ko) <bond_class2>`
+   * :doc:`fene (iko) <bond_fene>`
+   * :doc:`fene/expand (o) <bond_fene_expand>`
+   * :doc:`gromos (o) <bond_gromos>`
+   * :doc:`harmonic (iko) <bond_harmonic>`
+   * :doc:`harmonic/shift (o) <bond_harmonic_shift>`
+   * :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>`
+   * :doc:`mm3 <bond_mm3>`
+   * :doc:`morse (o) <bond_morse>`
+   * :doc:`nonlinear (o) <bond_nonlinear>`
+   * :doc:`oxdna/fene <bond_oxdna>`
+   * :doc:`oxdna2/fene <bond_oxdna>`
+   * :doc:`oxrna2/fene <bond_oxdna>`
+   * :doc:`quartic (o) <bond_quartic>`
+   * :doc:`table (o) <bond_table>`
 
 .. _angle:
 
-Angle\_style potentials
+Angle_style potentials
-===================================
+======================
 
-All LAMMPS :doc:`angle\_style <angle_style>` commands.  Some styles have
+All LAMMPS :doc:`angle_style <angle_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
 parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.
 
-+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
+.. table_from_list::
-| :doc:`none <angle_none>`                             | :doc:`zero <angle_zero>`                         | :doc:`hybrid <angle_hybrid>`                       |                                              |
+   :columns: 4
-+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
-|                                                      |                                                  |                                                    |                                              |
-+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
-| :doc:`charmm (iko) <angle_charmm>`                   | :doc:`class2 (ko) <angle_class2>`                | :doc:`class2/p6 <angle_class2>`                    | :doc:`cosine (ko) <angle_cosine>`            |
-+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
-| :doc:`cosine/buck6d <angle_cosine_buck6d>`           | :doc:`cosine/delta (o) <angle_cosine_delta>`     | :doc:`cosine/periodic (o) <angle_cosine_periodic>` | :doc:`cosine/shift (o) <angle_cosine_shift>` |
-+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
-| :doc:`cosine/shift/exp (o) <angle_cosine_shift_exp>` | :doc:`cosine/squared (o) <angle_cosine_squared>` | :doc:`cross <angle_cross>`                         | :doc:`dipole (o) <angle_dipole>`             |
-+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
-| :doc:`fourier (o) <angle_fourier>`                   | :doc:`fourier/simple (o) <angle_fourier_simple>` | :doc:`harmonic (iko) <angle_harmonic>`             | :doc:`mm3 <angle_mm3>`                       |
-+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
-| :doc:`quartic (o) <angle_quartic>`                   | :doc:`sdk (o) <angle_sdk>`                       | :doc:`table (o) <angle_table>`                     |                                              |
-+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
-
-
-----------
 
+   * :doc:`none <angle_none>`
+   * :doc:`zero <angle_zero>`
+   * :doc:`hybrid <angle_hybrid>`
+   *
+   *
+   *
+   *
+   *
+   * :doc:`charmm (iko) <angle_charmm>`
+   * :doc:`class2 (ko) <angle_class2>`
+   * :doc:`class2/p6 <angle_class2>`
+   * :doc:`cosine (ko) <angle_cosine>`
+   * :doc:`cosine/buck6d <angle_cosine_buck6d>`
+   * :doc:`cosine/delta (o) <angle_cosine_delta>`
+   * :doc:`cosine/periodic (o) <angle_cosine_periodic>`
+   * :doc:`cosine/shift (o) <angle_cosine_shift>`
+   * :doc:`cosine/shift/exp (o) <angle_cosine_shift_exp>`
+   * :doc:`cosine/squared (o) <angle_cosine_squared>`
+   * :doc:`cross <angle_cross>`
+   * :doc:`dipole (o) <angle_dipole>`
+   * :doc:`fourier (o) <angle_fourier>`
+   * :doc:`fourier/simple (o) <angle_fourier_simple>`
+   * :doc:`harmonic (iko) <angle_harmonic>`
+   * :doc:`mm3 <angle_mm3>`
+   * :doc:`quartic (o) <angle_quartic>`
+   * :doc:`sdk (o) <angle_sdk>`
+   * :doc:`table (o) <angle_table>`
 
 .. _dihedral:
 
-Dihedral\_style potentials
+Dihedral_style potentials
-=========================================
+=========================
 
-All LAMMPS :doc:`dihedral\_style <dihedral_style>` commands.  Some styles
+All LAMMPS :doc:`dihedral_style <dihedral_style>` commands.  Some styles
 have accelerated versions.  This is indicated by additional letters in
 parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.
 
-+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
+.. table_from_list::
-| :doc:`none <dihedral_none>`               | :doc:`zero <dihedral_zero>`               | :doc:`hybrid <dihedral_hybrid>`           |                                                         |
+   :columns: 4
-+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
-|                                           |                                           |                                           |                                                         |
-+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
-| :doc:`charmm (iko) <dihedral_charmm>`     | :doc:`charmmfsw <dihedral_charmm>`        | :doc:`class2 (ko) <dihedral_class2>`      | :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>` |
-+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
-| :doc:`fourier (io) <dihedral_fourier>`    | :doc:`harmonic (iko) <dihedral_harmonic>` | :doc:`helix (o) <dihedral_helix>`         | :doc:`multi/harmonic (o) <dihedral_multi_harmonic>`     |
-+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
-| :doc:`nharmonic (o) <dihedral_nharmonic>` | :doc:`opls (iko) <dihedral_opls>`         | :doc:`quadratic (o) <dihedral_quadratic>` | :doc:`spherical <dihedral_spherical>`                   |
-+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
-| :doc:`table (o) <dihedral_table>`         | :doc:`table/cut <dihedral_table_cut>`     |                                           |                                                         |
-+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
-
-
-----------
 
+   * :doc:`none <dihedral_none>`
+   * :doc:`zero <dihedral_zero>`
+   * :doc:`hybrid <dihedral_hybrid>`
+   *
+   *
+   *
+   *
+   *
+   * :doc:`charmm (iko) <dihedral_charmm>`
+   * :doc:`charmmfsw <dihedral_charmm>`
+   * :doc:`class2 (ko) <dihedral_class2>`
+   * :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>`
+   * :doc:`fourier (io) <dihedral_fourier>`
+   * :doc:`harmonic (iko) <dihedral_harmonic>`
+   * :doc:`helix (o) <dihedral_helix>`
+   * :doc:`multi/harmonic (o) <dihedral_multi_harmonic>`
+   * :doc:`nharmonic (o) <dihedral_nharmonic>`
+   * :doc:`opls (iko) <dihedral_opls>`
+   * :doc:`quadratic (o) <dihedral_quadratic>`
+   * :doc:`spherical <dihedral_spherical>`
+   * :doc:`table (o) <dihedral_table>`
+   * :doc:`table/cut <dihedral_table_cut>`
 
 .. _improper:
 
-Improper\_style potentials
+Improper_style potentials
-=========================================
+=========================
 
-All LAMMPS :doc:`improper\_style <improper_style>` commands.  Some styles
+All LAMMPS :doc:`improper_style <improper_style>` commands.  Some styles
 have accelerated versions.  This is indicated by additional letters in
 parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.
 
-+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
+.. table_from_list::
-| :doc:`none <improper_none>`          | :doc:`zero <improper_zero>`             | :doc:`hybrid <improper_hybrid>`           |                                                         |
+   :columns: 4
-+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
-|                                      |                                         |                                           |                                                         |
-+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
-| :doc:`class2 (ko) <improper_class2>` | :doc:`cossq (o) <improper_cossq>`       | :doc:`cvff (io) <improper_cvff>`          | :doc:`distance <improper_distance>`                     |
-+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
-| :doc:`distharm <improper_distharm>`  | :doc:`fourier (o) <improper_fourier>`   | :doc:`harmonic (iko) <improper_harmonic>` | :doc:`inversion/harmonic <improper_inversion_harmonic>` |
-+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
-| :doc:`ring (o) <improper_ring>`      | :doc:`sqdistharm <improper_sqdistharm>` | :doc:`umbrella (o) <improper_umbrella>`   |                                                         |
-+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
 
-
+   * :doc:`none <improper_none>`
-.. _lws: http://lammps.sandia.gov
+   * :doc:`zero <improper_zero>`
-.. _ld: Manual.html
+   * :doc:`hybrid <improper_hybrid>`
-.. _lc: Commands_all.html
+   *
+   *
+   *
+   *
+   *
+   * :doc:`class2 (ko) <improper_class2>`
+   * :doc:`cossq (o) <improper_cossq>`
+   * :doc:`cvff (io) <improper_cvff>`
+   * :doc:`distance <improper_distance>`
+   * :doc:`distharm <improper_distharm>`
+   * :doc:`fourier (o) <improper_fourier>`
+   * :doc:`harmonic (iko) <improper_harmonic>`
+   * :doc:`inversion/harmonic <improper_inversion_harmonic>`
+   * :doc:`ring (o) <improper_ring>`
+   * :doc:`sqdistharm <improper_sqdistharm>`
+   * :doc:`umbrella (o) <improper_umbrella>`