Merge pull request #2064 from akohlmey/next_lammps_version

Update version strings for the next patch release

.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

@@ -68,11 +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 outside of <cstdio>, STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. There MUST NOT be any "using namespace XXX;" statements in headers. In the implementation file (<name>.cpp) system includes should be placed in angular brackets (<>) and for c-library functions the C++ style header files should be included (<cstdio> instead of <stdio.h>, or <cstring> instead of <string.h>). This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages.
+* For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no trailing whitespace, no lines over 80 characters. I/O is done via the C-style stdio library, style class header files should not import any system headers, STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. There MUST NOT be any "using namespace XXX;" statements in headers. In the implementation file (<name>.cpp) system includes should be placed in angular brackets (<>) and for c-library functions the C++ style header files should be included (<cstdio> instead of <stdio.h>, or <cstring> instead of <string.h>). This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages.
+* Source, style name, and documentation file should follow the following naming convention: style names should be lowercase and words separated by a forward slash; for a new fix style 'foo/bar', the class should be named FixFooBar, the name of the source files should be 'fix_foo_bar.h' and 'fix_foo_bar.cpp' and the corresponding documentation should be in a file 'fix_foo_bar.rst'.
 * If you want your contribution to be added as a user-contributed feature, and it is a single file (actually a `<name>.cpp` and `<name>.h` file) it can be rapidly added to the USER-MISC directory. Include the one-line entry to add to the USER-MISC/README file in that directory, along with the 2 source files. You can do this multiple times if you wish to contribute several individual features.
 * If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like USER-FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this USER-FOO directory.
 * Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code.
-* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are 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?

bench/POTENTIALS/CH.airebo

@@ -0,0 +1 @@
+../../potentials/CH.airebo

bench/POTENTIALS/CdTe.bop.table

@@ -0,0 +1 @@
+../../potentials/CdTe.bop.table

bench/POTENTIALS/Cu_u3.eam

@@ -1,305 +0,0 @@
-Cu functions (universal 3), SM Foiles et al, PRB, 33, 7983 (1986)
-   29     63.550         3.6150    FCC
-  500  5.0100200400801306e-04  500  1.0000000000000009e-02  4.9499999999999886e+00
-  0.                     -3.1561636903424350e-01 -5.2324876182494506e-01 -6.9740831416804383e-01 -8.5202525457518519e-01
- -9.9329216586042435e-01 -1.1246331970890324e+00 -1.2481882647347859e+00 -1.3654054700363645e+00 -1.4773214276236644e+00
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-  6.8271983168139705e-03  6.7032188559211503e-03  6.5814072030662141e-03  6.4617201320263939e-03  6.3441158405819764e-03
-  6.2285538676237207e-03  6.1149950163802147e-03  6.0034012832899109e-03  5.8937357920846312e-03  5.7859627326801166e-03
-  5.6800473044990030e-03  5.5759556638887986e-03  5.4736548753111791e-03  5.3731128660109428e-03  5.2742983838981461e-03
-  5.1771809583849582e-03  5.0817308639591330e-03  4.9879190862693046e-03  4.8957172905357560e-03  4.8050977921015592e-03
-  4.7160335289582467e-03  4.6284980360953021e-03  4.5424654215287241e-03  4.4579103438822931e-03  4.3748079913988880e-03
-  4.2931340622749670e-03  4.2128647462132407e-03  4.1339767071033873e-03  4.0564470667446839e-03  3.9802533895282599e-03
-  3.9053736680121076e-03  3.8317863093158128e-03  3.7594701222811860e-03  3.6884043053326127e-03  3.6185684349951674e-03
-  3.5499424550168301e-03  3.4825066660512660e-03  3.4162417158645347e-03  3.3511285900229004e-03  3.2871486030347646e-03
-  3.2242833899080170e-03  3.1625148980992668e-03  3.1018253798278661e-03  3.0421973847258310e-03  2.9836137528083811e-03
-  2.9260576077371064e-03  2.8695123503632708e-03  2.8139616525287708e-03  2.7593894511106498e-03  2.7057799422959966e-03
-  2.6531175760685227e-03  2.6013870509009052e-03  2.5505733086344240e-03  2.5006615295404683e-03  2.4516371275501436e-03
-  2.4034857456453340e-03  2.3561932514012535e-03  2.3097457326723414e-03  2.2641294934160616e-03  2.2193310496436136e-03
-  2.1753371254977782e-03  2.1321346494441173e-03  2.0897107505768314e-03  2.0480527550303662e-03  2.0071481824917164e-03
-  1.9669847428123305e-03  1.9275503327108034e-03  1.8888330325659355e-03  1.8508211032951805e-03  1.8135029833145980e-03
-  1.7768672855772646e-03  1.7409027946878666e-03  1.7055984640891586e-03  1.6709434133182904e-03  1.6369269253308227e-03
-  1.6035384438881917e-03  1.5707675710093030e-03  1.5386040644797400e-03  1.5070378354209296e-03  1.4760589459142243e-03
-  1.4456576066784674e-03  1.4158241748004133e-03  1.3865491515145517e-03  1.3578231800324136e-03  1.3296370434173130e-03
-  1.3019816625059188e-03  1.2748480938728074e-03  1.2482275278369870e-03  1.2221112865106742e-03  1.1964908218862064e-03
-  1.1713577139624703e-03  1.1467036689077198e-03  1.1225205172586891e-03  1.0988002121543120e-03  1.0755348276031765e-03
-  1.0527165567835728e-03  1.0303377103750150e-03  1.0083907149206553e-03  9.8686811121878604e-04  9.6576255274356815e-04
-  9.4506680409354657e-04  9.2477373946662708e-04  9.0487634116191706e-04  8.8536769810608137e-04  8.6624100440530968e-04
-  8.4748955791986991e-04  8.2910675886310736e-04  8.1108610842155551e-04  7.9342120739794852e-04  7.7610575487466887e-04
-  7.5913354689786591e-04  7.4249847518158968e-04  7.2619452583109687e-04  7.1021577808524222e-04  6.9455640307671332e-04
-  6.7921066261025093e-04  6.6417290795844214e-04  6.4943757867335500e-04  6.3499920141575628e-04  6.2085238879914031e-04
-  6.0699183824991856e-04  5.9341233088238896e-04  5.8010873038847818e-04  5.6707598194186137e-04  5.5430911111587280e-04
-  5.4180322281523891e-04  5.2955350022104025e-04  5.1755520374872563e-04  5.0580367001857793e-04  4.9429431083891986e-04
-  4.8302261220136561e-04  4.7198413328763435e-04  4.6117450548847222e-04  4.5058943143359842e-04  4.4022468403297037e-04
-  4.3007610552883886e-04  4.2013960655883260e-04  4.1041116522908330e-04  4.0088682619821882e-04  3.9156269977118005e-04
-  3.8243496100300207e-04  3.7349984881274514e-04  3.6475366510662147e-04  3.5619277391102898e-04  3.4781360051482253e-04
-  3.3961263062063513e-04  3.3158640950565685e-04  3.2373154119109092e-04  3.1604468762060252e-04  3.0852256784754707e-04
-  3.0116195723081836e-04  2.9395968663908575e-04  2.8691264166377101e-04  2.8001776184017647e-04  2.7327203987681688e-04
-  2.6667252089326854e-04  2.6021630166557681e-04  2.5390052988028163e-04  2.4772240339593181e-04  2.4167916951265550e-04
-  2.3576812424967210e-04  2.2998661163024531e-04  2.2433202297460642e-04  2.1880179620031078e-04  2.1339341513026532e-04
-  2.0810440880823181e-04  2.0293235082175821e-04  1.9787485863260665e-04  1.9292959291436311e-04  1.8809425689761319e-04
-  1.8336659572205580e-04  1.7874439579616125e-04  1.7422548416372047e-04  1.6980772787763936e-04  1.6548903338088530e-04
-  1.6126734589430591e-04  1.5714064881157744e-04  1.5310696310104604e-04  1.4916434671449329e-04  1.4531089400280153e-04
-  1.4154473513841234e-04  1.3786403554466153e-04  1.3426699533172857e-04  1.3075184873951283e-04  1.2731686358694039e-04
-  1.2396034072819674e-04  1.2068061351527565e-04  1.1747604726729168e-04  1.1434503874632306e-04  1.1128601563955686e-04
-  1.0829743604811193e-04  1.0537778798212988e-04  1.0252558886227753e-04  9.9739385027582898e-05  9.7017751249615057e-05
-  9.4359290252773662e-05  9.1762632240957511e-05  8.9226434430383569e-05  8.6749380588361721e-05  8.4330180578390864e-05
-  8.1967569911181246e-05  7.9660309301724484e-05  7.7407184232279429e-05  7.5207004521348451e-05  7.3058603898526649e-05
-  7.0960839585107720e-05  6.8912591880629977e-05  6.6912763755002085e-05  6.4960280446513426e-05  6.3054089065330086e-05
-  6.1193158202771814e-05  5.9376477546041213e-05  5.7603057498502742e-05  5.5871928805544500e-05  5.4182142185708361e-05
-  5.2532767967318744e-05  5.0922895730446966e-05  4.9351633954125953e-05  4.7818109668823321e-05  4.6321468114150300e-05
-  4.4860872401664663e-05  4.3435503182825573e-05  4.2044558321957873e-05  4.0687252574273750e-05  3.9362817268785450e-05
-  3.8070499996214428e-05  3.6809564301621984e-05  3.5579289382025496e-05  3.4378969788611451e-05  3.3207915133769052e-05
-  3.2065449802711312e-05  3.0950912669766876e-05  2.9863656819185611e-05  2.8803049270468119e-05  2.7768470708167169e-05
-  2.6759315216115260e-05  2.5774990015931323e-05  2.4814915209964844e-05  2.3878523528387922e-05  2.2965260080560611e-05
-  2.2074582110528148e-05  2.1205958756658535e-05  2.0358870815317476e-05  1.9532810508535560e-05  1.8727281255713447e-05
-  1.7941797449145505e-05  1.7175884233475961e-05  1.6429077288930018e-05  1.5700922618341645e-05  1.4990976337865471e-05
-  1.4298804471386687e-05  1.3623982748522034e-05  1.2966096406226424e-05  1.2324739993882115e-05  1.1699517181902770e-05
-  1.1090040573734860e-05  1.0495931521266495e-05  9.9168199435395021e-06  9.3523441487842465e-06  8.8021506596591475e-06
-  8.2658940417265321e-06  7.7432367350197678e-06  7.2338488887770244e-06  6.7374081991923703e-06  6.2535997501888662e-06
-  5.7821158571569505e-06  5.3226559136389283e-06  4.8749262408651290e-06  4.4386399401326240e-06  4.0135167480073166e-06
-  3.5992828942305738e-06  3.1956709623667747e-06  2.8024197531120341e-06  2.4192741502208947e-06  2.0459849890155880e-06
-  1.6823089274468580e-06  1.3280083196495871e-06  9.8285109196557868e-07  6.4661062138351467e-07  3.1906561636122974e-07
-  0.                      0.                      0.                      0.                      0.
-
-

bench/POTENTIALS/Cu_u3.eam

@@ -0,0 +1 @@
+../../potentials/Cu_u3.eam

bench/POTENTIALS/Ni.adp

@@ -0,0 +1 @@
+../../potentials/Ni.adp

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 "${CMAKE_BUILD_TYPE}" BTYPE)
@@ -52,109 +46,85 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
 include(CheckCCompilerFlag)
 include(CheckIncludeFileCXX)
 
-if (${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
-  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
+# set required compiler flags and compiler/CPU arch specific optimizations
+if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
+  if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
+    set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
+  else()
+    set(CMAKE_TUNE_DEFAULT "-xHost")
+  endif()
 endif()
 
-# GNU compiler features
+if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
+  set(CMAKE_TUNE_DEFAULT "-ffast-math -march=native")
+endif()
+
+if(${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)
-if(BUILD_EXE)
-  set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically")
-  mark_as_advanced(LAMMPS_MACHINE)
-  if(LAMMPS_MACHINE)
-    set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}")
-  endif()
-  set(LAMMPS_BINARY lmp${LAMMPS_MACHINE})
+set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically")
+mark_as_advanced(LAMMPS_MACHINE)
+if(LAMMPS_MACHINE)
+  set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}")
 endif()
+set(LAMMPS_BINARY lmp${LAMMPS_MACHINE})
 
-option(BUILD_LIB "Build LAMMPS library" OFF)
-if(BUILD_LIB)
-  option(BUILD_SHARED_LIBS "Build shared library" OFF)
-  if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
-    set(CMAKE_POSITION_INDEPENDENT_CODE ON)
-  endif()
-  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()
+option(BUILD_SHARED_LIBS "Build shared library" OFF)
+if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
+  set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 endif()
 
 option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
 
-if(NOT BUILD_EXE AND NOT BUILD_LIB)
-  message(FATAL_ERROR "You need to at least enable one of two following options: BUILD_LIB or BUILD_EXE")
-endif()
+include(GNUInstallDirs)
+file(GLOB ALL_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
+file(GLOB MAIN_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
+list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})
+add_library(lammps ${ALL_SOURCES})
+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(LAMMPS_DEPS)
-set(LAMMPS_API_DEFINES)
-
-set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
+set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS 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-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
-  USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
-set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
-foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
+  USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION
+  USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+  USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
+set(SUFFIX_PACKAGES CORESHELL USER-OMP KOKKOS OPT USER-INTEL GPU)
+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
@@ -162,27 +132,44 @@ 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" ${MPI_FOUND})
 if(BUILD_MPI)
-  find_package(MPI REQUIRED)
-  include_directories(${MPI_CXX_INCLUDE_PATH})
-  list(APPEND LAMMPS_LINK_LIBS ${MPI_CXX_LIBRARIES})
-  option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
-  if(LAMMPS_LONGLONG_TO_LONG)
-    add_definitions(-DLAMMPS_LONGLONG_TO_LONG)
+  # We use a non-standard procedure to cross-compile with MPI on Windows
+  if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)
+    include(MPI4WIN)
+    target_link_libraries(lammps PUBLIC MPI::MPI_CXX)
+  else()
+    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)
-  list(APPEND LAMMPS_LINK_LIBS mpi_stubs)
+  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)")
@@ -190,8 +177,7 @@ 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})
-set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -DLAMMPS_${LAMMPS_SIZES}")
+target_compile_definitions(lammps PUBLIC -DLAMMPS_${LAMMPS_SIZES})
 
 # posix_memalign is not available on Windows
 if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
@@ -200,13 +186,12 @@ 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)
-  set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -DLAMMPS_EXCEPTIONS")
+  target_compile_definitions(lammps PUBLIC -DLAMMPS_EXCEPTIONS)
 endif()
 
 # "hard" dependencies between packages resulting
@@ -217,41 +202,53 @@ 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)
-
-# TODO: this is a temporary workaround until a better solution is found. AK 2019-05-30
-# GNU GCC 9.x uses settings incompatible with our use of 'default(none)' in OpenMP pragmas
-# where we assume older GCC semantics. For the time being, we disable OpenMP by default
-# for GCC 9.x and beyond. People may manually turn it on, but need to run the script
-# 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})
+if(OpenMP_FOUND)
+  check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
+  if(HAVE_OMP_H_INCLUDE)
+    set(BUILD_OMP_DEFAULT ON)
+  endif()
 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)
+  enable_language(C)
   find_package(LAPACK)
   find_package(BLAS)
   if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
-    if(CMAKE_GENERATOR STREQUAL "Ninja")
-      status(FATAL_ERROR "Cannot build internal linear algebra library with Ninja build tool due to lack for Fortran support")
+    include(CheckGeneratorSupport)
+    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 ${LAPACK_SOURCES})
-    set(BLAS_LIBRARIES linalg)
-    set(LAPACK_LIBRARIES linalg)
+    set_target_properties(linalg PROPERTIES OUTPUT_NAME lammps_linalg${LAMMPS_MACHINE})
+    set(BLAS_LIBRARIES "$<TARGET_FILE:linalg>")
+    set(LAPACK_LIBRARIES "$<TARGET_FILE:linalg>")
   else()
     list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
   endif()
@@ -262,9 +259,13 @@ find_package(JPEG QUIET)
 option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND})
 if(WITH_JPEG)
   find_package(JPEG REQUIRED)
-  add_definitions(-DLAMMPS_JPEG)
-  include_directories(${JPEG_INCLUDE_DIR})
-  list(APPEND LAMMPS_LINK_LIBS ${JPEG_LIBRARIES})
+  target_compile_definitions(lammps PRIVATE -DLAMMPS_JPEG)
+  if(CMAKE_VERSION VERSION_LESS 3.12)
+    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)
@@ -277,9 +278,8 @@ endif()
 if(WITH_PNG)
   find_package(PNG REQUIRED)
   find_package(ZLIB REQUIRED)
-  include_directories(${PNG_INCLUDE_DIRS} ${ZLIB_INCLUDE_DIRS})
-  list(APPEND LAMMPS_LINK_LIBS ${PNG_LIBRARIES} ${ZLIB_LIBRARIES})
-  add_definitions(-DLAMMPS_PNG)
+  target_link_libraries(lammps PRIVATE PNG::PNG ZLIB::ZLIB)
+  target_compile_definitions(lammps PRIVATE -DLAMMPS_PNG)
 endif()
 
 find_program(GZIP_EXECUTABLE gzip)
@@ -289,7 +289,7 @@ 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)
@@ -299,7 +299,7 @@ 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)
@@ -312,28 +312,25 @@ else()
   set(CUDA_REQUEST_PIC)
 endif()
 
-include(Packages/KSPACE)
-include(Packages/PYTHON)
-include(Packages/VORONOI)
-include(Packages/USER-SCAFACOS)
-include(Packages/USER-PLUMED)
-include(Packages/USER-MOLFILE)
-include(Packages/USER-NETCDF)
-include(Packages/USER-SMD)
-include(Packages/USER-QUIP)
-include(Packages/USER-QMMM)
-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(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
-  list(APPEND LAMMPS_LINK_LIBS -lwsock32 -lpsapi)
-endif()
+foreach(PKG_WITH_INCL KSPACE PYTHON VORONOI USER-COLVARS USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM
+        USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS)
+  if(PKG_${PKG_WITH_INCL})
+    include(Packages/${PKG_WITH_INCL})
+  endif()
+endforeach()
 
+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)   #
 ########################################################################
@@ -346,18 +343,7 @@ endforeach(HEADER)
 
 set(MATH_LIBRARIES "m" CACHE STRING "math library")
 mark_as_advanced( MATH_LIBRARIES )
-include(CheckLibraryExists)
-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})
+target_link_libraries(lammps PRIVATE ${MATH_LIBRARIES})
 
 ######################################
 # Generate Basic Style files
@@ -368,7 +354,7 @@ 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)
@@ -381,8 +367,8 @@ foreach(PKG ${DEFAULT_PACKAGES})
     # detects styles in package and adds them to global list
     RegisterStyles(${${PKG}_SOURCES_DIR})
 
-    list(APPEND LIB_SOURCES ${${PKG}_SOURCES})
-    include_directories(${${PKG}_SOURCES_DIR})
+    target_sources(lammps PRIVATE ${${PKG}_SOURCES})
+    target_include_directories(lammps PRIVATE ${${PKG}_SOURCES_DIR})
   endif()
 
   RegisterPackages(${${PKG}_SOURCES_DIR})
@@ -391,12 +377,12 @@ 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)
@@ -411,25 +397,20 @@ endforeach()
 ##############################################
 # add lib sources of (simple) enabled packages
 ############################################
-foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-COLVARS 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 ${PKG_LIB})
+    set_target_properties(${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)
       target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include ${HDF5_INCLUDE_DIRS})
-    elseif(PKG_LIB STREQUAL colvars)
-      target_compile_options(colvars PRIVATE -DLEPTON)
-      target_include_directories(colvars PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton/include)
-      target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
     else()
       target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB})
     endif()
@@ -437,30 +418,45 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
 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})
+  if(BUILD_MPI)
+    target_link_libraries(atc PRIVATE MPI::MPI_CXX)
+  else()
+    target_link_libraries(atc PRIVATE mpi_stubs)
+  endif()
+  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)
-include(Packages/QEQ)
-include(Packages/USER-OMP)
-include(Packages/USER-SDPD)
-include(Packages/KOKKOS)
-include(Packages/OPT)
-include(Packages/USER-INTEL)
-include(Packages/GPU)
+foreach(PKG_WITH_INCL CORESHELL QEQ USER-OMP USER-SDPD KOKKOS OPT USER-INTEL GPU)
+  if(PKG_${PKG_WITH_INCL})
+    include(Packages/${PKG_WITH_INCL})
+  endif()
+endforeach()
+
+######################################################################
+# 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
@@ -472,14 +468,14 @@ 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})
@@ -501,7 +497,7 @@ 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
@@ -509,93 +505,68 @@ 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)
-if(BUILD_LIB)
-  add_library(lammps ${LIB_SOURCES})
-  target_link_libraries(lammps ${LAMMPS_LINK_LIBS})
-  if(LAMMPS_DEPS)
-    add_dependencies(lammps ${LAMMPS_DEPS})
+set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h compute.h dihedral.h domain.h error.h fix.h force.h group.h improper.h
+  input.h info.h kspace.h lammps.h lattice.h library.h lmppython.h lmptype.h memory.h modify.h neighbor.h neigh_list.h output.h
+  pair.h pointers.h region.h timer.h universe.h update.h variable.h)
+if(LAMMPS_EXCEPTIONS)
+  list(APPEND LAMMPS_CXX_HEADERS exceptions.h)
+endif()
+
+set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
+set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
+target_include_directories(lammps PUBLIC $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>)
+file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps)
+foreach(_HEADER ${LAMMPS_CXX_HEADERS})
+  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_custom_target(${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER})
+  add_dependencies(lammps ${_HEADER})
+  if(BUILD_SHARED_LIBS)
+    install(FILES ${LAMMPS_SOURCE_DIR}/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
   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)
-  add_executable(lmp ${LMP_SOURCES})
-  if(BUILD_LIB)
-    target_link_libraries(lmp lammps)
-  else()
-    target_link_libraries(lmp ${LAMMPS_LINK_LIBS})
-    if(LAMMPS_DEPS)
-      add_dependencies(lmp ${LAMMPS_DEPS})
-    endif()
-  endif()
-
-  set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})
-  install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
-  install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1)
+endforeach()
+target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/includes>)
+add_library(LAMMPS::lammps ALIAS lammps)
+get_target_property(LAMMPS_DEFINES lammps INTERFACE_COMPILE_DEFINITIONS)
+set(LAMMPS_API_DEFINES)
+foreach(_DEF ${LAMMPS_DEFINES})
+  set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${_DEF}")
+endforeach()
+if(BUILD_SHARED_LIBS)
+  install(TARGETS lammps EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+  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)
 endif()
+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
-  if(NOT CMAKE_GENERATOR STREQUAL "Ninja")
-    message(STATUS "Skipping building 'chain.x' with Ninja build tool due to lack of Fortran support")
+  include(CheckGeneratorSupport)
+  if(CMAKE_GENERATOR_SUPPORT_FORTRAN AND CMAKE_Fortran_COMPILER)
     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()
@@ -625,12 +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)
-  find_package(PythonInterp)
-  if (PYTHONINTERP_FOUND)
+if(BUILD_SHARED_LIBS)
+  if(CMAKE_VERSION VERSION_LESS 3.12)
+    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}
@@ -651,10 +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))
-  find_package(PythonInterp)
-  if (PYTHONINTERP_FOUND)
-    execute_process(COMMAND ${PYTHON_EXECUTABLE}
+if(BUILD_SHARED_LIBS OR PKG_PYTHON)
+  if(CMAKE_VERSION VERSION_LESS 3.12)
+    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)
+    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")
@@ -668,69 +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}
-   Install path     ${CMAKE_INSTALL_PREFIX}
-   Compilers and Flags:
-   C++ Compiler     ${CMAKE_CXX_COMPILER}
-       Type         ${CMAKE_CXX_COMPILER_ID}
-       Version      ${CMAKE_CXX_COMPILER_VERSION}
-   C++ Flags        ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}
-   Defines          ${CPPFLAGS}")
+   Build type:       ${CMAKE_BUILD_TYPE}
+   Install path:     ${CMAKE_INSTALL_PREFIX}
+   Generator:        ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}
+-- <<< Compilers and Flags: >>>
+-- C++ Compiler:     ${CMAKE_CXX_COMPILER}
+      Type:          ${CMAKE_CXX_COMPILER_ID}
+      Version:       ${CMAKE_CXX_COMPILER_VERSION}
+      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}
-           Type     ${CMAKE_Fortran_COMPILER_ID}
-           Version  ${CMAKE_Fortran_COMPILER_VERSION}
-   Fortran Flags    ${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}")
+  message(STATUS "Fortran Compiler: ${CMAKE_Fortran_COMPILER}
+      Type:          ${CMAKE_Fortran_COMPILER_ID}
+      Version:       ${CMAKE_Fortran_COMPILER_VERSION}
+      Fortran Flags:${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}")
 endif()
 list (FIND LANGUAGES "C" _index)
 if (${_index} GREATER -1)
-  message(STATUS "C Compiler ${CMAKE_C_COMPILER}
-     Type     ${CMAKE_C_COMPILER_ID}
-     Version  ${CMAKE_C_COMPILER_VERSION}
-     C Flags  ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${BTYPE}}")
+  message(STATUS "C compiler:       ${CMAKE_C_COMPILER}
+      Type:          ${CMAKE_C_COMPILER_ID}
+      Version:       ${CMAKE_C_COMPILER_VERSION}
+      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:
-   Executable      ${CMAKE_EXE_LINKER_FLAGS}")
+  message(STATUS "Executable linker flags: ${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 +1,11 @@
+list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR})
+include(CMakeFindDependencyMacro)
+if(@BUILD_MPI@)
+  find_dependency(MPI REQUIRED CXX)
+endif()
+if(@PKG_KSPACE@)
+  if(@FFT@ STREQUAL "FFTW3")
+    find_dependency(@FFTW@ REQUIRED MODULE)
+  endif()
+endif()
+include("${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

@@ -1,17 +1,13 @@
 ###############################################################################
 # 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)
 
-  file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.txt)
-  file(GLOB PDF_EXTRA_SOURCES ${LAMMPS_DOC_DIR}/src/lammps_commands*.txt ${LAMMPS_DOC_DIR}/src/lammps_support.txt ${LAMMPS_DOC_DIR}/src/lammps_tutorials.txt)
-  list(REMOVE_ITEM DOC_SOURCES ${PDF_EXTRA_SOURCES})
+  file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
 
   add_custom_command(
     OUTPUT docenv
@@ -28,30 +24,49 @@ if(BUILD_DOC)
     COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
   )
 
-  set(RST_FILES "")
-  set(RST_DIR ${CMAKE_BINARY_DIR}/rst)
-  file(MAKE_DIRECTORY ${RST_DIR})
-  foreach(TXT_FILE ${DOC_SOURCES})
-    get_filename_component(FILENAME ${TXT_FILE} NAME_WE)
-    set(RST_FILE ${RST_DIR}/${FILENAME}.rst)
-    list(APPEND RST_FILES ${RST_FILE})
+  # download mathjax distribution and unpack to folder "mathjax"
+  file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
+    "${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 -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 ${RST_FILE}
-      DEPENDS requirements.txt docenv ${TXT_FILE}
-      COMMAND ${DOCENV_BINARY_DIR}/txt2rst -o ${RST_DIR} ${TXT_FILE}
+      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_command(
-    OUTPUT html
-    DEPENDS ${RST_FILES}
-    COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src ${RST_DIR}
-    COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${RST_DIR} html
-  )
-
   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_LIBRARIES    - List of libraries when using fftw3.
-#  FFTW3_FOUND        - True if fftw3 found.
+#  FFTW3_INCLUDE_DIRS  - where to find fftw3.h, etc.
+#  FFTW3_LIBRARIES     - List of libraries when using fftw3.
+#  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})
-
-set(FFTW3_LIBRARIES ${FFTW3_LIBRARY})
-set(FFTW3_INCLUDE_DIRS ${FFTW3_INCLUDE_DIR})
+find_library(FFTW3_OMP_LIBRARY NAMES fftw3_omp HINTS ${PC_FFTW3_LIBRARY_DIRS})
 
 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 FFTW3F headers and libraries.
+# Find the native single precision FFTW3 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})
-
-set(FFTW3F_LIBRARIES ${FFTW3F_LIBRARY})
-set(FFTW3F_INCLUDE_DIRS ${FFTW3F_INCLUDE_DIR})
+find_library(FFTW3F_OMP_LIBRARY NAMES fftw3f_omp HINTS ${PC_FFTW3F_LIBRARY_DIRS})
 
 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

@@ -1,59 +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
-#
-
-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()
-
-# 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)

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)
-  include_directories(${ZLIB_INCLUDE_DIRS})
-  list(APPEND LAMMPS_LINK_LIBS ${ZLIB_LIBRARIES})
-endif()
+find_package(ZLIB REQUIRED)
+target_link_libraries(lammps PRIVATE ZLIB::ZLIB)

cmake/Modules/Packages/CORESHELL.cmake

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

cmake/Modules/Packages/GPU.cmake

@@ -1,194 +1,371 @@
-if(PKG_GPU)
-    if (CMAKE_VERSION VERSION_LESS "3.1")
-      message(FATAL_ERROR "For the GPU package you need at least cmake-3.1")
-    endif()
-    set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
-    set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
-                    ${GPU_SOURCES_DIR}/fix_gpu.h
-                    ${GPU_SOURCES_DIR}/fix_gpu.cpp)
+set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
+set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
+                ${GPU_SOURCES_DIR}/fix_gpu.h
+                ${GPU_SOURCES_DIR}/fix_gpu.cpp)
 
-    set(GPU_API "opencl" CACHE STRING "API used by GPU package")
-    set(GPU_API_VALUES opencl cuda)
-    set_property(CACHE GPU_API PROPERTY STRINGS ${GPU_API_VALUES})
-    validate_option(GPU_API GPU_API_VALUES)
-    string(TOUPPER ${GPU_API} GPU_API)
+set(GPU_API "opencl" CACHE STRING "API used by GPU package")
+set(GPU_API_VALUES opencl cuda hip)
+set_property(CACHE GPU_API PROPERTY STRINGS ${GPU_API_VALUES})
+validate_option(GPU_API GPU_API_VALUES)
+string(TOUPPER ${GPU_API} GPU_API)
 
-    set(GPU_PREC "mixed" CACHE STRING "LAMMPS GPU precision")
-    set(GPU_PREC_VALUES double mixed single)
-    set_property(CACHE GPU_PREC PROPERTY STRINGS ${GPU_PREC_VALUES})
-    validate_option(GPU_PREC GPU_PREC_VALUES)
-    string(TOUPPER ${GPU_PREC} GPU_PREC)
+set(GPU_PREC "mixed" CACHE STRING "LAMMPS GPU precision")
+set(GPU_PREC_VALUES double mixed single)
+set_property(CACHE GPU_PREC PROPERTY STRINGS ${GPU_PREC_VALUES})
+validate_option(GPU_PREC GPU_PREC_VALUES)
+string(TOUPPER ${GPU_PREC} GPU_PREC)
 
-    if(GPU_PREC STREQUAL "DOUBLE")
-      set(GPU_PREC_SETTING "DOUBLE_DOUBLE")
-    elseif(GPU_PREC STREQUAL "MIXED")
-      set(GPU_PREC_SETTING "SINGLE_DOUBLE")
-    elseif(GPU_PREC STREQUAL "SINGLE")
-      set(GPU_PREC_SETTING "SINGLE_SINGLE")
-    endif()
-
-    file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
-    file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
-
-    if(GPU_API STREQUAL "CUDA")
-      find_package(CUDA REQUIRED)
-      find_program(BIN2C bin2c)
-      if(NOT BIN2C)
-        message(FATAL_ERROR "Could not find bin2c, use -DBIN2C=/path/to/bin2c to help cmake finding it.")
-      endif()
-      option(CUDPP_OPT "Enable CUDPP_OPT" ON)
-      option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF)
-      if(CUDA_MPS_SUPPORT)
-        set(GPU_CUDA_MPS_FLAGS "-DCUDA_PROXY")
-      endif()
-
-      set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
-
-      file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
-      list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
-
-      cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
-
-      if(CUDPP_OPT)
-        cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
-        file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
-        file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
-      endif()
-
-      # build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
-      # --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
-      set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH} ")
-      # Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
-      if((CUDA_VERSION VERSION_GREATER "3.1") AND (CUDA_VERSION VERSION_LESS "9.0"))
-        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_20,code=[sm_20,compute_20] ")
-      endif()
-      # Kepler (GPU Arch 3.x) is supported by CUDA 5 and later
-      if(CUDA_VERSION VERSION_GREATER "4.9")
-        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35] ")
-      endif()
-      # Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
-      if(CUDA_VERSION VERSION_GREATER "5.9")
-        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] ")
-      endif()
-      # Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
-      if(CUDA_VERSION VERSION_GREATER "7.9")
-        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] ")
-      endif()
-      # Volta (GPU Arch 7.0) is supported by CUDA 9 and later
-      if(CUDA_VERSION VERSION_GREATER "8.9")
-        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_70,code=[sm_70,compute_70] ")
-      endif()
-      # Turing (GPU Arch 7.5) is supported by CUDA 10 and later
-      if(CUDA_VERSION VERSION_GREATER "9.9")
-        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ")
-      endif()
-
-      cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
-              -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
-
-      cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
-              -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
-
-      foreach(CU_OBJ ${GPU_GEN_OBJS})
-        get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
-        string(REGEX REPLACE "^.*_lal_" "" CU_NAME "${CU_NAME}")
-        add_custom_command(OUTPUT ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
-          COMMAND ${BIN2C} -c -n ${CU_NAME} ${CU_OBJ} > ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
-          DEPENDS ${CU_OBJ}
-          COMMENT "Generating ${CU_NAME}_cubin.h")
-        list(APPEND GPU_LIB_SOURCES ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h)
-      endforeach()
-      set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "${LAMMPS_LIB_BINARY_DIR}/gpu/*_cubin.h")
-
-
-      add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
-      target_link_libraries(gpu ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
-      target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
-      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS})
-      if(CUDPP_OPT)
-        target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
-        target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
-      endif()
-
-      list(APPEND LAMMPS_LINK_LIBS gpu)
-
-      add_executable(nvc_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
-      target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR)
-      target_link_libraries(nvc_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
-      target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
-
-
-    elseif(GPU_API STREQUAL "OPENCL")
-      find_package(OpenCL REQUIRED)
-      set(OCL_TUNE "generic" CACHE STRING "OpenCL Device Tuning")
-      set(OCL_TUNE_VALUES intel fermi kepler cypress generic)
-      set_property(CACHE OCL_TUNE PROPERTY STRINGS ${OCL_TUNE_VALUES})
-      validate_option(OCL_TUNE OCL_TUNE_VALUES)
-      string(TOUPPER ${OCL_TUNE} OCL_TUNE)
-
-      include(OpenCLUtils)
-      set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
-
-      file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
-      list(REMOVE_ITEM GPU_LIB_CU
-        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu
-        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu
-        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu
-        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu
-        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu
-        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu
-        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu
-      )
-
-      foreach(GPU_KERNEL ${GPU_LIB_CU})
-          get_filename_component(basename ${GPU_KERNEL} NAME_WE)
-          string(SUBSTRING ${basename} 4 -1 KERNEL_NAME)
-          GenerateOpenCLHeader(${KERNEL_NAME} ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h ${OCL_COMMON_HEADERS} ${GPU_KERNEL})
-          list(APPEND GPU_LIB_SOURCES ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h)
-      endforeach()
-
-      GenerateOpenCLHeader(gayberne ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu)
-      GenerateOpenCLHeader(gayberne_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu)
-      GenerateOpenCLHeader(re_squared ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu)
-      GenerateOpenCLHeader(re_squared_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu)
-      GenerateOpenCLHeader(tersoff ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu)
-      GenerateOpenCLHeader(tersoff_zbl ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu)
-      GenerateOpenCLHeader(tersoff_mod ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu)
-
-      list(APPEND GPU_LIB_SOURCES
-        ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h
-        ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h
-        ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h
-        ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h
-        ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h
-        ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h
-        ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h
-      )
-
-      add_library(gpu STATIC ${GPU_LIB_SOURCES})
-      target_link_libraries(gpu ${OpenCL_LIBRARIES})
-      target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu ${OpenCL_INCLUDE_DIRS})
-      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -D${OCL_TUNE}_OCL -DMPI_GERYON -DUCL_NO_EXIT)
-      target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
-
-      list(APPEND LAMMPS_LINK_LIBS gpu)
-
-      add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
-      target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL)
-      target_link_libraries(ocl_get_devices PRIVATE ${OpenCL_LIBRARIES})
-      target_include_directories(ocl_get_devices PRIVATE ${OpenCL_INCLUDE_DIRS})
-    endif()
-
-    # GPU package
-    FindStyleHeaders(${GPU_SOURCES_DIR} FIX_CLASS fix_ FIX)
-
-    set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
-
-    # detects styles which have GPU version
-    RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)
-
-    get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
-
-    list(APPEND LIB_SOURCES ${GPU_SOURCES})
-    include_directories(${GPU_SOURCES_DIR})
+if(GPU_PREC STREQUAL "DOUBLE")
+  set(GPU_PREC_SETTING "DOUBLE_DOUBLE")
+elseif(GPU_PREC STREQUAL "MIXED")
+  set(GPU_PREC_SETTING "SINGLE_DOUBLE")
+elseif(GPU_PREC STREQUAL "SINGLE")
+  set(GPU_PREC_SETTING "SINGLE_SINGLE")
 endif()
+
+file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
+file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
+
+if(GPU_API STREQUAL "CUDA")
+  find_package(CUDA REQUIRED)
+  find_program(BIN2C bin2c)
+  if(NOT BIN2C)
+    message(FATAL_ERROR "Could not find bin2c, use -DBIN2C=/path/to/bin2c to help cmake finding it.")
+  endif()
+  option(CUDPP_OPT "Enable CUDPP_OPT" ON)
+  option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF)
+  if(CUDA_MPS_SUPPORT)
+    set(GPU_CUDA_MPS_FLAGS "-DCUDA_PROXY")
+  endif()
+
+  set(GPU_ARCH "sm_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()
+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

@@ -1,49 +1,63 @@
-if(PKG_KIM)
-  find_package(CURL)
-  if(CURL_FOUND)
-    include_directories(${CURL_INCLUDE_DIRS})
-    list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES})
-    add_definitions(-DLMP_KIM_CURL)
+set(KIM-API_MIN_VERSION 2.1.3)
+find_package(CURL)
+if(CURL_FOUND)
+  if(CMAKE_VERSION VERSION_LESS 3.12)
+    target_include_directories(lammps PRIVATE ${CURL_INCLUDE_DIRS})
+    target_link_libraries(lammps PRIVATE ${CURL_LIBRARIES})
+  else()
+    target_link_libraries(lammps PRIVATE CURL::libcurl)
   endif()
-  find_package(KIM-API QUIET)
+  target_compile_definitions(lammps PRIVATE -DLMP_KIM_CURL)
+  set(LMP_DEBUG_CURL OFF CACHE STRING "Set libcurl verbose mode on/off. If on, it displays a lot of verbose information about its operations.")
+  mark_as_advanced(LMP_DEBUG_CURL)
+  if(LMP_DEBUG_CURL)
+    target_compile_definitions(lammps PRIVATE -DLMP_DEBUG_CURL)
+  endif()
+  set(LMP_NO_SSL_CHECK OFF CACHE STRING "Tell libcurl to not verify the peer. If on, the connection succeeds regardless of the names in the certificate. Insecure - Use with caution!")
+  mark_as_advanced(LMP_NO_SSL_CHECK)
+  if(LMP_NO_SSL_CHECK)
+    target_compile_definitions(lammps PRIVATE -DLMP_NO_SSL_CHECK)
+  endif()
+endif()
+find_package(PkgConfig QUIET)
+set(DOWNLOAD_KIM_DEFAULT ON)
+if(PKG_CONFIG_FOUND)
+  pkg_check_modules(KIM-API QUIET libkim-api>=${KIM-API_MIN_VERSION})
   if(KIM-API_FOUND)
     set(DOWNLOAD_KIM_DEFAULT OFF)
-  else()
-    if (NOT DOWNLOAD_KIM)
-      message(WARNING "KIM-API package not found.  We will download and build our own")
-    endif()
-    set(DOWNLOAD_KIM_DEFAULT ON)
   endif()
-  option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT})
-  if(DOWNLOAD_KIM)
-    if(CMAKE_GENERATOR STREQUAL "Ninja")
-      message(FATAL_ERROR "Cannot build downloaded KIM-API library with Ninja build tool")
-    endif()
-    message(STATUS "KIM-API download requested - we will build our own")
-    include(CheckLanguage)
-    include(ExternalProject)
-    enable_language(C)
-    check_language(Fortran)
-    if(NOT CMAKE_Fortran_COMPILER)
-      message(FATAL_ERROR "Compiling the KIM-API library requires a Fortran compiler")
-    endif()
-    ExternalProject_Add(kim_build
-      URL https://s3.openkim.org/kim-api/kim-api-2.1.2.txz
-      URL_MD5 6ac52e14ef52967fc7858220b208cba5
-      BINARY_DIR build
-      CMAKE_ARGS -DCMAKE_C_COMPILER=${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${CMAKE_SHARED_LIBRARY_SUFFIX})
-    list(APPEND LAMMPS_DEPS kim_build)
-  else()
-    find_package(KIM-API REQUIRED)
-  endif()
-  list(APPEND LAMMPS_LINK_LIBS "${KIM-API_LDFLAGS}")
-  include_directories(${KIM-API_INCLUDE_DIRS})
+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)
+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

@@ -1,53 +1,122 @@
-if(PKG_KOKKOS)
+########################################################################
+# consistency checks and Kokkos options/settings required by LAMMPS
+if(Kokkos_ENABLE_CUDA)
+  message(STATUS "KOKKOS: Enabling CUDA LAMBDA function support")
+  set(Kokkos_ENABLE_CUDA_LAMBDA ON CACHE BOOL "" FORCE)
+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)
+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 ${LAMMPS_LIB_BINARY_DIR}/kokkos)
-  add_definitions(-DLMP_KOKKOS)
   add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
 
   set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
                           ${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
                           ${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src
                           ${LAMMPS_LIB_KOKKOS_BIN_DIR})
-  include_directories(${Kokkos_INCLUDE_DIRS})
-  list(APPEND LAMMPS_LINK_LIBS kokkos)
-
-  set(KOKKOS_PKG_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/KOKKOS)
-  set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/atom_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/neighbor_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/neigh_list_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/neigh_bond_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/fix_nh_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.cpp
-                         ${KOKKOS_PKG_SOURCES_DIR}/npair_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)
-
-  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})
+  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)
-  set(FFTW "FFTW3")
-  if(FFT_SINGLE)
-    set(FFTW "FFTW3F")
-    add_definitions(-DFFT_SINGLE)
-  endif()
-  find_package(${FFTW} QUIET)
-  if(${FFTW}_FOUND)
-    set(FFT "FFTW3" CACHE STRING "FFT library for KSPACE package")
-  else()
-    set(FFT "KISS" CACHE STRING "FFT library for KSPACE package")
-  endif()
-  set(FFT_VALUES KISS FFTW3 MKL)
-  set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES})
-  validate_option(FFT FFT_VALUES)
-  string(TOUPPER ${FFT} FFT)
-
-  if(FFT STREQUAL "FFTW3")
-    find_package(${FFTW} REQUIRED)
-    add_definitions(-DFFT_FFTW3)
-    include_directories(${${FFTW}_INCLUDE_DIRS})
-    list(APPEND LAMMPS_LINK_LIBS ${${FFTW}_LIBRARIES})
-  elseif(FFT STREQUAL "MKL")
-    find_package(MKL REQUIRED)
-    add_definitions(-DFFT_MKL)
-    include_directories(${MKL_INCLUDE_DIRS})
-    list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES})
-  else()
-    # last option is KISSFFT
-    add_definitions(-DFFT_KISS)
-  endif()
-
-  set(FFT_PACK "array" CACHE STRING "Optimization for FFT")
-  set(FFT_PACK_VALUES array pointer memcpy)
-  set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES})
-  validate_option(FFT_PACK FFT_PACK_VALUES)
-  if(NOT FFT_PACK STREQUAL "array")
-    string(TOUPPER ${FFT_PACK} FFT_PACK)
-    add_definitions(-DFFT_PACK_${FFT_PACK})
-  endif()
+option(FFT_SINGLE "Use single precision FFTs instead of double precision FFTs" OFF)
+set(FFTW "FFTW3")
+if(FFT_SINGLE)
+  set(FFTW "FFTW3F")
+  target_compile_definitions(lammps PUBLIC -DFFT_SINGLE)
+endif()
+find_package(${FFTW} QUIET)
+if(${FFTW}_FOUND)
+  set(FFT "FFTW3" CACHE STRING "FFT library for KSPACE package")
+else()
+  set(FFT "KISS" CACHE STRING "FFT library for KSPACE package")
+endif()
+set(FFT_VALUES KISS FFTW3 MKL)
+set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES})
+validate_option(FFT FFT_VALUES)
+string(TOUPPER ${FFT} FFT)
+
+if(FFT STREQUAL "FFTW3")
+  find_package(${FFTW} REQUIRED)
+  target_compile_definitions(lammps PUBLIC -DFFT_FFTW3)
+  target_link_libraries(lammps PUBLIC ${FFTW}::${FFTW})
+  if(FFTW3_OMP_LIBRARY OR FFTW3F_OMP_LIBRARY)
+    option(FFT_FFTW_THREADS "Use threaded FFTW library" ON)
+  else()
+    option(FFT_FFTW_THREADS "Use threaded FFT library" OFF)
+  endif()
+
+  if(FFT_FFTW_THREADS)
+    if(FFTW3_OMP_LIBRARY OR FFTW3F_OMP_LIBRARY)
+	target_compile_definitions(lammps PRIVATE -DFFT_FFTW_THREADS)
+	target_link_libraries(lammps PRIVATE ${FFTW}::${FFTW}_OMP)
+    else()
+      message(FATAL_ERROR "Need OpenMP enabled FFTW3 library for FFT_THREADS")
+    endif()
+  endif()
+elseif(FFT STREQUAL "MKL")
+  find_package(MKL REQUIRED)
+  target_compile_definitions(lammps PRIVATE -DFFT_MKL)
+  option(FFT_MKL_THREADS "Use threaded MKL FFT" ON)
+  if(FFT_MKL_THREADS)
+    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 +1,44 @@
-if(PKG_LATTE)
-  enable_language(Fortran)
-  find_package(LATTE)
-  if(LATTE_FOUND)
-    set(DOWNLOAD_LATTE_DEFAULT OFF)
-  else()
-    set(DOWNLOAD_LATTE_DEFAULT ON)
-  endif()
-  option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
-  if(DOWNLOAD_LATTE)
-    if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
-      message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
-    endif()
-    if(CMAKE_GENERATOR STREQUAL "Ninja")
-      message(FATAL_ERROR "Cannot build downloaded LATTE library with Ninja build tool")
-    endif()
-    message(STATUS "LATTE download requested - we will build our own")
-    include(ExternalProject)
-    ExternalProject_Add(latte_build
-      URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz
-      URL_MD5 85ac414fdada2d04619c8f936344df14
-      SOURCE_SUBDIR cmake
-      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC}
-      -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
-      -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=${CMAKE_Fortran_FLAGS}
-      -DCMAKE_Fortran_FLAGS_${BTYPE}=${CMAKE_Fortran_FLAGS_${BTYPE}} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-    )
-    ExternalProject_get_property(latte_build INSTALL_DIR)
-    set(LATTE_LIBRARIES ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/liblatte.a)
-    list(APPEND LAMMPS_DEPS latte_build)
-  else()
-    find_package(LATTE)
-    if(NOT LATTE_FOUND)
-      message(FATAL_ERROR "LATTE library not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
-    endif()
-  endif()
-  list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES})
+enable_language(Fortran)
+
+# using lammps in a super-build setting
+if(TARGET LATTE::latte)
+  target_link_libraries(lammps PRIVATE LATTE::latte)
+  return()
+endif()
+
+find_package(LATTE)
+if(LATTE_FOUND)
+  set(DOWNLOAD_LATTE_DEFAULT OFF)
+else()
+  set(DOWNLOAD_LATTE_DEFAULT ON)
+endif()
+option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
+if(DOWNLOAD_LATTE)
+  message(STATUS "LATTE download requested - we will build our own")
+  include(ExternalProject)
+  ExternalProject_Add(latte_build
+    URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz
+    URL_MD5 85ac414fdada2d04619c8f936344df14
+    SOURCE_SUBDIR cmake
+    CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} -DCMAKE_INSTALL_LIBDIR=lib
+    -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
+    -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=${CMAKE_Fortran_FLAGS}
+    -DCMAKE_Fortran_FLAGS_${BTYPE}=${CMAKE_Fortran_FLAGS_${BTYPE}} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+    -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM} -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
+    BUILD_BYPRODUCTS <INSTALL_DIR>/lib/liblatte.a
+  )
+  ExternalProject_get_property(latte_build INSTALL_DIR)
+  add_library(LAMMPS::LATTE UNKNOWN IMPORTED)
+  set_target_properties(LAMMPS::LATTE PROPERTIES
+    IMPORTED_LOCATION "${INSTALL_DIR}/lib/liblatte.a"
+    INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
+  target_link_libraries(lammps PRIVATE LAMMPS::LATTE)
+  add_dependencies(LAMMPS::LATTE latte_build)
+else()
+  find_package(LATTE)
+  if(NOT LATTE_FOUND)
+    message(FATAL_ERROR "LATTE library not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
+  endif()
+  # latte needs lapack
+  target_link_libraries(lammps PRIVATE LATTE::latte ${LAPACK_LIBRARIES})
 endif()

cmake/Modules/Packages/MESSAGE.cmake

@@ -1,29 +1,32 @@
-if(PKG_MESSAGE)
-  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)
+if(LAMMPS_SIZES STREQUAL BIGBIG)
+  message(FATAL_ERROR "The MESSAGE Package is not compatible with -DLAMMPS_BIGBIG")
 endif()
+option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
+file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F
+    ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c
+    ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
+
+add_library(cslib STATIC ${cslib_SOURCES})
+target_compile_definitions(cslib PRIVATE -DLAMMPS_${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 +1,45 @@
-if(PKG_MSCG)
-  find_package(GSL REQUIRED)
-  find_package(MSCG QUIET)
-  if(MSGC_FOUND)
-    set(DOWNLOAD_MSCG_DEFAULT OFF)
-  else()
-    set(DOWNLOAD_MSCG_DEFAULT ON)
-  endif()
-  option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
-  if(DOWNLOAD_MSCG)
-    if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
-      message(FATAL_ERROR "For downlading MSCG you need at least cmake-3.7")
-    endif()
-    if(CMAKE_GENERATOR STREQUAL "Ninja")
-      message(FATAL_ERROR "Cannot build downloaded MSCG library with Ninja build tool")
-    endif()
-    include(ExternalProject)
-    if(NOT LAPACK_FOUND)
-      set(EXTRA_MSCG_OPTS "-DLAPACK_LIBRARIES=${CMAKE_CURRENT_BINARY_DIR}/liblinalg.a")
-    endif()
-    ExternalProject_Add(mscg_build
-      URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz
-      URL_MD5 8c45e269ee13f60b303edd7823866a91
-      SOURCE_SUBDIR src/CMake
-      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} ${EXTRA_MSCG_OPTS}
-      BUILD_COMMAND make mscg INSTALL_COMMAND ""
-      )
-    ExternalProject_get_property(mscg_build BINARY_DIR)
-    set(MSCG_LIBRARIES ${BINARY_DIR}/libmscg.a)
-    ExternalProject_get_property(mscg_build SOURCE_DIR)
-    set(MSCG_INCLUDE_DIRS ${SOURCE_DIR}/src)
-    list(APPEND LAMMPS_DEPS mscg_build)
-    if(NOT LAPACK_FOUND)
-      file(MAKE_DIRECTORY ${MSCG_INCLUDE_DIRS})
-      add_dependencies(mscg_build linalg)
-    endif()
-  else()
-    find_package(MSCG)
-    if(NOT MSCG_FOUND)
-      message(FATAL_ERROR "MSCG not found, help CMake to find it by setting MSCG_LIBRARY and MSCG_INCLUDE_DIRS, or set DOWNLOAD_MSCG=ON to download it")
-    endif()
-  endif()
-  list(APPEND LAMMPS_LINK_LIBS ${MSCG_LIBRARIES} ${GSL_LIBRARIES} ${LAPACK_LIBRARIES})
-  include_directories(${MSCG_INCLUDE_DIRS})
+find_package(GSL REQUIRED)
+find_package(MSCG QUIET)
+if(MSGC_FOUND)
+  set(DOWNLOAD_MSCG_DEFAULT OFF)
+else()
+  set(DOWNLOAD_MSCG_DEFAULT ON)
 endif()
+option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
+if(DOWNLOAD_MSCG)
+  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)
+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 ${LAMMPS_SOURCE_DIR}/OPT)
-    set(OPT_SOURCES)
-    set_property(GLOBAL PROPERTY "OPT_SOURCES" "${OPT_SOURCES}")
+  set(OPT_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/OPT)
+  set(OPT_SOURCES)
+  set_property(GLOBAL PROPERTY "OPT_SOURCES" "${OPT_SOURCES}")
 
-    # detects styles which have OPT version
-    RegisterStylesExt(${OPT_SOURCES_DIR} opt OPT_SOURCES)
+  # detects styles which have OPT version
+  RegisterStylesExt(${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 ${OPT_SOURCES})
-    include_directories(${OPT_SOURCES_DIR})
-endif()
+  target_sources(lammps PRIVATE ${OPT_SOURCES})
+  target_include_directories(lammps PRIVATE ${OPT_SOURCES_DIR})

cmake/Modules/Packages/PYTHON.cmake

@@ -1,6 +1,9 @@
-if(PKG_PYTHON)
-  find_package(PythonLibs REQUIRED)
-  add_definitions(-DLMP_PYTHON)
-  include_directories(${PYTHON_INCLUDE_DIR})
-  list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY})
+if(CMAKE_VERSION VERSION_LESS 3.12)
+  find_package(PythonLibs REQUIRED) # Deprecated since version 3.12
+  target_include_directories(lammps PRIVATE ${PYTHON_INCLUDE_DIR})
+  target_link_libraries(lammps PRIVATE ${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)
-  file(GLOB QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix*.h)
-  file(GLOB QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix*.cpp)
+set(QEQ_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/QEQ)
+file(GLOB QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix*.h)
+file(GLOB QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix*.cpp)
 
-  if(NOT PKG_MANYBODY)
-    list(REMOVE_ITEM QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix_qeq_fire.h)
-    list(REMOVE_ITEM QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix_qeq_fire.cpp)
-  endif()
-  set_property(GLOBAL PROPERTY "QEQ_SOURCES" "${QEQ_SOURCES}")
-
-  foreach(MY_HEADER ${QEQ_HEADERS})
-    AddStyleHeader(${MY_HEADER} FIX)
-  endforeach()
-
-  get_property(QEQ_SOURCES GLOBAL PROPERTY QEQ_SOURCES)
-  list(APPEND LIB_SOURCES ${QEQ_SOURCES})
-  include_directories(${QEQ_SOURCES_DIR})
+if(NOT PKG_MANYBODY)
+  list(REMOVE_ITEM QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix_qeq_fire.h)
+  list(REMOVE_ITEM QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix_qeq_fire.cpp)
 endif()
+set_property(GLOBAL PROPERTY "QEQ_SOURCES" "${QEQ_SOURCES}")
+
+foreach(MY_HEADER ${QEQ_HEADERS})
+  AddStyleHeader(${MY_HEADER} FIX)
+endforeach()
+
+get_property(QEQ_SOURCES GLOBAL PROPERTY QEQ_SOURCES)
+target_sources(lammps PRIVATE ${QEQ_SOURCES})
+target_include_directories(lammps PRIVATE ${QEQ_SOURCES_DIR})

cmake/Modules/Packages/USER-COLVARS.cmake

@@ -0,0 +1,30 @@
+set(COLVARS_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars)
+
+file(GLOB COLVARS_SOURCES ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
+
+# Build Lepton by default
+option(COLVARS_LEPTON "Build and link the Lepton library" ON)
+
+if(COLVARS_LEPTON)
+  set(LEPTON_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton)
+  file(GLOB LEPTON_SOURCES ${LEPTON_DIR}/src/[^.]*.cpp)
+  add_library(lepton STATIC ${LEPTON_SOURCES})
+  # Change the define below to LEPTON_BUILDING_SHARED_LIBRARY when linking Lepton as a DLL with MSVC
+  target_compile_definitions(lepton PRIVATE -DLEPTON_BUILDING_STATIC_LIBRARY)
+  set_target_properties(lepton PROPERTIES OUTPUT_NAME lammps_lepton${LAMMPS_MACHINE})
+  target_include_directories(lepton PRIVATE ${LEPTON_DIR}/include)
+endif()
+
+add_library(colvars STATIC ${COLVARS_SOURCES})
+target_compile_definitions(colvars PRIVATE -DLAMMPS_${LAMMPS_SIZES})
+set_target_properties(colvars PROPERTIES OUTPUT_NAME lammps_colvars${LAMMPS_MACHINE})
+target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
+target_link_libraries(lammps PRIVATE colvars)
+
+if(COLVARS_LEPTON)
+  target_link_libraries(lammps PRIVATE lepton)
+  target_compile_definitions(colvars PRIVATE -DLEPTON)
+  # Disable the line below when linking Lepton as a DLL with MSVC
+  target_compile_definitions(colvars PRIVATE -DLEPTON_USE_STATIC_LIBRARIES)
+  target_include_directories(colvars PUBLIC ${LEPTON_DIR}/include)
+endif()

cmake/Modules/Packages/USER-H5MD.cmake

@@ -1,8 +1,8 @@
-if(PKG_USER-H5MD)
-  enable_language(C)
+enable_language(C)
 
-  find_package(HDF5 REQUIRED)
-  target_link_libraries(h5md ${HDF5_LIBRARIES})
-  target_include_directories(h5md PRIVATE ${HDF5_INCLUDE_DIRS})
-  include_directories(${HDF5_INCLUDE_DIRS})
+if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.12)
+  cmake_policy(SET CMP0074 NEW)
 endif()
+find_package(HDF5 REQUIRED)
+target_link_libraries(h5md PRIVATE ${HDF5_LIBRARIES})
+target_include_directories(h5md PUBLIC ${HDF5_INCLUDE_DIRS})

cmake/Modules/Packages/USER-INTEL.cmake

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

@@ -1,10 +1,8 @@
-if(PKG_USER-MOLFILE)
-  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 ${CMAKE_DL_LIBS})
-  endif()
-  list(APPEND LAMMPS_LINK_LIBS molfile)
+set(MOLFILE_INCLUDE_DIRS "${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()
+target_link_libraries(lammps PRIVATE molfile)

cmake/Modules/Packages/USER-NETCDF.cmake

@@ -1,6 +1,27 @@
-if(PKG_USER-NETCDF)
-  find_package(NetCDF REQUIRED)
-  include_directories(${NETCDF_INCLUDE_DIRS})
-  list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES})
-  add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
+# USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
+# NetCDF library enables dump style "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
+if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.12)
+  cmake_policy(SET CMP0074 NEW)
 endif()
+if(NOT BUILD_MPI)
+  find_package(NetCDF REQUIRED)
+else()
+  find_package(NetCDF)
+  if(NETCDF_FOUND)
+    find_package(PNetCDF)
+  else()
+    find_package(PNetCDF REQUIRED)
+  endif()
+endif()
+
+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 ${USER-OMP_SOURCES_DIR}/thr_data.cpp
-                         ${USER-OMP_SOURCES_DIR}/thr_omp.cpp
-                         ${USER-OMP_SOURCES_DIR}/fix_omp.cpp
-                         ${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp
-                         ${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp
-                         ${USER-OMP_SOURCES_DIR}/domain_omp.cpp)
-    add_definitions(-DLMP_USER_OMP)
-    set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}")
+  set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP)
+  set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
+                       ${USER-OMP_SOURCES_DIR}/thr_omp.cpp
+                       ${USER-OMP_SOURCES_DIR}/fix_omp.cpp
+                       ${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp
+                       ${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp
+                       ${USER-OMP_SOURCES_DIR}/domain_omp.cpp)
+  target_compile_definitions(lammps PRIVATE -DLMP_USER_OMP)
+  set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}")
 
-    # detects styles which have USER-OMP version
-    RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
-    RegisterFixStyle(${USER-OMP_SOURCES_DIR}/fix_omp.h)
+  # detects styles which have USER-OMP version
+  RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
+  RegisterFixStyle(${USER-OMP_SOURCES_DIR}/fix_omp.h)
 
-    get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
+  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)
-      list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_nh_asphere_omp.cpp)
-    endif()
+  if(PKG_ASPHERE)
+    list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_nh_asphere_omp.cpp)
+  endif()
 
-    if(PKG_RIGID)
-      list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp)
-    endif()
+  if(PKG_RIGID)
+    list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp)
+  endif()
 
-    if(PKG_USER-REAXC)
-      list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/reaxc_bond_orders_omp.cpp
-                                   ${USER-OMP_SOURCES_DIR}/reaxc_hydrogen_bonds_omp.cpp
-                                   ${USER-OMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp
-                                   ${USER-OMP_SOURCES_DIR}/reaxc_bonds_omp.cpp
-                                   ${USER-OMP_SOURCES_DIR}/reaxc_init_md_omp.cpp
-                                   ${USER-OMP_SOURCES_DIR}/reaxc_torsion_angles_omp.cpp
-                                   ${USER-OMP_SOURCES_DIR}/reaxc_forces_omp.cpp
-                                   ${USER-OMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp
-                                   ${USER-OMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp)
-    endif()
+  if(PKG_USER-REAXC)
+    list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/reaxc_bond_orders_omp.cpp
+                                 ${USER-OMP_SOURCES_DIR}/reaxc_hydrogen_bonds_omp.cpp
+                                 ${USER-OMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp
+                                 ${USER-OMP_SOURCES_DIR}/reaxc_bonds_omp.cpp
+                                 ${USER-OMP_SOURCES_DIR}/reaxc_init_md_omp.cpp
+                                 ${USER-OMP_SOURCES_DIR}/reaxc_torsion_angles_omp.cpp
+                                 ${USER-OMP_SOURCES_DIR}/reaxc_forces_omp.cpp
+                                 ${USER-OMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp
+                                 ${USER-OMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp)
+  endif()
 
-    list(APPEND LIB_SOURCES ${USER-OMP_SOURCES})
-    include_directories(${USER-OMP_SOURCES_DIR})
-endif()
+  target_sources(lammps PRIVATE ${USER-OMP_SOURCES})
+  target_include_directories(lammps PRIVATE ${USER-OMP_SOURCES_DIR})

cmake/Modules/Packages/USER-PLUMED.cmake

@@ -1,91 +1,98 @@
-if(PKG_USER-PLUMED)
-  set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")
-  set(PLUMED_MODE_VALUES static shared runtime)
-  set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})
-  validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
-  string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
+set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")
+set(PLUMED_MODE_VALUES static shared runtime)
+set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})
+validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
+string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
 
-  set(PLUMED_LINK_LIBS "")
-  if(PLUMED_MODE STREQUAL "STATIC")
-    find_package(LAPACK REQUIRED)
-    find_package(BLAS REQUIRED)
-    find_package(GSL REQUIRED)
-    list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
-    list(APPEND PLUMED_LINK_LIBS ${LAPACK_LIBRARIES} ${GSL_LIBRARIES})
-    find_package(ZLIB QUIET)
-    if(ZLIB_FOUND)
-      list(APPEND PLUMED_LINK_LIBS ${ZLIB_LIBRARIES})
-    endif()
+set(PLUMED_LINK_LIBS)
+if(PLUMED_MODE STREQUAL "STATIC")
+  find_package(LAPACK REQUIRED)
+  find_package(BLAS REQUIRED)
+  find_package(GSL REQUIRED)
+  list(APPEND PLUMED_LINK_LIBS ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} GSL::gsl)
+  find_package(ZLIB QUIET)
+  if(ZLIB_FOUND)
+    list(APPEND PLUMED_LINK_LIBS ZLIB::ZLIB)
   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()
+  find_package(FFTW3 QUIET)
+  if(FFTW3_FOUND)
+    list(APPEND PLUMED_LINK_LIBS FFTW3::FFTW3)
   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/v2.5.2/plumed-src-2.5.2.tgz
-      URL_MD5 bd2f18346c788eb54e1e52f4f6acf41a
-      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(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 +1,6 @@
-if(PKG_USER-QMMM)
-  enable_language(Fortran)
-  enable_language(C)
+enable_language(C)
 
-  message(WARNING "Building QMMM with CMake is still experimental")
-  find_package(QE REQUIRED)
-  include_directories(${QE_INCLUDE_DIRS})
-  list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES})
-endif()
+add_library(qmmm STATIC ${LAMMPS_LIB_SOURCE_DIR}/qmmm/libqmmm.c)
+set_target_properties(qmmm PROPERTIES OUTPUT_NAME lammps_qmmm${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)
-  find_package(QUIP REQUIRED)
-  list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES})
-endif()
+enable_language(Fortran)
+find_package(QUIP REQUIRED)
+target_link_libraries(lammps PRIVATE QUIP::QUIP ${LAPACK_LIBRARIES})

cmake/Modules/Packages/USER-SCAFACOS.cmake

@@ -1,62 +1,59 @@
-if(PKG_USER-SCAFACOS)
-  enable_language(Fortran)
-  enable_language(C)
+enable_language(Fortran)
+enable_language(C)
 
-  find_package(GSL REQUIRED)
-  find_package(PkgConfig QUIET)
-  set(DOWNLOAD_SCAFACOS_DEFAULT ON)
-  if(PKG_CONFIG_FOUND)
-    pkg_check_modules(SCAFACOS QUIET scafacos)
-    if(SCAFACOS_FOUND)
-      set(DOWNLOAD_SCAFACOS_DEFAULT OFF)
-    endif()
+find_package(GSL REQUIRED)
+find_package(PkgConfig QUIET)
+find_package(MPI REQUIRED)
+set(DOWNLOAD_SCAFACOS_DEFAULT ON)
+if(PKG_CONFIG_FOUND)
+  pkg_check_modules(SCAFACOS QUIET scafacos)
+  if(SCAFACOS_FOUND)
+    set(DOWNLOAD_SCAFACOS_DEFAULT OFF)
   endif()
-  option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
-  if(DOWNLOAD_SCAFACOS)
-    if(CMAKE_GENERATOR STREQUAL "Ninja")
-      message(FATAL_ERROR "Cannot build downloaded ScaFaCoS library with Ninja build tool")
-    endif()
-    message(STATUS "ScaFaCoS download requested - we will build our own")
-    include(ExternalProject)
-    ExternalProject_Add(scafacos_build
-      URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
-      URL_MD5 bd46d74e3296bd8a444d731bb10c1738
-      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc
-                                               --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
-                                               --with-internal-fftw --with-internal-pfft
-                                               --with-internal-pnfft ${CONFIGURE_REQUEST_PIC}
-                                               FC=${CMAKE_MPI_Fortran_COMPILER}
-                                               CXX=${CMAKE_MPI_CXX_COMPILER}
-                                               CC=${CMAKE_MPI_C_COMPILER}
-                                               F77=
-    )
-    ExternalProject_get_property(scafacos_build INSTALL_DIR)
-    set(SCAFACOS_BUILD_DIR ${INSTALL_DIR})
-    set(SCAFACOS_INCLUDE_DIRS ${SCAFACOS_BUILD_DIR}/include)
-    list(APPEND LAMMPS_DEPS scafacos_build)
-    # list and order from pkg_config file of ScaFaCoS build
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs.a)
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_direct.a)
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_ewald.a)
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fmm.a)
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p2nfft.a)
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p3m.a)
-    list(APPEND LAMMPS_LINK_LIBS ${GSL_LIBRARIES})
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_near.a)
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_gridsort.a)
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_resort.a)
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_redist.a)
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_common.a)
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pnfft.a)
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pfft.a)
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3_mpi.a)
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3.a)
-    list(APPEND LAMMPS_LINK_LIBS ${MPI_Fortran_LIBRARIES})
-    list(APPEND LAMMPS_LINK_LIBS ${MPI_C_LIBRARIES})
-  else()
-    find_package(PkgConfig REQUIRED)
-    pkg_check_modules(SCAFACOS REQUIRED scafacos)
-    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_LDFLAGS})
-  endif()
-  include_directories(${SCAFACOS_INCLUDE_DIRS})
+endif()
+option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
+if(DOWNLOAD_SCAFACOS)
+  message(STATUS "ScaFaCoS download requested - we will build our own")
+  include(ExternalProject)
+  ExternalProject_Add(scafacos_build
+    URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
+    URL_MD5 bd46d74e3296bd8a444d731bb10c1738
+    CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc
+                                             --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
+                                             --with-internal-fftw --with-internal-pfft
+                                             --with-internal-pnfft ${CONFIGURE_REQUEST_PIC}
+                                             FC=${CMAKE_MPI_Fortran_COMPILER}
+                                             CXX=${CMAKE_MPI_CXX_COMPILER}
+                                             CC=${CMAKE_MPI_C_COMPILER}
+                                             F77=
+    BUILD_BYPRODUCTS
+      <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
+      <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
+  )
+  ExternalProject_get_property(scafacos_build INSTALL_DIR)
+  file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
+  add_library(LAMMPS::SCAFACOS UNKNOWN IMPORTED)
+  set_target_properties(LAMMPS::SCAFACOS PROPERTIES
+    IMPORTED_LOCATION "${INSTALL_DIR}/lib/libfcs.a"
+    INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include"
+    INTERFACE_LINK_LIBRARIES "${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")
+  target_link_libraries(lammps PRIVATE LAMMPS::SCAFACOS)
+  add_dependencies(LAMMPS::SCAFACOS scafacos_build)
+else()
+  find_package(PkgConfig REQUIRED)
+  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)
-  if(NOT PKG_RIGID)
-    list(REMOVE_ITEM hlist ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.h)
-    list(REMOVE_ITEM LIB_SOURCES ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.cpp)
-  endif()
-  set_property(GLOBAL PROPERTY FIX "${hlist}")
-
-  include_directories(${USER-SDPD_SOURCES_DIR})
+get_property(hlist GLOBAL PROPERTY FIX)
+if(NOT PKG_RIGID)
+  list(REMOVE_ITEM hlist ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.h)
+  get_target_property(LAMMPS_SOURCES lammps SOURCES)
+  list(REMOVE_ITEM LAMMPS_SOURCES ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.cpp)
+  set_property(TARGET lammps PROPERTY SOURCES ${LAMMPS_SOURCES})
 endif()
+set_property(GLOBAL PROPERTY FIX "${hlist}")
+
+target_include_directories(lammps PRIVATE ${USER-SDPD_SOURCES_DIR})

cmake/Modules/Packages/USER-SMD.cmake

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

cmake/Modules/Packages/VORONOI.cmake

@@ -1,45 +1,48 @@
-if(PKG_VORONOI)
-  find_package(VORO)
-  if(VORO_FOUND)
-    set(DOWNLOAD_VORO_DEFAULT OFF)
-  else()
-    set(DOWNLOAD_VORO_DEFAULT ON)
-  endif()
-  option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT})
-  if(DOWNLOAD_VORO)
-    if(CMAKE_GENERATOR STREQUAL "Ninja")
-      message(FATAL_ERROR "Cannot build downloaded Voro++ library with Ninja build tool")
-    endif()
-    message(STATUS "Voro++ download requested - we will build our own")
-    include(ExternalProject)
-
-    if(BUILD_SHARED_LIBS)
-      set(VORO_BUILD_CFLAGS "${CMAKE_SHARED_LIBRARY_CXX_FLAGS} ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
-    else()
-      set(VORO_BUILD_CFLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
-    endif()
-    if(APPLE)
-      get_filename_component(VORO_CXX ${CMAKE_CXX_COMPILER} NAME_WE)
-      set(VORO_BUILD_OPTIONS CXX=${VORO_CXX} CFLAGS=${VORO_BUILD_CFLAGS})
-    else()
-      set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
-    endif()
-
-    ExternalProject_Add(voro_build
-      URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
-      URL_MD5 2338b824c3b7b25590e18e8df5d68af9
-      CONFIGURE_COMMAND "" BUILD_COMMAND make ${VORO_BUILD_OPTIONS} BUILD_IN_SOURCE 1 INSTALL_COMMAND ""
-      )
-    ExternalProject_get_property(voro_build SOURCE_DIR)
-    set(VORO_LIBRARIES ${SOURCE_DIR}/src/libvoro++.a)
-    set(VORO_INCLUDE_DIRS ${SOURCE_DIR}/src)
-    list(APPEND LAMMPS_DEPS voro_build)
-  else()
-    find_package(VORO)
-    if(NOT VORO_FOUND)
-      message(FATAL_ERROR "Voro++ library not found. Help CMake to find it by setting VORO_LIBRARY and VORO_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
-    endif()
-  endif()
-  include_directories(${VORO_INCLUDE_DIRS})
-  list(APPEND LAMMPS_LINK_LIBS ${VORO_LIBRARIES})
+find_package(VORO)
+if(VORO_FOUND)
+  set(DOWNLOAD_VORO_DEFAULT OFF)
+else()
+  set(DOWNLOAD_VORO_DEFAULT ON)
+endif()
+option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT})
+if(DOWNLOAD_VORO)
+  message(STATUS "Voro++ download requested - we will build our own")
+  include(ExternalProject)
+
+  if(BUILD_SHARED_LIBS)
+    set(VORO_BUILD_CFLAGS "${CMAKE_SHARED_LIBRARY_CXX_FLAGS} ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
+  else()
+    set(VORO_BUILD_CFLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
+  endif()
+  if(APPLE)
+    get_filename_component(VORO_CXX ${CMAKE_CXX_COMPILER} NAME_WE)
+    set(VORO_BUILD_OPTIONS CXX=${VORO_CXX} CFLAGS=${VORO_BUILD_CFLAGS})
+  else()
+    set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
+  endif()
+
+  ExternalProject_Add(voro_build
+    URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
+    URL_MD5 2338b824c3b7b25590e18e8df5d68af9
+    PATCH_COMMAND patch -b -p0 < ${LAMMPS_LIB_SOURCE_DIR}/voronoi/voro-make.patch
+    CONFIGURE_COMMAND ""
+    BUILD_COMMAND make ${VORO_BUILD_OPTIONS}
+    BUILD_IN_SOURCE 1
+    INSTALL_COMMAND ""
+    BUILD_BYPRODUCTS <SOURCE_DIR>/src/libvoro++.a
+    )
+  ExternalProject_get_property(voro_build SOURCE_DIR)
+  file(MAKE_DIRECTORY ${SOURCE_DIR}/src)
+  add_library(LAMMPS::VORO UNKNOWN IMPORTED)
+  set_target_properties(LAMMPS::VORO PROPERTIES
+    IMPORTED_LOCATION "${SOURCE_DIR}/src/libvoro++.a"
+    INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/src")
+  target_link_libraries(lammps PRIVATE LAMMPS::VORO)
+  add_dependencies(LAMMPS::VORO voro_build)
+else()
+  find_package(VORO)
+  if(NOT VORO_FOUND)
+    message(FATAL_ERROR "Voro++ library not found. Help CMake to find it by setting VORO_LIBRARY and VORO_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
+  endif()
+  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 ${SCRIPT_NAME})
-      set_tests_properties(${TEST_NAME} PROPERTIES WORKING_DIRECTORY ${PARENT_DIR})
+      add_test(NAME ${TEST_NAME} COMMAND $<TARGET_FILE:lmp> -in ${SCRIPT_NAME} 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-TALLY USER-UEF USER-VTK USER-YAFF)
+        USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
+        USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

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-TALLY USER-UEF USER-VTK USER-YAFF)
+        USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
+        USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)

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
-                 REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI USER-ATC USER-AWPMD
-                 USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
-                 USER-DPD USER-DRUDE USER-EFF USER-FEP USER-INTEL USER-MANIFOLD
-                 USER-MEAMC USER-MESO USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE
-                 USER-OMP USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SDPD
-                 USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-YAFF)
+                 GRANULAR KSPACE LATTE MANYBODY MC MISC MOLECULE OPT PERI
+                 POEMS QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
+                 USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
+                 USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
+                 USER-FEP USER-INTEL USER-MANIFOLD USER-MEAMC USER-MESODPD
+                 USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE USER-OMP
+                 USER-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC
+                 USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
+                 USER-YAFF)
 
 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
-        GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI
-        PYTHON QEQ REPLICA RIGID SHOCK SRD VORONOI
-        USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD
-        USER-DRUDE USER-FEP USER-MEAMC USER-MESO
-        USER-MISC USER-MOFFF USER-OMP USER-PLUMED USER-PHONON USER-REAXC
-        USER-SPH USER-SMD USER-UEF USER-YAFF)
+set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL
+        DIPOLE GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI
+        POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
+        USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
+        USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC USER-MESODPD
+        USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION
+        USER-REAXC USER-SDPD USER-SPH USER-SMD USER-UEF USER-YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)
 endforeach()
+
+set(BUILD_TOOLS ON CACHE BOOL "" FORCE)

doc/.gitignore

@@ -1,8 +1,12 @@
 /old
 /html
+/html-offline
 /latex
+/mathjax
 /spelling
 /LAMMPS.epub
 /LAMMPS.mobi
 /Manual.pdf
 /Developer.pdf
+/doctrees
+/docenv

doc/Makefile

@@ -1,17 +1,18 @@
 # Makefile for LAMMPS documentation
 
 SHELL         = /bin/bash
-SHA1          = $(shell echo ${USER}-${PWD} | python utils/sha1sum.py)
-BUILDDIR      = /tmp/lammps-docs-$(SHA1)
-RSTDIR        = $(BUILDDIR)/rst
+BUILDDIR      = ${CURDIR}
+RSTDIR        = $(BUILDDIR)/src
 VENV          = $(BUILDDIR)/docenv
+MATHJAX       = $(BUILDDIR)/mathjax
 TXT2RST       = $(VENV)/bin/txt2rst
-ANCHORCHECK   = $(VENV)/bin/doc_anchor_check
+ANCHORCHECK   = $(VENV)/bin/rst_anchor_check
 
 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
@@ -27,82 +28,83 @@ VIRTUALENV     = virtualenv
 HAS_VIRTUALENV = YES
 endif
 
-SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
-SOURCES=$(filter-out $(wildcard src/lammps_commands*.txt) src/lammps_support.txt src/lammps_tutorials.txt,$(wildcard src/*.txt))
-OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
+ifeq ($(shell which pdflatex >/dev/null 2>&1; echo $$?), 0)
+HAS_PDFLATEX = YES
+endif
 
-.PHONY: help clean-all clean epub mobi html pdf old 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 "  pdf        create Developer.pdf and Manual.pdf in this dir"
-	@echo "  old        create old-style HTML doc pages and Manual.pdf in old dir"
-	@echo "  fetch      fetch HTML and PDF files from LAMMPS web site"
-	@echo "  epub       create ePUB format manual for e-book readers"
-	@echo "  mobi       convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
+	@echo "  html          create HTML doc pages in html dir"
+	@echo "  pdf           create Developer.pdf and Manual.pdf in this dir"
+	@echo "  fetch         fetch HTML and PDF files from LAMMPS web site"
+	@echo "  epub          create ePUB format manual for e-book readers"
+	@echo "  mobi          convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
 	@echo "                      (requires ebook-convert tool from calibre)"
-	@echo "  clean      remove all intermediate RST files"
-	@echo "  clean-all  reset the entire build environment"
-	@echo "  txt2html   build txt2html tool"
+	@echo "  clean         remove all intermediate RST files"
+	@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)/* utils/txt2html/txt2html.exe
+	rm -rf $(BUILDDIR)/docenv $(BUILDDIR)/doctrees $(BUILDDIR)/mathjax Manual.pdf Developer.pdf
 
-clean:
-	rm -rf $(RSTDIR) html old epub latex
-	rm -rf spelling
+clean: clean-spelling
+	rm -rf html epub latex
 
 clean-spelling:
 	rm -rf spelling
 
-html: $(OBJECTS) $(ANCHORCHECK)
+html: $(ANCHORCHECK) $(MATHJAX)
 	@(\
 		. $(VENV)/bin/activate ;\
-		cp -r src/* $(RSTDIR)/ ;\
 		sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
 		echo "############################################" ;\
-		doc_anchor_check src/*.txt ;\
+		rst_anchor_check src/*.rst ;\
+		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]*
-	@rm -rf html/USER/*/.[sg]*
-	@rm -rf html/USER/*/*.[sg]*
+	@mkdir -p html/_static/mathjax
+	@cp -r $(MATHJAX)/es5 html/_static/mathjax/
 	@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 -r src/* $(RSTDIR)/ ;\
-        cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ;\
+		cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ; env PYTHONWARNINGS= \
 		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/
 	@cp src/JPG/*.* epub/JPG
 	@(\
 		. $(VENV)/bin/activate ;\
-		cp -r src/* $(RSTDIR)/ ;\
 		sphinx-build $(SPHINXEXTRA) -b epub -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
 		deactivate ;\
 	)
@@ -115,7 +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; \
@@ -124,57 +127,35 @@ pdf: $(OBJECTS) $(ANCHORCHECK)
 		cd ../../; \
 	)
 	@(\
-                . $(VENV)/bin/activate ;\
-                cp -r src/* $(RSTDIR)/ ;\
-                sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
-                echo "############################################" ;\
-                doc_anchor_check src/*.txt ;\
-                echo "############################################" ;\
-                deactivate ;\
+		. $(VENV)/bin/activate ;\
+		sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
+		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 ;\
 	)
 	@cd latex && \
-          sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \
-	  mv temp Makefile && \
-	  sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \
-	  mv tmp.tex LAMMPS.tex && \
-	  sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
-	  mv tmp.tex LAMMPS.tex && \
-	  make && \
-	  make && \
-	  mv LAMMPS.pdf ../Manual.pdf && \
-	  cd ../;
+		sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \
+		mv temp Makefile && \
+		sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \
+		mv tmp.tex LAMMPS.tex && \
+		sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
+		mv tmp.tex LAMMPS.tex && \
+		make && \
+		make && \
+		make && \
+		mv LAMMPS.pdf ../Manual.pdf && \
+		cd ../;
 	@rm -rf latex/_sources
 	@rm -rf latex/PDF
 	@rm -rf latex/USER
 	@cp -r src/PDF latex/PDF
-	@cp -r src/USER latex/USER
 	@rm -rf latex/PDF/.[sg]*
-	@rm -rf latex/USER/.[sg]*
-	@rm -rf latex/USER/*/.[sg]*
-	@rm -rf latex/USER/*/*.[sg]*
 	@echo "Build finished. Manual.pdf and Developer.pdf are in this directory."
 
-old: utils/txt2html/txt2html.exe
-	@rm -rf old
-	@mkdir old; mkdir old/Eqs; mkdir old/JPG; mkdir old/PDF
-	@cd src; ../utils/txt2html/txt2html.exe -b *.txt; \
-	  mv *.html ../old; \
-	  cp Eqs/*.jpg ../old/Eqs; \
-	  cp JPG/* ../old/JPG; \
-	  cp PDF/* ../old/PDF;
-	@(      set -e;\
-		cd src/Developer; \
-		pdflatex developer; \
-		pdflatex developer; \
-		mv developer.pdf ../../old/Developer.pdf; \
-		cd ../../old; \
-	        for s in `echo ../src/*.txt | sed -e 's,\.\./src/,,g' -e 's/ \(pairs\|bonds\|angles\|dihedrals\|impropers\|commands_list\|fixes\|computes\).txt/ /g' | sed -e 's,\.txt,\.html,g'` ; \
-			do grep -q ^$$s ../src/lammps.book || \
-			echo WARNING: doc file $$s missing in src/lammps.book; done; \
-		htmldoc --batch ../src/lammps.book;          \
-	)
-
-
 fetch:
 	@rm -rf html_www Manual_www.pdf Developer_www.pdf
 	@curl -s -o Manual_www.pdf http://lammps.sandia.gov/doc/Manual.pdf
@@ -183,38 +164,45 @@ fetch:
 	@tar xzf lammps-doc.tar.gz
 	@rm -f lammps-doc.tar.gz
 
-txt2html: utils/txt2html/txt2html.exe
-
 anchor_check : $(ANCHORCHECK)
 	@(\
 		. $(VENV)/bin/activate ;\
-		doc_anchor_check src/*.txt ;\
+		rst_anchor_check src/*.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 ;\
 	)
 
 # ------------------------------------------
 
-utils/txt2html/txt2html.exe: utils/txt2html/txt2html.cpp
-	g++ -O -Wall -o $@ $<
-
-$(RSTDIR)/%.rst : src/%.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

@@ -5,7 +5,7 @@ sub-directories and optionally 2 PDF files and an ePUB file:
 
 src             content files for LAMMPS documentation
 html            HTML version of the LAMMPS manual (see html/Manual.html)
-tools           tools and settings for building the documentation
+utils           utilities and settings for building the documentation
 Manual.pdf      large PDF version of entire manual
 Developer.pdf   small PDF with info about how LAMMPS is structured
 LAMMPS.epub     Manual in ePUB format
@@ -25,17 +25,12 @@ the fetched documentation will include those changes (but your source
 code will not, unless you update your local repository).
 
 (b) You can build the HTML and PDF files yourself, by typing "make
-html" followed by "make pdf".  Note that the PDF make requires the
-HTML files already exist.  This requires various tools including
-Sphinx, which the build process will attempt to download and install
-on your system, if not already available.  See more details below.
-
-(c) You can genererate an older, simpler, less-fancy style of HTML
-documentation by typing "make old".  This will create an "old"
-directory.  This can be useful if (b) does not work on your box for
-some reason, or you want to quickly view the HTML version of a doc
-page you have created or edited yourself within the src directory.
-E.g. if you are planning to submit a new feature to LAMMPS.
+html" or by "make pdf", respectively.  This requires various tools
+including the Python documentation processing tool Sphinx, which the
+build process will attempt to download and install on your system into
+a python virtual environment, if not already available.  The PDF file
+will require a working LaTeX installation with several add-on packages
+in addition to the Python/Sphinx setup.  See more details below.
 
 ----------------
 
@@ -46,11 +41,10 @@ Options:
 
 make html         # generate HTML in html dir using Sphinx
 make pdf          # generate 2 PDF files (Manual.pdf,Developer.pdf)
-                  #   in this dir via htmldoc and pdflatex
-make old          # generate old-style HTML pages in old dir via txt2html
+                  #   in this dir via Sphinx and PDFLaTeX
 make fetch        # fetch HTML doc pages and 2 PDF files from web site
                   #   as a tarball and unpack into html dir and 2 PDFs
-make epub         # generate LAMMPS.epub in ePUB format using Sphinx 
+make epub         # generate LAMMPS.epub in ePUB format using Sphinx
 make clean        # remove intermediate RST files created by HTML build
 make clean-all    # remove entire build folder and any cached data
 
@@ -94,8 +88,23 @@ This will install virtualenv from the Python Package Index.
 
 Installing prerequisites for PDF build
 
-[TBA]
-
+Same as for HTML plus a compatible LaTeX installation with
+support for PDFLaTeX. Also the following LaTeX packages need
+to be installed (e.g. from texlive):
+- amsmath
+- babel
+- capt-of
+- cmap
+- fncychap
+- framed
+- geometry
+- hyperref
+- hypcap
+- needspace
+- times
+- tabulary
+- upquote
+- wrapfig
 ----------------
 
 Installing prerequisites for epub build
@@ -103,7 +112,11 @@ Installing prerequisites for epub build
 ## ePUB
 
 Same as for HTML. This uses the same tools and configuration
-files as the HTML tree.
+files as the HTML tree. The ePUB format conversion currently
+does not support processing mathematical expressions via MathJAX,
+so there will be limitations on some pages. For the time being
+until this is resolved, building and using the PDF format file
+is recommended instead.
 
 For converting the generated ePUB file to a mobi format file
 (for e-book readers like Kindle, that cannot read ePUB), you

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`
-  and `doc/src/lammps.book`
+  `doc/src/Commands_*.rst`, `doc/src/{fixes,computes,pairs,bonds,...}.rst`
   * check whether manual cleanly translates with `make html` and `make pdf`
+  * if documentation is (still) provided as a .txt file, convert to .rst
+  and remove the .txt file. For files in doc/txt the conversion is automatic.
+  * remove all .txt files in `doc/txt` that are out of sync with their .rst counterparts in `doc/src`
   * check spelling of manual with `make spelling` in doc folder
+  * check style tables and command lists with `make style_check`
   * new source files in packages should be added to `src/.gitignore`
   * removed or renamed files in packages should be added to `src/Purge.list`
   * C++ source files should use C++ style include files for accessing
@@ -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
-in the C++98 standard.  Some files thus must use the older style until
-the minimum C++ standard requirement of LAMMPS is lifted to C++11 or
-even beyond (examples: `#include <stdint.h>` versus `#include <cstdint>`
-or `#include <inttypes.h>` versus `#include <cinttypes>`).
+`#include <cctypes>` instead of `#include <stdlib.h>` or
+`#include<ctypes.h>` ).
 
 ### C++ Standard Compliance
 
-LAMMPS core files currently correspond to the C++98 standard. Files
-requiring C++11 or later are only permitted in (optional) packages
-and particularly packages that are not part of the list of commonly
-used packages such as MOLECULE, KSPACE, MANYBODY, or RIGID.
-
-Also, LAMMPS uses the C-style stdio library for I/O instead of iostreams.
-Since using both at the same time can cause problems, iostreams should
-be avoided where possible.
+LAMMPS core files use standard conforming C++ compatible with the
+C++11 standard, unless explicitly noted.  Also, LAMMPS uses the C-style
+stdio library for I/O instead of iostreams.  Since using both at the
+same time can cause problems, iostreams should be avoided where possible.
 
 ### Lean Header Files
 

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "7 August 2019" "2019-08-07"
+.TH LAMMPS "5 May 2020" "2020-05-5"
 .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

@@ -0,0 +1 @@
+/false_positives.txt

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

@@ -0,0 +1,24 @@
+Build LAMMPS
+************
+
+LAMMPS is built as a library and an executable from source code using
+either traditional makefiles for use with GNU make (which may require
+manual editing), or using a build environment generated by CMake (Unix
+Makefiles, Ninja, Xcode, Visual Studio, KDevelop, CodeBlocks and more).
+
+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
+
+   Build_cmake
+   Build_make
+   Build_link
+   Build_basics
+   Build_settings
+   Build_package
+   Build_extras
+   Build_windows
+   Build_development

doc/src/Build.txt

@@ -1,51 +0,0 @@
-"Previous Section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Run_head.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-Build LAMMPS :h2
-
-LAMMPS can be built as an executable or library from source code via
-either traditional makefiles (which may require manual editing)
-for use with GNU make or gmake, or a build environment generated by CMake
-(Unix Makefiles, Xcode, Visual Studio, KDevelop or more).  As an
-alternative you can download a package with pre-built executables
-as described on the "Install"_Install.html doc page.
-
-<!-- RST
-
-.. toctree::
-   :maxdepth: 1
-
-   Build_cmake
-   Build_make
-   Build_link
-   Build_basics
-   Build_settings
-   Build_package
-   Build_extras
-   Build_windows
-   Build_development
-
-END_RST -->
-
-<!-- HTML_ONLY -->
-
-"Build LAMMPS with CMake"_Build_cmake.html
-"Build LAMMPS with make"_Build_make.html
-"Link LAMMPS as a library to another code"_Build_link.html
-"Basic build options"_Build_basics.html
-"Optional build settings"_Build_settings.html
-"Include packages in build"_Build_package.html
-"Packages with extra build options"_Build_extras.html
-"Notes for building LAMMPS on Windows"_Build_windows.html
-"Development build options (CMake only)"_Build_development.html  :all(b)
-
-If you have problems building LAMMPS, it is often due to software
-issues on your local machine.  If you can, find a local expert to
-help.  If you're still stuck, send an email to the "LAMMPS mail
-list"_http://lammps.sandia.gov/mail.html.

doc/src/Build_basics.rst

@@ -0,0 +1,560 @@
+Basic build options
+===================
+
+The following topics are covered on this page, for building both with
+CMake and make:
+
+* :ref:`Serial vs parallel build <serial>`
+* :ref:`Choice of compiler and compile/link options <compile>`
+* :ref:`Build 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 is written to use the ubiquitous `MPI (Message Passing Interface)
+<https://en.wikipedia.org/wiki/Message_Passing_Interface>`_ library API
+for distributed memory parallel computation.  You need to have such a
+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.
+
+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**\ :
+
+.. 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 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 named ``lmp`` unless
+the ``LAMMPS_MACHINE`` option is set.  When setting ``LAMMPS_MACHINE=name``
+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``.
+
+.. code-block:: bash
+
+   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
+
+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):
+
+.. code-block:: make
+
+   CC =            g++
+   LINK =          g++
+   MPI_INC =       -I../STUBS
+   MPI_PATH =      -L../STUBS
+   MPI_LIB =       -lmpi_stubs
+
+You also need to build the STUBS library for your platform before making
+LAMMPS itself.  A ``make serial`` build does this for you automatically,
+otherwise, type ``make mpi-stubs`` from the src directory, or ``make``
+from the ``src/STUBS`` dir.  If the build fails, you may need to edit
+the ``STUBS/Makefile`` for your platform.  The stubs library does not
+provide MPI/IO functions required by some LAMMPS packages,
+e.g. ``MPIIO`` or ``USER-LB``, and thus is not compatible with those
+packages.
+
+.. note::
+
+   The file ``src/STUBS/mpi.c`` provides a CPU timer function called
+   ``MPI_Wtime()`` that calls ``gettimeofday()``.  If your operating system
+   does not support ``gettimeofday()``, you will 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.
+
+**MPI and OpenMP support 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.
+
+The majority of OpenMP (threading) support in LAMMPS is provided by the
+``USER-OMP`` package; see the :doc:`Speed omp <Speed_omp>` doc page for
+details. The ``USER-INTEL`` package also includes OpenMP threading (it
+is compatible with ``USER-OMP`` and will usually fall back on styles
+from that package, if a ``USER-INTEL`` does not exist) and adds
+vectorization support when compiled with compatible compilers, in
+particular the Intel compilers on top of OpenMP. Also, the ``KOKKOS``
+package can be compiled to include OpenMP threading.
+
+In addition, there are a few commands in LAMMPS that have native OpenMP
+support included as well.  These are commands in the ``MPIIO``,
+``SNAP``, ``USER-DIFFRACTION``, and ``USER-DPD`` packages.  In addition
+some packages support OpenMP threading indirectly through the libraries
+they interface to: e.g. ``LATTE``, ``KSPACE``, and ``USER-COLVARS``.
+See the :doc:`Packages details <Packages_details>` doc page for more
+info on these packages and the doc pages for their respective commands
+for OpenMP threading info.
+
+For CMake, if you use ``BUILD_OMP=yes``, you can use these packages
+and turn on their native OpenMP support and turn on their native OpenMP
+support at run time, by setting the ``OMP_NUM_THREADS`` environment
+variable before you launch LAMMPS.
+
+For building via conventional make, the ``CCFLAGS`` and ``LINKFLAGS``
+variables in Makefile.machine need to include the compiler flag that
+enables OpenMP. For GNU compilers it is ``-fopenmp``\ .  For (recent) Intel
+compilers it is ``-qopenmp``\ .  If you are using a different compiler,
+please refer to its documentation.
+
+.. _default-none-issues:
+
+**OpenMP Compiler compatibility info**\ :
+
+Some compilers do not fully support the ``default(none)`` directive
+and others (e.g. GCC version 9 and beyond, 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 maximum
+performance.  Vendor provided compilers for a specific hardware can
+produce faster code than open-source compilers like the GNU compilers.
+On the most common x86 hardware most popular C++ compilers are quite
+similar in performance of C/C++ code at high optimization levels.  When
+using the ``USER-INTEL`` package, there is a distinct advantage in using
+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**\ :
+
+By default CMake will use a compiler it finds according to internal
+preferences and it will add optimization flags appropriate to that
+compiler and any :doc:`accelerator packages <Speed_packages>` you have
+included in the build.
+
+You can tell CMake to look for a specific compiler with 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
+
+   -D CMAKE_CXX_COMPILER=name            # name of C++ compiler
+   -D CMAKE_C_COMPILER=name              # name of C compiler
+   -D CMAKE_Fortran_COMPILER=name        # name of Fortran compiler
+
+   -D CMAKE_CXX_FLAGS=string             # flags to use with C++ compiler
+   -D CMAKE_C_FLAGS=string               # flags to use with C compiler
+   -D CMAKE_Fortran_FLAGS=string         # flags to use with Fortran compiler
+
+A few example command lines are:
+
+.. code-block:: bash
+
+   # Building with GNU Compilers:
+   cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
+   # Building with Intel Compilers:
+   cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
+   # Building with LLVM/Clang Compilers:
+   cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
+
+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 a summary to the screen
+   which compilers it is using and what flags and settings will be used
+   for the  compilation.  Note that if the top-level compiler is mpicxx,
+   it is simply a wrapper on a real compiler.  The underlying compiler
+   info is what CMake will try to determine and report.  You should check
+   to confirm you are using the compiler and optimization flags you want.
+
+**Makefile.machine settings for traditional make**\ :
+
+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``):
+
+.. code-block:: bash
+
+   CC =            mpicxx
+   CCFLAGS =       -g -O3
+   LINK =          mpicxx
+   LINKFLAGS =     -g -O
+
+Serial build with GNU gcc (see ``src/MAKE/Makefile.serial``):
+
+.. code-block:: make
+
+   CC =            g++
+   CCFLAGS =       -g -O3
+   LINK =          g++
+   LINKFLAGS =     -g -O
+
+
+.. note::
+
+   If compilation stops with a message like the following:
+
+   .. code-block::
+
+      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
+   Makefile.intel_cpu             # USER-INTEL package for CPUs
+   Makefile.intel_coprocessor     # USER-INTEL package for KNLs
+   Makefile.gpu                   # GPU package
+   Makefile.kokkos_cuda_mpi       # KOKKOS package for GPUs
+   Makefile.kokkos_omp            # KOKKOS package for CPUs (OpenMP)
+   Makefile.kokkos_phi            # KOKKOS package for KNLs (OpenMP)
+
+----------
+
+.. _exe:
+
+Build the LAMMPS executable and library
+---------------------------------------
+
+LAMMPS is always built as a library of C++ classes plus an executable.
+The executable is a simple ``main()`` function that sets up MPI and then
+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 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.
+
+.. code-block:: bash
+
+   -D BUILD_SHARED_LIBS=value   # yes or no (default)
+   -D LAMMPS_MACHINE=name       # name = mpi, serial, mybox, titan, laptop, etc
+                                # no default value
+
+The compilation will always produce a LAMMPS library and an executable
+linked to it.  By default this will be a static library named
+``liblammps.a`` and an executable named ``lmp`` Setting
+``BUILD_SHARED_LIBS=yes`` will instead produce a shared library called
+``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.
+
+.. code-block:: bash
+
+   make machine               # build LAMMPS executable lmp_machine
+   make mode=static machine   # same as "make machine"
+   make mode=shared machine   # build LAMMPS shared lib liblammps_machine.so instead
+
+The "static" build will generate a static library called
+``liblammps_machine.a`` and an executable named ``lmp_machine``\ , while
+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 creating a shared library, all the libraries it depends on
+must be compiled to be compatible with shared libraries.  This should be
+the case for libraries included with LAMMPS, such as the dummy MPI
+library in ``src/STUBS`` or any package libraries in the ``lib``
+directory, since they are always built in a shared library compatible
+way using the ``-fPIC`` compiler switch.  However, if an auxiliary
+library (like MPI or FFTW) does not exist as a compatible format, the
+shared library linking step may generate an error.  This means you will
+need to install a compatible version of the auxiliary library.  The
+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, as a shared library
+in the default /usr/local/lib location:
+
+.. _mpich: https://www.mpich.org
+
+.. code-block:: bash
+
+   ./configure --enable-shared
+   make
+   make install
+
+You may need to use ``sudo make install`` in place of the last line if
+you do not have write privileges for ``/usr/local/lib`` or use the
+``--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
+----------------------------------------
+
+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
+
+**Documentation make option**\ :
+
+The following make commands can be issued in the doc folder of the
+LAMMPS source distribution.
+
+.. code-block:: bash
+
+  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
+manual pages so that you can browse them with a web browser locally on
+your system.
+
+.. note::
+
+   You can also download a tarball of the documentation for the
+   current LAMMPS version (HTML and PDF files), from the website
+   `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
+------------------------------
+
+Some tools described in :doc:`Auxiliary tools <Tools>` can be built directly
+using CMake or Make.
+
+**CMake build3**\ :
+
+.. code-block:: bash
+
+   -D BUILD_TOOLS=value       # yes or no (default)
+
+The generated binaries will also become part of the LAMMPS installation
+(see below).
+
+**Traditional make**\ :
+
+.. code-block:: bash
+
+   cd lammps/tools
+   make all              # build all binaries of tools
+   make binary2txt       # build only binary2txt tool
+   make chain            # build only chain tool
+   make micelle2d        # build only micelle2d tool
+   make thermo_extract   # build only thermo_extract tool
+
+----------
+
+.. _install:
+
+Install LAMMPS after a build
+------------------------------------------
+
+After building LAMMPS, you may wish to copy the LAMMPS executable of
+library, along with other LAMMPS files (library header, doc files) to
+a globally visible place on your system, for others to access.  Note
+that you may need super-user privileges (e.g. sudo) if the directory
+you want to copy files to is protected.
+
+**CMake build**\ :
+
+.. code-block:: bash
+
+   cmake -D CMAKE_INSTALL_PREFIX=path [options ...] ../cmake
+   make                        # perform make after CMake command
+   make install                # perform the installation into prefix
+
+**Traditional make**\ :
+
+There is no "install" option in the ``src/Makefile`` for LAMMPS.  If
+you wish to do this you will need to first build LAMMPS, then manually
+copy the desired LAMMPS files to the appropriate system directories.

doc/src/Build_basics.txt

@@ -1,359 +0,0 @@
-"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-Basic build options :h3
-
-The following topics are covered on this page, for building both with
-CMake and make:
-
-"Serial vs parallel build"_#serial
-"Choice of compiler and compile/link options"_#compile
-"Build LAMMPS as an executable or a library"_#exe
-"Build the LAMMPS documentation"_#doc
-"Install LAMMPS after a build"_#install :ul
-
-:line
-
-Serial vs parallel build :h4,link(serial)
-
-LAMMPS can be built to run in parallel using the ubiquitous "MPI
-(message-passing
-interface)"_https://en.wikipedia.org/wiki/Message_Passing_Interface
-library.  Or it can built to run on a single processor (serial)
-without MPI.  It can also be built with support for OpenMP threading
-(see more discussion below).
-
-[CMake variables]:
-
--D BUILD_MPI=value        # yes or no, default is yes if CMake finds MPI, else no
--D BUILD_OMP=value        # yes or no (default)
--D LAMMPS_MACHINE=name    # name = mpi, serial, mybox, titan, laptop, etc
-                          # no default value :pre
-
-The executable created by CMake (after running make) is lmp_name.  If
-the LAMMPS_MACHINE variable is not specified, the executable is just
-lmp.  Using BUILD_MPI=no will produce a serial executable.
-
-[Traditional make]:
-
-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 :pre         # uses Makefile.mybox to produce lmp_mybox :pre
-
-Serial build (see src/MAKE/Makefile.serial):
-
-MPI_INC =       -I../STUBS
-MPI_PATH =      -L../STUBS
-MPI_LIB =	-lmpi_stubs :pre
-
-For a parallel build, if MPI is installed on your system in the usual
-place (e.g. under /usr/local), you do not need to specify the 3
-variables MPI_INC, MPI_PATH, MPI_LIB.  The MPI wrapper on the compiler
-(e.g. mpicxx, mpiCC) knows where to find the needed include and
-library files.  Failing this, these 3 variables can be used to specify
-where the mpi.h file (MPI_INC), and the MPI library files (MPI_PATH)
-are found, and the name of the library files (MPI_LIB).
-
-For a serial build, you need to specify the 3 variables, as shown
-above.
-
-For a serial LAMMPS build, use the dummy MPI library provided in
-src/STUBS.  You also need to build the STUBS library for your platform
-before making LAMMPS itself.  A "make serial" build does this for.
-Otherwise, type "make mpi-stubs" from the src directory, or "make"
-from the src/STUBS dir.  If the build fails, you will need to edit the
-STUBS/Makefile for your platform.
-
-The file STUBS/mpi.c provides a CPU timer function called MPI_Wtime()
-that calls gettimeofday() .  If your system doesn't support
-gettimeofday() , you'll need to insert code to call another timer.
-Note that the ANSI-standard function clock() rolls over after an hour
-or so, and is therefore insufficient for timing long LAMMPS
-simulations.
-
-[CMake and make info]:
-
-If you are installing MPI yourself, we recommend MPICH2 from Argonne
-National Laboratory or OpenMPI.  MPICH can be downloaded from the
-"Argonne MPI site"_http://www.mcs.anl.gov/research/projects/mpich2/.
-OpenMPI can be downloaded from the "OpenMPI
-site"_http://www.open-mpi.org.  Other MPI packages should also work.
-If you are running on a large parallel machine, your system admins or
-the vendor should have already installed a version of MPI, which is
-likely to be faster than a self-installed MPICH or OpenMPI, so find
-out how to build and link with it.
-
-The majority of OpenMP (threading) support in LAMMPS is provided by
-the USER-OMP package; see the "Speed omp"_Speed_omp.html doc page for
-details. The USER-INTEL package also provides OpenMP support (it is
-compatible with USER-OMP) and adds vectorization support when compiled
-with the Intel compilers on top of that. Also, the KOKKOS package can
-be compiled for using OpenMP threading.
-
-However, there are a few commands in LAMMPS that have native OpenMP
-support.  These are commands in the MPIIO, SNAP, USER-DIFFRACTION, and
-USER-DPD packages.  In addition some packages support OpenMP threading
-indirectly through the libraries they interface to: e.g. LATTE and
-USER-COLVARS.  See the "Packages details"_Packages_details.html doc
-page for more info on these packages and the doc pages for their
-respective commands for OpenMP threading info.
-
-For CMake, if you use BUILD_OMP=yes, you can use these packages and
-turn on their native OpenMP support and turn on their native OpenMP
-support at run time, by setting the OMP_NUM_THREADS environment
-variable before you launch LAMMPS.
-
-For building via conventional make, the CCFLAGS and LINKFLAGS
-variables in Makefile.machine need to include the compiler flag that
-enables OpenMP. For GNU compilers it is -fopenmp.  For (recent) Intel
-compilers it is -qopenmp.  If you are using a different compiler,
-please refer to its documentation.
-
-[OpenMP Compiler compatibility info]: :link(default-none-issues)
-
-Some compilers do not fully support the 'default(none)' directive
-and others (e.g. GCC version 9 and beyond) may implement OpenMP 4.0
-semantics, which are incompatible with the OpenMP 3.1 directives used
-in LAMMPS (for maximal compatibility with compiler versions in use).
-In those case, all 'default(none)' directives (which aid in detecting
-incorrect and unwanted sharing) can be replaced with 'default(shared)'
-while dropping all 'shared()' directives. The script
-'src/USER-OMP/hack_openmp_for_pgi_gcc9.sh' can be used to automate
-this conversion.
-
-:line
-
-Choice of compiler and compile/link options :h4,link(compile)
-
-The choice of compiler and compiler flags can be important for
-performance.  Vendor compilers can produce faster code than
-open-source compilers like GNU.  On boxes with Intel CPUs, we suggest
-trying the "Intel C++ compiler"_intel.
-
-:link(intel,https://software.intel.com/en-us/intel-compilers)
-
-On parallel clusters or supercomputers which use "modules" for their
-compile/link environments, you can often access different compilers by
-simply loading the appropriate module before building LAMMPS.
-
-[CMake variables]:
-
--D CMAKE_CXX_COMPILER=name            # name of C++ compiler
--D CMAKE_C_COMPILER=name              # name of C compiler
--D CMAKE_Fortran_COMPILER=name        # name of Fortran compiler :pre
-
--D CMAKE_CXX_FLAGS=string             # flags to use with C++ compiler
--D CMAKE_C_FLAGS=string               # flags to use with C compiler
--D CMAKE_Fortran_FLAGS=string         # flags to use with Fortran compiler :pre
-
-By default CMake will use a compiler it finds and it will add
-optimization flags appropriate to that compiler and any "accelerator
-packages"_Speed_packages.html you have included in the build.
-
-You can tell CMake to look for a specific compiler with these variable
-settings.  Likewise you can specify the FLAGS variables if you want to
-experiment with alternate optimization flags.  You should specify all
-3 compilers, so that the small number of LAMMPS source files written
-in C or Fortran are built with a compiler consistent with the one used
-for all the C++ files:
-
-Building with GNU Compilers:
-cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
-Building with Intel Compilers:
-cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
-Building with LLVM/Clang Compilers:
-cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang :pre
-
-NOTE: When the cmake command completes, it prints info to the screen
-as to which compilers it is using, and what flags will be used in the
-compilation.  Note that if the top-level compiler is mpicxx, it is
-simply a wrapper on a real compiler.  The underlying compiler info is
-what will be listed in the CMake output.  You should check to insure
-you are using the compiler and optimization flags are the ones you
-want.
-
-[Makefile.machine settings]:
-
-Parallel build (see src/MAKE/Makefile.mpi):
-
-CC =		mpicxx
-CCFLAGS =	-g -O3
-LINK =		mpicxx
-LINKFLAGS =	-g -O :pre
-
-Serial build (see src/MAKE/Makefile.serial):
-
-CC =		g++
-CCFLAGS =	-g -O3
-LINK =		g++
-LINKFLAGS =	-g -O :pre
-
-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 "accelerator
-packages"_Speed_packages.html included, they have specific
-optimization flags that are either required or recommended for optimal
-performance.  You need to include these in the CCFLAGS and LINKFLAGS
-settings above.  For details, see the individual package doc pages
-listed on the "Speed packages"_Speed_packages.html 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:
-
-Makefile.opt                   # OPT package
-Makefile.omp                   # USER-OMP package
-Makefile.intel_cpu             # USER-INTEL package for CPUs
-Makefile.intel_coprocessor     # USER-INTEL package for KNLs
-Makefile.gpu                   # GPU package
-Makefile.kokkos_cuda_mpi       # KOKKOS package for GPUs
-Makefile.kokkos_omp            # KOKKOS package for CPUs (OpenMP)
-Makefile.kokkos_phi            # KOKKOS package for KNLs (OpenMP) :pre
-
-:line
-
-Build LAMMPS as an executable or a library :h4,link(exe)
-
-LAMMPS can be built as either an executable or as a static or shared
-library.  The LAMMPS library can be called from another application or
-a scripting language.  See the "Howto couple"_Howto_couple.html doc
-page for more info on coupling LAMMPS to other codes.  See the
-"Python"_Python_head.html doc page for more info on wrapping and
-running LAMMPS from Python via its library interface.
-
-[CMake variables]:
-
--D BUILD_EXE=value           # yes (default) or no
--D BUILD_LIB=value           # yes or no (default)
--D BUILD_SHARED_LIBS=value   # yes or no (default)
--D LAMMPS_LIB_SUFFIX=name    # name = mpi, serial, mybox, titan, laptop, etc
-                             # no default value :pre
-
-
-Setting BUILD_EXE=no will not produce an executable.  Setting
-BUILD_LIB=yes will produce a static library named liblammps.a.
-Setting both BUILD_LIB=yes and BUILD_SHARED_LIBS=yes will produce a
-shared library named liblammps.so. If LAMMPS_LIB_SUFFIX is set the generated
-libraries will be named liblammps_name.a or liblammps_name.so instead.
-
-[Traditional make]:
-
-cd lammps/src
-make machine               # build LAMMPS executable lmp_machine
-make mode=lib machine      # build LAMMPS static lib liblammps_machine.a
-make mode=shlib machine    # build LAMMPS shared lib liblammps_machine.so :pre
-
-The two library builds also create generic soft links, named
-liblammps.a and liblammps.so, which point to the liblammps_machine
-files.
-
-[CMake and make info]:
-
-Note that for a shared library to be usable by a calling program, all
-the auxiliary libraries it depends on must also exist as shared
-libraries.  This will be the case for libraries included with LAMMPS,
-such as the dummy MPI library in src/STUBS or any package libraries in
-the lib/packages directory, since they are always built as shared
-libraries using the -fPIC switch.  However, if a library like MPI or
-FFTW does not exist as a shared library, the shared library build will
-generate an error.  This means you will need to install a shared
-library version of the auxiliary library.  The build instructions for
-the library should tell you how to do this.
-
-As an example, here is how to build and install the "MPICH
-library"_mpich, a popular open-source version of MPI, distributed by
-Argonne National Lab, as a shared library in the default
-/usr/local/lib location:
-
-:link(mpich,http://www-unix.mcs.anl.gov/mpi)
-
-./configure --enable-shared
-make
-make install :pre
-
-You may need to use "sudo make install" in place of the last line if
-you do not have write privileges for /usr/local/lib.  The end result
-should be the file /usr/local/lib/libmpich.so.
-
-:line
-
-Build the LAMMPS documentation :h4,link(doc)
-
-[CMake variable]:
-
--D BUILD_DOC=value       # yes or no (default) :pre
-
-This will create the HTML doc pages within the CMake build directory.
-The reason to do this is if you want to "install" LAMMPS on a system
-after the CMake build via "make install", and include the doc pages in
-the install.
-
-[Traditional make]:
-
-cd lammps/doc
-make html       # html doc pages
-make pdf        # single Manual.pdf file :pre
-
-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.
-
-:line
-
-Build LAMMPS tools :h4,link(tools)
-
-Some tools described in "Auxiliary tools"_Tools.html can be built directly
-using CMake or Make.
-
-[CMake variable]:
-
--D BUILD_TOOLS=value       # yes or no (default) :pre
-
-The generated binaries will also become part of the LAMMPS installation (see below)
-
-[Traditional make]:
-
-cd lammps/tools
-make all              # build all binaries of tools
-make binary2txt       # build only binary2txt tool
-make chain            # build only chain tool
-make micelle2d        # build only micelle2d tool
-make thermo_extract   # build only thermo_extract tool
-:pre
-
-:line
-
-
-Install LAMMPS after a build :h4,link(install)
-
-After building LAMMPS, you may wish to copy the LAMMPS executable of
-library, along with other LAMMPS files (library header, doc files) to
-a globally visible place on your system, for others to access.  Note
-that you may need super-user privileges (e.g. sudo) if the directory
-you want to copy files to is protected.
-
-[CMake variable]:
-
-cmake -D CMAKE_INSTALL_PREFIX=path \[options ...\] ../cmake
-make                        # perform make after CMake command
-make install                # perform the installation into prefix :pre
-
-[Traditional make]:
-
-There is no "install" option in the src/Makefile for LAMMPS.  If you
-wish to do this you will need to first build LAMMPS, then manually
-copy the desired LAMMPS files to the appropriate system directories.

doc/src/Build_cmake.rst

@@ -0,0 +1,180 @@
+Build LAMMPS with CMake
+=======================
+
+This page describes how to use `CMake <https://cmake.org>`_ in general
+to build LAMMPS.  Details for specific compile time settings and options
+to enable and configure add-on packages are discussed with those
+packages.  Links to those pages on the :doc:`Build overview <Build>`
+page.
+
+The following text assumes some familiarity with CMake and focuses on
+using the command line tool ``cmake`` and what settings are supported
+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 generate a build environment in a new directory.  For that purpose
+you can use either the command-line utility ``cmake`` (or ``cmake3``),
+the text-mode UI utility ``ccmake`` (or ``ccmake3``) or the graphical
+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
+
+   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")
+
+This will create and change into a folder called ``build``, then run the
+configuration step to generate build files for the default build command
+and then launch that build command to compile LAMMPS.  During the
+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.
+
+Compilation can take a long time, since LAMMPS is a large project with
+many features. If your machine has multiple CPU cores (most do these
+days), you can speed this up by compiling sources in parallel with
+``make -j N`` (with N being the maximum number of concurrently executed
+tasks).  Also installation of the `ccache <https://ccache.dev/>`_ (=
+Compiler Cache) software may speed up repeated compilation even more,
+e.g. during code development.
+
+After the initial build, whenever you edit LAMMPS source files, enable
+or disable packages, change compiler flags or build options, you must
+re-compile and relink the LAMMPS executable with ``cmake --build .`` (or
+``make``).  If the compilation fails for some reason, try running
+``cmake .`` and then compile again. The included dependency tracking
+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
+
+   make install    # optional, copy compiled files into installation location
+
+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``.
+
+.. _cmake_options:
+
+Configuration and build options
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+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
+^^^^^^^^^^^^^^^^
+
+Check if your machine already has CMake installed:
+
+.. code-block:: bash
+
+   which cmake             # do you have it?
+   which cmake3            # version 3 may have this name
+   cmake --version         # what specific version you have
+
+On clusters or supercomputers which use environment modules to manage
+software packages, do this:
+
+.. code-block:: bash
+
+   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
+
+Most Linux distributions offer pre-compiled cmake packages through their
+package management system. If you do not have CMake or a recent enough
+version (Note: for CentOS 7.x you need to enable the EPEL repository),
+you can download the latest version from `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/>`_.