Merge pull request #2305 from akohlmey/next_patch_version

Update version strings for updated patch release

.gitattributes

@@ -0,0 +1,3 @@
+.gitattributes export-ignore
+.gitignore export-ignore
+.github export-ignore

.github/CODEOWNERS

@@ -10,6 +10,7 @@ lib/molfile/*         @akohlmey
 lib/qmmm/*            @akohlmey
 lib/vtk/*             @rbberger
 lib/kim/*             @ellio167
+lib/mesont/*          @iafoss
 
 # whole packages
 src/COMPRESS/*        @akohlmey
@@ -22,10 +23,10 @@ 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
+src/USER-MESONT/*     @iafoss
 src/USER-MOFFF/*      @hheenen
 src/USER-MOLFILE/*    @akohlmey
 src/USER-NETCDF/*     @pastewka
@@ -46,7 +47,7 @@ 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
 
@@ -112,14 +113,23 @@ src/fix_nh.*              @athomps
 src/info.*                @akohlmey @rbberger
 src/timer.*               @akohlmey
 src/min*                  @sjplimp @stanmoore1
+src/utils.*               @akohlmey @rbberger
 
 # tools
 tools/msi2lmp/*       @akohlmey
 tools/emacs/*         @HaoZeke
+tools/singularity/*   @akohlmey @rbberger
+tools/code_standard/* @rbberger
+tools/valgrind/*      @akohlmey
+
+# tests
+unittest/*            @akohlmey @rbberger
 
 # cmake
 cmake/*               @junghans @rbberger
 cmake/Modules/Packages/USER-COLVARS.cmake @junghans @rbberger @giacomofiorin
+cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
+cmake/presets/*.cmake @junghans @rbberger @akohlmey
 
 # python
 python/*              @rbberger

.github/CONTRIBUTING.md

@@ -75,7 +75,9 @@ Here is a checklist of steps you need to follow to submit a single file or user
 * Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code.
 * You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). The text files can include mathematical expressions and symbol in ".. math::" sections or ":math:" expressions or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html`, `make pdf` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file.  For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`.
 * For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/USER for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind
-* 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.
+* For new utility functions or class (i.e. anything that does not depend on a LAMMPS object), new unit tests should be added to the unittest tree.
+* When adding a new LAMMPS style, a .yaml file with a test configuration and reference data should be added for the styles where a suitable tester program already exists (e.g. pair styles, bond styles, etc.).
+* If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the <name>.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide.
 
 Finally, as a general rule-of-thumb, the more clear and self-explanatory you make your documentation and README files, and the easier you make it for people to get started, e.g. by providing example scripts, the more likely it is that users will try out your new feature.
 

.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
@@ -34,11 +34,12 @@ _Please check the fields below as they are completed **after** the pull request
 - [ ] The added/updated documentation is integrated and tested with the documentation build system
 - [ ] The feature has been verified to work with the conventional build system
 - [ ] The feature has been verified to work with the CMake based build system
+- [ ] Suitable tests have been added to the unittest tree.
 - [ ] A package specific README file has been included or updated
 - [ ] One or more example input decks are included
 
 **Further Information, Files, and Links**
 
-_Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)_
+<!--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)-->
 
 

.github/codecov.yml

@@ -0,0 +1,29 @@
+comment: false
+coverage:
+  notify:
+    slack:
+      default:
+        url: "secret:HWZbvgtc6OD7F3v3PfrK3/rzCJvScbh69Fi1CkLwuHK0+wIBIHVR+Q5i7q6F9Ln4OChbiRGtYAEUUsT8/jmBu4qDpIi8mx746codc0z/Z3aafLd24pBrCEPLvdCfIZxqPnw3TuUgGhwmMDZf0+thg8YNUr/MbOZ7Li2L6+ZbYuA="
+        threshold: 10%
+        only_pulls: false
+        branches:
+          - "master"
+        flags:
+          - "unit"
+        paths:
+          - "src"
+  status:
+    project:
+        default:
+            branches:
+              - "master"
+            paths:
+              - "src"
+            informational: true
+    patch:
+        default:
+            branches:
+              - "master"
+            paths:
+              - "src"
+            informational: true

bench/FERMI/README

@@ -1,51 +0,0 @@
-These are input scripts used to run versions of several of the
-benchmarks in the top-level bench directory using the GPU accelerator
-package.  The results of running these scripts on two different machines
-(a desktop with 2 Tesla GPUs and the ORNL Titan supercomputer) are shown
-on the "GPU (Fermi)" section of the Benchmark page of the LAMMPS WWW
-site: lammps.sandia.gov/bench.
-
-Examples are shown below of how to run these scripts.  This assumes
-you have built 3 executables with the GPU package
-installed, e.g.
-
-lmp_linux_single
-lmp_linux_mixed
-lmp_linux_double
-
-------------------------------------------------------------------------
-
-To run on just CPUs (without using the GPU styles),
-do something like the following:
-
-mpirun -np 1 lmp_linux_double -v x 8 -v y 8 -v z 8 -v t 100 < in.lj
-mpirun -np 12 lmp_linux_double -v x 16 -v y 16 -v z 16 -v t 100 < in.eam
-
-The "xyz" settings determine the problem size.  The "t" setting
-determines the number of timesteps.
-
-These mpirun commands run on a single node.  To run on multiple
-nodes, scale up the "-np" setting.
-
-------------------------------------------------------------------------
-
-To run with the GPU package, do something like the following:
-
-mpirun -np 12 lmp_linux_single -sf gpu -v x 32 -v y 32 -v z 64 -v t 100 < in.lj
-mpirun -np 8 lmp_linux_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 64 -v t 100 < in.eam
-
-The "xyz" settings determine the problem size.  The "t" setting
-determines the number of timesteps.  The "np" setting determines how
-many MPI tasks (per node) the problem will run on.  The numeric
-argument to the "-pk" setting is the number of GPUs (per node); 1 GPU
-is the default.  Note that you can use more MPI tasks than GPUs (per
-node) with the GPU package.
-
-These mpirun commands run on a single node.  To run on multiple nodes,
-scale up the "-np" setting, and control the number of MPI tasks per
-node via a "-ppn" setting.
-
-------------------------------------------------------------------------
-
-If the script has "titan" in its name, it was run on the Titan
-supercomputer at ORNL.

bench/FERMI/in.eam

@@ -1,24 +0,0 @@
-# bulk Cu lattice
-
-units		metal
-atom_style	atomic
-
-lattice		fcc 3.615
-region		box block 0 $x 0 $y 0 $z
-create_box	1 box
-create_atoms	1 box
-
-pair_style	eam
-pair_coeff	1 1 Cu_u3.eam
-
-velocity	all create 1600.0 376847 loop geom
-
-neighbor	1.0 bin
-neigh_modify    every 1 delay 5 check yes
-
-fix		1 all nve
-
-timestep	0.005
-thermo		50
-
-run		$t

bench/FERMI/in.eam.titan

@@ -1,37 +0,0 @@
-# bulk Cu lattice
-
-newton          off
-package         gpu force/neigh 0 0 1
-processors      * * * grid numa
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	yy equal 20*$y
-variable	zz equal 20*$z
-
-units		metal
-atom_style	atomic
-
-lattice		fcc 3.615
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-create_box	1 box
-create_atoms	1 box
-
-pair_style	eam/gpu
-pair_coeff	1 1 Cu_u3.eam
-
-velocity	all create 1600.0 376847 loop geom
-
-neighbor	1.0 bin
-neigh_modify    every 1 delay 5 check yes
-
-fix		1 all nve
-
-timestep	0.005
-thermo		50
-
-run             15
-run		100

bench/FERMI/in.lj

@@ -1,22 +0,0 @@
-# 3d Lennard-Jones melt
-
-units		lj
-atom_style	atomic
-
-lattice		fcc 0.8442
-region		box block 0 $x 0 $y 0 $z
-create_box	1 box
-create_atoms	1 box
-mass		1 1.0
-
-velocity	all create 1.44 87287 loop geom
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0 2.5
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 20 check no
-
-fix		1 all nve
-
-run		$t

bench/FERMI/in.lj.titan

@@ -1,35 +0,0 @@
-# 3d Lennard-Jones melt
-
-newton          off
-package         gpu force/neigh 0 0 1
-processors      * * * grid numa
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	yy equal 20*$y
-variable	zz equal 20*$z
-
-units		lj
-atom_style	atomic
-
-lattice		fcc 0.8442
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-create_box	1 box
-create_atoms	1 box
-mass		1 1.0
-
-velocity	all create 1.44 87287 loop geom
-
-pair_style	lj/cut/gpu 2.5
-pair_coeff	1 1 1.0 1.0 2.5
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 20 check no
-
-fix		1 all nve
-
-run             15
-run		100

bench/FERMI/in.rhodo

@@ -1,30 +0,0 @@
-# Rhodopsin model
-
-units           real  
-neigh_modify    delay 5 every 1   
-
-atom_style      full  
-atom_modify	map hash
-bond_style      harmonic 
-angle_style     charmm 
-dihedral_style  charmm 
-improper_style  harmonic 
-pair_style      lj/charmm/coul/long 8.0 10.0 
-pair_modify     mix arithmetic 
-kspace_style    pppm 1e-4 
-
-read_data       data.rhodo
-
-replicate	$x $y $z
-
-fix             1 all shake 0.0001 5 0 m 1.0 a 232
-fix             2 all npt temp 300.0 300.0 100.0 &
-		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
-
-special_bonds   charmm
- 
-thermo          50
-thermo_style    multi 
-timestep        2.0
-
-run		$t

bench/FERMI/in.rhodo.scaled.titan

@@ -1,39 +0,0 @@
-# Rhodopsin model
-
-newton          off
-package         gpu force/neigh 0 0 1
-processors      * * * grid numa
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-units           real  
-neigh_modify    delay 5 every 1   
-
-atom_style      full  
-atom_modify	map hash
-bond_style      harmonic 
-angle_style     charmm 
-dihedral_style  charmm 
-improper_style  harmonic 
-pair_style      lj/charmm/coul/long/gpu 8.0 ${cutoff}
-pair_modify     mix arithmetic 
-kspace_style    pppm/gpu 1e-4 
-
-read_data       data.rhodo
-
-replicate	$x $y $z
-
-fix             1 all shake 0.0001 5 0 m 1.0 a 232
-fix             2 all npt temp 300.0 300.0 100.0 &
-		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
-
-special_bonds   charmm
- 
-thermo          50
-# thermo_style    multi 
-timestep        2.0
-
-run             15
-run		100

bench/FERMI/in.rhodo.split.titan

@@ -1,42 +0,0 @@
-# Rhodopsin model
-
-newton          off
-package         gpu force/neigh 0 0 1
-partition	yes 1 processors * * * grid twolevel ${grid} * * * &
-		part 1 2 multiple
-partition	yes 2 processors * * * part 1 2 multiple
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-units           real  
-neigh_modify    delay 5 every 1   
-
-atom_style      full  
-atom_modify	map hash
-bond_style      harmonic 
-angle_style     charmm 
-dihedral_style  charmm 
-improper_style  harmonic 
-pair_style      lj/charmm/coul/long/gpu 8.0 ${cutoff}
-pair_modify     mix arithmetic 
-kspace_style    pppm/gpu 1e-4 
-
-read_data       data.rhodo
-
-replicate	$x $y $z
-
-fix             1 all shake 0.0001 5 0 m 1.0 a 232
-fix             2 all npt temp 300.0 300.0 100.0 &
-		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
-
-special_bonds   charmm
- 
-thermo          50
-# thermo_style    multi 
-timestep        2.0
-
-run_style       verlet/split
-run             15
-run		100

bench/POTENTIALS/Ni.meam

@@ -1,2 +0,0 @@
-rc = 4.0
-delr = 0.1

bench/POTENTIALS/Ni.meam

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

bench/POTENTIALS/Si.sw

@@ -1,17 +0,0 @@
-# Stillinger-Weber parameters for various elements and mixtures
-# multiple entries can be added to this file, LAMMPS reads the ones it needs
-# these entries are in LAMMPS "metal" units:
-#   epsilon = eV; sigma = Angstroms
-#   other quantities are unitless
-
-# format of a single entry (one or more lines):
-#   element 1, element 2, element 3, 
-#   epsilon, sigma, a, lambda, gamma, costheta0, A, B, p, q, tol
-
-# Here are the original parameters in metal units, for Silicon from:
-#
-# Stillinger and Weber,  Phys. Rev. B, v. 31, p. 5262, (1985)
-#
-
-Si Si Si 2.1683  2.0951  1.80  21.0  1.20  -0.333333333333
-         7.049556277  0.6022245584  4.0  0.0 0.0

bench/POTENTIALS/Si.sw

@@ -0,0 +1 @@
+../../potentials/Si.sw

bench/POTENTIALS/Si.tersoff

@@ -1,16 +0,0 @@
-# Tersoff parameters for various elements and mixtures
-# multiple entries can be added to this file, LAMMPS reads the ones it needs
-# these entries are in LAMMPS "metal" units:
-#   A,B = eV; lambda1,lambda2,lambda3 = 1/Angstroms; R,D = Angstroms
-#   other quantities are unitless
-
-# This is the Si parameterization from a particular Tersoff paper:
-# J. Tersoff, PRB, 37, 6991 (1988) 
-# See the SiCGe.tersoff file for different Si variants.
-
-# format of a single entry (one or more lines):
-#   element 1, element 2, element 3, 
-#   m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A
-
-Si  Si   Si  3.0 1.0 1.3258 4.8381 2.0417 0.0000 22.956
-             0.33675  1.3258  95.373  3.0  0.2  3.2394  3264.7

bench/POTENTIALS/Si.tersoff

@@ -0,0 +1 @@
+../../potentials/Si.tersoff

bench/POTENTIALS/in.meam

@@ -1,24 +0,0 @@
-# bulk Ni in MEAM
-
-units		metal
-atom_style	atomic
-
-lattice		fcc 3.52
-region		box block 0 20 0 20 0 20
-create_box	1 box
-create_atoms	1 box
-
-pair_style	meam
-pair_coeff	* * library.meam Ni4 Ni.meam Ni4
-
-velocity	all create 1600.0 376847 loop geom
-
-neighbor	1.0 bin
-neigh_modify    delay 5 every 1
-
-fix		1 all nve
-
-timestep	0.005
-thermo		50
-
-run		100

bench/POTENTIALS/in.reax

@@ -1,22 +0,0 @@
-# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
-
-units		real
-atom_style	charge
-
-read_data	data.reax
-
-#replicate	7 8 10
-replicate	7 8 5
-
-velocity	all create 300.0 9999
-
-pair_style	reax
-pair_coeff      * * ffield.reax 1 2 3 4
-
-timestep	0.1
-fix		2 all nve 
-
-thermo		10
-thermo_style	custom step temp ke pe pxx pyy pzz etotal
-
-run		100

bench/POTENTIALS/library.meam

@@ -1,162 +0,0 @@
-# meam data from vax files fcc,bcc,dia    11/4/92
-# elt        lat     z       ielement     atwt
-# alpha      b0      b1      b2           b3    alat    esub    asub
-# t0         t1              t2           t3            rozero  ibar
-
-'Sn5'       'dia'   4.      50           118.
-5.09        5.00   16.0    04.0          5.0  6.483   3.14     1.00
-1.0         2.00            5.756        -0.30         1.      0
-'Sn'        'dia'   4.      50           118.
-5.09        5.42    8.0     5.0          6.0  6.483   3.14     1.12
-1.0         3.0             5.707        +0.30         1.      0
-'Cu'        'fcc'   12.     29           63.54
-5.10570729  3.634   2.20    6            2.20  3.62    3.54    1.07
-1.0         3.13803254      2.49438711   2.95269237    1.      0
-'Ag'        'fcc'   12.     47           107.870
-5.89222008  4.456   2.20    6            2.20  4.08    2.85    1.06
-1.0         5.54097609      2.45015783   1.28843988    1.      0
-'Au'        'fcc'   12.     79           196.967
-6.34090112  5.449   2.20    6            2.20  4.07    3.93    1.04
-1.0         1.58956328      1.50776392   2.60609758    1.      0
-'Ni1'        'fcc'   12.     28           58.71
-4.99        2.45    2.20    6            2.20  3.52    4.45    1.10
-1.0         3.57            1.60         3.70           1.0    0
-'Ni2'        'fcc'   12.     28           58.71
-4.99        2.45    2.20    6            2.20  3.52    4.45    1.10
-1.0         3.57            1.60         3.70           1.0    3
-'Ni3'        'fcc'   12.     28           58.71
-4.99        2.45    1.50    6            1.50  3.52    4.45    1.10
-1.0         3.57            1.60         3.70           1.0    3
-'Ni4'        'fcc'   12.     28           58.71
-4.99        2.45    1.50    6            1.50  3.52    4.45    1.10
-1.0         3.57            1.60         3.70           1.0    0
-'Ni'        'fcc'   12.     28           58.71
-4.99        2.64    1.50    4.50         1.50  3.52    4.45    1.10
-1.0         1.692           4.987        3.683          1.0    1 
-'Nix'        'fcc'   12.     28           58.71
-4.99        2.64    1.50    4.50         1.50  3.52    4.45    1.10
-1.0         0.00            0.000        3.683          1.0    1 
-'Ni'        'fcc'   12.     28           58.71
-4.99        3.25    0.80    4            1.50  3.52    4.45    1.07
-1.0         -4.052          13.14        3.786		1.0    1
-'Pd'        'fcc'   12.     46           106.4
-6.43230473  4.975   2.20    6            2.20  3.89    3.91    1.01
-1.0         2.33573516      1.38343023   4.47989049    1.      0
-'Pt'        'fcc'   12.     78           195.09
-6.44221724  4.673   2.20    6            2.20  3.92    5.77    1.04
-1.0         2.73335406      -1.3759593   3.29322278    1.      0
-'Al'        'fcc'   12.     13           26.9815
-4.61        2.21    2.20    6.0          2.20  4.05    3.58    1.07
-1.0         -1.78           -2.21        8.01          0.6     0
-'Al'        'fcc'   12.     13           26.9815
-4.69        1.56    4.00    5.5          0.60  4.05    3.36    1.09
-1.0         -0.251          -3.450       8.298         0.6     1
-'Al'        'fcc'   12.     13           26.9815
-4.69	    1.58    1.00    6.0          0.60  4.05    3.36    1.09
-1.0         -0.808          -2.614       8.298         0.6     1
-'Pb'        'fcc'   12.     82           207.19
-6.0564428   5.306   2.20    6            2.20  4.95    2.04    1.01
-1.0         2.74022352      3.06323991   1.2           1.      0
-'Rh'        'fcc'   12.     45           102.905
-6.0045385   1.131   1.00    2            1.00  3.8     5.75    1.05
-1.0         2.9900          4.60231784   4.8           1.      0
-'Ir'        'fcc'   12.     77           192.2
-6.52315787  1.13    1.00    2            1.00  3.84    6.93    1.05
-1.0         1.50000         8.09942666   4.8           1.      0
-'Li'        'bcc'   8.      3            6.939
-2.97244804  1.425   1.00    1.00169907   1.00  3.509   1.65    0.87
-1.0         0.26395017      0.44431129   -0.2          1.      0 
-'Na'        'bcc'   8.      11           22.9898
-3.64280541  2.313   1.00    1.00173951   1.00  4.291   1.13    0.9
-1.0         3.55398839      0.68807569   -0.2          1.      0
-'K'         'bcc'   8.      19           39.102
-3.90128376  2.687   1.00    1.00186667   1.00  5.344   0.94    0.92
-1.0         5.09756981      0.69413264   -0.2          1.      0
-'V'         'bcc'   8.      23           50.942
-4.83265262  4.113   1.00    1.00095022   1.00  3.04    5.3     1
-1.0         4.20161301      4.09946561   -1            1.      0
-'Nb'        'bcc'   8.      41           92.906
-4.79306197  4.374   1.00    1.00101441   1.00  3.301   7.47    1
-1.0         3.75762849      3.82514598   -1            1.      0
-'Ta'        'bcc'   8.      73           180.948
-4.89528669  3.709   1.00    1.00099783   1.00  3.303   8.09    0.99
-1.0         6.08617812      3.35255804   -2.9          1.      0
-'Cr'        'bcc'   8.      24           51.996
-5.12169218  3.224   1.00    1.00048646   1.00  2.885   4.1     0.94
-1.0         -0.207535       12.2600006   -1.9          1.      0
-'Mo'        'bcc'   8.      42           95.94
-5.84872871  4.481   1.00    1.00065204   1.00  3.15    6.81    0.99
-1.0         3.47727181      9.48582009   -2.9          1.      0
-'W'         'bcc'   8.      74           183.85
-5.62777409  3.978   1.00    1.00065894   1.00  3.165   8.66    0.98
-1.0         3.16353338      8.24586928   -2.7          1.      0
-'WL'	    'bcc'   8	    74	         183.85
-5.6831	    6.54    1	    1	         1     3.1639  8.66    0.4
-1	    -0.6	    0.3	         -8.7	       1       3
-'Fe'        'bcc'   8.      26           55.847
-5.07292627  2.935   1.00    1.00080073   1.00  2.866   4.29    0.89
-1.0         5.13579244      4.12042448   -2.7          1.      0
-'Si'        'dia'   4.      14           28.086
-4.87        4.8     4.8     4.8          4.8   5.431   4.63    1.
-1.0         3.30            5.105        -0.80         1.      1
-'Si97'        'dia'   4.      14           28.086
-4.87        4.4     5.5     5.5          5.5   5.431   4.63    1.
-1.0         3.13            4.47         -1.80         2.05    0
-'Si92'        'dia'   4.      14           28.086
-4.87        4.4     5.5     5.5          5.5   5.431   4.63    1.
-1.0         3.13            4.47        -1.80          2.35    0
-'Six'	    'dia'   4	    14	         28.086
-4.87	    4.4	    5.5	    5.5	         5.5   5.431   4.63    1.0
-1.0	    2.05            4.47         -1.8	       2.05     0
-'Sixb'	    'dia'   4	    14	         28.086
-4.87	    4.4	    5.5	    5.5	         5.5   5.431   4.63    1.0
-1.0	    2.05            4.47         -1.8	       2.5     0
-'Mg'       'hcp'   12.      12           24.305
-5.45        2.70    0.0     0.35         3.0   3.20    1.55    1.11
-1.0         8.00            04.1         -02.0         1.0     0
-'C'         'dia'   4.      6            12.0111
-4.38        4.10    4.200   5.00         3.00  3.567   7.37    1.000
-1.0         5.0             9.34         -1.00         2.25    1
-'C'         'dia'   4.      6            12.0111
-4.38        5.20    3.87    4.00         4.50  3.567   7.37    1.278
-1.0         15.             2.09         -6.00         2.5     1
-'C'         'dia'   4.      6            12.0111
-4.38        4.50    4.00    3.50         4.80  3.567   7.37    1.00
-1.0         10.5            1.54         -8.75         3.2     1 
-'C'         'dia'   4.      6            12.0111
-4.38        3.30    2.80    1.50         3.20  3.567   7.37    1.00 
-1.0         10.3            1.54         -8.80         2.5     1 
-'C'         'dia'   4.      6            12.0111
-4.38        4.60    3.45    4.00         4.20  3.567   7.37    1.061
-1.0         15.0            1.74         -8.00         2.5     1
-'C'         'dia'   4.      6            12.0111
-4.38        4.50    4.00    3.50         4.80  3.567   7.37    1.00
-1.0         10.5            1.54         -8.75         3.2     1
-'h'         'dim'   1.      1            1.0079
-2.96        2.70    3.5     3.4          3.4   0.74    2.235   2.27
-1.0         0.19            0.00         0.00          20.00    0
-'h'         'dim'   1.      1            1.0079
-2.96        2.00    4.0     4.0          0.0   0.74    2.235   1.00
-1.0         -0.60           -0.80        -0.0          01.0    1
-'H'         'dim'   1.      1            1.0079
-2.96        2.96    3.0     3.0          3.0   0.74    2.235   2.50
-1.0         0.20            -0.10        0.0           0.5     0
-'H'         'dim'   1.      1            1.0079
-2.96        2.0     3.0     4.0          0.0   0.74    2.225   1.00
-1.0         -0.5            -1.00        0.0           0.15    1
-'H'         'dim'   1.      1            1.0079
-2.96        2.00    2.0     2.0          2.0   0.74    2.235   1.00
-1.0         -0.60           -0.80        -0.0          01.0    2
-'Hni'       'dim'   1.      1            1.0079
-2.96        2.96    3.0     3.0          3.0   0.74    2.235   2.50
-1.0         0.2             -0.1         0.0           0.5     0
-'Hni'         'dim'   1.      1            1.0079
-2.96        2.96    3.0     2.0          3.0   0.74    2.235   36.4
-1.0         0.2             6.0         0.0           22.8     0
-'Vac'       'fcc'   12.     1            1.
-0           0       0.0     0            0.0   1E+08   0       1  
-0           0               0             0             1.     0
-'zz'        'zzz'   99.     1            1.
-0           0       0.0     0            0.0    0.     0.     0.
-0           0               0             0             1.     0
-                                 

bench/POTENTIALS/library.meam

@@ -0,0 +1 @@
+../../potentials/library.meam

bench/POTENTIALS/log.16Mar18.meam.1

@@ -1,84 +0,0 @@
-LAMMPS (16 Mar 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
-  using 1 OpenMP thread(s) per MPI task
-# bulk Ni in MEAM
-
-units		metal
-atom_style	atomic
-
-lattice		fcc 3.52
-Lattice spacing in x,y,z = 3.52 3.52 3.52
-region		box block 0 20 0 20 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
-  1 by 1 by 1 MPI processor grid
-create_atoms	1 box
-Created 32000 atoms
-  Time spent = 0.00186539 secs
-
-pair_style	meam
-WARNING: The pair_style meam command is unsupported. Please use pair_style meam/c instead (../pair_meam.cpp:51)
-pair_coeff	* * library.meam Ni4 Ni.meam Ni4
-
-velocity	all create 1600.0 376847 loop geom
-
-neighbor	1.0 bin
-neigh_modify    delay 5 every 1
-
-fix		1 all nve
-
-timestep	0.005
-thermo		50
-
-run		100
-Neighbor list info ...
-  update every 1 steps, delay 5 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 5
-  ghost atom cutoff = 5
-  binsize = 2.5, bins = 29 29 29
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair meam, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-  (2) pair meam, perpetual, half/full from (1)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 55.91 | 55.91 | 55.91 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1600      -142400            0   -135782.09     20259.18 
-      50    885.10702   -139411.51            0   -135750.54    32425.433 
-     100     895.5097    -139454.3            0    -135750.3    31804.187 
-Loop time of 30.6278 on 1 procs for 100 steps with 32000 atoms
-
-Performance: 1.410 ns/day, 17.015 hours/ns, 3.265 timesteps/s
-99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 30.088     | 30.088     | 30.088     |   0.0 | 98.24
-Neigh   | 0.48914    | 0.48914    | 0.48914    |   0.0 |  1.60
-Comm    | 0.015916   | 0.015916   | 0.015916   |   0.0 |  0.05
-Output  | 0.00022554 | 0.00022554 | 0.00022554 |   0.0 |  0.00
-Modify  | 0.025481   | 0.025481   | 0.025481   |   0.0 |  0.08
-Other   |            | 0.009055   |            |       |  0.03
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    13576 ave 13576 max 13576 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    780360 ave 780360 max 780360 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  1.56072e+06 ave 1.56072e+06 max 1.56072e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1560720
-Ave neighs/atom = 48.7725
-Neighbor list builds = 8
-Dangerous builds = 0
-Total wall time: 0:00:30

bench/POTENTIALS/log.16Mar18.meam.4

@@ -1,84 +0,0 @@
-LAMMPS (16 Mar 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
-  using 1 OpenMP thread(s) per MPI task
-# bulk Ni in MEAM
-
-units		metal
-atom_style	atomic
-
-lattice		fcc 3.52
-Lattice spacing in x,y,z = 3.52 3.52 3.52
-region		box block 0 20 0 20 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
-  1 by 2 by 2 MPI processor grid
-create_atoms	1 box
-Created 32000 atoms
-  Time spent = 0.000587463 secs
-
-pair_style	meam
-WARNING: The pair_style meam command is unsupported. Please use pair_style meam/c instead (../pair_meam.cpp:51)
-pair_coeff	* * library.meam Ni4 Ni.meam Ni4
-
-velocity	all create 1600.0 376847 loop geom
-
-neighbor	1.0 bin
-neigh_modify    delay 5 every 1
-
-fix		1 all nve
-
-timestep	0.005
-thermo		50
-
-run		100
-Neighbor list info ...
-  update every 1 steps, delay 5 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 5
-  ghost atom cutoff = 5
-  binsize = 2.5, bins = 29 29 29
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair meam, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-  (2) pair meam, perpetual, half/full from (1)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 17.41 | 17.41 | 17.41 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1600      -142400            0   -135782.09     20259.18 
-      50    885.10702   -139411.51            0   -135750.54    32425.433 
-     100     895.5097    -139454.3            0    -135750.3    31804.187 
-Loop time of 8.21941 on 4 procs for 100 steps with 32000 atoms
-
-Performance: 5.256 ns/day, 4.566 hours/ns, 12.166 timesteps/s
-99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 8.0277     | 8.0384     | 8.0504     |   0.3 | 97.80
-Neigh   | 0.12555    | 0.12645    | 0.12713    |   0.2 |  1.54
-Comm    | 0.024279   | 0.036776   | 0.048389   |   4.5 |  0.45
-Output  | 9.4414e-05 | 0.00011903 | 0.00018597 |   0.0 |  0.00
-Modify  | 0.01252    | 0.012608   | 0.012795   |   0.1 |  0.15
-Other   |            | 0.005028   |            |       |  0.06
-
-Nlocal:    8000 ave 8045 max 7947 min
-Histogram: 1 0 0 1 0 0 0 1 0 1
-Nghost:    6066.75 ave 6120 max 6021 min
-Histogram: 1 0 1 0 0 0 1 0 0 1
-Neighs:    195090 ave 196403 max 193697 min
-Histogram: 1 0 0 1 0 0 0 1 0 1
-FullNghs:  390180 ave 392616 max 387490 min
-Histogram: 1 0 0 1 0 0 0 1 0 1
-
-Total # of neighbors = 1560720
-Ave neighs/atom = 48.7725
-Neighbor list builds = 8
-Dangerous builds = 0
-Total wall time: 0:00:08

bench/POTENTIALS/log.16Mar18.reax.1

@@ -1,86 +0,0 @@
-LAMMPS (16 Mar 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
-  using 1 OpenMP thread(s) per MPI task
-# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
-
-units		real
-atom_style	charge
-
-read_data	data.reax
-  orthogonal box = (0 0 0) to (9.49107 9.49107 6.99123)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  58 atoms
-
-#replicate	7 8 10
-replicate	7 8 5
-  orthogonal box = (0 0 0) to (66.4375 75.9285 34.9562)
-  1 by 1 by 1 MPI processor grid
-  16240 atoms
-  Time spent = 0.000834942 secs
-
-velocity	all create 300.0 9999
-
-pair_style	reax
-WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
-pair_coeff      * * ffield.reax 1 2 3 4
-
-timestep	0.1
-fix		2 all nve
-
-thermo		10
-thermo_style	custom step temp ke pe pxx pyy pzz etotal
-
-run		100
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 12
-  ghost atom cutoff = 12
-  binsize = 6, bins = 12 13 6
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair reax, perpetual
-      attributes: half, newton off
-      pair build: half/bin/newtoff
-      stencil: half/bin/3d/newtoff
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 115.8 | 115.8 | 115.8 Mbytes
-Step Temp KinEng PotEng Pxx Pyy Pzz TotEng 
-       0          300    14521.612   -1616144.2    22296.712   -29858.677    5721.0921   -1601622.5 
-      10    298.98728    14472.591   -1616093.9    21955.847   -24067.096     7389.148   -1601621.3 
-      20    294.76158    14268.045   -1615890.1    19179.258   -10513.494    10789.925     -1601622 
-      30    288.56967    13968.323   -1615591.2    13854.377      5833.02    13949.731   -1601622.9 
-      40    282.06725    13653.571   -1615278.2    6259.9845     19406.33    14947.939   -1601624.6 
-      50    274.84112    13303.787   -1614931.9   -2009.6832    26964.336    13346.855   -1601628.2 
-      60    266.20153    12885.585   -1614519.7   -8441.1641    28485.532    10195.429   -1601634.1 
-      70    259.17085    12545.262   -1614184.2   -11426.993    24941.516    6572.2953   -1601638.9 
-      80    259.73004     12572.33   -1614216.7   -10867.598    16928.461    3033.9021   -1601644.3 
-      90     269.2352    13032.431     -1614679   -7962.3129    4931.5317   -280.22164   -1601646.6 
-     100    280.67181    13586.024   -1615234.3   -3606.1519   -8769.8482   -2527.5887   -1601648.3 
-Loop time of 358.104 on 1 procs for 100 steps with 16240 atoms
-
-Performance: 0.002 ns/day, 9947.338 hours/ns, 0.279 timesteps/s
-99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 358.07     | 358.07     | 358.07     |   0.0 | 99.99
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.01623    | 0.01623    | 0.01623    |   0.0 |  0.00
-Output  | 0.0013328  | 0.0013328  | 0.0013328  |   0.0 |  0.00
-Modify  | 0.012679   | 0.012679   | 0.012679   |   0.0 |  0.00
-Other   |            | 0.006895   |            |       |  0.00
-
-Nlocal:    16240 ave 16240 max 16240 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    32428 ave 32428 max 32428 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    6.69975e+06 ave 6.69975e+06 max 6.69975e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 6699752
-Ave neighs/atom = 412.546
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:06:02

bench/POTENTIALS/log.16Mar18.reax.4

@@ -1,86 +0,0 @@
-LAMMPS (16 Mar 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
-  using 1 OpenMP thread(s) per MPI task
-# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
-
-units		real
-atom_style	charge
-
-read_data	data.reax
-  orthogonal box = (0 0 0) to (9.49107 9.49107 6.99123)
-  2 by 2 by 1 MPI processor grid
-  reading atoms ...
-  58 atoms
-
-#replicate	7 8 10
-replicate	7 8 5
-  orthogonal box = (0 0 0) to (66.4375 75.9285 34.9562)
-  2 by 2 by 1 MPI processor grid
-  16240 atoms
-  Time spent = 0.000491619 secs
-
-velocity	all create 300.0 9999
-
-pair_style	reax
-WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
-pair_coeff      * * ffield.reax 1 2 3 4
-
-timestep	0.1
-fix		2 all nve
-
-thermo		10
-thermo_style	custom step temp ke pe pxx pyy pzz etotal
-
-run		100
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 12
-  ghost atom cutoff = 12
-  binsize = 6, bins = 12 13 6
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair reax, perpetual
-      attributes: half, newton off
-      pair build: half/bin/newtoff
-      stencil: half/bin/3d/newtoff
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 35.58 | 35.68 | 35.77 Mbytes
-Step Temp KinEng PotEng Pxx Pyy Pzz TotEng 
-       0          300    14521.612   -1616144.1    22296.712   -29858.677    5721.0922   -1601622.5 
-      10    298.98728    14472.591   -1616093.8    21955.847   -24067.094     7389.149   -1601621.3 
-      20    294.76158    14268.044     -1615890    19179.258   -10513.494    10789.925     -1601622 
-      30    288.56967    13968.323   -1615591.2     13854.38    5833.0219    13949.731   -1601622.9 
-      40    282.06725    13653.571   -1615278.2     6259.981    19406.327    14947.938   -1601624.7 
-      50    274.84112    13303.787   -1614931.9   -2009.6844    26964.334    13346.855   -1601628.1 
-      60    266.20153    12885.585   -1614519.8   -8441.1628    28485.533    10195.428   -1601634.2 
-      70    259.17085    12545.262   -1614184.2   -11426.992    24941.517     6572.295     -1601639 
-      80    259.73004     12572.33   -1614216.8   -10867.596    16928.464    3033.9024   -1601644.5 
-      90     269.2352    13032.431     -1614679   -7962.3097    4931.5336   -280.21988   -1601646.5 
-     100    280.67181    13586.024   -1615234.3   -3606.1482   -8769.8463   -2527.5874   -1601648.3 
-Loop time of 97.054 on 4 procs for 100 steps with 16240 atoms
-
-Performance: 0.009 ns/day, 2695.944 hours/ns, 1.030 timesteps/s
-99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 94.83      | 95.764     | 96.883     |   9.2 | 98.67
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.16123    | 1.2801     | 2.2132     |  79.9 |  1.32
-Output  | 0.00056076 | 0.00066662 | 0.00095987 |   0.0 |  0.00
-Modify  | 0.0048354  | 0.0049006  | 0.0049515  |   0.1 |  0.01
-Other   |            | 0.004639   |            |       |  0.00
-
-Nlocal:    4060 ave 4080 max 4040 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost:    14972 ave 14992 max 14952 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs:    1.8135e+06 ave 1.82186e+06 max 1.80514e+06 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 7253988
-Ave neighs/atom = 446.674
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:01:38

bench/POTENTIALS/reax_defs.h

@@ -1,69 +0,0 @@
-#define PORTABLECOMMENTFLAG
-#ifndef PORTABLECOMMENTFLAG
-// This is just a way to have portable comments 
-// for both C++ and FORTRAN preprocessing.
- /* ///:EOH~                                                                 */
- /*                                                                          */
- /* This file contains array dimension parameters for all the main           */
- /* ReaxFF data structures, some of which need to be directly accessed       */
- /* by Grasp C++ functions. If they are set too small, the calculation       */
- /* will run out of allocated memory. If they are set too big, the machine   */
- /* will not be able to allocate enough memory.                              */
- /*                                                                          */
- 
- /*     NNEIGHMAXDEF =   Max number of neighbors / NATDEF                    */
- /*     NATDEF =         Max number of atoms                                 */
- /*     NATTOTDEF =      Max number of global atoms                          */
- /*     NSORTDEF =       Max number of atom types                            */
- /*     MBONDDEF =       Max number of bonds connected to one atom           */
- /*     NAVIBDEF =       for 2nd derivatives                                 */
- /*     NBOTYMDEF =      Max number of bond types                            */
- /*     NVATYMDEF =      Max number of valency angle types                   */
- /*     NTOTYMDEF =      Max number of torsion angle types                   */
- /*     NHBTYMDEF =      Max number of hydrogen bond types                   */
- /*     NODMTYMDEF =     Max number of off-diagonal Morse types              */
- /*     NBOALLMAXDEF =   Max number of all bonds                             */
- /*     NBOMAXDEF =      Max number of bonds                                 */
- /*     NHBMAXDEF =      Max number of  hydrogen bonds                       */
- /*     NVAMAXDEF =      Max number of valency angles                        */
- /*     NOPMAXDEF =      Max number of out of plane angles                   */
- /*     NTOMAXDEF =      Max number of torsion angles                        */
- /*     NPAMAXDEF =      Max number of general parameters in force field     */
- /*     NMOLMAXDEF =     Max number of molecules in system                   */
- /*     NMOLSETDEF =     Max number of molecules in training set             */
- /*     MRESTRADEF =     Max number of restraints                            */
- /*     MTREGDEF =       Max number of temperature regimes                   */
- /*     MTZONEDEF =      Max number of temperature zones                     */
- /*     MVREGDEF =       Max number of volume regimes                        */
- /*     MVZONEDEF =      Max number of volume zones                          */
- /*     MEREGDEF =       Max number of electric field regimes                */
- /*     MEZONEDEF =      Max number of electric field zones                  */
-#endif
-
-#define NNEIGHMAXDEF 200
-#define NATDEF 50000
-#define NATTOTDEF 1
-#define NSORTDEF 20
-#define MBONDDEF 20
-#define NAVIBDEF 50
-#define NBOTYMDEF 200
-#define NVATYMDEF 200
-#define NTOTYMDEF 200
-#define NHBTYMDEF 200
-#define NODMTYMDEF 20
-#define NBOALLMAXDEF 180000
-#define NBOMAXDEF 90000
-#define NHBMAXDEF 400000
-#define NVAMAXDEF 300000
-#define NOPMAXDEF 00010
-#define NTOMAXDEF 200000
-#define NPAMAXDEF 50
-#define NMOLMAXDEF 2000
-#define NMOLSETDEF 1500
-#define MRESTRADEF 100
-#define MTREGDEF 100
-#define MTZONEDEF 5
-#define MVREGDEF 100
-#define MVZONEDEF 6
-#define MEREGDEF 100
-#define MEZONEDEF 3

cmake/CMakeLists.txt

@@ -3,16 +3,24 @@
 # This file is part of LAMMPS
 # Created by Christoph Junghans and Richard Berger
 cmake_minimum_required(VERSION 3.10)
+# set policy to silence warnings about ignoring <PackageName>_ROOT but use it
+if(POLICY CMP0074)
+  cmake_policy(SET CMP0074 NEW)
+endif()
+########################################
 
 project(lammps CXX)
 set(SOVERSION 0)
-get_filename_component(LAMMPS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../src ABSOLUTE)
-get_filename_component(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib ABSOLUTE)
+
+get_filename_component(LAMMPS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/.. ABSOLUTE)
 get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
-get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUTE)
-get_filename_component(LAMMPS_TOOLS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../tools ABSOLUTE)
-get_filename_component(LAMMPS_PYTHON_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../python ABSOLUTE)
-get_filename_component(LAMMPS_POTENTIALS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../potentials ABSOLUTE)
+
+set(LAMMPS_SOURCE_DIR     ${LAMMPS_DIR}/src)
+set(LAMMPS_LIB_SOURCE_DIR ${LAMMPS_DIR}/lib)
+set(LAMMPS_DOC_DIR        ${LAMMPS_DIR}/doc)
+set(LAMMPS_TOOLS_DIR      ${LAMMPS_DIR}/tools)
+set(LAMMPS_PYTHON_DIR     ${LAMMPS_DIR}/python)
+set(LAMMPS_POTENTIALS_DIR ${LAMMPS_DIR}/potentials)
 
 find_package(Git)
 
@@ -24,6 +32,12 @@ endif()
 # Cmake modules/macros are in a subdirectory to keep this file cleaner
 set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules)
 
+# make sure LIBRARY_PATH is set if environment variable is set
+if (DEFINED ENV{LIBRARY_PATH})
+  list(APPEND CMAKE_LIBRARY_PATH "$ENV{LIBRARY_PATH}")
+  message(STATUS "Appending $ENV{LIBRARY_PATH} to CMAKE_LIBRARY_PATH: ${CMAKE_LIBRARY_PATH}")
+endif()
+
 include(LAMMPSUtils)
 
 get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h PROJECT_VERSION)
@@ -43,7 +57,6 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
 # compiler tests
 # these need ot be done early (before further tests).
 #####################################################################
-include(CheckCCompilerFlag)
 include(CheckIncludeFileCXX)
 
 # set required compiler flags and compiler/CPU arch specific optimizations
@@ -56,27 +69,10 @@ if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
   endif()
 endif()
 
-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 (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
-  option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
-  mark_as_advanced(ENABLE_COVERAGE)
-  if(ENABLE_COVERAGE)
-    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
-  endif()
-endif()
+set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
 
 ########################################################################
 # User input options                                                   #
@@ -108,11 +104,11 @@ install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
 option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
 
 set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
-  GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MOLECULE PERI POEMS QEQ
-  REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
+  GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS
+  QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
   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-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
   USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION
   USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
   USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
@@ -135,23 +131,20 @@ if(PKG_USER-ADIOS)
   target_link_libraries(lammps PRIVATE adios2::adios2)
 endif()
 
-if (CMAKE_SYSTEM_NAME STREQUAL Windows)
-  option(BUILD_MPI "Build MPI version" OFF)
-else()
-  # do MPI detection after language activation,
-  # in case MPI for these languages is required
+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()
 
 if(BUILD_MPI)
-  # We use a non-standard procedure to compile with MPI on windows
-  if (CMAKE_SYSTEM_NAME STREQUAL Windows)
+  # 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()
-    set(MPI_CXX_SKIP_MPICXX ON)
     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)
@@ -163,9 +156,6 @@ else()
   enable_language(C)
   file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
   add_library(mpi_stubs STATIC ${MPI_SOURCES})
-  if(NOT BUILD_SHARED_LIBS)
-    install(TARGETS mpi_stubs EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-  endif()
   set_target_properties(mpi_stubs PROPERTIES OUTPUT_NAME lammps_mpi_stubs${LAMMPS_MACHINE})
   target_include_directories(mpi_stubs PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS> $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/lammps/mpi>)
   install(FILES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps/mpi)
@@ -195,13 +185,14 @@ if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0")
   target_compile_definitions(lammps PRIVATE -DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
 endif()
 
-option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)
+option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" ${ENABLE_TESTING})
 if(LAMMPS_EXCEPTIONS)
   target_compile_definitions(lammps PUBLIC -DLAMMPS_EXCEPTIONS)
 endif()
 
 # "hard" dependencies between packages resulting
 # in an error instead of skipping over files
+pkg_depends(MLIAP SNAP)
 pkg_depends(MPIIO MPI)
 pkg_depends(USER-ATC MANYBODY)
 pkg_depends(USER-LB MPI)
@@ -240,6 +231,48 @@ if(BUILD_OMP)
   target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
 endif()
 
+# Compiler specific features for testing
+if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
+  option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
+  mark_as_advanced(ENABLE_COVERAGE)
+  if(ENABLE_COVERAGE)
+    if(CMAKE_VERSION VERSION_LESS 3.13)
+      if(CMAKE_CXX_FLAGS)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
+      else()
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage")
+      endif()
+    else()
+      target_compile_options(lammps PUBLIC --coverage)
+      target_link_options(lammps PUBLIC --coverage)
+    endif()
+  endif()
+endif()
+
+set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)")
+mark_as_advanced(ENABLE_SANITIZER)
+set(ENABLE_SANITIZER_VALUES none address leak thread undefined)
+set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES})
+validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
+string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)
+if(NOT ENABLE_SANITIZER STREQUAL "none")
+  if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
+    if(CMAKE_VERSION VERSION_LESS 3.13)
+      if(CMAKE_CXX_FLAGS)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
+      else()
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
+      endif()
+    else()
+      target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
+      target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
+    endif()
+  else()
+    message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.")
+    set(ENABLE_SANITIZER "none")
+  endif()
+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)
@@ -252,9 +285,6 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
     enable_language(Fortran)
     file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
     add_library(linalg STATIC ${LAPACK_SOURCES})
-    if(NOT BUILD_SHARED_LIBS)
-      install(TARGETS linalg EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-    endif()
     set_target_properties(linalg PROPERTIES OUTPUT_NAME lammps_linalg${LAMMPS_MACHINE})
     set(BLAS_LIBRARIES "$<TARGET_FILE:linalg>")
     set(LAPACK_LIBRARIES "$<TARGET_FILE:linalg>")
@@ -328,16 +358,10 @@ foreach(PKG_WITH_INCL KSPACE PYTHON VORONOI USER-COLVARS USER-MOLFILE USER-NETCD
   endif()
 endforeach()
 
-set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler specific optimization or instrumentation")
+set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler and machine specific optimization flags (compilation only)")
 separate_arguments(CMAKE_TUNE_FLAGS)
-include(CheckCXXCompilerFlag)
 foreach(_FLAG ${CMAKE_TUNE_FLAGS})
-  check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAG})
-  if(COMPILER_SUPPORTS${_FLAG})
-    target_compile_options(lammps PRIVATE ${_FLAG})
-  else()
-    message(WARNING "${_FLAG} found in CMAKE_TUNE_FLAGS, but not supported by the compiler, skipping")
-  endif()
+  target_compile_options(lammps PRIVATE ${_FLAG})
 endforeach()
 ########################################################################
 # Basic system tests (standard libraries, headers, functions, types)   #
@@ -359,6 +383,15 @@ target_link_libraries(lammps PRIVATE ${MATH_LIBRARIES})
 include(StyleHeaderUtils)
 RegisterStyles(${LAMMPS_SOURCE_DIR})
 
+########################################################
+# Fetch missing external files and archives for packages
+########################################################
+foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
+  if(PKG_${PKG})
+    FetchPotentials(${LAMMPS_SOURCE_DIR}/${PKG} ${LAMMPS_POTENTIALS_DIR})
+  endif()
+endforeach()
+
 ##############################################
 # add sources of enabled packages
 ############################################
@@ -405,17 +438,20 @@ endforeach()
 ##############################################
 # add lib sources of (simple) enabled packages
 ############################################
-foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD)
+foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT)
   if(PKG_${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}/[^.]*.c
-      ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
-    add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
-    if(NOT BUILD_SHARED_LIBS)
-      install(TARGETS ${PKG_LIB} EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+    if(PKG_LIB STREQUAL mesont)
+      enable_language(Fortran)
+      file(GLOB_RECURSE ${PKG_LIB}_SOURCES
+        ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.f90)
+    else()
+      file(GLOB_RECURSE ${PKG_LIB}_SOURCES
+        ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c
+        ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
     endif()
+    add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
     set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE})
     target_link_libraries(lammps PRIVATE ${PKG_LIB})
     if(PKG_LIB STREQUAL awpmd)
@@ -436,7 +472,12 @@ 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 PRIVATE ${LAPACK_LIBRARIES} MPI::MPI_CXX)
+  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()
@@ -497,7 +538,7 @@ execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HE
 # Generate lmpgitversion.h
 ######################################
 add_custom_target(gitversion COMMAND ${CMAKE_COMMAND}
-  -DCMAKE_CURRENT_SOURCE_DIR="${CMAKE_CURRENT_SOURCE_DIR}"
+  -DLAMMPS_DIR="${LAMMPS_DIR}"
   -DGIT_EXECUTABLE="${GIT_EXECUTABLE}"
   -DGIT_FOUND="${GIT_FOUND}"
   -DLAMMPS_STYLE_HEADERS_DIR="${LAMMPS_STYLE_HEADERS_DIR}"
@@ -522,14 +563,15 @@ endif()
 
 set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
 set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
-install(TARGETS lammps EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
 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})
-  install(FILES ${LAMMPS_SOURCE_DIR}/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
+  if(BUILD_SHARED_LIBS)
+    install(FILES ${LAMMPS_SOURCE_DIR}/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
+  endif()
 endforeach()
 target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/includes>)
 add_library(LAMMPS::lammps ALIAS lammps)
@@ -538,15 +580,16 @@ set(LAMMPS_API_DEFINES)
 foreach(_DEF ${LAMMPS_DEFINES})
   set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${_DEF}")
 endforeach()
-configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
-install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
-install(EXPORT LAMMPS_Targets FILE LAMMPS_Targets.cmake NAMESPACE LAMMPS:: DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
-file(GLOB MODULE_FILES ${CMAKE_CURRENT_SOURCE_DIR}/Modules/Find*.cmake)
-install(FILES ${MODULE_FILES} DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
-include(CMakePackageConfigHelpers)
-configure_file(LAMMPSConfig.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake @ONLY)
-write_basic_package_version_file("LAMMPSConfigVersion.cmake" VERSION ${PROJECT_VERSION} COMPATIBILITY ExactVersion)
-install(FILES "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake" "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfigVersion.cmake" DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
+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)
+  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)
@@ -556,10 +599,16 @@ if(BUILD_TOOLS)
 
   include(CheckGeneratorSupport)
   if(CMAKE_GENERATOR_SUPPORT_FORTRAN)
-    enable_language(Fortran)
-    add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
-    target_link_libraries(chain.x PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
-    install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR})
+    include(CheckLanguage)
+    check_language(Fortran)
+    if(CMAKE_Fortran_COMPILER)
+      enable_language(Fortran)
+      add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
+      target_link_libraries(chain.x PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+      install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR})
+    else()
+      message(WARNING "No suitable Fortran compiler found, skipping building 'chain.x'")
+    endif()
   else()
     message(WARNING "CMake build doesn't support fortran, skipping building 'chain.x'")
   endif()
@@ -600,6 +649,8 @@ install(
 ###############################################################################
 if(BUILD_SHARED_LIBS)
   if(CMAKE_VERSION VERSION_LESS 3.12)
+    # adjust so we find Python 3 versions before Python 2 on old systems with old CMake
+    set(Python_ADDITIONAL_VERSIONS 3.8 3.7 3.6 3.5)
     find_package(PythonInterp) # Deprecated since version 3.12
     if(PYTHONINTERP_FOUND)
         set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
@@ -651,6 +702,7 @@ endif()
 
 include(Testing)
 include(CodeCoverage)
+include(CodingStandard)
 
 ###############################################################################
 # Print package summary
@@ -695,6 +747,12 @@ if (${_index} GREATER -1)
 endif()
 message(STATUS "<<< Linker flags: >>>")
 message(STATUS "Executable name:  ${LAMMPS_BINARY}")
+if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
+  get_target_property(OPTIONS lammps LINK_OPTIONS)
+  if(OPTIONS)
+    message(STATUS "Linker options:   ${OPTIONS}")
+  endif()
+endif()
 if(CMAKE_EXE_LINKER_FLAGS)
   message(STATUS "Executable linker flags: ${CMAKE_EXE_LINKER_FLAGS}")
 endif()
@@ -705,6 +763,7 @@ else()
 endif()
 if(BUILD_MPI)
   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()
@@ -754,3 +813,6 @@ if(PKG_KSPACE)
     endif()
   endif()
 endif()
+if(BUILD_DOC)
+  message(STATUS "<<< Building HTML Manual >>>")
+endif()

cmake/LAMMPSConfig.cmake.in

@@ -1,87 +1,5 @@
-set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR})
 include(CMakeFindDependencyMacro)
 if(@BUILD_MPI@)
   find_dependency(MPI REQUIRED CXX)
 endif()
-if(@PKG_KSPACE@)
-  if(@FFT@ STREQUAL "FFTW3")
-    find_dependency(@FFTW@ REQUIRED MODULE)
-  endif()
-endif()
-if(NOT @BUILD_SHARED_LIBS@)
-  if(@BUILD_OMP@)
-    find_dependency(OpenMP REQUIRED)
-  endif()
-  if(@WITH_JPEG@)
-    find_dependency(JPEG REQUIRED)
-  endif()
-  if(@WITH_PNG@)
-    find_dependency(PNG REQUIRED)
-    find_dependency(ZLIB REQUIRED)
-  endif()
-  if(@PKG_KIM@)
-    find_dependency(PkgConfig REQUIRED)
-    pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=@KIM-API_MIN_VERSION@)
-    if(@CURL_FOUND@)
-      find_dependency(CURL REQUIRED)
-    endif()
-  endif()
-  if(@PKG_USER-SMD@)
-    find_dependency(Eigen3 NO_MODULE REQUIRED)
-  endif()
-  if(@PKG_USER-SCAFACOS@)
-    find_dependency(PkgConfig REQUIRED)
-    find_ependency(GSL REQUIRED)
-    find_dependency(MPI REQUIRED C Fortran)
-    pkg_check_modules(SCAFACOS REQUIRED IMPORTED_TARGET scafacos)
-  endif()
-  if(@PKG_PYTHON@ AND NOT CMAKE_VERSION VERSION_LESS 3.12)
-    find_package(Python REQUIRED COMPONENTS Development)
-  endif()
-  if(@PKG_COMPRESS@)
-    find_dependency(ZLIB REQUIRED)
-  endif()
-  if(@PKG_KOKKOS@)
-    if(@EXTERNAL_KOKKOS@)
-      find_dependency(Kokkos 3 REQUIRED)
-    endif()
-  endif()
-  if(@PKG_VORONOI@)
-    find_dependency(VORO REQUIRED)
-  endif()
-  if(@PKG_USER-INTEL@)
-    if(@INTEL_LRT_MODE@ STREQUAL "THREADS")
-      find_dependency(Threads REQUIRED)
-    endif()
-    if(@TBB_MALLOC_FOUND@)
-      find_ependency(TBB_MALLOC REQUIRED)
-    endif()
-  endif()
-  if(@PKG_USER-ADIOS@)
-    find_ependency(ADIOS2 REQUIRED)
-  endif()
-  if(@PKG_LATTE@)
-    find_ependency(LATTE REQUIRED)
-  endif()
-  if(@PKG_MESSAGE@)
-    if(@MESSAGE_ZMQ@)
-      find_ependency(ZMQ REQUIRED)
-    endif()
-  endif()
-  if(@PKG_MSCG@)
-    find_ependency(GSL REQUIRED)
-    find_ependency(MSCG REQUIRED)
-  endif()
-  if(@USER-NETCDF@)
-    if(@NETCDF_FOUND@)
-      find_ependency(NetCDF REQUIRED)
-    endif()
-    if(@PNETCDF_FOUND@)
-      find_ependency(PNetCDF REQUIRED)
-    endif()
-  endif()
-  if(@PKG_QUIP@)
-    find_ependency(QUIP REQUIRED)
-  endif()
-endif()
 include("${CMAKE_CURRENT_LIST_DIR}/LAMMPS_Targets.cmake")

cmake/Modules/CodeCoverage.cmake

@@ -15,14 +15,35 @@ if(ENABLE_COVERAGE)
             gen_coverage_xml
             COMMAND ${GCOVR_BINARY} -s -x -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.xml
             WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
-            COMMENT "Generating XML Coverage Report..."
+            COMMENT "Generating XML coverage report..."
         )
 
+        set(COVERAGE_HTML_DIR ${CMAKE_BINARY_DIR}/coverage_html)
+
+        add_custom_target(coverage_html_folder
+            COMMAND ${CMAKE_COMMAND} -E make_directory ${COVERAGE_HTML_DIR})
+
         add_custom_target(
             gen_coverage_html
-            COMMAND ${GCOVR_BINARY} -s  --html --html-details -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.html
+            COMMAND ${GCOVR_BINARY} -s  --html --html-details -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o ${COVERAGE_HTML_DIR}/index.html
             WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
-            COMMENT "Generating HTML Coverage Report..."
+            COMMENT "Generating HTML coverage report..."
         )
+        add_dependencies(gen_coverage_html coverage_html_folder)
+
+        add_custom_target(clean_coverage_html
+            ${CMAKE_COMMAND} -E remove_directory ${COVERAGE_HTML_DIR}
+            COMMENT "Deleting HTML coverage report..."
+        )
+
+        add_custom_target(reset_coverage
+            ${CMAKE_COMMAND} -E remove -f */*.gcda */*/*.gcda */*/*/*.gcda
+                              */*/*/*/*.gcda */*/*/*/*/*.gcda */*/*/*/*/*/*.gcda
+                              */*/*/*/*/*/*/*.gcda */*/*/*/*/*/*/*/*.gcda
+                              */*/*/*/*/*/*/*/*/*.gcda */*/*/*/*/*/*/*/*/*/*.gcda
+            WORKIND_DIRECTORY ${CMAKE_BINARY_DIR}
+            COMMENT "Deleting coverage data files..."
+        )
+        add_dependencies(reset_coverage clean_coverage_html)
     endif()
 endif()

cmake/Modules/CodingStandard.cmake

@@ -0,0 +1,34 @@
+if(CMAKE_VERSION VERSION_LESS 3.12)
+    find_package(PythonInterp 3.5 QUIET) # Deprecated since version 3.12
+    if(PYTHONINTERP_FOUND)
+        set(Python3_EXECUTABLE ${PYTHON_EXECUTABLE})
+        set(Python3_VERSION ${PYTHON_VERSION_STRING})
+    endif()
+else()
+    find_package(Python3 COMPONENTS Interpreter QUIET)
+endif()
+
+if (Python3_EXECUTABLE)
+    if(Python3_VERSION VERSION_GREATER_EQUAL 3.5)
+        add_custom_target(
+          check-whitespace
+          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .
+          WORKING_DIRECTORY  ${LAMMPS_DIR}
+          COMMENT "Check for whitespace errors")
+        add_custom_target(
+          check-permissions
+          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py .
+          WORKING_DIRECTORY  ${LAMMPS_DIR}
+          COMMENT "Check for permission errors")
+        add_custom_target(
+          fix-whitespace
+          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py -f .
+          WORKING_DIRECTORY  ${LAMMPS_DIR}
+          COMMENT "Fix whitespace errors")
+        add_custom_target(
+          fix-permissions
+          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py -f .
+          WORKING_DIRECTORY  ${LAMMPS_DIR}
+          COMMENT "Fix permission errors")
+    endif()
+endif()

cmake/Modules/Documentation.cmake

@@ -2,10 +2,19 @@
 # Build documentation
 ###############################################################################
 option(BUILD_DOC "Build LAMMPS HTML documentation" OFF)
-if(BUILD_DOC)
-  find_package(PythonInterp 3 REQUIRED)
 
-  set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)
+if(BUILD_DOC)
+  # Sphinx 3.x requires at least Python 3.5
+  if(CMAKE_VERSION VERSION_LESS 3.12)
+    find_package(PythonInterp 3.5 REQUIRED)
+    set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv -p ${PYTHON_EXECUTABLE})
+  else()
+    find_package(Python3 REQUIRED COMPONENTS Interpreter)
+    if(Python3_VERSION VERSION_LESS 3.5)
+      message(FATAL_ERROR "Python 3.5 and up is required to build the HTML documentation")
+    endif()
+    set(VIRTUALENV ${Python3_EXECUTABLE} -m virtualenv -p ${Python3_EXECUTABLE})
+  endif()
 
   file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
 
@@ -20,16 +29,15 @@ if(BUILD_DOC)
     OUTPUT requirements.txt
     DEPENDS docenv
     COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/utils/requirements.txt requirements.txt
-    COMMAND ${DOCENV_BINARY_DIR}/pip install -r requirements.txt --upgrade
     COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
+    COMMAND ${DOCENV_BINARY_DIR}/pip install --use-feature=2020-resolver -r requirements.txt --upgrade
   )
 
   # 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)
+  if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax/es5)
+    file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
+      "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
+      EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7)
     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)
@@ -37,11 +45,18 @@ if(BUILD_DOC)
   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/)
 
+  # for increased browser compatibility
+  if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/html/_static/polyfill.js)
+    file(DOWNLOAD "https://polyfill.io/v3/polyfill.min.js?features=es6"
+      "${CMAKE_CURRENT_BINARY_DIR}/html/_static/polyfill.js")
+  endif()
+
   # 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
+    COMMAND ${CMAKE_COMMAND} -E create_symlink Manual.html ${CMAKE_CURRENT_BINARY_DIR}/html/index.html
   )
 
   # copy selected image files to html output tree
@@ -56,17 +71,17 @@ if(BUILD_DOC)
   set(HTML_IMAGE_TARGETS "")
   foreach(_IMG ${HTML_EXTRA_IMAGES})
     string(PREPEND _IMG JPG/)
-    list(APPEND HTML_IMAGE_TARGETS "html/${_IMG}")
+    list(APPEND HTML_IMAGE_TARGETS "${CMAKE_CURRENT_BINARY_DIR}/html/${_IMG}")
     add_custom_command(
       OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/html/${_IMG}
-      DEPENDS ${LAMMPS_DOC_DIR}/src/${_IMG} html/JPG
+      DEPENDS ${LAMMPS_DOC_DIR}/src/${_IMG} ${CMAKE_CURRENT_BINARY_DIR}/html/JPG
       COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/src/${_IMG} ${CMAKE_BINARY_DIR}/html/${_IMG}
     )
   endforeach()
 
   add_custom_target(
     doc ALL
-    DEPENDS html html/_static/mathjax/es5 ${HTML_IMAGE_TARGETS}
+    DEPENDS html ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax/es5 ${HTML_IMAGE_TARGETS}
     SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES}
   )
 

cmake/Modules/FindClangFormat.cmake

@@ -0,0 +1,46 @@
+# Find clang-format
+find_program(ClangFormat_EXECUTABLE NAMES clang-format
+                                          clang-format-10.0
+                                          clang-format-9.0
+                                          clang-format-8.0
+                                          clang-format-7.0
+                                          clang-format-6.0
+                                     DOC "clang-format executable")
+mark_as_advanced(ClangFormat_EXECUTABLE)
+
+if(ClangFormat_EXECUTABLE)
+  # find version
+  execute_process(COMMAND ${ClangFormat_EXECUTABLE} --version
+                  OUTPUT_VARIABLE clang_format_version
+                  ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+
+  if(clang_format_version MATCHES "^clang-format version .*")
+    # Arch Linux
+    # clang-format version 10.0.0
+
+    # Ubuntu 18.04 LTS Output
+    # clang-format version 6.0.0-1ubuntu2 (tags/RELEASE_600/final)
+    string(REGEX REPLACE "clang-format version ([0-9.]+).*"
+                         "\\1"
+                         ClangFormat_VERSION
+                         "${clang_format_version}")
+  elseif(clang_format_version MATCHES ".*LLVM version .*")
+    # CentOS 7 Output
+    # LLVM (http://llvm.org/):
+    #   LLVM version 3.4.2
+    #   Optimized build.
+    #   Built Nov  1 2018 (15:06:24).
+    #   Default target: x86_64-redhat-linux-gnu
+    #   Host CPU: x86-64
+    string(REGEX REPLACE ".*LLVM version ([0-9.]+).*"
+                         "\\1"
+                         ClangFormat_VERSION
+                         "${clang_format_version}")
+  else()
+    set(ClangFormat_VERSION "0.0")
+  endif()
+endif()
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(ClangFormat REQUIRED_VARS ClangFormat_EXECUTABLE VERSION_VAR ClangFormat_VERSION)

cmake/Modules/FindLATTE.cmake

@@ -1,27 +0,0 @@
-# - Find latte
-# Find the native LATTE libraries.
-#
-#  LATTE_LIBRARIES    - List of libraries when using latte.
-#  LATTE_FOUND        - True if latte found.
-#
-
-find_library(LATTE_LIBRARY NAMES latte)
-
-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/FindTBB_MALLOC.cmake

@@ -6,12 +6,12 @@
 #  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
+find_library(TBB_MALLOC_LIBRARY NAMES tbbmalloc PATHS $ENV{TBBROOT}/lib/intel64/gcc4.8
+                                                      $ENV{TBBROOT}/lib/intel64/gcc4.7
                                                       $ENV{TBBROOT}/lib/intel64/gcc4.4
                                                       $ENV{TBBROOT}/lib/intel64/gcc4.1)
 

cmake/Modules/FindYAML.cmake

@@ -0,0 +1,30 @@
+# - Find libyaml
+# Find the native Yaml headers and libraries.
+#
+#  YAML_INCLUDE_DIRS - where to find yaml.h
+#  YAML_LIBRARIES    - List of libraries when using libyaml
+#  YAML_FOUND        - True if libyaml is found.
+#
+
+find_path(YAML_INCLUDE_DIR yaml.h PATH_SUFFIXES yaml)
+find_library(YAML_LIBRARY NAMES yaml)
+
+# handle the QUIET and REQUIRED arguments and
+# set YAML_FOUND to TRUE if all variables are non-zero
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(YAML DEFAULT_MSG YAML_LIBRARY YAML_INCLUDE_DIR)
+
+# Copy the results to the output variables and target.
+if(YAML_FOUND)
+  set(YAML_LIBRARIES ${YAML_LIBRARY})
+  set(YAML_INCLUDE_DIRS ${YAML_INCLUDE_DIR})
+
+  if(NOT TARGET Yaml::Yaml)
+    add_library(Yaml::Yaml UNKNOWN IMPORTED)
+    set_target_properties(Yaml::Yaml PROPERTIES
+      IMPORTED_LOCATION "${YAML_LIBRARY}"
+      INTERFACE_INCLUDE_DIRECTORIES "${YAML_INCLUDE_DIR}")
+  endif()
+endif()
+
+mark_as_advanced(YAML_INCLUDE_DIR YAML_LIBRARY)

cmake/Modules/GTest.cmake

@@ -0,0 +1,79 @@
+message(STATUS "Downloading and building Google Test library")
+
+if(CMAKE_BUILD_TYPE STREQUAL Debug)
+  set(GTEST_LIB_POSTFIX d)
+else()
+  set(GTEST_LIB_POSTFIX)
+endif()
+
+include(ExternalProject)
+set(GTEST_URL "https://github.com/google/googletest/archive/release-1.10.0.tar.gz" CACHE STRING "URL for GTest tarball")
+mark_as_advanced(GTEST_URL)
+ExternalProject_Add(googletest
+                    URL ${GTEST_URL}
+                    URL_MD5         ecd1fa65e7de707cd5c00bdac56022cd
+                    SOURCE_DIR      "${CMAKE_BINARY_DIR}/gtest-src"
+                    BINARY_DIR      "${CMAKE_BINARY_DIR}/gtest-build"
+                    CMAKE_ARGS      ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_GTEST_OPTS}
+                                    -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+                                    -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+                                    -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+                                    -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
+                                    -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
+                    BUILD_BYPRODUCTS <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest${GTEST_LIB_POSTFIX}.a
+                                     <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock${GTEST_LIB_POSTFIX}.a
+                                     <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest_main${GTEST_LIB_POSTFIX}.a
+                                     <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock_main${GTEST_LIB_POSTFIX}.a
+                    LOG_DOWNLOAD ON
+                    LOG_CONFIGURE ON
+                    LOG_BUILD ON
+                    INSTALL_COMMAND ""
+                    TEST_COMMAND    "")
+
+ExternalProject_Get_Property(googletest SOURCE_DIR)
+set(GTEST_INCLUDE_DIR ${SOURCE_DIR}/googletest/include)
+set(GMOCK_INCLUDE_DIR ${SOURCE_DIR}/googlemock/include)
+
+# workaround for CMake 3.10 on ubuntu 18.04
+file(MAKE_DIRECTORY ${GTEST_INCLUDE_DIR})
+file(MAKE_DIRECTORY ${GMOCK_INCLUDE_DIR})
+
+ExternalProject_Get_Property(googletest BINARY_DIR)
+set(GTEST_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest${GTEST_LIB_POSTFIX}.a)
+set(GMOCK_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock${GTEST_LIB_POSTFIX}.a)
+set(GTEST_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest_main${GTEST_LIB_POSTFIX}.a)
+set(GMOCK_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock_main${GTEST_LIB_POSTFIX}.a)
+
+# Prevent GoogleTest from overriding our compiler/linker options
+# when building with Visual Studio
+set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
+
+find_package(Threads QUIET)
+
+add_library(GTest::GTest UNKNOWN IMPORTED)
+set_target_properties(GTest::GTest PROPERTIES
+        IMPORTED_LOCATION ${GTEST_LIBRARY_PATH}
+        INTERFACE_INCLUDE_DIRECTORIES ${GTEST_INCLUDE_DIR}
+        INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
+add_dependencies(GTest::GTest googletest)
+
+add_library(GTest::GMock UNKNOWN IMPORTED)
+set_target_properties(GTest::GMock PROPERTIES
+        IMPORTED_LOCATION ${GMOCK_LIBRARY_PATH}
+        INTERFACE_INCLUDE_DIRECTORIES ${GMOCK_INCLUDE_DIR}
+        INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
+add_dependencies(GTest::GMock googletest)
+
+add_library(GTest::GTestMain UNKNOWN IMPORTED)
+set_target_properties(GTest::GTestMain PROPERTIES
+        IMPORTED_LOCATION ${GTEST_MAIN_LIBRARY_PATH}
+        INTERFACE_INCLUDE_DIRECTORIES ${GTEST_INCLUDE_DIR}
+        INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
+add_dependencies(GTest::GTestMain googletest)
+
+add_library(GTest::GMockMain UNKNOWN IMPORTED)
+set_target_properties(GTest::GMockMain PROPERTIES
+        IMPORTED_LOCATION ${GMOCK_MAIN_LIBRARY_PATH}
+        INTERFACE_INCLUDE_DIRECTORIES ${GMOCK_INCLUDE_DIR}
+        INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
+add_dependencies(GTest::GMockMain googletest)

cmake/Modules/LAMMPSUtils.cmake

@@ -85,3 +85,26 @@ function(GenerateBinaryHeader varname outfile files)
         file(APPEND ${outfile} "const unsigned int ${varname}_size = sizeof(${varname});\n")
     endforeach()
 endfunction(GenerateBinaryHeader)
+
+# fetch missing potential files
+function(FetchPotentials pkgfolder potfolder)
+  if (EXISTS "${pkgfolder}/potentials.txt")
+    set(LAMMPS_POTENTIALS_URL "https://download.lammps.org/potentials")
+    file(STRINGS "${pkgfolder}/potentials.txt" linelist REGEX "^[^#].")
+    foreach(line ${linelist})
+      string(FIND ${line} " " blank)
+      math(EXPR plusone "${blank}+1")
+      string(SUBSTRING ${line} 0 ${blank} pot)
+      string(SUBSTRING ${line} ${plusone} -1 sum)
+      if(EXISTS ${LAMMPS_POTENTIALS_DIR}/${pot})
+        file(MD5 "${LAMMPS_POTENTIALS_DIR}/${pot}" oldsum)
+      endif()
+      if(NOT sum STREQUAL oldsum)
+        message(STATUS "Checking external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
+        file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${CMAKE_BINARY_DIR}/${pot}"
+          EXPECTED_HASH MD5=${sum} SHOW_PROGRESS)
+        file(COPY "${CMAKE_BINARY_DIR}/${pot}" DESTINATION ${LAMMPS_POTENTIALS_DIR})
+      endif()
+    endforeach()
+  endif()
+endfunction(FetchPotentials)

cmake/Modules/MPI4WIN.cmake

@@ -23,3 +23,8 @@ set_target_properties(MPI::MPI_CXX PROPERTIES
   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/GPU.cmake

@@ -40,6 +40,17 @@ if(GPU_API STREQUAL "CUDA")
 
   set(GPU_ARCH "sm_50" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
 
+  # ensure that no *cubin.h files exist from a compile in the lib/gpu folder
+  file(GLOB GPU_LIB_OLD_CUBIN_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h)
+  if (GPU_LIB_OLD_CUBIN_HEADERS)
+    message(FATAL_ERROR "########################################################################\n"
+      "Found file(s) generated by the make-based build system in lib/gpu\n"
+      "Please run\n"
+      "  make -C ${LAMMPS_LIB_SOURCE_DIR}/gpu -f Makefile.serial clean\n"
+      "to remove\n"
+      "########################################################################")
+  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)
 
@@ -53,33 +64,44 @@ if(GPU_API STREQUAL "CUDA")
 
   # build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
   # --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
-  set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH} ")
+  set(GPU_CUDA_GENCODE "-arch=${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] ")
+  if((CUDA_VERSION VERSION_GREATER_EQUAL "3.2") AND (CUDA_VERSION VERSION_LESS "9.0"))
+    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_20,code=[sm_20,compute_20] ")
   endif()
-  # Kepler (GPU Arch 3.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] ")
+  # Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
+  if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
+    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] ")
+  endif()
+  # Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11
+  if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
+    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_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] ")
+  if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
+    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")
   endif()
   # Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
-  if(CUDA_VERSION VERSION_GREATER "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] ")
+  if(CUDA_VERSION VERSION_GREATER_EQUAL "8.0")
+    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")
   endif()
   # Volta (GPU Arch 7.0) is supported by CUDA 9 and later
-  if(CUDA_VERSION VERSION_GREATER "8.9")
-    string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_70,code=[sm_70,compute_70] ")
+  if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
+    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")
   endif()
   # Turing (GPU Arch 7.5) is supported by CUDA 10 and later
-  if(CUDA_VERSION VERSION_GREATER "9.9")
-    string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ")
+  if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
+    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
+  endif()
+  # Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
+  if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
+    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
+  endif()
+  if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
+    message(WARNING "Unsupported CUDA version. Use at your own risk.")
   endif()
 
-  cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
+  cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
           -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 ${CUDA_REQUEST_PIC}
@@ -115,7 +137,7 @@ if(GPU_API STREQUAL "CUDA")
 elseif(GPU_API STREQUAL "OPENCL")
   if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
     # download and unpack support binaries for compilation of windows binaries.
-    set(LAMMPS_THIRDPARTY_URL "http://download.lammps.org/thirdparty")
+    set(LAMMPS_THIRDPARTY_URL "https://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})
@@ -215,30 +237,41 @@ elseif(GPU_API STREQUAL "HIP")
 
     # 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=${HIP_ARCH} ")
+    set(HIP_CUDA_GENCODE "-arch=${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] ")
+    if((CUDA_VERSION VERSION_GREATER_EQUAL "3.2") 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] ")
+    # Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
+    if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
+      string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30]")
+    endif()
+    # Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11.0
+    if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
+      string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_35,code=[sm_35,compute_35]")
     endif()
     # Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
-    if(CUDA_VERSION VERSION_GREATER "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] ")
+    if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
+      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] ")
+    if(CUDA_VERSION VERSION_GREATER_EQUAL "8.0")
+      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] ")
+    if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
+      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] ")
+    if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
+      string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
+    endif()
+    # Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
+    if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
+      string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
+    endif()
+    if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
+      message(WARNING "Unsupported CUDA version. Use at your own risk.")
     endif()
   endif()
 
@@ -257,10 +290,17 @@ elseif(GPU_API STREQUAL "HIP")
     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")
+        if(HIP_COMPILER STREQUAL "clang")
+          add_custom_command(OUTPUT ${CUBIN_FILE}
+            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -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")
+        else()
+          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")
+        endif()
     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}
@@ -330,7 +370,7 @@ elseif(GPU_API STREQUAL "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 ${HIP_ROOT_DIR}/../include)
     target_include_directories(gpu PRIVATE ${CUDA_INCLUDE_DIRS})
     target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
 
@@ -338,6 +378,12 @@ elseif(GPU_API STREQUAL "HIP")
     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)
@@ -353,9 +399,11 @@ RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)
 
 get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
 
-target_link_libraries(gpu PRIVATE MPI::MPI_CXX)
-if(NOT BUILD_SHARED_LIBS)
-  install(TARGETS gpu EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+if(NOT BUILD_MPI)
+  # mpistubs is aliased to MPI::MPI_CXX, but older versions of cmake won't work forward the include path
+  target_link_libraries(gpu PRIVATE mpi_stubs)
+else()
+  target_link_libraries(gpu PRIVATE MPI::MPI_CXX)
 endif()
 target_compile_definitions(gpu PRIVATE -DLAMMPS_${LAMMPS_SIZES})
 set_target_properties(gpu PROPERTIES OUTPUT_NAME lammps_gpu${LAMMPS_MACHINE})

cmake/Modules/Packages/KIM.cmake

@@ -1,7 +1,12 @@
 set(KIM-API_MIN_VERSION 2.1.3)
 find_package(CURL)
 if(CURL_FOUND)
-  target_link_libraries(lammps PRIVATE CURL::libcurl)
+  if(CMAKE_VERSION VERSION_LESS 3.12)
+    target_include_directories(lammps PRIVATE ${CURL_INCLUDE_DIRS})
+    target_link_libraries(lammps PRIVATE ${CURL_LIBRARIES})
+  else()
+    target_link_libraries(lammps PRIVATE CURL::libcurl)
+  endif()
   target_compile_definitions(lammps PRIVATE -DLMP_KIM_CURL)
   set(LMP_DEBUG_CURL OFF CACHE STRING "Set libcurl verbose mode on/off. If on, it displays a lot of verbose information about its operations.")
   mark_as_advanced(LMP_DEBUG_CURL)
@@ -51,9 +56,6 @@ if(DOWNLOAD_KIM)
     INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include/kim-api")
   target_link_libraries(lammps PRIVATE LAMMPS::KIM)
   add_dependencies(LAMMPS::KIM kim_build)
-  if(NOT BUILD_SHARED_LIBS)
-    install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
-  endif()
 else()
   find_package(PkgConfig REQUIRED)
   pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=${KIM-API_MIN_VERSION})

cmake/Modules/Packages/KOKKOS.cmake

@@ -14,16 +14,30 @@ 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")
-  file(DOWNLOAD https://github.com/kokkos/kokkos/compare/3.0.00...stanmoore1:lammps.diff ${CMAKE_CURRENT_BINARY_DIR}/kokkos-lammps.patch)
+  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/3.0.00.tar.gz
-    URL_MD5 281c7093aa3a603276e93abdf4be23b9
-    PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/kokkos-lammps.patch
-    CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC}
-    -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DCMAKE_INSTALL_LIBDIR=lib
-    -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM} -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
+    URL https://github.com/kokkos/kokkos/archive/3.1.01.tar.gz
+    URL_MD5 3ccb2100f7fc316891e7dad3bc33fa37
+    CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
     BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
   )
   ExternalProject_get_property(kokkos_build INSTALL_DIR)
@@ -35,14 +49,8 @@ if(DOWNLOAD_KOKKOS)
     INTERFACE_LINK_LIBRARIES ${CMAKE_DL_LIBS})
   target_link_libraries(lammps PRIVATE LAMMPS::KOKKOS)
   add_dependencies(LAMMPS::KOKKOS kokkos_build)
-  if(NOT BUILD_SHARED_LIBS)
-    install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
-  endif()
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 3)
-  if(NOT Kokkos_FOUND)
-    message(FATAL_ERROR "KOKKOS library not found, help CMake to find it by setting KOKKOS_LIBRARY, or set DOWNLOAD_KOKKOS=ON to download it")
-  endif()
+  find_package(Kokkos 3.1.01 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
 else()
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)

cmake/Modules/Packages/KSPACE.cmake

@@ -2,7 +2,7 @@ option(FFT_SINGLE "Use single precision FFTs instead of double precision FFTs" O
 set(FFTW "FFTW3")
 if(FFT_SINGLE)
   set(FFTW "FFTW3F")
-  target_compile_definitions(lammps PUBLIC -DFFT_SINGLE)
+  target_compile_definitions(lammps PRIVATE -DFFT_SINGLE)
 endif()
 find_package(${FFTW} QUIET)
 if(${FFTW}_FOUND)
@@ -17,8 +17,8 @@ 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})
+  target_compile_definitions(lammps PRIVATE -DFFT_FFTW3)
+  target_link_libraries(lammps PRIVATE ${FFTW}::${FFTW})
   if(FFTW3_OMP_LIBRARY OR FFTW3F_OMP_LIBRARY)
     option(FFT_FFTW_THREADS "Use threaded FFTW library" ON)
   else()

cmake/Modules/Packages/LATTE.cmake

@@ -1,5 +1,12 @@
 enable_language(Fortran)
-find_package(LATTE)
+
+# using lammps in a super-build setting
+if(TARGET LATTE::latte)
+  target_link_libraries(lammps PRIVATE LATTE::latte)
+  return()
+endif()
+
+find_package(LATTE 1.2.2 CONFIG)
 if(LATTE_FOUND)
   set(DOWNLOAD_LATTE_DEFAULT OFF)
 else()
@@ -10,8 +17,8 @@ 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
+    URL https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz
+    URL_MD5 820e73a457ced178c08c71389a385de7
     SOURCE_SUBDIR cmake
     CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} -DCMAKE_INSTALL_LIBDIR=lib
     -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
@@ -27,13 +34,7 @@ if(DOWNLOAD_LATTE)
     INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
   target_link_libraries(lammps PRIVATE LAMMPS::LATTE)
   add_dependencies(LAMMPS::LATTE latte_build)
-  if(NOT BUILD_SHARED_LIBS)
-    install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
-  endif()
 else()
-  find_package(LATTE)
-  if(NOT LATTE_FOUND)
-    message(FATAL_ERROR "LATTE library not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
-  endif()
+  find_package(LATTE 1.2.2 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE LATTE::latte)
 endif()

cmake/Modules/Packages/MESSAGE.cmake

@@ -7,9 +7,6 @@ file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F
     ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
 
 add_library(cslib STATIC ${cslib_SOURCES})
-if(NOT BUILD_SHARED_LIBS)
-  install(TARGETS cslib EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-endif()
 target_compile_definitions(cslib PRIVATE -DLAMMPS_${LAMMPS_SIZES})
 set_target_properties(cslib PROPERTIES OUTPUT_NAME lammps_cslib${LAMMPS_MACHINE})
 if(BUILD_MPI)

cmake/Modules/Packages/MSCG.cmake

@@ -35,9 +35,6 @@ if(DOWNLOAD_MSCG)
     INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
   target_link_libraries(lammps PRIVATE LAMMPS::MSCG)
   add_dependencies(LAMMPS::MSCG mscg_build)
-  if(NOT BUILD_SHARED_LIBS)
-    install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
-  endif()
 else()
   find_package(MSCG)
   if(NOT MSCG_FOUND)

cmake/Modules/Packages/USER-COLVARS.cmake

@@ -9,9 +9,6 @@ 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})
-  if(NOT BUILD_SHARED_LIBS)
-    install(TARGETS lepton EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-  endif()
   # Change the define below to LEPTON_BUILDING_SHARED_LIBRARY when linking Lepton as a DLL with MSVC
   target_compile_definitions(lepton PRIVATE -DLEPTON_BUILDING_STATIC_LIBRARY)
   set_target_properties(lepton PROPERTIES OUTPUT_NAME lammps_lepton${LAMMPS_MACHINE})
@@ -19,9 +16,6 @@ if(COLVARS_LEPTON)
 endif()
 
 add_library(colvars STATIC ${COLVARS_SOURCES})
-if(NOT BUILD_SHARED_LIBS)
-  install(TARGETS colvars EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-endif()
 target_compile_definitions(colvars PRIVATE -DLAMMPS_${LAMMPS_SIZES})
 set_target_properties(colvars PROPERTIES OUTPUT_NAME lammps_colvars${LAMMPS_MACHINE})
 target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)

cmake/Modules/Packages/USER-INTEL.cmake

@@ -77,7 +77,7 @@ else()
     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})
+          target_compile_options(lammps PRIVATE ${_FLAG})
       endif()
     endforeach()
   endif()

cmake/Modules/Packages/USER-MOLFILE.cmake

@@ -1,8 +1,5 @@
 set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
 add_library(molfile INTERFACE)
-if(NOT BUILD_SHARED_LIBS)
-  install(TARGETS molfile EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-endif()
 target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
 # no need to link with -ldl on windows
 if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")

cmake/Modules/Packages/USER-NETCDF.cmake

@@ -1,11 +1,17 @@
 # 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"
-find_package(NetCDF)
-if(NETCDF_FOUND)
-  find_package(PNetCDF)
-else(NETCDF_FOUND)
-  find_package(PNetCDF REQUIRED)
-endif(NETCDF_FOUND)
+
+# may use NetCDF or PNetCDF with MPI, but must have NetCDF without
+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)

cmake/Modules/Packages/USER-PLUMED.cmake

@@ -70,16 +70,12 @@ if(DOWNLOAD_PLUMED)
   ExternalProject_get_property(plumed_build INSTALL_DIR)
   add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
   add_dependencies(LAMMPS::PLUMED plumed_build)
-  if(NOT BUILD_SHARED_LIBS)
-    install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
-  endif()
   if(PLUMED_MODE STREQUAL "STATIC")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_WRAPPER_CXX=1")
     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};${CMAKE_DL_LIBS}")
   elseif(PLUMED_MODE STREQUAL "RUNTIME")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_HAS_DLOPEN=1;__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${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 ${INSTALL_DIR}/include)
@@ -89,12 +85,11 @@ else()
   pkg_check_modules(PLUMED REQUIRED plumed)
   add_library(LAMMPS::PLUMED INTERFACE IMPORTED)
   if(PLUMED_MODE STREQUAL "STATIC")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_WRAPPER_CXX=1")
     include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
   elseif(PLUMED_MODE STREQUAL "SHARED")
     include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
   elseif(PLUMED_MODE STREQUAL "RUNTIME")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_HAS_DLOPEN=1;__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${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}")

cmake/Modules/Packages/USER-QMMM.cmake

@@ -1,12 +1,6 @@
 enable_language(C)
 
-if(NOT BUILD_SHARED_LIBS)
-  message(WARNING "It is recommended to use BUILD_SHARED_LIBS=yes with USER-QMMM")
-endif()
 add_library(qmmm STATIC ${LAMMPS_LIB_SOURCE_DIR}/qmmm/libqmmm.c)
-if(NOT BUILD_SHARED_LIBS)
-  install(TARGETS qmmm EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-endif()
 set_target_properties(qmmm PROPERTIES OUTPUT_NAME lammps_qmmm${LAMMPS_MACHINE})
 target_link_libraries(lammps PRIVATE qmmm)
 target_include_directories(qmmm PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/qmmm)

cmake/Modules/Packages/USER-SCAFACOS.cmake

@@ -14,10 +14,16 @@ 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")
+
+  # version 1.0.1 needs a patch to compile and linke cleanly with GCC 10 and later.
+  file(DOWNLOAD https://download.lammps.org/thirdparty/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
+          EXPECTED_HASH MD5=4baa1333bb28fcce102d505e1992d032)
+
   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
+    PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
     CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc
                                              --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
                                              --with-internal-fftw --with-internal-pfft
@@ -52,9 +58,6 @@ if(DOWNLOAD_SCAFACOS)
     INTERFACE_LINK_LIBRARIES "${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)
-  if(NOT BUILD_SHARED_LIBS)
-    install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
-  endif()
 else()
   find_package(PkgConfig REQUIRED)
   pkg_check_modules(SCAFACOS REQUIRED IMPORTED_TARGET scafacos)

cmake/Modules/Packages/USER-SMD.cmake

@@ -9,8 +9,8 @@ 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
+    URL https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz
+    URL_MD5 9e30f67e8531477de4117506fe44669b
     CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
   )
   ExternalProject_get_property(Eigen3_build SOURCE_DIR)
@@ -18,9 +18,6 @@ if(DOWNLOAD_EIGEN3)
   set_target_properties(LAMMPS::EIGEN3 PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}")
   target_link_libraries(lammps PRIVATE LAMMPS::EIGEN3)
   add_dependencies(LAMMPS::EIGEN3 Eigen3_build)
-  if(NOT BUILD_SHARED_LIBS)
-    install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
-  endif()
 else()
   find_package(Eigen3 NO_MODULE)
   mark_as_advanced(Eigen3_DIR)

cmake/Modules/Packages/VORONOI.cmake

@@ -24,7 +24,11 @@ if(DOWNLOAD_VORO)
   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 ""
+    PATCH_COMMAND patch -b -p0 < ${LAMMPS_LIB_SOURCE_DIR}/voronoi/voro-make.patch
+    CONFIGURE_COMMAND ""
+    BUILD_COMMAND make ${VORO_BUILD_OPTIONS}
+    BUILD_IN_SOURCE 1
+    INSTALL_COMMAND ""
     BUILD_BYPRODUCTS <SOURCE_DIR>/src/libvoro++.a
     )
   ExternalProject_get_property(voro_build SOURCE_DIR)
@@ -35,9 +39,6 @@ if(DOWNLOAD_VORO)
     INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/src")
   target_link_libraries(lammps PRIVATE LAMMPS::VORO)
   add_dependencies(LAMMPS::VORO voro_build)
-  if(NOT BUILD_SHARED_LIBS)
-    install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
-  endif()
 else()
   find_package(VORO)
   if(NOT VORO_FOUND)

cmake/Modules/Testing.cmake

@@ -3,49 +3,53 @@
 ###############################################################################
 option(ENABLE_TESTING "Enable testing" OFF)
 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")
-  mark_as_advanced(LAMMPS_TESTING_SOURCE_DIR LAMMPS_TESTING_GIT_TAG)
+  find_program(VALGRIND_BINARY NAMES valgrind)
+  # generate custom suppression file
+  file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "\n")
+  file(GLOB VALGRIND_SUPPRESSION_FILES ${LAMMPS_TOOLS_DIR}/valgrind/[^.]*.supp)
+  foreach(SUPP ${VALGRIND_SUPPRESSION_FILES})
+    file(READ ${SUPP} SUPPRESSIONS)
+    file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "${SUPPRESSIONS}")
+  endforeach()
+  set(VALGRIND_DEFAULT_OPTIONS "--leak-check=full --show-leak-kinds=all --track-origins=yes --suppressions=${CMAKE_BINARY_DIR}/lammps.supp")
 
-  if (CMAKE_VERSION VERSION_GREATER "3.10.3" AND NOT LAMMPS_TESTING_SOURCE_DIR)
-    include(FetchContent)
+  set(MEMORYCHECK_COMMAND "${VALGRIND_BINARY}" CACHE FILEPATH "Memory Check Command")
+  set(MEMORYCHECK_COMMAND_OPTIONS "${VALGRIND_DEFAULT_OPTIONS}" CACHE STRING "Memory Check Command Options")
 
-    FetchContent_Declare(lammps-testing
-      GIT_REPOSITORY https://github.com/lammps/lammps-testing.git
-      GIT_TAG ${LAMMPS_TESTING_GIT_TAG}
-    )
-
-    FetchContent_GetProperties(lammps-testing)
-    if(NOT lammps-testing_POPULATED)
-      message(STATUS "Downloading tests...")
-      FetchContent_Populate(lammps-testing)
+  # check if a faster linker is available.
+  # only verified with GNU and Clang compilers and new CMake
+  if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
+    if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
+        OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
+      include(CheckCXXCompilerFlag)
+      set(CMAKE_CUSTOM_LINKER_DEFAULT default)
+      check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG)
+      check_cxx_compiler_flag(-fuse-ld=gold HAVE_GOLD_LINKER_FLAG)
+      check_cxx_compiler_flag(-fuse-ld=bfd HAVE_BFD_LINKER_FLAG)
+      find_program(HAVE_LLD_LINKER_BIN lld ld.lld)
+      find_program(HAVE_GOLD_LINKER_BIN ld.gold)
+      find_program(HAVE_BFD_LINKER_BIN ld.bfd)
+      if(HAVE_LLD_LINKER_FLAG AND HAVE_LLD_LINKER_BIN)
+        set(CMAKE_CUSTOM_LINKER_DEFAULT lld)
+      elseif(HAVE_GOLD_LINKER_FLAG AND HAVE_GOLD_LINKER_BIN)
+        set(CMAKE_CUSTOM_LINKER_DEFAULT gold)
+      elseif(HAVE_BFD_LINKER_FLAG AND HAVE_BFD_LINKER_BIN)
+        set(CMAKE_CUSTOM_LINKER_DEFAULT bfd)
+      endif()
+      set(CMAKE_CUSTOM_LINKER_VALUES lld gold bfd default)
+      set(CMAKE_CUSTOM_LINKER ${CMAKE_CUSTOM_LINKER_DEFAULT} CACHE STRING "Choose a custom linker for faster linking (lld, gold, bfd, default)")
+      validate_option(CMAKE_CUSTOM_LINKER CMAKE_CUSTOM_LINKER_VALUES)
+      mark_as_advanced(CMAKE_CUSTOM_LINKER)
+      if(NOT "${CMAKE_CUSTOM_LINKER}" STREQUAL "default")
+        target_link_options(lammps PUBLIC -fuse-ld=${CMAKE_CUSTOM_LINKER})
+      endif()
     endif()
-
-    set(LAMMPS_TESTING_SOURCE_DIR ${lammps-testing_SOURCE_DIR})
-  elseif(NOT LAMMPS_TESTING_SOURCE_DIR)
-    message(WARNING "Full test-suite requires CMake >= 3.11 or copy of\n"
-                    "https://github.com/lammps/lammps-testing in LAMMPS_TESTING_SOURCE_DIR")
   endif()
 
-  add_test(NAME ShowHelp COMMAND $<TARGET_FILE:lmp> -help)
+  include(CTest)
 
-  if(EXISTS ${LAMMPS_TESTING_SOURCE_DIR})
-    message(STATUS "Running test discovery...")
-
-    file(GLOB_RECURSE TEST_SCRIPTS ${LAMMPS_TESTING_SOURCE_DIR}/tests/core/*/in.*)
-    foreach(script_path ${TEST_SCRIPTS})
-      get_filename_component(TEST_NAME ${script_path} EXT)
-      get_filename_component(SCRIPT_NAME ${script_path} NAME)
-      get_filename_component(PARENT_DIR ${script_path} DIRECTORY)
-      string(SUBSTRING ${TEST_NAME} 1 -1 TEST_NAME)
-      string(REPLACE "-" "_" TEST_NAME ${TEST_NAME})
-      string(REPLACE "+" "_" TEST_NAME ${TEST_NAME})
-      set(TEST_NAME "test_core_${TEST_NAME}_serial")
-      add_test(NAME ${TEST_NAME} COMMAND $<TARGET_FILE:lmp> -in ${SCRIPT_NAME} WORKING_DIRECTORY ${PARENT_DIR})
-    endforeach()
-    list(LENGTH TEST_SCRIPTS NUM_TESTS)
-
-    message(STATUS "Found ${NUM_TESTS} tests.")
-  endif()
+  enable_testing()
+  get_filename_component(LAMMPS_UNITTEST_DIR ${LAMMPS_SOURCE_DIR}/../unittest ABSOLUTE)
+  get_filename_component(LAMMPS_UNITTEST_BIN ${CMAKE_BINARY_DIR}/unittest ABSOLUTE)
+  add_subdirectory(${LAMMPS_UNITTEST_DIR} ${LAMMPS_UNITTEST_BIN})
 endif()

cmake/Modules/generate_lmpgitversion.cmake

@@ -3,17 +3,19 @@ set(temp_git_commit "(unknown)")
 set(temp_git_branch "(unknown)")
 set(temp_git_describe "(unknown)")
 set(temp_git_info "false")
-if(GIT_FOUND AND EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/../.git)
+
+message(STATUS "Git Directory: ${LAMMPS_DIR}/.git")
+if(GIT_FOUND AND EXISTS ${LAMMPS_DIR}/.git)
   set(temp_git_info "true")
-  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse HEAD
+  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${LAMMPS_DIR} rev-parse HEAD
     OUTPUT_VARIABLE temp_git_commit
     ERROR_QUIET
     OUTPUT_STRIP_TRAILING_WHITESPACE)
-  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse --abbrev-ref HEAD
+  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${LAMMPS_DIR} rev-parse --abbrev-ref HEAD
     OUTPUT_VARIABLE temp_git_branch
     ERROR_QUIET
     OUTPUT_STRIP_TRAILING_WHITESPACE)
-  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. describe --dirty=-modified
+  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${LAMMPS_DIR} describe --dirty=-modified
     OUTPUT_VARIABLE temp_git_describe
     ERROR_QUIET
     OUTPUT_STRIP_TRAILING_WHITESPACE)

cmake/presets/all_off.cmake

@@ -8,7 +8,7 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
         USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
         USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
         USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD
-        USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
+        USER-MESONT 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-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
         USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)

cmake/presets/all_on.cmake

@@ -10,7 +10,7 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
         USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
         USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
         USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD
-        USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
+        USER-MESONT 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-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
         USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)

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)

cmake/presets/download.cmake

@@ -0,0 +1,17 @@
+# preset that turns on packages with automatic downloads of sources of potentials
+# compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time.
+
+set(ALL_PACKAGES KIM LATTE MSCG VORONOI USER-PLUMED USER-SCAFACOS USER-SMD USER-MESONT)
+
+foreach(PKG ${ALL_PACKAGES})
+  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
+endforeach()
+
+set(DOWNLOAD_KIM ON CACHE BOOL "" FORCE)
+set(DOWNLOAD_LATTE ON CACHE BOOL "" FORCE)
+set(DOWNLOAD_MSCG ON CACHE BOOL "" FORCE)
+set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
+set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
+set(DOWNLOAD_PLUMED ON CACHE BOOL "" FORCE)
+set(DOWNLOAD_SCAFACOS ON CACHE BOOL "" 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/mingw-cross.cmake

@@ -1,10 +1,10 @@
 set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-                 GRANULAR KSPACE LATTE MANYBODY MC MISC MOLECULE OPT PERI
-                 POEMS QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
+                 GRANULAR KSPACE LATTE MANYBODY MC MISC MLIAP MOLECULE OPT
+                 PERI POEMS QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
                  USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
                  USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
                  USER-FEP USER-INTEL USER-MANIFOLD USER-MEAMC USER-MESODPD
-                 USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE USER-OMP
+                 USER-MESONT USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE USER-OMP
                  USER-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC
                  USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
                  USER-YAFF)

cmake/presets/most.cmake

@@ -2,13 +2,13 @@
 # external libraries. Compared to all_on.cmake some more unusual packages
 # are removed. The resulting binary should be able to run most inputs.
 
-set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL
-        DIPOLE GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI
+set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
+        GRANULAR KSPACE MANYBODY MC MISC MLIAP MOLECULE OPT PERI
         POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
-        USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
-        USER-DPD USER-DRUDE USER-FEP USER-MEAMC USER-MESODPD
+        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-SPH USER-SMD USER-UEF USER-YAFF)
+        USER-REAXC USER-SDPD USER-SPH USER-SMD USER-UEF USER-YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)

cmake/presets/nolib.cmake

@@ -3,7 +3,7 @@
 
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MPIIO MSCG PYTHON
         VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB
-        USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP
+        USER-MOLFILE USER-MESONT USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP
         USER-SCAFACOS USER-SMD USER-VTK)
 
 foreach(PKG ${PACKAGES_WITH_LIB})

doc/Makefile

@@ -83,7 +83,7 @@ html: $(ANCHORCHECK) $(MATHJAX)
 	@rm -rf html/JPG
 	@cp -r src/PDF html/PDF
 	@mkdir -p html/JPG
-	@cp `grep -A2 '\.\. .*\(image\|figure\)::' src/*.rst | grep ':target:' | sed -e 's,.*:target: JPG/,src/JPG/,' | sort | uniq` html/JPG/
+	@cp `grep -A2 '\.\. .*\(image\|figure\)::' src/*.rst | grep ':target: JPG' | sed -e 's,.*:target: JPG/,src/JPG/,' | sort | uniq` html/JPG/
 	@rm -rf html/PDF/.[sg]*
 	@mkdir -p html/_static/mathjax
 	@cp -r $(MATHJAX)/es5 html/_static/mathjax/
@@ -194,9 +194,7 @@ $(VENV):
 		$(VIRTUALENV) -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
 		pip install --upgrade pip; \
-		pip install Sphinx; \
-		pip install sphinxcontrib-spelling ;\
-		pip install breathe; \
+		pip install --use-feature=2020-resolver -r requirements.txt; \
 		deactivate;\
 	)
 

doc/github-development-workflow.md

@@ -25,10 +25,10 @@ In the interest of consistency, ONLY ONE of the core LAMMPS developers
 should doing the merging itself.  This is currently
 [@akohlmey](https://github.com/akohlmey) (Axel Kohlmeyer).
 If this assignment needs to be changed, it shall be done right after a
-stable release.  If the currently assigned developer cannot merge outstanding pull 
-requests in a timely manner, or in other extenuating circumstances, 
+stable release.  If the currently assigned developer cannot merge outstanding pull
+requests in a timely manner, or in other extenuating circumstances,
 other core LAMMPS developers with merge rights can merge pull requests,
-when necessary. 
+when necessary.
 
 ## Pull Requests
 

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
 
@@ -72,7 +65,7 @@ Header files will typically contain the definition of a (single) class.
 These header files should have as few include statements as possible.
 This is particularly important for classes that implement a "style" and
 thus use a macro of the kind `SomeStyle(some/name,SomeName)`. These will
-all be included in the auto-generated `"some_style.h"` files which 
+all be included in the auto-generated `"some_style.h"` files which
 results in a high potential for direct or indirect symbol name clashes.
 
 In the ideal case, the header would only include one file defining the

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "15 April 2020" "2020-04-15"
+.TH LAMMPS "24 August 2020" "2020-08-24"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/requirements.txt

@@ -0,0 +1,4 @@
+Sphinx
+sphinxcontrib-spelling
+breathe
+Pygments

doc/src/Build_basics.rst

@@ -193,14 +193,17 @@ 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:
+variables (listed below) 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 (applied to compilation only), to be used
+for adding compiler or host specific optimization flags in addition to
+the "flags" variables listed below. You may 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
 
@@ -225,15 +228,11 @@ A few example command lines are:
 
 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 
+`-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=``.
+default this variable is empty.
 
 .. note::
 
@@ -372,7 +371,8 @@ 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**\ :
+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
@@ -462,7 +462,8 @@ 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**\ :
+Documentation make option
+^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The following make commands can be issued in the doc folder of the
 LAMMPS source distribution.
@@ -489,7 +490,8 @@ your system.
    current LAMMPS version (HTML and PDF files), from the website
    `download page <https://lammps.sandia.gov/download.html>`_.
 
-**CMake build option**\ :
+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
@@ -512,7 +514,8 @@ Build LAMMPS tools
 Some tools described in :doc:`Auxiliary tools <Tools>` can be built directly
 using CMake or Make.
 
-**CMake build3**\ :
+CMake build
+^^^^^^^^^^^
 
 .. code-block:: bash
 
@@ -521,7 +524,8 @@ using CMake or Make.
 The generated binaries will also become part of the LAMMPS installation
 (see below).
 
-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^
 
 .. code-block:: bash
 
@@ -545,7 +549,8 @@ 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**\ :
+CMake build
+^^^^^^^^^^^
 
 .. code-block:: bash
 
@@ -553,7 +558,8 @@ you want to copy files to is protected.
    make                        # perform make after CMake command
    make install                # perform the installation into prefix
 
-**Traditional make**\ :
+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

doc/src/Build_cmake.rst

@@ -107,7 +107,7 @@ re-compile and relink the LAMMPS executable with ``cmake --build .`` (or
 ``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``).
+executables with ``cmake --build . --target clean`` (or ``make clean``).
 
 After compilation, you may optionally install the LAMMPS executable into
 your system with:

doc/src/Build_development.rst

@@ -8,8 +8,8 @@ useful during development, testing or debugging.
 
 .. _compilation:
 
-Verify compilation flags
-------------------------
+Monitor compilation flags
+-------------------------
 
 Sometimes it is necessary to verify the complete sequence of compilation flags
 generated by the CMake build. To enable a more verbose output during
@@ -19,7 +19,8 @@ compilation you can use the following option.
 
    -D CMAKE_VERBOSE_MAKEFILE=value    # value = no (default) or yes
 
-Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1:
+Another way of doing this without reconfiguration is calling make with
+variable VERBOSE set to 1:
 
 .. code-block:: bash
 
@@ -33,77 +34,385 @@ Address, Undefined Behavior, and Thread Sanitizer Support
 ---------------------------------------------------------
 
 Compilers such as GCC and Clang support generating instrumented binaries
-which use different sanitizer libraries to detect problems in code
+which use different sanitizer libraries to detect problems in the code
 during run-time. They can detect issues like:
 
  - `memory leaks <https://clang.llvm.org/docs/AddressSanitizer.html>`_
  - `undefined behavior <https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html>`_
  - `data races <https://clang.llvm.org/docs/ThreadSanitizer.html>`_
 
-Please note that this kind of instrumentation usually comes with a small
-performance hit (much less than using tools like `Valgrind
-<https://valgrind.org>`_).  The to enable these features additional
-compiler flags need to be added to the compilation and linking stages.
-This is most easily done through setting the ``CMAKE_TUNE_FLAGS``
-variable during configuration. Examples:
+Please note that this kind of instrumentation usually comes with a
+performance hit (but much less than using tools like `Valgrind
+<https://valgrind.org>`_ with a more low level approach).  The to enable
+these features additional compiler flags need to be added to the
+compilation and linking stages.  This is done through setting the
+``ENABLE_SANITIZER`` variable during configuration. Examples:
 
 .. code-block:: bash
 
-   -D CMAKE_TUNE_FLAGS=-fsanitize=address    # enable address sanitizer / memory leak checker
-   -D CMAKE_TUNE_FLAGS=-fsanitize=undefined  # enable undefined behavior sanitizer
-   -D CMAKE_TUNE_FLAGS=-fsanitize=thread     # enable thread sanitizer
+   -D ENABLE_SANITIZER=none       # no sanitizer active (default)
+   -D ENABLE_SANITIZER=address    # enable address sanitizer / memory leak checker
+   -D ENABLE_SANITIZER=leak       # enable memory leak checker (only)
+   -D ENABLE_SANITIZER=undefined  # enable undefined behavior sanitizer
+   -D ENABLE_SANITIZER=thread     # enable thread sanitizer
 
 ----------
 
 .. _testing:
 
-Code Coverage and Testing
----------------------------------------
+Code Coverage and Unit Testing
+------------------------------
 
-We do extensive regression testing of the LAMMPS code base on a continuous
-basis. Some of the logic to do this has been added to the CMake build so
-developers can run the tests directly on their workstation.
+The LAMMPS code is subject to multiple levels of automated testing
+during development: integration testing (i.e. whether the code compiles
+on various platforms and with a variety of settings), unit testing
+(i.e. whether certain individual parts of the code produce the expected
+results for given inputs), run testing (whether selected complete input
+decks run without crashing for multiple configurations), and regression
+testing (i.e. whether selected input examples reproduce the same
+results over a given number of steps and operations within a given
+error margin).  The status of this automated testing can be viewed on
+`https://ci.lammps.org <https://ci.lammps.org>`_.
+
+The unit testing facility is integrated into the CMake build process
+of the LAMMPS source code distribution itself.  It can be enabled by
+setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
+It requires the `YAML <http://pyyaml.org/>`_ library and development
+headers to compile and will download and compile a recent version of the
+`Googletest <https://github.com/google/googletest/>`_ C++ test framework
+for implementing the tests.
+
+After compilation is complete, the unit testing is started in the build
+folder using the ``ctest`` command, which is part of the CMake software.
+The output of this command will be looking something like this::
+
+   [...]$ ctest
+   Test project /home/akohlmey/compile/lammps/build-testing
+         Start  1: MolPairStyle:hybrid-overlay
+   1/109 Test  #1: MolPairStyle:hybrid-overlay .........   Passed    0.02 sec
+         Start  2: MolPairStyle:hybrid
+   2/109 Test  #2: MolPairStyle:hybrid .................   Passed    0.01 sec
+         Start  3: MolPairStyle:lj_class2
+    [...]
+         Start 107: PotentialFileReader
+ 107/109 Test #107: PotentialFileReader ................   Passed    0.04 sec
+         Start 108: EIMPotentialFileReader
+ 108/109 Test #108: EIMPotentialFileReader .............   Passed    0.03 sec
+         Start 109: TestSimpleCommands
+ 109/109 Test #109: TestSimpleCommands .................   Passed    0.02 sec
+
+   100% tests passed, 0 tests failed out of 26
+
+   Total Test time (real) =  25.57 sec
+
+
+The ``ctest`` command has many options, the most important ones are:
+
+.. list-table::
+
+   * - Option
+     - Function
+   * - -V
+     - verbose output: display output of individual test runs
+   * - -j <num>
+     - parallel run: run <num> tests in parallel
+   * - -R <regex>
+     - run subset of tests matching the regular expression <regex>
+   * - -E <regex>
+     - exclude subset of tests matching the regular expression <regex>
+   * - -N
+     - dry-run: display list of tests without running them
+   * - -T memcheck
+     - run tests with valgrind memory checker (if available)
+
+In its full implementation, the unit test framework will consist of multiple
+kinds of tests implemented in different programming languages (C++, C, Python,
+Fortran) and testing different aspects of the LAMMPS software and its features.
+At the moment only tests for "force styles" are implemented. More on those
+in the next section.
 
 .. note::
 
-   this is incomplete and only represents a small subset of tests that we run
+   The unit test framework is new and still under development.
+   The coverage is only minimal and will be expanded over time.
+   Tests styles of the same kind of style (e.g. pair styles or
+   bond styles) are performed with the same executable using
+   different input files in YAML format.  So to add a test for
+   another pair style can be done by copying the YAML file and
+   editing the style settings and then running the individual test
+   program with a flag to update the computed reference data.
+   Detailed documentation about how to add new test program and
+   the contents of the YAML files for existing test programs
+   will be provided in time as well.
+
+Unit tests for force styles
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+A large part of LAMMPS are different "styles" for computing non-bonded
+and bonded interactions selected through the :doc:`pair_style`,
+:doc:`bond_style`, :doc:`angle_style`, :doc:`dihedral_style`,
+:doc:`improper_style`, and :doc:`kspace_style`.  Since these all share
+common interfaces, it is possible to write generic test programs that
+will call those common interfaces for small test systems with less than
+100 atoms and compare the results with pre-recorded reference results.
+A test run is then a a collection multiple individual test runs each
+with many comparisons to reference results based on template input
+files, individual command settings, relative error margins, and
+reference data stored in a YAML format file with ``.yaml``
+suffix. Currently the programs ``test_pair_style``, ``test_bond_style``, and
+``test_angle_style`` are implemented.  They will compare forces, energies and
+(global) stress for all atoms after a ``run 0`` calculation and after a
+few steps of MD with :doc:`fix nve <fix_nve>`, each in multiple variants
+with different settings and also for multiple accelerated styles. If a
+prerequisite style or package is missing, the individual tests are
+skipped.  All tests will be executed on a single MPI process, so using
+the CMake option ``-D BUILD_MPI=off`` can significantly speed up testing,
+since this will skip the MPI initialization for each test run.
+Below is an example command and output:
+
+.. parsed-literal::
+
+   [tests]$ test_pair_style mol-pair-lj_cut.yaml
+   [==========] Running 6 tests from 1 test suite.
+   [----------] Global test environment set-up.
+   [----------] 6 tests from PairStyle
+   [ RUN      ] PairStyle.plain
+   [       OK ] PairStyle.plain (24 ms)
+   [ RUN      ] PairStyle.omp
+   [       OK ] PairStyle.omp (18 ms)
+   [ RUN      ] PairStyle.intel
+   [       OK ] PairStyle.intel (6 ms)
+   [ RUN      ] PairStyle.opt
+   [  SKIPPED ] PairStyle.opt (0 ms)
+   [ RUN      ] PairStyle.single
+   [       OK ] PairStyle.single (7 ms)
+   [ RUN      ] PairStyle.extract
+   [       OK ] PairStyle.extract (6 ms)
+   [----------] 6 tests from PairStyle (62 ms total)
+
+   [----------] Global test environment tear-down
+   [==========] 6 tests from 1 test suite ran. (63 ms total)
+   [  PASSED  ] 5 tests.
+   [  SKIPPED ] 1 test, listed below:
+   [  SKIPPED ] PairStyle.opt
+
+In this particular case, 5 out of 6 sets of tests were conducted, the
+tests for the ``lj/cut/opt`` pair style was skipped, since the tests
+executable did not include it.  To learn what individual tests are performed,
+you (currently) need to read the source code.  You can use code coverage
+recording (see next section) to confirm how well the tests cover the code
+paths in the individual source files.
+
+The force style test programs have a common set of options:
+
+.. list-table::
+
+   * - Option
+     - Function
+   * - -g <newfile>
+     - regenerate reference data in new YAML file
+   * - -u
+     - update reference data in the original YAML file
+   * - -s
+     - print error statistics for each group of comparisons
+   * - -v
+     - verbose output: also print the executed LAMMPS commands
+
+The ``ctest`` tool has no mechanism to directly pass flags to the individual
+test programs, but a workaround has been implemented where these flags can be
+set in an environment variable ``TEST_ARGS``. Example:
 
 .. code-block:: bash
 
-   -D ENABLE_TESTING=value               # enable simple run tests of LAMMPS, value = no (default) or yes
-   -D LAMMPS_TESTING_SOURCE_DIR=path     # path to lammps-testing repository (option if in custom location)
-   -D LAMMPS_TESTING_GIT_TAG=value       # version of lammps-testing repository that should be used, value = master (default) or custom git commit or tag
+   env TEST_ARGS=-s ctest -V -R BondStyle
 
-If you enable testing in the CMake build it will create an additional
-target called "test". You can run them with:
+To add a test for a style that is not yet covered, it is usually best
+to copy a YAML file for a similar style to a new file, edit the details
+of the style (how to call it, how to set its coefficients) and then
+run test command with either the *-g* and the replace the initial
+test file with the regenerated one or the *-u* option.  The *-u* option
+will destroy the original file, if the generation run does not complete,
+so using *-g* is recommended unless the YAML file is fully tested
+and working.
+
+.. admonition:: Recommendations and notes for YAML files
+   :class: note
+
+   - The reference results should be recorded without any code
+     optimization or related compiler flags enabled.
+   - The ``epsilon`` parameter defines the relative precision with which
+     the reference results must be met.  The test geometries often have
+     high and low energy parts and thus a significant impact from
+     floating-point math truncation errors is to be expected. Some
+     functional forms and potentials are more noisy than others, so this
+     parameter needs to be adjusted. Typically a value around 1.0e-13
+     can be used, but it may need to be as large as 1.0e-8 in some
+     cases.
+   - The tests for pair styles from OPT, USER-OMP and USER-INTEL are
+     performed with automatically rescaled epsilon to account for
+     additional loss of precision from code optimizations and different
+     summation orders.
+   - When compiling with (aggressive) compiler optimization, some tests
+     are likely to fail.  It is recommended to inspect the individual
+     tests in detail to decide, whether the specific error for a specific
+     property is acceptable (it often is), or this may be an indication
+     of mis-compiled code (or an undesired large loss of precision due
+     to significant reordering of operations and thus less error cancellation).
+
+Unit tests for timestepping related fixes
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+A substantial subset of :doc:`fix styles <fix>` are invoked regularly
+during MD timestepping and manipulate per-atom properties like
+positions, velocities, and forces.  For those fix styles, testing can be
+done in a very similar fashion as for force fields and thus there is a
+test program `test_fix_timestep` that shares a lot of code, properties,
+and command line flags with the force field style testers described in
+the previous section.
+
+This tester will set up a small molecular system run with verlet run
+style for 4 MD steps, then write a binary restart and continue for
+another 4 MD steps. At this point coordinates and velocities are
+recorded and compared to reference data. Then the system is cleared,
+restarted and running the second 4 MD steps again and the data is
+compared to the same reference. That is followed by another restart
+after which per atom type masses are replaced with per-atom masses and
+the second 4 MD steps are repeated again and compared to the same
+reference.  Also global scalar and vector data of the fix is recorded
+and compared.  If the fix is a thermostat and thus the internal property
+``t_target`` can be extracted, then this is compared to the reference
+data.  The tests are repeated with the respa run style.
+
+If the fix has a multi-threaded version in the USER-OMP package, then
+the entire set of tests is repeated for that version as well.
+
+For this to work, some additional conditions have to be met by the
+YAML format test inputs.
+
+- The fix to be tested (and only this fix), should be listed in the
+  ``prerequisites:`` section
+- The fix to be tested must be specified in the ``post_commands:``
+  section with the fix-ID ``test``.  This section may contain other
+  commands and other fixes (e.g. an instance of fix nve for testing
+  a thermostat or force manipulation fix)
+- For fixes that can tally contributions to the global virial, the
+  line ``fix_modify test virial yes`` should be included in the
+  ``post_commands:`` section of the test input.
+- For thermostat fixes the target temperature should be ramped from
+  an arbitrary value (e.g. 50K) to a pre-defined target temperature
+  entered as ``${t_target}``.
+- For fixes that have thermostatting support included, but do not
+  have it enabled in the input (e.g. fix rigid with default settings),
+  the ``post_commands:`` section should contain the line
+  ``variable t_target delete`` to disable the target temperature ramp
+  check to avoid false positives.
+
+Use custom linker for faster link times when ENABLE_TESTING is active
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+When compiling LAMMPS with enabled tests, most test executables will
+need to be linked against the LAMMPS library.  Since this can be a very
+large library with many C++ objects when many packages are enabled, link
+times can become very long on machines that use the GNU BFD linker (e.g.
+Linux systems).  Alternatives like the ``lld`` linker of the LLVM project
+or the ``gold`` linker available with GNU binutils can speed up this step
+substantially. CMake will by default test if any of the two can be
+enabled and use it when ``ENABLE_TESTING`` is active.  It can also be
+selected manually through the ``CMAKE_CUSTOM_LINKER`` CMake variable.
+Allowed values are ``lld``, ``gold``, ``bfd``, or ``default``.  The
+``default`` option will use the system default linker otherwise, the
+linker is chosen explicitly.  This option is only available for the
+GNU or Clang C++ compiler.
+
+Tests for other components and utility functions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Additional tests that validate utility functions or specific components
+of LAMMPS are implemented as standalone executable which may, or may not
+require creating a suitable LAMMPS instance.  These tests are more specific
+and do not require YAML format input files.  To add a test, either an
+existing source file needs to be extended or a new file added, which in turn
+requires additions to the ``CMakeLists.txt`` file in the source folder.
+
+Collect and visualize code coverage metrics
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+You can also collect code coverage metrics while running LAMMPS or the
+tests by enabling code coverage support during the CMake configuration:
 
 .. code-block:: bash
 
-   cmake --build . test
+   -D ENABLE_COVERAGE=on  # enable coverage measurements (off by default)
 
-The test cases used come from the lammps-testing repository. They are
-derivatives of the examples folder with some modifications to make the
-run faster.
+This will instrument all object files to write information about which
+lines of code were accessed during execution in files next to the
+corresponding object files.  These can be post-processed to visually
+show the degree of coverage and which code paths are accessed and which
+are not taken.  When working on unit tests (see above), this can be
+extremely helpful to determine which parts of the code are not executed
+and thus what kind of tests are still missing. The coverage data is
+cumulative, i.e. new data is added with each new run.
 
-You can also collect code coverage metrics while running the tests by
-enabling coverage support during building.
+Enabling code coverage will also add the following build targets to
+generate coverage reports after running the LAMMPS executable or the
+unit tests:
 
 .. code-block:: bash
 
-   -D ENABLE_COVERAGE=value  # enable coverage measurements, value = no (default) or yes
+   make gen_coverage_html   # generate coverage report in HTML format
+   make gen_coverage_xml    # generate coverage report in XML format
+   make clean_coverage_html # delete folder with HTML format coverage report
+   make reset_coverage      # delete all collected coverage data and HTML output
 
-This will also add the following targets to generate coverage reports
-after running the LAMMPS executable:
-
-.. code-block:: bash
-
-   make test               # run tests first!
-   make gen_coverage_html  # generate coverage report in HTML format
-   make gen_coverage_xml   # generate coverage report in XML format
-
-These reports require GCOVR to be installed. The easiest way to do this
-to install it via pip:
+These reports require `GCOVR <https://gcovr.com/>`_ to be installed. The easiest way
+to do this to install it via pip:
 
 .. code-block:: bash
 
    pip install git+https://github.com/gcovr/gcovr.git
+
+After post-processing with ``gen_coverage_html`` the results are in
+a folder ``coverage_html`` and can be viewed with a web browser.
+The images below illustrate how the data is presented.
+
+.. list-table::
+
+      * - .. figure:: JPG/coverage-overview-top.png
+             :target: JPG/coverage-overview-top.png
+
+          Top of the overview page
+
+        - .. figure:: JPG/coverage-overview-manybody.png
+             :target: JPG/coverage-overview-manybody.png
+
+          Styles with good coverage
+
+        - .. figure:: JPG/coverage-file-top.png
+             :target: JPG/coverage-file-top.png
+
+          Top of individual source page
+
+        - .. figure:: JPG/coverage-file-branches.png
+             :target: JPG/coverage-file-branches.png
+
+          Source page with branches
+
+Coding style utilities
+----------------------
+
+To aid with enforcing some of the coding style conventions in LAMMPS
+some additional build targets have been added. These require Python 3.5
+or later and will only work on Unix-like operating and file systems.
+The following options are available.
+
+.. code-block:: bash
+
+   make check-whitespace    # generate coverage report in HTML format
+   make fix-whitespace      # generate coverage report in XML format
+   make check-permissions   # delete folder with HTML format coverage report
+   make fix-permissions     # delete all collected coverage data and HTML output
+
+For the code in the ``unittest`` tree we are using the `clang-format`
+tool (Clang version 8.0 or later is required). If available, the source
+code files in the ``unittest`` tree can be updated to conform to the
+formatting settings using ``make format-tests``.

doc/src/Build_link.rst

@@ -1,12 +1,12 @@
 Link LAMMPS as a library to another code
 ========================================
 
-LAMMPS is designed as a library of C++ objects and can thus be
+LAMMPS is designed as a library of C++ objects that can be
 integrated into other applications including Python scripts.
 The files ``src/library.cpp`` and ``src/library.h`` define a
 C-style API for using LAMMPS as a library.  See the :doc:`Howto
-library <Howto_library>` doc page for a description of the interface
-and how to extend it for your needs.
+library <Howto_library>` page for a description of the interface
+and how to use it for your needs.
 
 The :doc:`Build basics <Build_basics>` doc page explains how to build
 LAMMPS as either a shared or static library.  This results in a file
@@ -31,18 +31,18 @@ the suffix ``.so.0`` (or some other number).
    communicator with a subset of MPI ranks to the function creating the
    LAMMPS instance.
 
-----------
-
-**Link with LAMMPS as a static library**\ :
+Link with LAMMPS as a static library
+------------------------------------
 
 The calling application can link to LAMMPS as a static library with
 compilation and link commands as in the examples shown below.  These
-are examples for a code written in C in the file *caller.c*.
+are examples for a code written in C in the file ``caller.c``.
 The benefit of linking to a static library is, that the resulting
 executable is independent of that library since all required
 executable code from the library is copied into the calling executable.
 
-*CMake build*\ :
+CMake build
+^^^^^^^^^^^
 
 This assumes that LAMMPS has been configured without setting a
 ``LAMMPS_MACHINE`` name, installed with "make install", and the
@@ -55,7 +55,8 @@ The commands to compile and link a coupled executable are then:
    mpicc -c -O $(pkgconf liblammps --cflags) caller.c
    mpicxx -o caller caller.o -$(pkgconf liblammps --libs)
 
-*Traditional make*\ :
+Traditional make
+^^^^^^^^^^^^^^^^
 
 This assumes that LAMMPS has been compiled in the folder
 ``${HOME}/lammps/src`` with "make mpi". The commands to compile and link
@@ -83,20 +84,20 @@ LAMMPS library without any optional packages that depend on libraries
 need to include all flags, libraries, and paths for the coupled
 executable, that are also required to link the LAMMPS executable.
 
-*CMake build*\ :
+CMake build
+^^^^^^^^^^^
 
 When using CMake, additional libraries with sources in the lib folder
 are built, but not included in ``liblammps.a`` and (currently) not
-installed with "make install" and not included in the *pkgconfig*
+installed with ``make install`` and not included in the ``pkgconfig``
 configuration file.  They can be found in the top level build folder,
 but you have to determine the necessary link flags manually.  It is
 therefore recommended to either use the traditional make procedure to
 build and link with a static library or build and link with a shared
 library instead.
 
-.. TODO: this needs to be updated to reflect that latest CMake changes after they are complete.
-
-*Traditional make*\ :
+Traditional make
+^^^^^^^^^^^^^^^^
 
 After you have compiled a static LAMMPS library using the conventional
 build system for example with "make mode=static serial". And you also
@@ -110,10 +111,10 @@ change to:
    g++ -o caller caller.o -L${HOME}/lammps/lib/poems \
      -L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src -llammps_serial -lpoems -lmpi_stubs
 
-Note, that you need to link with "g++" instead of "gcc", since the
-LAMMPS library is C++ code.  You can display the currently applied
-settings for building LAMMPS for the "serial" machine target by using
-the command:
+Note, that you need to link with ``g++`` instead of ``gcc`` even if you have
+written your code in C, since LAMMPS itself is C++ code.  You can display the
+currently applied settings for building LAMMPS for the "serial" machine target
+by using the command:
 
 .. code-block:: bash
 
@@ -123,25 +124,24 @@ Which should output something like:
 
 .. code-block:: bash
 
-   # Compiler: 
+   # Compiler:
    CXX=g++
-   # Linker: 
+   # Linker:
    LD=g++
-   # Compilation: 
+   # Compilation:
    CXXFLAGS=-g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -I${HOME}/compile/lammps/lib/poems -I${HOME}/compile/lammps/src/STUBS
-   # Linking: 
+   # Linking:
    LDFLAGS=-g -O
-   # Libraries: 
+   # Libraries:
    LDLIBS=-L${HOME}/compile/lammps/src -llammps_serial -L${HOME}/compile/lammps/lib/poems -L${HOME}/compile/lammps/src/STUBS -lpoems -lmpi_stubs
 
 From this you can gather the necessary paths and flags.  With
 makefiles for other *machine* configurations you need to do the
-equivalent and replace "serial" with the corresponding *machine* name
+equivalent and replace "serial" with the corresponding "machine" name
 of the makefile.
 
-----------
-
-**Link with LAMMPS as a shared library**\ :
+Link with LAMMPS as a shared library
+------------------------------------
 
 When linking to LAMMPS built as a shared library, the situation becomes
 much simpler, as all dependent libraries and objects are either included
@@ -151,7 +151,8 @@ linking the calling executable.  Only the *-I* flags are needed.  So the
 example case from above of the serial version static LAMMPS library with
 the POEMS package installed becomes:
 
-*CMake build*\ :
+CMake build
+^^^^^^^^^^^
 
 The commands with a shared LAMMPS library compiled with the CMake
 build process are the same as for the static library.
@@ -161,10 +162,11 @@ build process are the same as for the static library.
    mpicc -c -O $(pkgconf liblammps --cflags) caller.c
    mpicxx -o caller caller.o -$(pkgconf --libs)
 
-*Traditional make*\ :
+Traditional make
+^^^^^^^^^^^^^^^^
 
 The commands with a shared LAMMPS library compiled with the
-traditional make build using "make mode=shared serial" becomes:
+traditional make build using ``make mode=shared serial`` becomes:
 
 .. code-block:: bash
 
@@ -231,29 +233,3 @@ If a required library is missing, you would get a 'not found' entry:
         libc.so.6 => /usr/lib64/libc.so.6 (0x00007fb7c7b5d000)
         /lib64/ld-linux-x86-64.so.2 (0x00007fb7c80a2000)
 
-----------
-
-**Calling the LAMMPS library**\ :
-
-Either flavor of library (static or shared) allows one or more LAMMPS
-objects to be instantiated from the calling program. When used from a
-C++ program, most of the symbols and functions in LAMMPS are wrapped
-in a ``LAMMPS_NS`` namespace; you can safely use any of its classes and
-methods from within the calling code, as needed, and you will not incur
-conflicts with functions and variables in your code that share the name.
-This, however, does not extend to all additional libraries bundled with
-LAMMPS in the lib folder and some of the low-level code of some packages.
-
-To be compatible with C, Fortran, Python programs, the library has a simple
-C-style interface, provided in ``src/library.cpp`` and ``src/library.h``.
-
-See the :doc:`Python library <Python_library>` doc page for a
-description of the Python interface to LAMMPS, which wraps the C-style
-interface from a shared library through the `ctypes python module <ctypes_>`_.
-
-See the sample codes in ``examples/COUPLE/simple`` for examples of C++ and
-C and Fortran codes that invoke LAMMPS through its library interface.
-Other examples in the COUPLE directory use coupling ideas discussed on
-the :doc:`Howto couple <Howto_couple>` doc page.
-
-.. _ctypes: https://docs.python.org/3/library/ctypes.html

doc/src/Build_package.rst

@@ -45,7 +45,8 @@ packages:
 The mechanism for including packages is simple but different for CMake
 versus make.
 
-**CMake build**\ :
+CMake build
+^^^^^^^^^^^
 
 .. code-block:: csh
 
@@ -72,7 +73,8 @@ once with CMake.
    invoke cmake.  CMake will give an error if that is not the case,
    indicating how you can un-install all packages in the src dir.
 
-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^
 
 .. code-block:: bash
 
@@ -108,7 +110,8 @@ once with make.
    within the same command.  You can include or exclude multiple packages
    in a single make command, e.g. make yes-colloid no-manybody.
 
-**CMake and make info**\ :
+CMake and make info
+^^^^^^^^^^^^^^^^^^^
 
 Any package can be included or excluded in a LAMMPS build, independent
 of all other packages.  However, some packages include files derived
@@ -132,7 +135,8 @@ src directory.
 
 .. _cmake_presets:
 
-**CMake shortcuts for installing many packages**\ :
+CMake presets for installing many packages
+""""""""""""""""""""""""""""""""""""""""""
 
 Instead of specifying all the CMake options via the command-line,
 CMake allows initializing its settings cache using script files.
@@ -148,13 +152,14 @@ one of them as a starting point and customize it to your needs.
 
 .. code-block:: bash
 
-    cmake -C ../cmake/presets/minimal.cmake [OPTIONS] ../cmake  # enable just a few core packages
-    cmake -C ../cmake/presets/most.cmake    [OPTIONS] ../cmake  # enable most packages
-    cmake -C ../cmake/presets/nolib.cmake   [OPTIONS] ../cmake  # disable packages that do require extra libraries or tools
-    cmake -C ../cmake/presets/clang.cmake   [OPTIONS] ../cmake  # change settings to use the Clang compilers by default
-    cmake -C ../cmake/presets/intel.cmake   [OPTIONS] ../cmake  # change settings to use the Intel compilers by default
-    cmake -C ../cmake/presets/all_on.cmake  [OPTIONS] ../cmake  # enable all packages
-    cmake -C ../cmake/presets/all_off.cmake [OPTIONS] ../cmake  # disable all packages
+    cmake -C ../cmake/presets/minimal.cmake  [OPTIONS] ../cmake  # enable just a few core packages
+    cmake -C ../cmake/presets/most.cmake     [OPTIONS] ../cmake  # enable most packages
+    cmake -C ../cmake/presets/download.cmake [OPTIONS] ../cmake  # enable packages which download sources or potential files
+    cmake -C ../cmake/presets/nolib.cmake    [OPTIONS] ../cmake  # disable packages that do require extra libraries or tools
+    cmake -C ../cmake/presets/clang.cmake    [OPTIONS] ../cmake  # change settings to use the Clang compilers by default
+    cmake -C ../cmake/presets/intel.cmake    [OPTIONS] ../cmake  # change settings to use the Intel compilers by default
+    cmake -C ../cmake/presets/all_on.cmake   [OPTIONS] ../cmake  # enable all packages
+    cmake -C ../cmake/presets/all_off.cmake  [OPTIONS] ../cmake  # disable all packages
     mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake  #  compile with MinGW cross compilers
 
 .. note::
@@ -164,7 +169,8 @@ one of them as a starting point and customize it to your needs.
    in a single cmake run, or change settings incrementally by running
    cmake with new flags.
 
-**Example:**
+Example
+"""""""
 
 .. code-block:: bash
 
@@ -184,7 +190,8 @@ one of them as a starting point and customize it to your needs.
 
 ----------
 
-**Make shortcuts for installing many packages**\ :
+Make shortcuts for installing many packages
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The following commands are useful for managing package source files
 and their installation when building LAMMPS via traditional make.

doc/src/Build_settings.rst

@@ -44,7 +44,8 @@ require use of an FFT library to compute 1d FFTs.  The KISS FFT
 library is included with LAMMPS but other libraries can be faster.
 LAMMPS can use them if they are available on your system.
 
-**CMake variables**\ :
+CMake build
+^^^^^^^^^^^
 
 .. code-block:: bash
 
@@ -74,7 +75,12 @@ to assist:
    -D FFT_MKL_THREADS=on       # enable using threaded FFTs with MKL libraries
    -D MKL_LIBRARIES=path
 
-**Makefile.machine settings**\ :
+Traditional make
+^^^^^^^^^^^^^^^^
+
+To change the FFT library to be used and its options, you have to edit
+your machine Makefile. Below are examples how the makefile variables
+could be changed.
 
 .. code-block:: make
 
@@ -104,7 +110,8 @@ As with CMake, you do not need to set paths in ``FFT_INC`` or ``FFT_PATH``, if
 the compiler can find the FFT header and library files in its default search path.
 You must specify ``FFT_LIB`` with the appropriate FFT libraries to include in the link.
 
-**CMake and make info**\ :
+CMake build
+^^^^^^^^^^^
 
 The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS
 distribution.  It is portable across all platforms.  Depending on the size
@@ -127,7 +134,7 @@ download it from `www.fftw.org <http://www.fftw.org>`_.  LAMMPS requires
 version 3.X; the legacy version 2.1.X is no longer supported.
 
 Building FFTW for your box should be as simple as ``./configure; make;
-make install``\ .  The install command typically requires root privileges
+make install``.  The install command typically requires root privileges
 (e.g. invoke it via sudo), unless you specify a local directory with
 the "--prefix" option of configure.  Type ``./configure --help`` to see
 various options.
@@ -169,20 +176,25 @@ ARRAY mode.
 
 .. _size:
 
-Size of LAMMPS data types
+Size of LAMMPS integer types
 ------------------------------------
 
-LAMMPS has a few integer data types which can be defined as 4-byte or
-8-byte integers.  The default setting of "smallbig" is almost always
-adequate.
+LAMMPS has a few integer data types which can be defined as either
+4-byte (= 32-bit) or 8-byte (= 64-bit) integers at compile time.
+The default setting of "smallbig" is almost always adequate.
 
-**CMake variable**\ :
+CMake build
+^^^^^^^^^^^
 
 .. code-block:: bash
 
    -D LAMMPS_SIZES=value   # smallbig (default) or bigbig or smallsmall
 
-**Makefile.machine setting**\ :
+Traditional build
+^^^^^^^^^^^^^^^^^
+
+If you want a setting different from the default, you need to edit your
+machine Makefile.
 
 .. code-block:: make
 
@@ -190,7 +202,8 @@ adequate.
 
 The default setting is ``-DLAMMPS_SMALLBIG`` if nothing is specified
 
-**CMake and make info**\ :
+CMake and make info
+^^^^^^^^^^^^^^^^^^^
 
 The default "smallbig" setting allows for simulations with:
 
@@ -251,7 +264,8 @@ PNG image files.  Likewise the :doc:`dump movie <dump_image>` command
 outputs movie files in MPEG format.  Using these options requires the
 following settings:
 
-**CMake variables**\ :
+CMake build
+^^^^^^^^^^^
 
 .. code-block:: bash
 
@@ -276,7 +290,8 @@ variables:
    -D ZLIB_LIBRARIES=path      # path to libz.a (.so) file
    -D FFMPEG_EXECUTABLE=path   # path to ffmpeg executable
 
-**Makefile.machine settings**\ :
+Traditional make
+^^^^^^^^^^^^^^^^
 
 .. code-block:: make
 
@@ -295,7 +310,8 @@ with a list of graphics libraries to include in the link.  You must
 insure ffmpeg is in a directory where LAMMPS can find it at runtime,
 that is a directory in your PATH environment variable.
 
-**CMake and make info**\ :
+CMake and make info
+^^^^^^^^^^^^^^^^^^^
 
 Using ``ffmpeg`` to output movie files requires that your machine
 supports the "popen" function in the standard runtime library.
@@ -318,7 +334,8 @@ If this option is enabled, large files can be read or written with
 gzip compression by several LAMMPS commands, including
 :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
 
-**CMake variables**\ :
+CMake build
+^^^^^^^^^^^
 
 .. code-block:: bash
 
@@ -326,13 +343,15 @@ gzip compression by several LAMMPS commands, including
                             # default is yes if CMake can find gzip, else no
    -D GZIP_EXECUTABLE=path  # path to gzip executable if CMake cannot find it
 
-**Makefile.machine setting**\ :
+Traditional make
+^^^^^^^^^^^^^^^^
 
 .. code-block:: make
 
    LMP_INC = -DLAMMPS_GZIP
 
-**CMake and make info**\ :
+CMake and make info
+^^^^^^^^^^^^^^^^^^^
 
 This option requires that your machine supports the "popen()" function
 in the standard runtime library and that a gzip executable can be
@@ -363,7 +382,8 @@ pointers that are aligned to 16-byte boundaries. Using SSE vector
 instructions efficiently, however, requires memory blocks being
 aligned on 64-byte boundaries.
 
-**CMake variable**\ :
+CMake build
+^^^^^^^^^^^
 
 .. code-block:: bash
 
@@ -374,7 +394,8 @@ and revert to using the malloc() C-library function instead.  When
 compiling LAMMPS for Windows systems, malloc() will always be used
 and this setting ignored.
 
-**Makefile.machine setting**\ :
+Traditional make
+^^^^^^^^^^^^^^^^
 
 .. code-block:: make
 
@@ -398,13 +419,15 @@ types, the following setting will be needed.  It converts "long long"
 to a "long" data type, which should be the desired 8-byte integer on
 those systems:
 
-**CMake variable**\ :
+CMake build
+^^^^^^^^^^^
 
 .. code-block:: bash
 
    -D LAMMPS_LONGLONG_TO_LONG=value     # yes or no (default)
 
-**Makefile.machine setting**\ :
+Traditional make
+^^^^^^^^^^^^^^^^
 
 .. code-block:: make
 
@@ -420,17 +443,26 @@ Exception handling when using LAMMPS as a library
 This setting is useful when external codes drive LAMMPS as a library.
 With this option enabled, LAMMPS errors do not kill the calling code.
 Instead, the call stack is unwound and control returns to the caller,
-e.g. to Python. Of course the calling code has to be set up to
-*catch* exceptions from within LAMMPS.
+e.g. to Python. Of course, the calling code has to be set up to
+*catch* exceptions thrown from within LAMMPS.
 
-**CMake variable**\ :
+CMake build
+^^^^^^^^^^^
 
 .. code-block:: bash
 
    -D LAMMPS_EXCEPTIONS=value        # yes or no (default)
 
-**Makefile.machine setting**\ :
+Traditional make
+^^^^^^^^^^^^^^^^
 
 .. code-block:: make
 
    LMP_INC = -DLAMMPS_EXCEPTIONS
+
+.. note::
+
+   When LAMMPS is running in parallel, it is not always possible to
+   cleanly recover from an exception since not all parallel ranks may
+   throw an exception and thus other MPI ranks may get stuck waiting for
+   messages from the ones with errors.

doc/src/Build_windows.rst

@@ -38,7 +38,7 @@ optional Windows feature allows you to run the bash shell from Ubuntu
 from within Windows and from there on, you can pretty much use that
 shell like you are running on an Ubuntu Linux machine (e.g. installing
 software via apt-get and more). For more details on that, please
-see :doc:`this tutorial <Howto_bash>`
+see :doc:`this tutorial <Howto_wsl>`
 
 .. _gnu:
 

doc/src/Commands_all.rst

@@ -46,13 +46,6 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`dimension <dimension>`
    * :doc:`displace_atoms <displace_atoms>`
    * :doc:`dump <dump>`
-   * :doc:`dump atom/adios <dump_adios>`
-   * :doc:`dump custom/adios <dump_adios>`
-   * :doc:`dump image <dump_image>`
-   * :doc:`dump movie <dump_image>`
-   * :doc:`dump netcdf <dump_netcdf>`
-   * :doc:`dump netcdf/mpiio <dump_netcdf>`
-   * :doc:`dump vtk <dump_vtk>`
    * :doc:`dump_modify <dump_modify>`
    * :doc:`dynamical_matrix <dynamical_matrix>`
    * :doc:`echo <echo>`
@@ -94,6 +87,7 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`package <package>`
    * :doc:`pair_coeff <pair_coeff>`
    * :doc:`pair_modify <pair_modify>`
+   * :doc:`pair_style <pair_style>`
    * :doc:`pair_write <pair_write>`
    * :doc:`partition <partition>`
    * :doc:`prd <prd>`
@@ -107,7 +101,8 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`region <region>`
    * :doc:`replicate <replicate>`
    * :doc:`rerun <rerun>`
-   * :doc:`reset_ids <reset_ids>`
+   * :doc:`reset_atom_ids <reset_atom_ids>`
+   * :doc:`reset_mol_ids <reset_mol_ids>`
    * :doc:`reset_timestep <reset_timestep>`
    * :doc:`restart <restart>`
    * :doc:`run <run>`

doc/src/Commands_bond.rst

@@ -46,6 +46,7 @@ OPT.
    * :doc:`oxdna2/fene <bond_oxdna>`
    * :doc:`oxrna2/fene <bond_oxdna>`
    * :doc:`quartic (o) <bond_quartic>`
+   * :doc:`special <bond_special>`
    * :doc:`table (o) <bond_table>`
 
 .. _angle:

doc/src/Commands_compute.rst

@@ -42,7 +42,7 @@ KOKKOS, o = USER-OMP, t = OPT.
    * :doc:`com <compute_com>`
    * :doc:`com/chunk <compute_com_chunk>`
    * :doc:`contact/atom <compute_contact_atom>`
-   * :doc:`coord/atom <compute_coord_atom>`
+   * :doc:`coord/atom (k) <compute_coord_atom>`
    * :doc:`damage/atom <compute_damage_atom>`
    * :doc:`dihedral <compute_dihedral>`
    * :doc:`dihedral/local <compute_dihedral_local>`
@@ -79,15 +79,14 @@ KOKKOS, o = USER-OMP, t = OPT.
    * :doc:`ke/atom/eff <compute_ke_atom_eff>`
    * :doc:`ke/eff <compute_ke_eff>`
    * :doc:`ke/rigid <compute_ke_rigid>`
-   * :doc:`meso/e/atom <compute_meso_e_atom>`
-   * :doc:`meso/rho/atom <compute_meso_rho_atom>`
-   * :doc:`meso/t/atom <compute_meso_t_atom>`
+   * :doc:`mesont <compute_mesont>`
+   * :doc:`mliap <compute_mliap>`
    * :doc:`momentum <compute_momentum>`
    * :doc:`msd <compute_msd>`
    * :doc:`msd/chunk <compute_msd_chunk>`
    * :doc:`msd/nongauss <compute_msd_nongauss>`
    * :doc:`omega/chunk <compute_omega_chunk>`
-   * :doc:`orientorder/atom <compute_orientorder_atom>`
+   * :doc:`orientorder/atom (k) <compute_orientorder_atom>`
    * :doc:`pair <compute_pair>`
    * :doc:`pair/local <compute_pair_local>`
    * :doc:`pe <compute_pe>`
@@ -124,6 +123,7 @@ KOKKOS, o = USER-OMP, t = OPT.
    * :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>`
    * :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>`
    * :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>`
+   * :doc:`smd/ulsph/effm <compute_smd_ulsph_effm>`
    * :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>`
    * :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>`
    * :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>`
@@ -133,6 +133,9 @@ KOKKOS, o = USER-OMP, t = OPT.
    * :doc:`sna/atom <compute_sna_atom>`
    * :doc:`snad/atom <compute_sna_atom>`
    * :doc:`snav/atom <compute_sna_atom>`
+   * :doc:`sph/e/atom <compute_sph_e_atom>`
+   * :doc:`sph/rho/atom <compute_sph_rho_atom>`
+   * :doc:`sph/t/atom <compute_sph_t_atom>`
    * :doc:`spin <compute_spin>`
    * :doc:`stress/atom <compute_stress_atom>`
    * :doc:`stress/mop <compute_stress_mop>`
@@ -161,5 +164,6 @@ KOKKOS, o = USER-OMP, t = OPT.
    * :doc:`torque/chunk <compute_torque_chunk>`
    * :doc:`vacf <compute_vacf>`
    * :doc:`vcm/chunk <compute_vcm_chunk>`
+   * :doc:`viscosity/cos <compute_viscosity_cos>`
    * :doc:`voronoi/atom <compute_voronoi_atom>`
    * :doc:`xrd <compute_xrd>`

doc/src/Commands_fix.rst

@@ -22,6 +22,7 @@ OPT.
 .. table_from_list::
    :columns: 5
 
+   * :doc:`accelerate/cos <fix_accelerate_cos>`
    * :doc:`adapt <fix_adapt>`
    * :doc:`adapt/fep <fix_adapt_fep>`
    * :doc:`addforce <fix_addforce>`
@@ -41,6 +42,7 @@ OPT.
    * :doc:`bocs <fix_bocs>`
    * :doc:`bond/break <fix_bond_break>`
    * :doc:`bond/create <fix_bond_create>`
+   * :doc:`bond/create/angle <fix_bond_create>`
    * :doc:`bond/react <fix_bond_react>`
    * :doc:`bond/swap <fix_bond_swap>`
    * :doc:`box/relax <fix_box_relax>`
@@ -94,10 +96,9 @@ OPT.
    * :doc:`lb/viscous <fix_lb_viscous>`
    * :doc:`lineforce <fix_lineforce>`
    * :doc:`manifoldforce <fix_manifoldforce>`
-   * :doc:`meso <fix_meso>`
    * :doc:`meso/move <fix_meso_move>`
-   * :doc:`meso/stationary <fix_meso_stationary>`
    * :doc:`momentum (k) <fix_momentum>`
+   * :doc:`momentum/chunk <fix_momentum>`
    * :doc:`move <fix_move>`
    * :doc:`mscg <fix_mscg>`
    * :doc:`msst <fix_msst>`
@@ -148,6 +149,7 @@ OPT.
    * :doc:`oneway <fix_oneway>`
    * :doc:`orient/bcc <fix_orient>`
    * :doc:`orient/fcc <fix_orient>`
+   * :doc:`orient/eco <fix_orient_eco>`
    * :doc:`phonon <fix_phonon>`
    * :doc:`pimd <fix_pimd>`
    * :doc:`planeforce <fix_planeforce>`
@@ -201,6 +203,8 @@ OPT.
    * :doc:`smd/move_tri_surf <fix_smd_move_triangulated_surface>`
    * :doc:`smd/setvel <fix_smd_setvel>`
    * :doc:`smd/wall_surface <fix_smd_wall_surface>`
+   * :doc:`sph <fix_sph>`
+   * :doc:`sph/stationary <fix_sph_stationary>`
    * :doc:`spring <fix_spring>`
    * :doc:`spring/chunk <fix_spring_chunk>`
    * :doc:`spring/rg <fix_spring_rg>`
@@ -241,3 +245,4 @@ OPT.
    * :doc:`wall/region <fix_wall_region>`
    * :doc:`wall/region/ees <fix_wall_ees>`
    * :doc:`wall/srd <fix_wall_srd>`
+   * :doc:`widom <fix_widom>`

doc/src/Commands_input.rst

@@ -31,9 +31,9 @@ does something different than this sequence:
    run      100
 
 In the first case, the specified timestep (0.5 fs) is used for two
-simulations of 100 timesteps each.  In the 2nd case, the default
-timestep (1.0 fs) is used for the 1st 100 step simulation and a 0.5 fs
-timestep is used for the 2nd one.
+simulations of 100 timesteps each.  In the second case, the default
+timestep (1.0 fs) is used for the first 100 step simulation and a 0.5 fs
+timestep is used for the second one.
 
 (2) Some commands are only valid when they follow other commands.  For
 example you cannot set the temperature of a group of atoms until atoms

doc/src/Commands_pair.rst

@@ -78,7 +78,7 @@ OPT.
    * :doc:`coul/long/soft (o) <pair_fep_soft>`
    * :doc:`coul/msm (o) <pair_coul>`
    * :doc:`coul/slater/cut <pair_coul_slater>`
-   * :doc:`coul/slater/long <pair_coul_slater>`   
+   * :doc:`coul/slater/long <pair_coul_slater>`
    * :doc:`coul/shield <pair_coul_shield>`
    * :doc:`coul/streitz <pair_coul>`
    * :doc:`coul/wolf (ko) <pair_coul>`
@@ -92,8 +92,8 @@ OPT.
    * :doc:`drip <pair_drip>`
    * :doc:`eam (gikot) <pair_eam>`
    * :doc:`eam/alloy (gikot) <pair_eam>`
-   * :doc:`eam/cd (o) <pair_eam>`
-   * :doc:`eam/cd/old (o) <pair_eam>`
+   * :doc:`eam/cd <pair_eam>`
+   * :doc:`eam/cd/old <pair_eam>`
    * :doc:`eam/fs (gikot) <pair_eam>`
    * :doc:`edip (o) <pair_edip>`
    * :doc:`edip/multi <pair_edip>`
@@ -136,22 +136,22 @@ OPT.
    * :doc:`lj/class2/soft <pair_fep_soft>`
    * :doc:`lj/cubic (go) <pair_lj_cubic>`
    * :doc:`lj/cut (gikot) <pair_lj>`
-   * :doc:`lj/cut/coul/cut (gko) <pair_lj>`
+   * :doc:`lj/cut/coul/cut (gko) <pair_lj_cut_coul>`
    * :doc:`lj/cut/coul/cut/soft (o) <pair_fep_soft>`
-   * :doc:`lj/cut/coul/debye (gko) <pair_lj>`
-   * :doc:`lj/cut/coul/dsf (gko) <pair_lj>`
-   * :doc:`lj/cut/coul/long (gikot) <pair_lj>`
+   * :doc:`lj/cut/coul/debye (gko) <pair_lj_cut_coul>`
+   * :doc:`lj/cut/coul/dsf (gko) <pair_lj_cut_coul>`
+   * :doc:`lj/cut/coul/long (gikot) <pair_lj_cut_coul>`
    * :doc:`lj/cut/coul/long/cs <pair_cs>`
    * :doc:`lj/cut/coul/long/soft (o) <pair_fep_soft>`
-   * :doc:`lj/cut/coul/msm (go) <pair_lj>`
-   * :doc:`lj/cut/coul/wolf (o) <pair_lj>`
+   * :doc:`lj/cut/coul/msm (go) <pair_lj_cut_coul>`
+   * :doc:`lj/cut/coul/wolf (o) <pair_lj_cut_coul>`
    * :doc:`lj/cut/dipole/cut (go) <pair_dipole>`
    * :doc:`lj/cut/dipole/long (g) <pair_dipole>`
    * :doc:`lj/cut/dipole/sf (go) <pair_dipole>`
    * :doc:`lj/cut/soft (o) <pair_fep_soft>`
    * :doc:`lj/cut/thole/long (o) <pair_thole>`
-   * :doc:`lj/cut/tip4p/cut (o) <pair_lj>`
-   * :doc:`lj/cut/tip4p/long (got) <pair_lj>`
+   * :doc:`lj/cut/tip4p/cut (o) <pair_lj_cut_tip4p>`
+   * :doc:`lj/cut/tip4p/long (got) <pair_lj_cut_tip4p>`
    * :doc:`lj/cut/tip4p/long/soft (o) <pair_fep_soft>`
    * :doc:`lj/expand (gko) <pair_lj_expand>`
    * :doc:`lj/expand/coul/long (g) <pair_lj_expand>`
@@ -180,8 +180,10 @@ OPT.
    * :doc:`meam/spline (o) <pair_meam_spline>`
    * :doc:`meam/sw/spline <pair_meam_sw_spline>`
    * :doc:`mesocnt <pair_mesocnt>`
+   * :doc:`mesont/tpm <pair_mesont_tpm>`
    * :doc:`mgpt <pair_mgpt>`
    * :doc:`mie/cut (g) <pair_mie>`
+   * :doc:`mliap <pair_mliap>`
    * :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
    * :doc:`momb <pair_momb>`
    * :doc:`morse (gkot) <pair_morse>`
@@ -227,7 +229,6 @@ OPT.
    * :doc:`smd/ulsph <pair_smd_ulsph>`
    * :doc:`smtbq <pair_smtbq>`
    * :doc:`snap (k) <pair_snap>`
-   * :doc:`snap (k) <pair_snap>`
    * :doc:`soft (go) <pair_soft>`
    * :doc:`sph/heatconduction <pair_sph_heatconduction>`
    * :doc:`sph/idealgas <pair_sph_idealgas>`

doc/src/Developer/developer.tex

@@ -142,7 +142,7 @@ follows:
   minimize.
 
 \item The Special class walks the bond topology of a molecular system
-  to find 1st, 2nd, 3rd neighbors of each atom.  It is invoked by
+  to find first, second, third neighbors of each atom.  It is invoked by
   several commands, like read\_data, read\_restart, and replicate.
 
 \item The Atom class stores all per-atom arrays.  More precisely, they

doc/src/Errors_debug.rst

@@ -23,7 +23,7 @@ We use it to show how to identify the origin of a segmentation fault.
      double *special_lj = force->special_lj;
      int newton_pair = force->newton_pair;
   +  double comx = 0.0;
-   
+
      inum = list->inum;
      ilist = list->ilist;
   @@ -134,8 +135,10 @@ void PairLJCut::compute(int eflag, int vflag)
@@ -31,7 +31,7 @@ We use it to show how to identify the origin of a segmentation fault.
          }
        }
   -  }
-   
+
   +    comx += atom->rmass[i]*x[i][0]; /* BUG */
   +  }
   +  printf("comx = %g\n",comx);
@@ -42,7 +42,7 @@ After recompiling LAMMPS and running the input you should get something like thi
 
 .. code-block:
 
-   $ ./lmp -in in.melt 
+   $ ./lmp -in in.melt
    LAMMPS (19 Mar 2020)
    OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
      using 1 OpenMP thread(s) per MPI task
@@ -98,11 +98,11 @@ drop back to the GDB prompt.
      Unit style    : lj
      Current step  : 0
      Time step     : 0.005
-   
+
    Program received signal SIGSEGV, Segmentation fault.
    0x00000000006653ab in LAMMPS_NS::PairLJCut::compute (this=0x829740, eflag=1, vflag=<optimized out>) at /home/akohlmey/compile/lammps/src/pair_lj_cut.cpp:139
    139      comx += atom->rmass[i]*x[i][0]; /* BUG */
-   (gdb) 
+   (gdb)
 
 Now typing the command "where" will show the stack of functions starting from
 the current function back to "main()".
@@ -119,7 +119,7 @@ the current function back to "main()".
    #4  0x0000000000410ad3 in LAMMPS_NS::Input::execute_command (this=0x7d1410) at /home/akohlmey/compile/lammps/src/input.cpp:864
    #5  0x00000000004111fb in LAMMPS_NS::Input::file (this=0x7d1410) at /home/akohlmey/compile/lammps/src/input.cpp:229
    #6  0x000000000040933a in main (argc=<optimized out>, argv=<optimized out>) at /home/akohlmey/compile/lammps/src/main.cpp:65
-   (gdb) 
+   (gdb)
 
 You can also print the value of variables and see if there is anything
 unexpected.  Segmentation faults, for example, commonly happen when a
@@ -189,12 +189,12 @@ the console are not mixed.
 
 .. code-block::
 
-   $ valgrind ./lmp -in in.melt 
+   $ valgrind ./lmp -in in.melt
    ==1933642== Memcheck, a memory error detector
    ==1933642== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
    ==1933642== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info
    ==1933642== Command: ./lmp -in in.melt
-   ==1933642== 
+   ==1933642==
    LAMMPS (19 Mar 2020)
    OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
      using 1 OpenMP thread(s) per MPI task
@@ -228,7 +228,7 @@ the console are not mixed.
    ==1933642==    by 0x4111FA: LAMMPS_NS::Input::file() (input.cpp:229)
    ==1933642==    by 0x409339: main (main.cpp:65)
    ==1933642==  Address 0x0 is not stack'd, malloc'd or (recently) free'd
-   ==1933642== 
+   ==1933642==
 
 As you can see, the stack trace information is similar to that obtained
 from GDB. In addition you get a more specific hint about what cause the

doc/src/Errors_messages.rst

@@ -381,7 +381,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    are defined.
 
 *Bond atom missing in box size check*
-   The 2nd atoms needed to compute a particular bond is missing on this
+   The second atom needed to compute a particular bond is missing on this
    processor.  Typically this is because the pairwise cutoff is set too
    short or the bond has blown apart and an atom is too far away.
 
@@ -391,7 +391,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    the atoms are too far apart to make a valid bond.
 
 *Bond atom missing in image check*
-   The 2nd atom in a particular bond is missing on this processor.
+   The second atom in a particular bond is missing on this processor.
    Typically this is because the pairwise cutoff is set too short or the
    bond has blown apart and an atom is too far away.
 
@@ -401,12 +401,12 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    are too far apart to make a valid bond.
 
 *Bond atoms %d %d missing on proc %d at step %ld*
-   The 2nd atom needed to compute a particular bond is missing on this
+   The second atom needed to compute a particular bond is missing on this
    processor.  Typically this is because the pairwise cutoff is set too
    short or the bond has blown apart and an atom is too far away.
 
 *Bond atoms missing on proc %d at step %ld*
-   The 2nd atom needed to compute a particular bond is missing on this
+   The second atom needed to compute a particular bond is missing on this
    processor.  Typically this is because the pairwise cutoff is set too
    short or the bond has blown apart and an atom is too far away.
 
@@ -1374,7 +1374,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    template does not qualify.
 
 *Cannot use fix box/relax on a 2nd non-periodic dimension*
-   When specifying an off-diagonal pressure component, the 2nd of the two
+   When specifying an off-diagonal pressure component, the second of the two
    dimensions must be periodic.  E.g. if the xy component is specified,
    then the y dimension must be periodic.
 
@@ -1388,7 +1388,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    also keyword tri or xy, this is wrong.
 
 *Cannot use fix box/relax with tilt factor scaling on a 2nd non-periodic dimension*
-   When specifying scaling on a tilt factor component, the 2nd of the two
+   When specifying scaling on a tilt factor component, the second of the two
    dimensions must be periodic.  E.g. if the xy component is specified,
    then the y dimension must be periodic.
 
@@ -1429,7 +1429,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    This would be changing the same box dimension twice.
 
 *Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension*
-   When specifying an off-diagonal pressure component, the 2nd of the two
+   When specifying an off-diagonal pressure component, the second of the two
    dimensions must be periodic.  E.g. if the xy component is specified,
    then the y dimension must be periodic.
 
@@ -1447,13 +1447,13 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    Self-explanatory.
 
 *Cannot use fix nvt/npt/nph with xy scaling when y is non-periodic dimension*
-   The 2nd dimension in the barostatted tilt factor must be periodic.
+   The second dimension in the barostatted tilt factor must be periodic.
 
 *Cannot use fix nvt/npt/nph with xz scaling when z is non-periodic dimension*
-   The 2nd dimension in the barostatted tilt factor must be periodic.
+   The second dimension in the barostatted tilt factor must be periodic.
 
 *Cannot use fix nvt/npt/nph with yz scaling when z is non-periodic dimension*
-   The 2nd dimension in the barostatted tilt factor must be periodic.
+   The second dimension in the barostatted tilt factor must be periodic.
 
 *Cannot use fix pour rigid and not molecule*
    Self-explanatory.
@@ -7192,7 +7192,7 @@ keyword to allow for additional bonds to be formed
    does not exist.
 
 *Replacing a fix, but new style != old style*
-   A fix ID can be used a 2nd time, but only if the style matches the
+   A fix ID can be used a second time, but only if the style matches the
    previous fix.  In this case it is assumed you with to reset a fix's
    parameters.  This error may mean you are mistakenly re-using a fix ID
    when you do not intend to.

doc/src/Errors_warnings.rst

@@ -43,17 +43,17 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    Self-explanatory.
 
 *Bond atom missing in box size check*
-   The 2nd atoms needed to compute a particular bond is missing on this
+   The second atom needed to compute a particular bond is missing on this
    processor.  Typically this is because the pairwise cutoff is set too
    short or the bond has blown apart and an atom is too far away.
 
 *Bond atom missing in image check*
-   The 2nd atom in a particular bond is missing on this processor.
+   The second atom in a particular bond is missing on this processor.
    Typically this is because the pairwise cutoff is set too short or the
    bond has blown apart and an atom is too far away.
 
 *Bond atoms missing at step %ld*
-   The 2nd atom needed to compute a particular bond is missing on this
+   The second atom needed to compute a particular bond is missing on this
    processor.  Typically this is because the pairwise cutoff is set too
    short or the bond has blown apart and an atom is too far away.
 
@@ -118,6 +118,24 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    incorrect periodic images of atoms in interaction lists.  To avoid, either use
    :doc:`pair style zero <pair_zero>` with a suitable cutoff or use :doc:`comm_modify cutoff <comm_modify>`.
 
+*Communication cutoff is shorter than a bond length based estimate. This may lead to errors.*
+
+   Since LAMMPS stores topology data with individual atoms, all atoms
+   comprising a bond, angle, dihedral or improper must be present on any
+   sub-domain that "owns" the atom with the information, either as a
+   local or a ghost atom. The communication cutoff is what determines up
+   to what distance from a sub-domain boundary ghost atoms are created.
+   The communication cutoff is by default the largest non-bonded cutoff
+   plus the neighbor skin distance, but for short or non-bonded cutoffs
+   and/or long bonds, this may not be sufficient. This warning indicates
+   that there is an increased risk of a simulation stopping unexpectedly
+   because of Bond/Angle/Dihedral/Improper atoms missing.  It can be
+   silenced by manually setting the communication cutoff via
+   :doc:`comm_modify cutoff <comm_modify>`.  However, since the
+   heuristic used to determine the estimate is not always accurate, it
+   is not changed automatically and the warning may be ignored depending
+   on the specific system being simulated.
+
 *Communication cutoff is too small for SNAP micro load balancing, increased to %lf*
    Self-explanatory.
 
@@ -486,7 +504,7 @@ This will most likely cause errors in kinetic fluctuations.
    a new style.
 
 *No Kspace calculation with verlet/split*
-   The 2nd partition performs a kspace calculation so the kspace_style
+   The second partition performs a kspace calculation so the kspace_style
    command must be used.
 
 *No automatic unit conversion to XTC file format conventions possible for units lj*

doc/src/Examples.rst

@@ -163,7 +163,7 @@ Here is how you can run and visualize one of the sample problems:
 
 Running the simulation produces the files *dump.indent* and
 *log.lammps*\ .  You can visualize the dump file of snapshots with a
-variety of 3rd-party tools highlighted on the
+variety of third-party tools highlighted on the
 `Visualization <https://lammps.sandia.gov/viz.html>`_ page of the LAMMPS
 web site.
 

doc/src/Howto.rst

@@ -19,7 +19,7 @@ Tutorials howto
    Howto_cmake
    Howto_github
    Howto_pylammps
-   Howto_bash
+   Howto_wsl
 
 General howto
 =============

doc/src/Howto_bash.rst

@@ -1,264 +0,0 @@
-Using LAMMPS with Bash on Windows
-=================================
-
-**written by Richard Berger**
-
-----------
-
-Starting with Windows 10 you can install Linux tools directly in Windows. This
-allows you to compile LAMMPS following the same procedure as on a real Ubuntu
-Linux installation. Software can be easily installed using the package manager
-via apt-get and all files are accessible in both the Windows Explorer and your
-Linux shell (bash). This avoids switching to a different operating system or
-installing a virtual machine. Everything runs on Windows.
-
-.. seealso::
-
-   You can find more detailed information at the `Windows Subsystem for Linux Installation Guide for Windows 10 <https://docs.microsoft.com/en-us/windows/wsl/install-win10>`_.
-
-Installing Bash on Windows
---------------------------
-
-Prerequisites
-^^^^^^^^^^^^^
-
-* Windows 10 (64bit only)
-* Latest updates installed
-
-Enable developer mode
-^^^^^^^^^^^^^^^^^^^^^
-
-You enable this feature by first opening Windows Settings and enabling
-Developer mode. Go to the Windows settings and search for "developer". This
-will allow you to install software which comes from outside of the Windows
-Store.  You might be prompted to reboot your compute. Please do so.
-
-.. image:: JPG/bow_tutorial_01_small.png
-   :target: JPG/bow_tutorial_01.png
-
-.. image:: JPG/bow_tutorial_02_small.png
-   :target: JPG/bow_tutorial_02.png
-
-.. image:: JPG/bow_tutorial_03_small.png
-   :target: JPG/bow_tutorial_03.png
-
-Install Windows Subsystem for Linux
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Next you must ensure that the Window Subsystem for Linux is installed. Again,
-search for "enable windows features" in the Settings dialog. This opens a
-dialog with a list of features you can install. Add a checkmark to Windows
-Subsystem for Linux (Beta) and press OK.
-
-.. image:: JPG/bow_tutorial_04_small.png
-   :target: JPG/bow_tutorial_04.png
-
-.. image:: JPG/bow_tutorial_05.png
-   :target: JPG/bow_tutorial_05.png
-
-Install Bash for Windows
-^^^^^^^^^^^^^^^^^^^^^^^^
-
-After installation completes, type "bash" in the Windows Start menu search.
-Select the first found option. This will launch a command-line window which
-will prompt you about installing Ubuntu on Windows. Confirm with "y" and press
-enter. This will then download Ubuntu for Windows.
-
-.. image:: JPG/bow_tutorial_06.png
-
-.. image:: JPG/bow_tutorial_07.png
-
-During installation, you will be asked for a new password. This will be used
-for installing new software and running commands with sudo.
-
-.. image:: JPG/bow_tutorial_08.png
-
-Type exit to close the command-line window.
-
-Go to the Start menu and type "bash" again. This time you will see a "Bash on
-Ubuntu on Windows" Icon. Start this program.
-
-.. image:: JPG/bow_tutorial_09.png
-
-Congratulations, you have installed **Bash on Ubuntu on Windows**\ .
-
-.. image:: JPG/bow_tutorial_10.png
-
-----------
-
-Compiling LAMMPS in Bash on Windows
------------------------------------
-
-The installation of LAMMPS in this environment is identical to working inside
-of a real Ubuntu Linux installation. At the time writing, it uses Ubuntu 16.04.
-
-Installing prerequisite packages
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-First upgrade all existing packages using
-
-.. code-block:: bash
-
-   sudo apt update
-   sudo apt upgrade -y
-
-Next install the following packages, which include compilers and libraries
-needed for various LAMMPS features:
-
-.. code-block:: bash
-
-   sudo apt install -y build-essential ccache gfortran openmpi-bin libopenmpi-dev libfftw3-dev libjpeg-dev libpng-dev python-dev python-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev hdf5-tools
-
-Files in Ubuntu on Windows
-^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-When you launch "Bash on Ubuntu on Windows" you will start out in your Linux
-user home directory /home/[username]\ . You can access your Windows user directory
-using the /mnt/c/Users/[username] folder.
-
-Download LAMMPS
-^^^^^^^^^^^^^^^
-
-Obtain a copy of the LAMMPS code and go into it using "cd"
-
-Option 1: Downloading LAMMPS tarball using wget
-"""""""""""""""""""""""""""""""""""""""""""""""
-
-.. code-block:: bash
-
-   wget https://lammps.sandia.gov/tars/lammps-stable.tar.gz
-   tar xvzf lammps-stable.tar.gz
-   cd lammps-31Mar17
-
-Option 2: Obtaining LAMMPS code from GitHub
-"""""""""""""""""""""""""""""""""""""""""""
-
-.. code-block:: bash
-
-   git clone https://github.com/lammps/lammps.git
-   cd lammps
-
-Compiling LAMMPS
-^^^^^^^^^^^^^^^^
-
-At this point you can compile LAMMPS like on Ubuntu Linux.
-
-Compiling serial version
-""""""""""""""""""""""""
-
-.. code-block:: bash
-
-   cd src/
-   make -j 4 serial
-
-This will create an executable called lmp_serial in the src/ directory
-
-Compiling MPI version
-"""""""""""""""""""""
-
-.. code-block:: bash
-
-   cd src/
-   make -j 4 mpi
-
-This will create an executable called lmp_mpi in the src/ directory
-
-----------
-
-Finally, please note the absolute path of your src folder. You can get this using
-
-.. code-block:: bash
-
-   pwd
-
-or
-
-.. code-block:: bash
-
-   echo $PWD
-
-To run any examples you need the location of the executable. For now, let us
-save this location in a temporary variable
-
-.. code-block:: bash
-
-   LAMMPS_DIR=$PWD
-
-----------
-
-Running an example script
-^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Once compiled you can execute some of the LAMMPS examples. Switch into the
-examples/melt folder
-
-.. code-block:: bash
-
-   cd ../examples/melt
-
-The full path of the serial executable is $LAMMPS_DIR/lmp_serial, while the mpi
-version is $LAMMPS_DIR/lmp_mpi. You can run the melt example with either
-version as follows:
-
-.. code-block:: bash
-
-   $LAMMPS_DIR/lmp_serial -in in.melt
-
-or
-
-.. code-block:: bash
-
-   mpirun -np 4 $LAMMPS_DIR/lmp_mpi -in in.melt
-
-Note the use of our variable $LAMMPS_DIR, which expands into the full path of
-the LAMMPS src folder we saved earlier.
-
-Adding your executable directory to your PATH
-"""""""""""""""""""""""""""""""""""""""""""""
-
-You can avoid having to type the full path of your LAMMPS binary by adding its
-parent folder to the PATH environment variable as follows:
-
-.. code-block:: bash
-
-   export PATH=$LAMMPS_DIR:$PATH
-
-Input scripts can then be run like this:
-
-.. code-block:: bash
-
-   lmp_serial -in in.melt
-
-or
-
-.. code-block:: bash
-
-   mpirun -np 4 lmp_mpi -in in.melt
-
-However, this PATH variable will not persist if you close your bash window.
-To persist this setting edit the $HOME/.bashrc file using your favorite editor
-and add this line
-
-.. code-block:: bash
-
-   export PATH=/full/path/to/your/lammps/src:$PATH
-
-**Example:**
-
-For an executable lmp_serial with a full path
-
-.. code-block:: bash
-
-   /home/richard/lammps/src/lmp_serial
-
-the PATH variable should be
-
-.. code-block:: bash
-
-   export PATH=/home/richard/lammps/src:$PATH
-
-.. note::
-
-   This should give you a jump start when trying to run LAMMPS on Windows.
-   To become effective in this environment I encourage you to look into Linux
-   tutorials explaining Bash and Basic Unix commands (e.g., `Linux Journey <https://linuxjourney.com>`_)