Merge pull request #2374 from akohlmey/next_patch_version

Step version strings for the next 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
@@ -25,6 +26,7 @@ src/USER-COLVARS/*    @giacomofiorin
 src/USER-INTEL/*      @wmbrownintel
 src/USER-MANIFOLD/*   @Pakketeretet2
 src/USER-MEAMC/*      @martok
+src/USER-MESONT/*     @iafoss
 src/USER-MOFFF/*      @hheenen
 src/USER-MOLFILE/*    @akohlmey
 src/USER-NETCDF/*     @pastewka
@@ -111,14 +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

@@ -67,6 +67,7 @@ How quickly your contribution will be integrated depends largely on how much eff
 
 Here is a checklist of steps you need to follow to submit a single file or user package for our consideration. Following these steps will save both you and us time. See existing files in packages in the source directory for examples. If you are uncertain, please ask on the lammps-users mailing list.
 
+* C++ source code must be compatible with the C++-11 standard. Packages may require a later standard, if justified.
 * All source files you provide must compile with the most current version of LAMMPS with multiple configurations. In particular you need to test compiling LAMMPS from scratch with `-DLAMMPS_BIGBIG` set in addition to the default `-DLAMMPS_SMALLBIG` setting. Your code will need to work correctly in serial and in parallel using MPI.
 * For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no trailing whitespace, no lines over 80 characters. I/O is done via the C-style stdio library, style class header files should not import any system headers, STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. There MUST NOT be any "using namespace XXX;" statements in headers. In the implementation file (<name>.cpp) system includes should be placed in angular brackets (<>) and for c-library functions the C++ style header files should be included (<cstdio> instead of <stdio.h>, or <cstring> instead of <string.h>). This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages.
 * Source, style name, and documentation file should follow the following naming convention: style names should be lowercase and words separated by a forward slash; for a new fix style 'foo/bar', the class should be named FixFooBar, the name of the source files should be 'fix_foo_bar.h' and 'fix_foo_bar.cpp' and the corresponding documentation should be in a file 'fix_foo_bar.rst'.
@@ -75,7 +76,9 @@ 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/PULL_REQUEST_TEMPLATE.md

@@ -2,7 +2,7 @@
 
 <!--Briefly describe the new feature(s), enhancement(s), or bugfix(es) included in this pull request.-->
 
-**Related Issues**
+**Related Issue(s)**
 
 <!--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-->
 
@@ -34,6 +34,7 @@ By submitting this pull request, I agree, that my contribution will be included
 - [ ] The added/updated documentation is integrated and tested with the documentation build system
 - [ ] The feature has been verified to work with the conventional build system
 - [ ] The feature has been verified to work with the CMake based build system
+- [ ] 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
 

.github/PULL_REQUEST_TEMPLATE/bug_fix.md

@@ -9,34 +9,37 @@ assignees: ''
 
 **Summary**
 
-<!--Briefly describe the bug or bugs, that are eliminated by this pull request.-->
+<!--Briefly describe the bug(s) 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 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-->
+<!--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**
 
-By submitting this pull request I implicitly accept, that my submission is subject to the same licensing terms as the files that are modified.
+By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).
 
 **Backward Compatibility**
 
-<!--Please state whether any changes in the pull request 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-->
 
 **Detailed Description**
 
 <!--Provide any relevant details about how the fixed bug can be reproduced, how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected-->
 
-## Post Submission Checklist
+**Post Submission Checklist**
 
-<!--Please check the fields below as they are completed *after* the pull request is submitted-->
-- [ ] The code in this pull request is complete
+<!--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
+- [ ] Corresponding author information is complete
 - [ ] The source code follows the LAMMPS formatting guidelines
+- [ ] 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.
 
-## 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)-->

.github/PULL_REQUEST_TEMPLATE/maintenance_refactoring.md

@@ -13,23 +13,31 @@ assignees: ''
 
 **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 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-->
+<!--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**
 
-By submitting this pull request I implicitly accept, that my submission is subject to the same licensing terms as the files that are modified.
+By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).
+
+**Backward Compatibility**
+
+<!--Please state whether any changes in the pull request will break backward compatibility for inputs, and - if yes - explain what has been changed and why-->
 
 **Detailed Description**
 
-<!--Provide any relevant details about the included changes.-->
+<!--Provide any relevant details about how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected-->
 
-## Post Submission Checklist
+**Post Submission Checklist**
 
 <!--Please check the fields below as they are completed *after* the pull request is submitted-->
 - [ ] The pull request is complete
 - [ ] The source code follows the LAMMPS formatting guidelines
+- [ ] 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.
+
 

.github/PULL_REQUEST_TEMPLATE/new_feature.md

@@ -11,32 +11,29 @@ assignees: ''
 
 <!--Briefly describe the new feature(s) included in this pull request.-->
 
-**Related Issues**
+**Related Issue(s)**
 
-<!--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 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 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 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**
 
-<!--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):
+By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).
 
 **Backward Compatibility**
 
-<!--Please state 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 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 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 feature(s) are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected-->
 
-## Post Submission Checklist
+**Post Submission Checklist**
 
-<!--Please check the fields below as they are completed *after* the pull request has been submitted-->
+<!--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
@@ -46,10 +43,11 @@ My contribution may be licensed as LGPL (for use as a library with proprietary s
 - [ ] 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
+**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)-->
 

.github/PULL_REQUEST_TEMPLATE/update_enhancement.md

@@ -11,17 +11,21 @@ assignees: ''
 
 <!--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.-->
 
+**Related Issue(s)**
+
+<!--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-->
 
 **Licensing**
 
-By submitting this pull request I implicitly accept, that my submission is subject to the same licensing terms as the original package or feature(s) that are updated or amended by this pull request.
+By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).
 
 **Backward Compatibility**
 
-<!--Please state whether any changes in the pull request 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**
 
@@ -29,11 +33,19 @@ By submitting this pull request I implicitly accept, that my submission is subje
 
 **Post Submission Checklist**
 
-<!--Please check the fields below as they are completed-->
+<!--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
-- [ ] Suitable updates to the existing docs are included
-- [ ] One or more example input decks are included
+- [ ] Licensing information is complete
+- [ ] Corresponding author information is complete
 - [ ] The source code follows the LAMMPS formatting guidelines
+- [ ] Suitable updates to the existing docs are included
+- [ ] The 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 updated or added to the unittest tree.
+- [ ] A package specific README file has been updated
+- [ ] One or more example input decks are included
 
 **Further Information, Files, and Links**
 

.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)
@@ -189,13 +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)
@@ -221,10 +218,9 @@ if(BUILD_OMP)
     message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
   endif()
 
-  if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 8.99.9)) OR
-      ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 9.99.9)) OR
-      ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 18.99.9))
-      )
+  if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR
+      ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
+      ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
     # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
     # Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe.
     target_compile_definitions(lammps PRIVATE -DLAMMPS_OMP_COMPAT=4)
@@ -234,6 +230,68 @@ 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()
+
+#######################################
+# add custom target for IWYU analysis
+#######################################
+set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool")
+mark_as_advanced(ENABLE_IWYU)
+if(ENABLE_IWYU)
+  find_program(IWYU_EXE NAMES include-what-you-use iwyu)
+  find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py)
+  if (IWYU_EXE AND IWYU_TOOL)
+    add_custom_target(
+      iwyu
+      ${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp
+      COMMENT "Running IWYU")
+    add_dependencies(iwyu lammps)
+  else()
+    message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable"
+      "and the iwyu-tool/iwyu_tool script installed in your PATH")
+  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)
@@ -254,14 +312,13 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
   endif()
 endif()
 
-
 find_package(JPEG QUIET)
 option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND})
 if(WITH_JPEG)
   find_package(JPEG REQUIRED)
   target_compile_definitions(lammps PRIVATE -DLAMMPS_JPEG)
   if(CMAKE_VERSION VERSION_LESS 3.12)
-    target_include_directories(lammps PRIVATE ${JPEG_INCLUDE_DIR})
+    target_include_directories(lammps PRIVATE ${JPEG_INCLUDE_DIRS})
     target_link_libraries(lammps PRIVATE ${JPEG_LIBRARIES})
   else()
     target_link_libraries(lammps PRIVATE JPEG::JPEG)
@@ -319,17 +376,10 @@ 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})
-  string(REGEX REPLACE "[=\"]" "" _FLAGX ${_FLAG})
-  check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAGX})
-  if(COMPILER_SUPPORTS${_FLAGX})
-    target_compile_options(lammps PRIVATE ${_FLAG})
-  else()
-    message(WARNING "${_FLAG} found in CMAKE_TUNE_FLAGS, but not supported by the compiler, skipping")
-  endif()
+  target_compile_options(lammps PRIVATE ${_FLAG})
 endforeach()
 ########################################################################
 # Basic system tests (standard libraries, headers, functions, types)   #
@@ -351,6 +401,15 @@ 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} ${LAMMPS_POTENTIALS_DIR})
+  endif()
+endforeach()
+
 ##############################################
 # add sources of enabled packages
 ############################################
@@ -397,13 +456,19 @@ endforeach()
 ##############################################
 # add lib sources of (simple) enabled packages
 ############################################
-foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD)
+foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT)
   if(PKG_${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)
+    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})
@@ -491,7 +556,7 @@ 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}"
@@ -538,8 +603,6 @@ if(BUILD_SHARED_LIBS)
   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)
@@ -553,11 +616,17 @@ if(BUILD_TOOLS)
   install(TARGETS binary2txt DESTINATION ${CMAKE_INSTALL_BINDIR})
 
   include(CheckGeneratorSupport)
-  if(CMAKE_GENERATOR_SUPPORT_FORTRAN AND CMAKE_Fortran_COMPILER)
-    enable_language(Fortran)
-    add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
-    target_link_libraries(chain.x PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
-    install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR})
+  if(CMAKE_GENERATOR_SUPPORT_FORTRAN)
+    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()
@@ -598,6 +667,8 @@ 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})
@@ -649,6 +720,7 @@ endif()
 
 include(Testing)
 include(CodeCoverage)
+include(CodingStandard)
 
 ###############################################################################
 # Print package summary
@@ -693,6 +765,12 @@ 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()
@@ -753,3 +831,6 @@ if(PKG_KSPACE)
     endif()
   endif()
 endif()
+if(BUILD_DOC)
+  message(STATUS "<<< Building HTML Manual >>>")
+endif()

cmake/LAMMPSConfig.cmake.in

@@ -1,11 +1,5 @@
-list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR})
 include(CMakeFindDependencyMacro)
 if(@BUILD_MPI@)
   find_dependency(MPI REQUIRED CXX)
 endif()
-if(@PKG_KSPACE@)
-  if(@FFT@ STREQUAL "FFTW3")
-    find_dependency(@FFTW@ REQUIRED MODULE)
-  endif()
-endif()
 include("${CMAKE_CURRENT_LIST_DIR}/LAMMPS_Targets.cmake")

cmake/Modules/CodeCoverage.cmake

@@ -3,11 +3,16 @@
 #
 # Requires latest gcovr (for GCC 8.1 support):#
 # pip install git+https://github.com/gcovr/gcovr.git
+#
+# For Python coverage the coverage package needs to be installed
 ###############################################################################
 if(ENABLE_COVERAGE)
     find_program(GCOVR_BINARY gcovr)
     find_package_handle_standard_args(GCOVR DEFAULT_MSG GCOVR_BINARY)
 
+    find_program(COVERAGE_BINARY coverage)
+    find_package_handle_standard_args(COVERAGE DEFAULT_MSG COVERAGE_BINARY)
+
     if(GCOVR_FOUND)
         get_filename_component(ABSOLUTE_LAMMPS_SOURCE_DIR ${LAMMPS_SOURCE_DIR} ABSOLUTE)
 
@@ -15,14 +20,61 @@ 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()
+
+    if(COVERAGE_FOUND)
+        set(PYTHON_COVERAGE_HTML_DIR ${CMAKE_BINARY_DIR}/python_coverage_html)
+        add_custom_command(
+            OUTPUT ${CMAKE_BINARY_DIR}/unittest/python/.coverage
+            COMMAND ${COVERAGE_BINARY} combine
+            WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
+            COMMENT "Combine Python coverage files..."
+        )
+
+        add_custom_target(
+            gen_python_coverage_html
+            COMMAND ${COVERAGE_BINARY} html -d ${PYTHON_COVERAGE_HTML_DIR}
+            DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage
+            WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
+            COMMENT "Generating HTML Python coverage report..."
+        )
+
+        add_custom_target(
+            gen_python_coverage_xml
+            COMMAND ${COVERAGE_BINARY} xml -o ${CMAKE_BINARY_DIR}/python_coverage.xml
+            DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage
+            WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
+            COMMENT "Generating XML Python coverage report..."
         )
     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

@@ -2,73 +2,106 @@
 # 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()
+  find_package(Doxygen 1.8.10 REQUIRED)
 
   file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
 
+
   add_custom_command(
     OUTPUT docenv
     COMMAND ${VIRTUALENV} docenv
   )
 
   set(DOCENV_BINARY_DIR ${CMAKE_BINARY_DIR}/docenv/bin)
+  set(DOCENV_REQUIREMENTS_FILE ${LAMMPS_DOC_DIR}/utils/requirements.txt)
+
+  set(SPHINX_CONFIG_DIR ${LAMMPS_DOC_DIR}/utils/sphinx-config)
+  set(SPHINX_CONFIG_FILE_TEMPLATE ${SPHINX_CONFIG_DIR}/conf.py.in)
+  set(SPHINX_STATIC_DIR  ${SPHINX_CONFIG_DIR}/_static)
+
+  # configuration and static files are copied to binary dir to avoid collisions with parallel builds
+  set(DOC_BUILD_DIR ${CMAKE_CURRENT_BINARY_DIR}/doc)
+  set(DOC_BUILD_CONFIG_FILE ${DOC_BUILD_DIR}/conf.py)
+  set(DOC_BUILD_STATIC_DIR ${DOC_BUILD_DIR}/_static)
+  set(DOXYGEN_BUILD_DIR ${DOC_BUILD_DIR}/doxygen)
+  set(DOXYGEN_XML_DIR ${DOXYGEN_BUILD_DIR}/xml)
+
+  # copy entire configuration folder to doc build directory
+  # files in _static are automatically copied during sphinx-build, so no need to copy them individually
+  file(COPY ${SPHINX_CONFIG_DIR}/ DESTINATION ${DOC_BUILD_DIR})
+
+  # configure paths in conf.py, since relative paths change when file is copied
+  configure_file(${SPHINX_CONFIG_FILE_TEMPLATE} ${DOC_BUILD_CONFIG_FILE})
 
   add_custom_command(
-    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
+    OUTPUT ${DOC_BUILD_DIR}/requirements.txt
+    DEPENDS docenv ${DOCENV_REQUIREMENTS_FILE}
+    COMMAND ${CMAKE_COMMAND} -E copy ${DOCENV_REQUIREMENTS_FILE} ${DOC_BUILD_DIR}/requirements.txt
+    COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade pip
     COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
+    COMMAND ${DOCENV_BINARY_DIR}/pip install --use-feature=2020-resolver -r ${DOC_BUILD_DIR}/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 ${DOC_BUILD_STATIC_DIR}/mathjax/es5)
+    file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
+      "${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)
+    execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax)
   endif()
-  file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax)
-  file(COPY ${CMAKE_CURRENT_BINARY_DIR}/mathjax/es5 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax/)
 
-  # note, this may run in parallel with other tasks, so we must not use multiple processes here
+  # for increased browser compatibility
+  if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/polyfill.js)
+    file(DOWNLOAD "https://polyfill.io/v3/polyfill.min.js?features=es6"
+      "${DOC_BUILD_STATIC_DIR}/polyfill.js")
+  endif()
+
+  # set up doxygen and add targets to run it
+  file(MAKE_DIRECTORY ${DOXYGEN_BUILD_DIR})
+  file(COPY ${LAMMPS_DOC_DIR}/doxygen/lammps-logo.png DESTINATION ${DOXYGEN_BUILD_DIR}/lammps-logo.png)
+  configure_file(${LAMMPS_DOC_DIR}/doxygen/Doxyfile.in ${DOXYGEN_BUILD_DIR}/Doxyfile)
+  get_target_property(LAMMPS_SOURCES lammps SOURCES)
   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
+    OUTPUT ${DOXYGEN_XML_DIR}/index.xml
+    DEPENDS ${DOC_SOURCES} ${LAMMPS_SOURCES}
+    COMMAND Doxygen::doxygen ${DOXYGEN_BUILD_DIR}/Doxyfile WORKING_DIRECTORY ${DOXYGEN_BUILD_DIR}
+    COMMAND ${CMAKE_COMMAND} -E touch ${DOXYGEN_XML_DIR}/run.stamp
   )
 
-  # copy selected image files to html output tree
-  file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/html/JPG)
-  set(HTML_EXTRA_IMAGES balance_nonuniform.jpg balance_rcb.jpg
-    balance_uniform.jpg bow_tutorial_01.png bow_tutorial_02.png
-    bow_tutorial_03.png bow_tutorial_04.png bow_tutorial_05.png
-    dump1.jpg dump2.jpg examples_mdpd.gif gran_funnel.png gran_mixer.png
-    hop1.jpg hop2.jpg saed_ewald_intersect.jpg saed_mesh.jpg
-    screenshot_atomeye.jpg screenshot_gl.jpg screenshot_pymol.jpg
-    screenshot_vmd.jpg sinusoid.jpg xrd_mesh.jpg)
-  set(HTML_IMAGE_TARGETS "")
-  foreach(_IMG ${HTML_EXTRA_IMAGES})
-    string(PREPEND _IMG JPG/)
-    list(APPEND HTML_IMAGE_TARGETS "html/${_IMG}")
-    add_custom_command(
-      OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/html/${_IMG}
-      DEPENDS ${LAMMPS_DOC_DIR}/src/${_IMG} html/JPG
-      COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/src/${_IMG} ${CMAKE_BINARY_DIR}/html/${_IMG}
-    )
-  endforeach()
+  if(EXISTS ${DOXYGEN_XML_DIR}/run.stamp)
+    set(SPHINX_EXTRA_OPTS "-E")
+  else()
+    set(SPHINX_EXTRA_OPTS "")
+  endif()
+  add_custom_command(
+    OUTPUT html
+    DEPENDS ${DOC_SOURCES} docenv ${DOC_BUILD_DIR}/requirements.txt ${DOXYGEN_XML_DIR}/index.xml ${BUILD_DOC_CONFIG_FILE}
+    COMMAND ${DOCENV_BINARY_DIR}/sphinx-build ${SPHINX_EXTRA_OPTS} -b html -c ${DOC_BUILD_DIR} -d ${DOC_BUILD_DIR}/doctrees ${LAMMPS_DOC_DIR}/src ${DOC_BUILD_DIR}/html
+    COMMAND ${CMAKE_COMMAND} -E create_symlink Manual.html ${DOC_BUILD_DIR}/html/index.html
+    COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src/PDF ${DOC_BUILD_DIR}/html/PDF
+    COMMAND ${CMAKE_COMMAND} -E remove -f ${DOXYGEN_XML_DIR}/run.stamp
+  )
 
   add_custom_target(
     doc ALL
-    DEPENDS html html/_static/mathjax/es5 ${HTML_IMAGE_TARGETS}
+    DEPENDS html ${DOC_BUILD_STATIC_DIR}/mathjax/es5
     SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES}
   )
 
-  install(DIRECTORY ${CMAKE_BINARY_DIR}/html DESTINATION ${CMAKE_INSTALL_DOCDIR})
+  install(DIRECTORY ${DOC_BUILD_DIR}/html DESTINATION ${CMAKE_INSTALL_DOCDIR})
 endif()

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/Packages/COMPRESS.cmake

@@ -1,2 +1,10 @@
 find_package(ZLIB REQUIRED)
 target_link_libraries(lammps PRIVATE ZLIB::ZLIB)
+
+find_package(PkgConfig REQUIRED)
+pkg_check_modules(Zstd IMPORTED_TARGET libzstd>=1.4)
+
+if(Zstd_FOUND)
+    target_compile_definitions(lammps PRIVATE -DLAMMPS_ZSTD)
+    target_link_libraries(lammps PRIVATE PkgConfig::Zstd)
+endif()

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_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}

cmake/Modules/Packages/KOKKOS.cmake

@@ -35,8 +35,8 @@ if(DOWNLOAD_KOKKOS)
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
   include(ExternalProject)
   ExternalProject_Add(kokkos_build
-    URL https://github.com/kokkos/kokkos/archive/3.1.00.tar.gz
-    URL_MD5 f638a6c786f748a602b26faa0e96ebab
+    URL https://github.com/kokkos/kokkos/archive/3.2.00.tar.gz
+    URL_MD5 81569170fe232e5e64ab074f7cca5e50
     CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
     BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
   )
@@ -50,10 +50,7 @@ if(DOWNLOAD_KOKKOS)
   target_link_libraries(lammps PRIVATE LAMMPS::KOKKOS)
   add_dependencies(LAMMPS::KOKKOS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 3.1)
-  if(NOT Kokkos_FOUND)
-    message(FATAL_ERROR "KOKKOS library version 3.1 or later not found, help CMake to find it by setting KOKKOS_LIBRARY, or set DOWNLOAD_KOKKOS=ON to download it")
-  endif()
+  find_package(Kokkos 3.2.00 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)
@@ -17,18 +17,18 @@ string(TOUPPER ${FFT} FFT)
 
 if(FFT STREQUAL "FFTW3")
   find_package(${FFTW} REQUIRED)
-  target_compile_definitions(lammps PUBLIC -DFFT_FFTW3)
-  target_link_libraries(lammps PUBLIC ${FFTW}::${FFTW})
-  if(FFTW3_OMP_LIBRARY OR FFTW3F_OMP_LIBRARY)
+  target_compile_definitions(lammps PRIVATE -DFFT_FFTW3)
+  target_link_libraries(lammps PRIVATE ${FFTW}::${FFTW})
+  if(FFTW3_OMP_LIBRARIES OR FFTW3F_OMP_LIBRARIES)
     option(FFT_FFTW_THREADS "Use threaded FFTW library" ON)
   else()
     option(FFT_FFTW_THREADS "Use threaded FFT library" OFF)
   endif()
 
   if(FFT_FFTW_THREADS)
-    if(FFTW3_OMP_LIBRARY OR FFTW3F_OMP_LIBRARY)
-	target_compile_definitions(lammps PRIVATE -DFFT_FFTW_THREADS)
-	target_link_libraries(lammps PRIVATE ${FFTW}::${FFTW}_OMP)
+    if(FFTW3_OMP_LIBRARIES OR FFTW3F_OMP_LIBRARIES)
+      target_compile_definitions(lammps PRIVATE -DFFT_FFTW_THREADS)
+      target_link_libraries(lammps PRIVATE ${FFTW}::${FFTW}_OMP)
     else()
       message(FATAL_ERROR "Need OpenMP enabled FFTW3 library for FFT_THREADS")
     endif()

cmake/Modules/Packages/LATTE.cmake

@@ -6,7 +6,7 @@ if(TARGET LATTE::latte)
   return()
 endif()
 
-find_package(LATTE)
+find_package(LATTE 1.2.2 CONFIG)
 if(LATTE_FOUND)
   set(DOWNLOAD_LATTE_DEFAULT OFF)
 else()
@@ -17,8 +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}
@@ -35,10 +35,6 @@ if(DOWNLOAD_LATTE)
   target_link_libraries(lammps PRIVATE LAMMPS::LATTE)
   add_dependencies(LAMMPS::LATTE latte_build)
 else()
-  find_package(LATTE)
-  if(NOT LATTE_FOUND)
-    message(FATAL_ERROR "LATTE library not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
-  endif()
-  # latte needs lapack
-  target_link_libraries(lammps PRIVATE LATTE::latte ${LAPACK_LIBRARIES})
+  find_package(LATTE 1.2.2 REQUIRED CONFIG)
+  target_link_libraries(lammps PRIVATE LATTE::latte)
 endif()

cmake/Modules/Packages/MSCG.cmake

@@ -38,7 +38,7 @@ if(DOWNLOAD_MSCG)
 else()
   find_package(MSCG)
   if(NOT MSCG_FOUND)
-    message(FATAL_ERROR "MSCG not found, help CMake to find it by setting MSCG_LIBRARY and MSCG_INCLUDE_DIRS, or set DOWNLOAD_MSCG=ON to download it")
+    message(FATAL_ERROR "MSCG not found, help CMake to find it by setting MSCG_LIBRARY and MSCG_INCLUDE_DIR, or set DOWNLOAD_MSCG=ON to download it")
   endif()
   target_link_libraries(lammps PRIVATE MSCG::MSCG)
 endif()

cmake/Modules/Packages/PYTHON.cmake

@@ -1,7 +1,7 @@
 if(CMAKE_VERSION VERSION_LESS 3.12)
   find_package(PythonLibs REQUIRED) # Deprecated since version 3.12
-  target_include_directories(lammps PRIVATE ${PYTHON_INCLUDE_DIR})
-  target_link_libraries(lammps PRIVATE ${PYTHON_LIBRARY})
+  target_include_directories(lammps PRIVATE ${PYTHON_INCLUDE_DIRS})
+  target_link_libraries(lammps PRIVATE ${PYTHON_LIBRARIES})
 else()
   find_package(Python REQUIRED COMPONENTS Development)
   target_link_libraries(lammps PRIVATE Python::Python)

cmake/Modules/Packages/USER-COLVARS.cmake

@@ -2,6 +2,8 @@ set(COLVARS_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars)
 
 file(GLOB COLVARS_SOURCES ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
 
+option(COLVARS_DEBUG "Debugging messages for Colvars (quite verbose)" OFF)
+
 # Build Lepton by default
 option(COLVARS_LEPTON "Build and link the Lepton library" ON)
 
@@ -16,11 +18,18 @@ if(COLVARS_LEPTON)
 endif()
 
 add_library(colvars STATIC ${COLVARS_SOURCES})
-target_compile_definitions(colvars PRIVATE -DLAMMPS_${LAMMPS_SIZES})
+target_compile_definitions(colvars PRIVATE -DCOLVARS_LAMMPS)
 set_target_properties(colvars PROPERTIES OUTPUT_NAME lammps_colvars${LAMMPS_MACHINE})
 target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
+# The line below is needed to locate math_eigen_impl.h
+target_include_directories(colvars PRIVATE ${LAMMPS_SOURCE_DIR})
 target_link_libraries(lammps PRIVATE colvars)
 
+if(COLVARS_DEBUG)
+  # Need to export the macro publicly to also affect the proxy
+  target_compile_definitions(colvars PUBLIC -DCOLVARS_DEBUG)
+endif()
+
 if(COLVARS_LEPTON)
   target_link_libraries(lammps PRIVATE lepton)
   target_compile_definitions(colvars PRIVATE -DLEPTON)

cmake/Modules/Packages/USER-H5MD.cmake

@@ -1,8 +1,5 @@
 enable_language(C)
 
-if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.12)
-  cmake_policy(SET CMP0074 NEW)
-endif()
 find_package(HDF5 REQUIRED)
 target_link_libraries(h5md PRIVATE ${HDF5_LIBRARIES})
 target_include_directories(h5md PUBLIC ${HDF5_INCLUDE_DIRS})

cmake/Modules/Packages/USER-INTEL.cmake

@@ -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

@@ -1,4 +1,5 @@
-set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
+set(MOLFILE_INCLUDE_DIR "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
+set(MOLFILE_INCLUDE_DIRS "${MOLFILE_INCLUDE_DIR}")
 add_library(molfile INTERFACE)
 target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
 # no need to link with -ldl on windows

cmake/Modules/Packages/USER-NETCDF.cmake

@@ -1,8 +1,7 @@
 # USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
 # NetCDF library enables dump style "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
-if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.12)
-  cmake_policy(SET CMP0074 NEW)
-endif()
+
+# may use NetCDF or PNetCDF with MPI, but must have NetCDF without
 if(NOT BUILD_MPI)
   find_package(NetCDF REQUIRED)
 else()

cmake/Modules/Packages/USER-PLUMED.cmake

@@ -55,8 +55,8 @@ if(DOWNLOAD_PLUMED)
   endif()
   include(ExternalProject)
   ExternalProject_Add(plumed_build
-    URL https://github.com/plumed/plumed2/releases/download/v2.6.0/plumed-src-2.6.0.tgz
-    URL_MD5 204d2edae58d9b10ba3ad460cad64191
+    URL https://github.com/plumed/plumed2/releases/download/v2.6.1/plumed-src-2.6.1.tgz
+    URL_MD5 89a9a450fc6025299fe16af235957163
     BUILD_IN_SOURCE 1
     CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
                                              ${CONFIGURE_REQUEST_PIC}

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

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)

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/iwyu/iwyu-extra-map.imp

@@ -0,0 +1,7 @@
+[
+  { include: [ "<bits/types/struct_rusage.h>", private, "<sys/resource.h>", public ] },
+  { include: [ "<bits/exception.h>", public, "<exception>", public ] },
+  { include: [ "@<Eigen/.*>", private, "<Eigen/Eigen>", public ] },
+  { include: [ "@<gtest/.*>", private, "\"gtest/gtest.h\"", public ] },
+  { include: [ "@<gmock/.*>", private, "\"gmock/gmock.h\"", public ] },
+]

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/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/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

@@ -2,8 +2,8 @@
 # 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-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
         USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC USER-MESODPD

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/.gitignore

@@ -1,6 +1,7 @@
 /old
 /html
 /html-offline
+/epub
 /latex
 /mathjax
 /spelling
@@ -10,3 +11,9 @@
 /Developer.pdf
 /doctrees
 /docenv
+/doxygen-warn.log
+/utils/sphinx-config/conf.py
+/doxygen/Doxyfile
+*.el
+/utils/sphinx-config/_static/mathjax
+/utils/sphinx-config/_static/polyfill.js

doc/Makefile

@@ -1,21 +1,35 @@
 # Makefile for LAMMPS documentation
 
-SHELL         = /bin/bash
-BUILDDIR      = ${CURDIR}
-RSTDIR        = $(BUILDDIR)/src
-VENV          = $(BUILDDIR)/docenv
-MATHJAX       = $(BUILDDIR)/mathjax
-TXT2RST       = $(VENV)/bin/txt2rst
-ANCHORCHECK   = $(VENV)/bin/rst_anchor_check
+SHELL          = /bin/bash
+HAS_BASH       = YES
+ifeq (,$(wildcard $(SHELL)))
+OSHELL         := $(SHELL)
+override SHELL = /bin/sh
+HAS_BASH       = NO
+endif
+BUILDDIR       = ${CURDIR}
+RSTDIR         = $(BUILDDIR)/src
+VENV           = $(BUILDDIR)/docenv
+TXT2RST        = $(VENV)/bin/txt2rst
+ANCHORCHECK    = $(VENV)/bin/rst_anchor_check
+SPHINXCONFIG   = $(BUILDDIR)/utils/sphinx-config
+MATHJAX        = $(SPHINXCONFIG)/_static/mathjax
+POLYFILL       = $(SPHINXCONFIG)/_static/polyfill.js
 
-PYTHON        = $(shell which python3)
+PYTHON         = $(shell which python3)
+DOXYGEN        = $(shell which doxygen)
 VIRTUALENV     = virtualenv
 HAS_PYTHON3    = NO
 HAS_VIRTUALENV = NO
+HAS_DOXYGEN    = NO
 HAS_PDFLATEX   = NO
 
 ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 0)
-HAS_PYTHON3 = YES
+HAS_PYTHON3    = YES
+endif
+
+ifeq ($(shell which doxygen >/dev/null 2>&1; echo $$?), 0)
+HAS_DOXYGEN    = YES
 endif
 
 ifeq ($(shell which virtualenv-3 >/dev/null 2>&1; echo $$?), 0)
@@ -33,16 +47,24 @@ HAS_PDFLATEX = YES
 endif
 
 
-SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
+#SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())') $(shell test -f $(BUILDDIR)/doxygen/xml/run.stamp && printf -- "-E")
 
-.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check
+# temporarily disable caching so that the hack for the sphinx-tabs extensions to get proper non-html output works
+SPHINXEXTRA = -E -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
+
+# grab list of sources from doxygen config file.
+# we only want to use explicitly listed files.
+DOXYFILES      = $(shell sed -n -e 's/\#.*$$//' -e '/^ *INPUT \+=/,/^[A-Z_]\+ \+=/p' doxygen/Doxyfile.in | sed -e 's/@LAMMPS_SOURCE_DIR@/..\/src/g' -e 's/\\//g' -e 's/ \+/ /' -e 's/[A-Z_]\+ \+= *\(YES\|NO\|\)//') 
+
+.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check xmlgen
 
 # ------------------------------------------
 
 help:
+	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@echo "Please use \`make <target>' where <target> is one of"
 	@echo "  html          create HTML doc pages in html dir"
-	@echo "  pdf           create Developer.pdf and Manual.pdf in this dir"
+	@echo "  pdf           create Manual.pdf in this dir"
 	@echo "  fetch         fetch HTML and PDF files from LAMMPS web site"
 	@echo "  epub          create ePUB format manual for e-book readers"
 	@echo "  mobi          convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
@@ -57,23 +79,33 @@ help:
 # ------------------------------------------
 
 clean-all: clean
-	rm -rf $(BUILDDIR)/docenv $(BUILDDIR)/doctrees $(BUILDDIR)/mathjax Manual.pdf Developer.pdf
+	rm -rf $(BUILDDIR)/docenv $(MATHJAX) $(BUILDDIR)/LAMMPS.mobi $(BUILDDIR)/LAMMPS.epub $(BUILDDIR)/Manual.pdf
 
 clean: clean-spelling
-	rm -rf html epub latex
+	rm -rf $(BUILDDIR)/html $(BUILDDIR)/epub $(BUILDDIR)/latex $(BUILDDIR)/doctrees $(BUILDDIR)/doxygen/xml $(BUILDDIR)/doxygen-warn.log $(BUILDDIR)/doxygen/Doxyfile $(SPHINXCONFIG)/conf.py
 
 clean-spelling:
-	rm -rf spelling
+	rm -rf $(BUILDDIR)/spelling
 
-html: $(ANCHORCHECK) $(MATHJAX)
+$(SPHINXCONFIG)/conf.py: $(SPHINXCONFIG)/conf.py.in
+	sed -e 's,@DOXYGEN_XML_DIR@,$(BUILDDIR)/doxygen/xml,g'   \
+	    -e 's,@LAMMPS_SOURCE_DIR@,$(BUILDDIR)/../src,g'    \
+	    -e 's,@LAMMPS_PYTHON_DIR@,$(BUILDDIR)/../python,g' \
+	    -e 's,@LAMMPS_DOC_DIR@,$(BUILDDIR),g' $< > $@
+
+html: xmlgen $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX) $(POLYFILL)
+	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
+	@$(MAKE) $(MFLAGS) -C graphviz all
 	@(\
-		. $(VENV)/bin/activate ;\
-		sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
+		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
+		ln -sf Manual.html html/index.html;\
+		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		echo "############################################" ;\
 		rst_anchor_check src/*.rst ;\
-		python utils/check-packages.py -s ../src -d src ;\
+		python $(BUILDDIR)/utils/check-packages.py -s ../src -d src ;\
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
-		python utils/check-styles.py -s ../src -d src ;\
+		python $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)
@@ -82,30 +114,30 @@ html: $(ANCHORCHECK) $(MATHJAX)
 	@rm -rf html/USER
 	@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/
 	@rm -rf html/PDF/.[sg]*
-	@mkdir -p html/_static/mathjax
-	@cp -r $(MATHJAX)/es5 html/_static/mathjax/
 	@echo "Build finished. The HTML pages are in doc/html."
 
-spelling: $(VENV) utils/sphinx-config/false_positives.txt
+spelling: xmlgen $(VENV) $(SPHINXCONFIG)/false_positives.txt
+	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@(\
-		. $(VENV)/bin/activate ;\
-		cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ; env PYTHONWARNINGS= \
-		sphinx-build -b spelling -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) spelling ;\
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
+		cp $(SPHINXCONFIG)/false_positives.txt $(RSTDIR)/ ; env PYTHONWARNINGS= \
+		sphinx-build -b spelling -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) spelling ;\
+		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		deactivate ;\
 	)
 	@echo "Spell check finished."
 
-epub: $(VENV)
+epub: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
+	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
+	@$(MAKE) $(MFLAGS) -C graphviz all
 	@mkdir -p epub/JPG
 	@rm -f LAMMPS.epub
-	@cp src/JPG/lammps-logo.png epub/
 	@cp src/JPG/*.* epub/JPG
 	@(\
 		. $(VENV)/bin/activate ;\
-		sphinx-build $(SPHINXEXTRA) -b epub -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
+		sphinx-build $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
+		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		deactivate ;\
 	)
 	@mv  epub/LAMMPS.epub .
@@ -117,18 +149,14 @@ mobi: epub
 	@ebook-convert LAMMPS.epub LAMMPS.mobi
 	@echo "Conversion finished. The MOBI manual file is created."
 
-pdf: $(ANCHORCHECK)
+pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
+	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
+	@$(MAKE) $(MFLAGS) -C graphviz all
 	@if [ "$(HAS_PDFLATEX)" == "NO" ] ; then echo "PDFLaTeX was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
 	@(\
-		cd src/Developer; \
-		pdflatex developer; \
-		pdflatex developer; \
-		mv developer.pdf ../../Developer.pdf; \
-		cd ../../; \
-	)
-	@(\
-		. $(VENV)/bin/activate ;\
-		sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
+		sphinx-build $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
+		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		echo "############################################" ;\
 		rst_anchor_check src/*.rst ;\
 		python utils/check-packages.py -s ../src -d src ;\
@@ -144,9 +172,9 @@ pdf: $(ANCHORCHECK)
 		mv tmp.tex LAMMPS.tex && \
 		sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
 		mv tmp.tex LAMMPS.tex && \
-		make && \
-		make && \
-		make && \
+		$(MAKE) $(MFLAGS) && \
+		$(MAKE) $(MFLAGS) && \
+		$(MAKE) $(MFLAGS) && \
 		mv LAMMPS.pdf ../Manual.pdf && \
 		cd ../;
 	@rm -rf latex/_sources
@@ -154,12 +182,11 @@ pdf: $(ANCHORCHECK)
 	@rm -rf latex/USER
 	@cp -r src/PDF latex/PDF
 	@rm -rf latex/PDF/.[sg]*
-	@echo "Build finished. Manual.pdf and Developer.pdf are in this directory."
+	@echo "Build finished. Manual.pdf is in this directory."
 
 fetch:
-	@rm -rf html_www Manual_www.pdf Developer_www.pdf
+	@rm -rf html_www Manual_www.pdf
 	@curl -s -o Manual_www.pdf http://lammps.sandia.gov/doc/Manual.pdf
-	@curl -s -o Developer_www.pdf http://lammps.sandia.gov/doc/Developer.pdf
 	@curl -s -o lammps-doc.tar.gz http://lammps.sandia.gov/tars/lammps-doc.tar.gz
 	@tar xzf lammps-doc.tar.gz
 	@rm -f lammps-doc.tar.gz
@@ -185,23 +212,33 @@ package_check : $(VENV)
 		deactivate ;\
 	)
 
+xmlgen : doxygen/xml/index.xml
+
+doxygen/Doxyfile: doxygen/Doxyfile.in
+	sed -e 's/@LAMMPS_SOURCE_DIR@/..\/..\/src/g' $< > $@
+
+doxygen/xml/index.xml : $(VENV) doxygen/Doxyfile $(DOXYFILES)
+	@(cd doxygen; $(DOXYGEN) Doxyfile && touch xml/run.stamp)
 # ------------------------------------------
 
 $(VENV):
-	@if [ "$(HAS_PYTHON3)" == "NO" ] ; then echo "Python3 was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
-	@if [ "$(HAS_VIRTUALENV)" == "NO" ] ; then echo "virtualenv was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
+	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
+	@if [ "$(HAS_PYTHON3)" == "NO" ] ; then echo "python3 was not found! Please see README for further instructions" 1>&2; exit 1; fi
+	@if [ "$(HAS_DOXYGEN)" == "NO" ] ; then echo "doxygen was not found! Please see README for further instructions" 1>&2; exit 1; fi
+	@if [ "$(HAS_VIRTUALENV)" == "NO" ] ; then echo "virtualenv was not found! Please see README for further instructions" 1>&2; exit 1; fi
 	@( \
 		$(VIRTUALENV) -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
 		pip install --upgrade pip; \
-		pip install Sphinx; \
-		pip install sphinxcontrib-spelling ;\
-		pip install breathe; \
+		pip install --use-feature=2020-resolver -r $(BUILDDIR)/utils/requirements.txt; \
 		deactivate;\
 	)
 
 $(MATHJAX):
-	@git clone --depth 1 https://github.com/mathjax/MathJax.git mathjax
+	@git clone --depth 1 https://github.com/mathjax/MathJax.git $@
+
+$(POLYFILL): $(MATHJAX)
+	@curl -s -o $@ "https://polyfill.io/v3/polyfill.min.js?features=es6"
 
 $(TXT2RST) $(ANCHORCHECK): $(VENV)
 	@( \

doc/README

@@ -1,97 +1,60 @@
 LAMMPS Documentation
 
-Depending on how you obtained LAMMPS, this directory has 2 or 3
-sub-directories and optionally 2 PDF files and an ePUB file:
+Depending on how you obtained LAMMPS and whether you have built
+the manual yourself, this directory has a varying number of
+sub-directories and files. Here is a list with descriptions:
 
-src             content files for LAMMPS documentation
-html            HTML version of the LAMMPS manual (see html/Manual.html)
-utils           utilities and settings for building the documentation
-Manual.pdf      large PDF version of entire manual
-Developer.pdf   small PDF with info about how LAMMPS is structured
-LAMMPS.epub     Manual in ePUB format
+README            this file
+src               content files for LAMMPS documentation
+html              HTML version of the LAMMPS manual (see html/Manual.html)
+utils             utilities and settings for building the documentation
+Manual.pdf        PDF version of entire manual
+Developer.pdf     PDF with info about how LAMMPS is structured
+LAMMPS.epub       Manual in ePUB format
+LAMMPS.mobi       Manual in MOBI (Kindle) format
+lammps.1          man page for the lammps command
+msi2lmp.1         man page for the msi2lmp command
+mathjax           code and fonts for rendering math in html
+doctree           temporary data
+docenv            python virtual environment for generating the manual
+doxygen           Doxygen configuration and output
+.gitignore        list of files and folders to be ignored by git
+doxygen-warn.log  logfile with warnings from running doxygen
 
-If you downloaded LAMMPS as a tarball from the web site, all these
-directories and files should be included.
+and:
 
-If you downloaded LAMMPS from the public SVN or Git repositories, then
-the HTML and PDF files are not included.  Instead you need to create
-them, in one of three ways:
+github-development-workflow.md   notes on the LAMMPS development workflow
+include-file-conventions.md      notes on LAMMPS' include file conventions
+documentation_conventions.md     notes on writing documentation for LAMMPS
+
+If you downloaded a LAMMPS tarball from lammps.sandia.gov, then the html
+folder and the PDF manual should be included. If you downloaded LAMMPS
+from GitHub then you either need to download them or build them.
 
 (a) You can "fetch" the current HTML and PDF files from the LAMMPS web
 site.  Just type "make fetch".  This should create a html_www dir and
-Manual_www.pdf/Developer_www.pdf files.  Note that if new LAMMPS
-features have been added more recently than the date of your version,
-the fetched documentation will include those changes (but your source
-code will not, unless you update your local repository).
+Manual_www.pdf/Developer_www.pdf files.  These files will always
+represent the latest published patch/development version of LAMMPS.
 
-(b) You can build the HTML and PDF files yourself, by typing "make
-html" or by "make pdf", respectively.  This requires various tools
-including the Python documentation processing tool Sphinx, which the
-build process will attempt to download and install on your system into
-a python virtual environment, if not already available.  The PDF file
-will require a working LaTeX installation with several add-on packages
-in addition to the Python/Sphinx setup.  See more details below.
+(b) You can build the HTML and PDF files yourself, by typing "make html"
+or by "make pdf", respectively.  This requires various tools and files.
+Some of them have to be installed (more on that below).  For the rest the
+build process will attempt to download and install into a python virtual
+environment and local folders.
 
 ----------------
 
-The generation of all documentation is managed by the Makefile in this
-dir.
+Installing prerequisites for the documentation build
 
-Options:
+To run the HTML documention build toolchain, python 3.x, doxygen, git,
+and virtualenv have to be installed.  Also internet access is initially
+required to download external files and tools.
 
-make html         # generate HTML in html dir using Sphinx
-make pdf          # generate 2 PDF files (Manual.pdf,Developer.pdf)
-                  #   in this dir via Sphinx and PDFLaTeX
-make fetch        # fetch HTML doc pages and 2 PDF files from web site
-                  #   as a tarball and unpack into html dir and 2 PDFs
-make epub         # generate LAMMPS.epub in ePUB format using Sphinx
-make clean        # remove intermediate RST files created by HTML build
-make clean-all    # remove entire build folder and any cached data
-
-----------------
-
-Installing prerequisites for HTML build
-
-To run the HTML documention build toolchain, Python 3 and virtualenv
-have to be installed.  Here are instructions for common setups:
-
-# Ubuntu
-
-sudo apt-get install python-virtualenv
-
-# Fedora (up to version 21)
-# Red Hat Enterprise Linux or CentOS (up to version 7.x)
-
-sudo yum install python3-virtualenv
-
-# Fedora (since version 22)
-
-sudo dnf install python3-virtualenv
-
-# MacOS X
-
-## Python 3
-
-Download the latest Python 3 MacOS X package from
-https://www.python.org and install it.  This will install both Python
-3 and pip3.
-
-## virtualenv
-
-Once Python 3 is installed, open a Terminal and type
-
-pip3 install virtualenv
-
-This will install virtualenv from the Python Package Index.
-
-----------------
-
-Installing prerequisites for PDF build
-
-Same as for HTML plus a compatible LaTeX installation with
-support for PDFLaTeX. Also the following LaTeX packages need
-to be installed (e.g. from texlive):
+Building the PDF format manual requires in addition a compatible LaTeX
+installation with support for PDFLaTeX and several add-on LaTeX packages
+installed.  This includes:
 - amsmath
+- anysize
 - babel
 - capt-of
 - cmap
@@ -105,24 +68,13 @@ to be installed (e.g. from texlive):
 - tabulary
 - upquote
 - wrapfig
+
+Building the EPUB format requires LaTeX installation with the same packages
+as for the PDF format plus the 'dvipng' command to convert the embedded math
+into images. The MOBI format is generated from the EPUB format file by using
+the tool 'ebook-convert' from the 'calibre' e-book management software
+(https://calibre-ebook.com).
 ----------------
 
-Installing prerequisites for epub build
-
-## ePUB
-
-Same as for HTML. This uses the same tools and configuration
-files as the HTML tree. The ePUB format conversion currently
-does not support processing mathematical expressions via MathJAX,
-so there will be limitations on some pages. For the time being
-until this is resolved, building and using the PDF format file
-is recommended instead.
-
-For converting the generated ePUB file to a mobi format file
-(for e-book readers like Kindle, that cannot read ePUB), you
-also need to have the 'ebook-convert' tool from the "calibre"
-software installed. http://calibre-ebook.com/
-You first create the ePUB file with 'make epub' and then do:
-
-ebook-convert LAMMPS.epub LAMMPS.mobi
-
+More details this can be found in the manual itself. The online
+version is at: https://lammps.sandia.gov/doc/Manual_build.html

doc/documentation_conventions.md

@@ -0,0 +1,93 @@
+# Outline of LAMMPS documentation file conventions
+
+This purpose of this document is to provide a point of reference
+for LAMMPS developers and contributors as to what conventions
+should be used to structure and format files in the LAMMPS manual.
+
+Last change: 2020-04-23
+
+## File format and tools
+
+In fall 2019, the LAMMPS documentation file format has changed from
+a home grown minimal markup designed to generate HTML format files
+from a mostly plain text format to using the reStructuredText file
+format.  For a transition period all files in the old .txt format
+were transparently converted to .rst and then processed.  The txt2rst
+tool is still included in the distribution to obtain an initial .rst
+file for integration into the manual.  Since the transition to
+reStructured text as source format, many of the artifacts or the
+translation have been removed though and parts of the documentation
+refactored and expanded to take advantage of the capabilities
+reStructuredText and associated tools.  The conversion from the
+source to the final formats (HTML, PDF, and optionally e-book
+reader formats ePUB and MOBI) is mostly automated and controlled
+by a Makefile in the `doc` folder. This makefile assumes that the
+processing is done on a Unix-like machine and Python 3.5 or later
+and a matching virtualenv module are available.  Additional Python
+packages (like the Sphinx tool and several extensions) are
+transparently installed into a virtual environment over the
+internet using the `pip` package manager.  Further requirements
+and details are discussed in the manual.
+
+## Work in progress
+
+The refactoring and improving of the documentation is an ongoing
+process, so statements in this document may not always be fully
+up-to-date.  If in doubt, contact the LAMMPS developers.
+
+## General structure
+
+The layout and formatting of added files should follow the example
+of the existing files.  Since those are directly derived from their
+former .txt format versions and the manual has been maintained in
+that format for many years, there is a large degree of consistency
+already, so comparision with similar files should give you a good
+idea what kind of information and sections are needed.
+
+## Formatting conventions
+
+Filenames, folders, paths, (shell) commands, definitions, makefile
+settings and similar should be formatted as "literals" with
+double backward quotes bracketing the item: \`\`path/to/some/file\`\`
+
+Keywords and options are formatted in italics:  \*option\*
+
+Mathematical expressions, equations, symbols are typeset using
+either a `.. math:`` block or the `:math:` role.
+
+Groups of shell commands or LAMMPS input script or C/C++ source
+code should be typeset into a `.. code-block::` section. A syntax
+highlighting extension for LAMMPS input scripts is provided, so
+`LAMMPS` can be used to indicate the language in the code block
+in addition to `bash`, `c`, or `python`.  When no syntax style
+is indicated, no syntax highlighting is performed.
+
+As an alternative, e.g. to typeset the syntax of file formats
+a `.. parsed-literal::` block can be used, which allows some
+formatting directives, which means that related characters need
+to be escaped with a preceding backslash: `\*`.
+
+Special remarks can be highlighted with a `.. note::` block and
+strong warnings can be put into a `.. warning::` block.
+
+## Required steps when adding a custom style to LAMMPS
+
+When adding a new style (e.g. pair style or a compute or a fix)
+or a new command, it is **required** to include the corresponding
+documentation.  Those are often new files that need to be added.
+In order to be included in the documentation, those new files
+need to be reference in a `.. toctree::` block.  Most of those
+use patterns with wildcards, so the addition will be automatic.
+However, those additions also need to be added to some lists of
+styles or commands.  The `make style\_check` command will perform
+a test and report any missing entries and list the affected files.
+Any references defined with `.. \_refname:` have to be unique
+across all documentation files and this can be checked for with
+`make anchor\_check`.  Finally, a spell-check should be done,
+which is triggered via `make spelling`.  Any offenses need to
+be corrected and false positives should be added to the file
+`utils/sphinx-config/false\_positives.txt`.
+
+## Required additional steps when adding a new package to LAMMPS
+
+TODO

doc/doxygen/.gitignore

@@ -0,0 +1 @@
+/xml

doc/doxygen/Doxyfile.in

@@ -0,0 +1,532 @@
+# Doxyfile 1.8.15 -*- makefile -*-
+
+DOXYFILE_ENCODING      = UTF-8
+PROJECT_NAME           = "LAMMPS Programmer's Guide"
+PROJECT_NUMBER         = "24 August 2020"
+PROJECT_BRIEF          = "Documentation of the LAMMPS library interface and Python wrapper"
+PROJECT_LOGO           = lammps-logo.png
+CREATE_SUBDIRS         = NO
+ALLOW_UNICODE_NAMES    = NO
+OUTPUT_LANGUAGE        = English
+OUTPUT_TEXT_DIRECTION  = LTR
+
+BRIEF_MEMBER_DESC      = YES
+REPEAT_BRIEF           = YES
+
+ALWAYS_DETAILED_SEC    = NO
+INLINE_INHERITED_MEMB  = NO
+FULL_PATH_NAMES        = NO
+INHERIT_DOCS           = YES
+TAB_SIZE               = 2
+
+# When enabled doxygen tries to link words that correspond to documented
+# classes, or namespaces to their corresponding documentation. Such a link can
+# be prevented in individual cases by putting a % sign in front of the word or
+# globally by setting AUTOLINK_SUPPORT to NO.
+# The default value is: YES.
+AUTOLINK_SUPPORT       = YES
+
+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
+# to include (a tag file for) the STL sources as input, then you should set this
+# tag to YES in order to let doxygen match functions declarations and
+# definitions whose arguments contain STL classes (e.g. func(std::string);
+# versus func(std::string) {}). This also make the inheritance and collaboration
+# diagrams that involve STL classes more complete and accurate.
+# The default value is: NO.
+
+BUILTIN_STL_SUPPORT    = YES
+IDL_PROPERTY_SUPPORT   = NO
+
+# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
+# cache is used to resolve symbols given their name and scope. Since this can be
+# an expensive process and often the same symbol appears multiple times in the
+# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
+# doxygen will become slower. If the cache is too large, memory is wasted. The
+# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
+# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
+# symbols. At the end of a run doxygen will report the cache usage and suggest
+# the optimal cache size from a speed point of view.
+# Minimum value: 0, maximum value: 9, default value: 0.
+
+LOOKUP_CACHE_SIZE      = 2
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in
+# documentation are documented, even if no documentation was available. Private
+# class members and static file members will be hidden unless the
+# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
+# Note: This will also disable the warnings about undocumented members that are
+# normally produced when WARNINGS is set to YES.
+# The default value is: NO.
+
+EXTRACT_ALL            = NO
+
+# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
+# be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PRIVATE        = YES
+
+# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
+# scope will be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PACKAGE        = YES
+
+# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be
+# included in the documentation.
+# The default value is: NO.
+
+EXTRACT_STATIC         = YES
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
+# locally in source files will be included in the documentation. If set to NO,
+# only classes defined in header files are included. Does not have any effect
+# for Java sources.
+# The default value is: YES.
+
+EXTRACT_LOCAL_CLASSES  = YES
+
+# If this flag is set to YES, the members of anonymous namespaces will be
+# extracted and appear in the documentation as a namespace called
+# 'anonymous_namespace{file}', where file will be replaced with the base name of
+# the file that contains the anonymous namespace. By default anonymous namespace
+# are hidden.
+# The default value is: NO.
+
+EXTRACT_ANON_NSPACES   = YES
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
+# undocumented members inside documented classes or files. If set to NO these
+# members will be included in the various overviews, but no documentation
+# section is generated. This option has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
+
+HIDE_UNDOC_MEMBERS     = YES
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy. If set
+# to NO, these classes will be included in the various overviews. This option
+# has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
+
+HIDE_UNDOC_CLASSES     = YES
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
+# (class|struct|union) declarations. If set to NO, these declarations will be
+# included in the documentation.
+# The default value is: NO.
+
+HIDE_FRIEND_COMPOUNDS  = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
+# documentation blocks found inside the body of a function. If set to NO, these
+# blocks will be appended to the function's detailed documentation block.
+# The default value is: NO.
+
+HIDE_IN_BODY_DOCS      = NO
+
+# The INTERNAL_DOCS tag determines if documentation that is typed after a
+# \internal command is included. If the tag is set to NO then the documentation
+# will be excluded. Set it to YES to include the internal documentation.
+# The default value is: NO.
+
+INTERNAL_DOCS          = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file
+# names in lower-case letters. If set to YES, upper-case letters are also
+# allowed. This is useful if you have classes or files whose names only differ
+# in case and if your file system supports case sensitive file names. Windows
+# and Mac users are advised to set this option to NO.
+# The default value is: system dependent.
+
+CASE_SENSE_NAMES       = YES
+
+# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
+# their full class and namespace scopes in the documentation. If set to YES, the
+# scope will be hidden.
+# The default value is: NO.
+
+HIDE_SCOPE_NAMES       = YES
+
+# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will
+# append additional text to a page's title, such as Class Reference. If set to
+# YES the compound reference will be hidden.
+# The default value is: NO.
+
+HIDE_COMPOUND_REFERENCE= NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
+# the files that are included by a file in the documentation of that file.
+# The default value is: YES.
+
+SHOW_INCLUDE_FILES     = NO
+
+# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
+# grouped member an include statement to the documentation, telling the reader
+# which file to include in order to use the member.
+# The default value is: NO.
+
+SHOW_GROUPED_MEMB_INC  = NO
+
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
+# files with double quotes in the documentation rather than with sharp brackets.
+# The default value is: NO.
+
+FORCE_LOCAL_INCLUDES   = NO
+
+# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
+# documentation for inline members.
+# The default value is: YES.
+
+INLINE_INFO            = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
+# (detailed) documentation of file and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order.
+# The default value is: YES.
+
+SORT_MEMBER_DOCS       = NO
+
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
+# descriptions of file, namespace and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order. Note that
+# this will also influence the order of the classes in the class list.
+# The default value is: NO.
+
+SORT_BRIEF_DOCS        = NO
+
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
+# (brief and detailed) documentation of class members so that constructors and
+# destructors are listed first. If set to NO the constructors will appear in the
+# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
+# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
+# member documentation.
+# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
+# detailed member documentation.
+# The default value is: NO.
+
+SORT_MEMBERS_CTORS_1ST = NO
+
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
+# of group names into alphabetical order. If set to NO the group names will
+# appear in their defined order.
+# The default value is: NO.
+
+SORT_GROUP_NAMES       = NO
+
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
+# fully-qualified names, including namespaces. If set to NO, the class list will
+# be sorted only by class name, not including the namespace part.
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
+# Note: This option applies only to the class list, not to the alphabetical
+# list.
+# The default value is: NO.
+
+SORT_BY_SCOPE_NAME     = NO
+
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
+# type resolution of all parameters of a function it will reject a match between
+# the prototype and the implementation of a member function even if there is
+# only one candidate or it is obvious which candidate to choose by doing a
+# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
+# accept a match between prototype and implementation in such cases.
+# The default value is: NO.
+
+STRICT_PROTO_MATCHING  = NO
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo
+# list. This list is created by putting \todo commands in the documentation.
+# The default value is: YES.
+
+GENERATE_TODOLIST      = YES
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test
+# list. This list is created by putting \test commands in the documentation.
+# The default value is: YES.
+
+GENERATE_TESTLIST      = YES
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug
+# list. This list is created by putting \bug commands in the documentation.
+# The default value is: YES.
+
+GENERATE_BUGLIST       = YES
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO)
+# the deprecated list. This list is created by putting \deprecated commands in
+# the documentation.
+# The default value is: YES.
+
+GENERATE_DEPRECATEDLIST= YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional documentation
+# sections, marked by \if <section_label> ... \endif and \cond <section_label>
+# ... \endcond blocks.
+
+ENABLED_SECTIONS       =
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
+# initial value of a variable or macro / define can have for it to appear in the
+# documentation. If the initializer consists of more lines than specified here
+# it will be hidden. Use a value of 0 to hide initializers completely. The
+# appearance of the value of individual variables and macros / defines can be
+# controlled using \showinitializer or \hideinitializer command in the
+# documentation regardless of this setting.
+# Minimum value: 0, maximum value: 10000, default value: 30.
+
+MAX_INITIALIZER_LINES  = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
+# the bottom of the documentation of classes and structs. If set to YES, the
+# list will mention the files that were used to generate the documentation.
+# The default value is: YES.
+
+SHOW_USED_FILES        = YES
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
+# will remove the Files entry from the Quick Index and from the Folder Tree View
+# (if specified).
+# The default value is: YES.
+
+SHOW_FILES             = NO
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
+# page. This will remove the Namespaces entry from the Quick Index and from the
+# Folder Tree View (if specified).
+# The default value is: YES.
+
+SHOW_NAMESPACES        = YES
+
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
+# popen()) the command command input-file, where command is the value of the
+# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
+# by doxygen. Whatever the program writes to standard output is used as the file
+# version. For an example see the documentation.
+
+FILE_VERSION_FILTER    =
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
+# by doxygen. The layout file controls the global structure of the generated
+# output files in an output format independent way. To create the layout file
+# that represents doxygen's defaults, run doxygen with the -l option. You can
+# optionally specify a file name after the option, if omitted DoxygenLayout.xml
+# will be used as the name of the layout file.
+#
+# Note that if you run doxygen from a directory containing a file called
+# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
+# tag is left empty.
+
+LAYOUT_FILE            =
+
+# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
+# the reference definitions. This must be a list of .bib files. The .bib
+# extension is automatically appended if omitted. This requires the bibtex tool
+# to be installed. See also https://en.wikipedia.org/wiki/BibTeX for more info.
+# For LaTeX the style of the bibliography can be controlled using
+# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
+# search path. See also \cite for info how to create references.
+
+CITE_BIB_FILES         =
+
+#---------------------------------------------------------------------------
+# Configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated to
+# standard output by doxygen. If QUIET is set to YES this implies that the
+# messages are off.
+# The default value is: NO.
+
+QUIET                  = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
+# this implies that the warnings are on.
+#
+# Tip: Turn warnings on while writing the documentation.
+# The default value is: YES.
+
+WARNINGS               = YES
+
+# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate
+# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
+# will automatically be disabled.
+# The default value is: YES.
+
+WARN_IF_UNDOCUMENTED   = YES
+
+# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as not documenting some parameters
+# in a documented function, or documenting parameters that don't exist or using
+# markup commands wrongly.
+# The default value is: YES.
+
+WARN_IF_DOC_ERROR      = YES
+
+# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
+# are documented, but have no documentation for their parameters or return
+# value. If set to NO, doxygen will only warn about wrong or incomplete
+# parameter documentation, but not about the absence of documentation. If
+# EXTRACT_ALL is set to YES then this flag will automatically be disabled.
+# The default value is: NO.
+
+WARN_NO_PARAMDOC       = YES
+
+# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when
+# a warning is encountered.
+# The default value is: NO.
+
+WARN_AS_ERROR          = NO
+
+# The WARN_FORMAT tag determines the format of the warning messages that doxygen
+# can produce. The string should contain the $file, $line, and $text tags, which
+# will be replaced by the file and line number from which the warning originated
+# and the warning text. Optionally the format may contain $version, which will
+# be replaced by the version of the file (if it could be obtained via
+# FILE_VERSION_FILTER)
+# The default value is: $file:$line: $text.
+
+WARN_FORMAT            = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning and error
+# messages should be written. If left blank the output is written to standard
+# error (stderr).
+
+WARN_LOGFILE           = "../doxygen-warn.log"
+
+#---------------------------------------------------------------------------
+# Configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag is used to specify the files and/or directories that contain
+# documented source files. You may enter file names like myfile.cpp or
+# directories like /usr/src/myproject. Separate the files or directories with
+# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
+# Note: If this tag is empty the current directory is searched.
+
+INPUT                  = @LAMMPS_SOURCE_DIR@/utils.cpp                 \
+                         @LAMMPS_SOURCE_DIR@/utils.h                   \
+                         @LAMMPS_SOURCE_DIR@/library.cpp               \
+                         @LAMMPS_SOURCE_DIR@/library.h                 \
+                         @LAMMPS_SOURCE_DIR@/lammps.cpp                \
+                         @LAMMPS_SOURCE_DIR@/lammps.h                  \
+                         @LAMMPS_SOURCE_DIR@/lmptype.h                 \
+                         @LAMMPS_SOURCE_DIR@/atom.cpp                  \
+                         @LAMMPS_SOURCE_DIR@/atom.h                    \
+                         @LAMMPS_SOURCE_DIR@/input.cpp                 \
+                         @LAMMPS_SOURCE_DIR@/input.h                   \
+                         @LAMMPS_SOURCE_DIR@/tokenizer.cpp             \
+                         @LAMMPS_SOURCE_DIR@/tokenizer.h               \
+                         @LAMMPS_SOURCE_DIR@/text_file_reader.cpp      \
+                         @LAMMPS_SOURCE_DIR@/text_file_reader.h        \
+                         @LAMMPS_SOURCE_DIR@/potential_file_reader.cpp \
+                         @LAMMPS_SOURCE_DIR@/potential_file_reader.h   \
+                         @LAMMPS_SOURCE_DIR@/my_page.cpp               \
+                         @LAMMPS_SOURCE_DIR@/my_page.h                 \
+                         @LAMMPS_SOURCE_DIR@/my_pool_chunk.cpp         \
+                         @LAMMPS_SOURCE_DIR@/my_pool_chunk.h           \
+                         @LAMMPS_SOURCE_DIR@/math_eigen.h              \
+
+# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
+# directories that are symbolic links (a Unix file system feature) are excluded
+# from the input.
+# The default value is: NO.
+
+EXCLUDE_SYMLINKS       = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to output
+#---------------------------------------------------------------------------
+
+GENERATE_HTML          = NO
+GENERATE_LATEX         = NO
+GENERATE_XML           = YES
+XML_OUTPUT             = xml
+XML_PROGRAMLISTING     = YES
+XML_NS_MEMB_FILE_SCOPE = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all
+# C-preprocessor directives found in the sources and include files.
+# The default value is: YES.
+
+#ENABLE_PREPROCESSING   = YES
+ENABLE_PREPROCESSING   = NO
+
+# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names
+# in the source code. If set to NO, only conditional compilation will be
+# performed. Macro expansion can be done in a controlled way by setting
+# EXPAND_ONLY_PREDEF to YES.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+MACRO_EXPANSION        = NO
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
+# the macro expansion is limited to the macros specified with the PREDEFINED and
+# EXPAND_AS_DEFINED tags.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+EXPAND_ONLY_PREDEF     = NO
+
+# If the SEARCH_INCLUDES tag is set to YES, the include files in the
+# INCLUDE_PATH will be searched if a #include is found.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+SEARCH_INCLUDES        = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that
+# contain include files that are not input files but should be processed by the
+# preprocessor.
+# This tag requires that the tag SEARCH_INCLUDES is set to YES.
+
+INCLUDE_PATH           =
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
+# patterns (like *.h and *.hpp) to filter out the header-files in the
+# directories. If left blank, the patterns specified with FILE_PATTERNS will be
+# used.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+INCLUDE_FILE_PATTERNS  =
+
+# The PREDEFINED tag can be used to specify one or more macro names that are
+# defined before the preprocessor is started (similar to the -D option of e.g.
+# gcc). The argument of the tag is a list of macros of the form: name or
+# name=definition (no spaces). If the definition and the "=" are omitted, "=1"
+# is assumed. To prevent a macro definition from being undefined via #undef or
+# recursively expanded use the := operator instead of the = operator.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+PREDEFINED             =
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
+# tag can be used to specify a list of macro names that should be expanded. The
+# macro definition that is found in the sources will be used. Use the PREDEFINED
+# tag if you want to use a different macro definition that overrules the
+# definition found in the source code.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+EXPAND_AS_DEFINED      =
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
+# remove all references to function-like macros that are alone on a line, have
+# an all uppercase name, and do not end with a semicolon. Such function macros
+# are typically used for boiler-plate code, and will confuse the parser if not
+# removed.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+SKIP_FUNCTION_MACROS   = YES
+

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
 
@@ -136,7 +136,8 @@ Here are some items to check:
     * string.h -> cstring
     * time.h -> ctime
     * Do NOT replace (as they are C++-11): `inttypes.h` and `stdint.h`.
-  * Code should follow the C++-98 standard. C++-11 is only accepted
+  * Code must follow the C++-11 standard. C++98-only is no longer accepted
+  * Code should use `nullptr` instead of `NULL` where applicable.
   in individual special purpose packages
   * indentation is 2 spaces per level
   * there should be NO tabs and no trailing whitespace (review the "checkstyle" test on pull requests)
@@ -145,6 +146,8 @@ Here are some items to check:
   Forward declarations should be used instead when possible.
   * iostreams should be avoided. LAMMPS uses stdio from the C-library.
   * use of STL in headers and class definitions should be avoided.
+  exception is <string>, but it won't need to be explicitly included
+  since pointers.h already includes it. so std::string can be used directly.
   * there MUST NOT be any "using namespace XXX;" statements in headers.
   * static class members should be avoided at all cost.
   * anything storing atom IDs should be using `tagint` and not `int`.
@@ -152,6 +155,8 @@ Here are some items to check:
   compiling LAMMPS with `-DLAMMPS_BIGBIG`.
   * when including both `lmptype.h` (and using defines or macros from it)
   and `mpi.h`, `lmptype.h` must be included first.
+  * see https://github.com/lammps/lammps/blob/master/doc/include-file-conventions.md
+  for general include file conventions and best practices
   * when pair styles are added, check if settings for flags like
   `single_enable`, `writedata`, `reinitflag`, `manybody_flag`
   and others are correctly set and supported.

doc/graphviz/.gitignore

@@ -0,0 +1,3 @@
+/*.png
+/*.svg
+/*.pdf

doc/graphviz/Makefile

@@ -0,0 +1,29 @@
+# Makefile for generating images with graphviz
+#
+BUILDDIR   = ${CURDIR}/..
+IMGDIR     = $(BUILDDIR)/src/JPG
+IMGSRC     = $(wildcard *.dot)
+IMGPNG     = $(IMGSRC:%.dot=$(IMGDIR)/%.png)
+
+HAS_DOT        = NO
+ifeq ($(shell which dot >/dev/null 2>&1; echo $$?), 0)
+HAS_DOT        = YES
+endif
+
+all:    $(IMGPNG)
+
+clean:
+	rm -f $(IMGSVG) $(IMGPDF) $(IMGPNG) *~
+
+ifeq ($(HAS_DOT),YES)
+$(IMGDIR)/%.png: %.dot
+	dot -Tpng -o $@ $<
+endif
+
+ifeq ($(HAS_DOT),NO)
+$(IMGDIR)/%.png: %.dot
+	@echo '###################################################'
+	@echo '# Need to install "graphviz" to regenerate graphs #'
+	@echo '###################################################'
+endif
+

doc/graphviz/lammps-classes.dot

@@ -0,0 +1,90 @@
+// LAMMPS Class topology
+digraph lammps {
+    rankdir="LR"
+    La [shape=circle label="LAMMPS"]
+    At [shape=box label="Atom" color=blue]
+    Ci [shape=box label="CiteMe"]
+    Co [shape=box label="Comm" color=blue]
+    Do [shape=box label="Domain" color=blue]
+    Er [shape=box label="Error" color=blue]
+    Fo [shape=box label="Force" color=blue]
+    Gr [shape=box label="Group" color=blue]
+    In [shape=box label="Input" color=blue]
+    Ko [shape=box label="KokkosLMP"]
+    Ak [shape=box label="AtomKK" color=blue]
+    Mk [shape=box label="MemoryKK" color=blue]
+    Me [shape=box label="Memory" color=blue]
+    Mo [shape=box label="Modify" color=blue]
+    Ne [shape=box label="Neighbor" color=blue]
+    Ou [shape=box label="Output" color=blue]
+    Py [shape=box label="Python" color=blue]
+    Up [shape=box label="Update" color=blue]
+    Un [shape=box label="Universe" color=blue]
+    Ti [shape=box label="Timer" color=blue]
+    Rg [label="Region" color=red]
+    Rb [shape=box label="RegionBlock"]
+    Rs [shape=box label="RegionSphere"]
+    Av [label="AtomVec" color=red]
+    It [label="Integrate" color=red]
+    Mi [label="Min" color=red]
+    Pa [label="Pair" color=red]
+    Bo [label="Bond" color=red]
+    An [label="Angle" color=red]
+    Di [label="Dihedral" color=red]
+    Im [label="Improper" color=red]
+    Ks [label="Kspace" color=red]
+    Du [label="Dump" color=red]
+    Fi [label="Fix" color=red]
+    Cp [label="Compute" color=red]
+    Th [label="Thermo"]
+    Va [label="Variable"]
+    Ew [shape=box label="Ewald"]
+    Pp [shape=box label="PPPM"]
+    Ff [label="FFT3d"]
+    Re [label="Remap"]
+    Gc [label="GridComm"]
+    Cb [shape=box label="CommBrick"]
+    Ct [shape=box label="CommTiled"]
+    Aa [shape=box label="AtomVecAtomic"]
+    Am [shape=box label="AtomVecMolecular"]
+    Lj [shape=box label="PairLJCut"]
+    Lo [shape=box label="PairLJCutOMP"]
+    Lg [shape=box label="PairLJCutGPU"]
+    Te [shape=box label="PairTersoff"]
+    Bh [shape=box label="BondHarmonic"]
+    Bf [shape=box label="BondFENE"]
+    Fa [shape=box label="FixAveTime"]
+    Fn [shape=box label="FixNVE"]
+    Fh [shape=box label="FixNH"]
+    Fp [shape=box label="FixNPT"]
+    Ft [shape=box label="FixNVT"]
+    Da [shape=box label="DumpAtom"]
+    Dc [shape=box label="DumpCustom"]
+    Dg [shape=box label="DumpCFG"]
+    Ve [shape=box label="Verlet"]
+    Rr [shape=box label="Respa"]
+    Po [shape=box label="PPPMOmp"]
+    La -> {At Ci Co Do Er Fo Gr In Ko Ak Mk Me Mo Ne Ou Py Ti Up Un} [penwidth=2]
+    Do -> {Rg} [penwidth=2]
+    Co -> {Cb Ct} [style=dashed penwidth=2]
+    Rg -> {Rb Rs} [style=dashed penwidth=2]
+    In -> Va [penwidth=2]
+    Mo -> {Fi Cp} [penwidth=2]
+    Fo -> {Pa Bo An Di Im Ks} [penwidth=2]
+    Ks -> {Ew Pp} [style=dashed penwidth=2]
+    Pp -> {Ff Re Gc} [penwidth=2]
+    Pp -> {Po} [style=dashed penwidth=2]
+    Up -> {It Mi} [penwidth=2]
+    It -> {Ve Rr} [style=dashed penwidth=2]
+    Ou -> {Du Th} [penwidth=2]
+    Du -> {Da Dc} [style=dashed penwidth=2]
+    Dc -> {Dg} [style=dashed penwidth=2]
+    At -> Av [penwidth=2]
+    Av -> {Aa Am} [style=dashed penwidth=2]
+    Pa -> {Lj Te} [style=dashed penwidth=2]
+    Lj -> {Lo Lg} [style=dashed penwidth=2]
+    Bo -> {Bh Bf} [style=dashed penwidth=2]
+    Fi -> {Fa Fn Fh} [style=dashed penwidth=2]
+    Fh -> {Fp Ft} [style=dashed penwidth=2]
+}
+

doc/include-file-conventions.md

@@ -3,7 +3,7 @@
 This purpose of this document is to provide a point of reference
 for LAMMPS developers and contributors as to what include files
 and definitions to put where into LAMMPS source.
-Last change 2019-07-05
+Last change 2020-08-31
 
 ## Table of Contents
 
@@ -65,7 +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
@@ -91,29 +91,31 @@ statements should follow the "include what you use" principle.
 
 Include files should be included in this order:
 * the header matching the implementation (`some_class.h` for file `some_class.cpp`)
-* mpi.h
-* system and library headers (anything that is using angular brackets; C-library headers first, then C++)
+* mpi.h  (only if needed)
 * LAMMPS local headers (preferably in alphabetical order)
+* system and library headers (anything that is using angular brackets; preferably in alphabetical order)
+* conditional include statements (i.e. anything bracketed with ifdefs)
 
 ### Special Cases and Exceptions
 
 #### pointers.h
 
-The `pointer.h` header file also includes `cstdio` and `lmptype.h`
-(and through it `stdint.h`, `intttypes.h`, cstdlib, and `climits`).
+The `pointer.h` header file also includes (in this order) `lmptype.h`,
+`mpi.h`, `cstddef`, `cstdio`, `string`, `utils.h`, and `fmt/format.h`
+and through `lmptype.h` indirectly also `climits`, `cstdlib`, `cinttypes`.
 This means any header including `pointers.h` can assume that `FILE`,
-`NULL`, `INT_MAX` are defined.
+`NULL`, `INT_MAX` are defined, and the may freely use the std::string
+for arguments. Corresponding implementation files do not need to include
+those headers.
 
 ## Tools
 
 The [Include What You Use tool](https://include-what-you-use.org/)
 can be used to provide supporting information about compliance with
-the rules listed here.  There are some limitations and the IWYU tool
-may give incorrect advice.  The tools is activated by setting the
-CMake variable `CMAKE_CXX_INCLUDE_WHAT_YOU_USE` variable to the
-path of the `include-what-you-use` command.  When activated, the
-tool will be run after each compilation and provide suggestions for
-which include files should be added or removed.
+the rules listed here.  Through setting `-DENABLE_IWYU=on` when running
+CMake, a custom build target is added that will enable recording
+the compilation commands and then run the `iwyu_tool` using the
+recorded compilation commands information when typing `make iwyu`.
 
 ## Legacy Code
 

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "5 May 2020" "2020-05-5"
+.TH LAMMPS "18 September 2020" "2020-09-18"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/src/Build_basics.rst

@@ -32,74 +32,80 @@ LAMMPS are also written with support for shared memory parallelization
 using the `OpenMP <https://en.wikipedia.org/wiki/OpenMP>`_ threading
 standard. A more detailed discussion of that is below.
 
-**CMake build**\ :
+.. tabs::
 
-.. code-block:: bash
+   .. tab:: CMake build
 
-   -D BUILD_MPI=value        # yes or no, default is yes if CMake finds MPI, else no
-   -D BUILD_OMP=value        # yes or no, default is yes if a compatible compiler is detected
-   -D LAMMPS_MACHINE=name    # name = mpi, serial, mybox, titan, laptop, etc
-                             # no default value
+      .. code-block:: bash
 
-The executable created by CMake (after running make) is named ``lmp`` unless
-the ``LAMMPS_MACHINE`` option is set.  When setting ``LAMMPS_MACHINE=name``
-the executable will be called ``lmp_name``.  Using ``BUILD_MPI=no`` will
-enforce building a serial executable using the MPI STUBS library.
+         -D BUILD_MPI=value        # yes or no, default is yes if CMake finds MPI, else no
+         -D BUILD_OMP=value        # yes or no, default is yes if a compatible compiler is detected
+         -D LAMMPS_MACHINE=name    # name = mpi, serial, mybox, titan, laptop, etc
+                                   # no default value
 
-**Traditional make**\ :
+      The executable created by CMake (after running make) is named
+      ``lmp`` unless the ``LAMMPS_MACHINE`` option is set.  When setting
+      ``LAMMPS_MACHINE=name`` the executable will be called
+      ``lmp_name``.  Using ``BUILD_MPI=no`` will enforce building a
+      serial executable using the MPI STUBS library.
 
-The build with traditional makefiles has to be done inside the source folder ``src``.
+   .. tab:: Traditional make
 
-.. code-block:: bash
+      The build with traditional makefiles has to be done inside the source folder ``src``.
 
-   make mpi                # parallel build, produces lmp_mpi using Makefile.mpi
-   make serial             # serial build, produces lmp_serial using Makefile/serial
-   make mybox              # uses Makefile.mybox to produce lmp_mybox
+      .. code-block:: bash
 
-Any ``make machine`` command will look up the make settings from a file
-``Makefile.machine`` in the folder ``src/MAKE`` or one of its
-sub-directories ``MINE``, ``MACHINES``, or ``OPTIONS``, create a folder
-``Obj_machine`` with all objects and generated files and an executable
-called ``lmp_machine``\ .  The standard parallel build with ``make mpi``
-assumes a standard MPI installation with MPI compiler wrappers where all
-necessary compiler and linker flags to get access and link with the
-suitable MPI headers and libraries are set by the wrapper programs.  For
-other cases or the serial build, you have to adjust the make file
-variables ``MPI_INC``, ``MPI_PATH``, ``MPI_LIB`` as well as ``CC`` and
-``LINK``\ .  To enable OpenMP threading usually a compiler specific flag
-needs to be added to the compile and link commands.  For the GNU
-compilers, this is ``-fopenmp``\ , which can be added to the ``CC`` and
-``LINK`` makefile variables.
+         make mpi                # parallel build, produces lmp_mpi using Makefile.mpi
+         make serial             # serial build, produces lmp_serial using Makefile/serial
+         make mybox              # uses Makefile.mybox to produce lmp_mybox
 
-For the serial build the following make variables are set (see src/MAKE/Makefile.serial):
+      Any ``make machine`` command will look up the make settings from a
+      file ``Makefile.machine`` in the folder ``src/MAKE`` or one of its
+      sub-directories ``MINE``, ``MACHINES``, or ``OPTIONS``, create a
+      folder ``Obj_machine`` with all objects and generated files and an
+      executable called ``lmp_machine``\ .  The standard parallel build
+      with ``make mpi`` assumes a standard MPI installation with MPI
+      compiler wrappers where all necessary compiler and linker flags to
+      get access and link with the suitable MPI headers and libraries
+      are set by the wrapper programs.  For other cases or the serial
+      build, you have to adjust the make file variables ``MPI_INC``,
+      ``MPI_PATH``, ``MPI_LIB`` as well as ``CC`` and ``LINK``\ .  To
+      enable OpenMP threading usually a compiler specific flag needs to
+      be added to the compile and link commands.  For the GNU compilers,
+      this is ``-fopenmp``\ , which can be added to the ``CC`` and
+      ``LINK`` makefile variables.
 
-.. code-block:: make
+      For the serial build the following make variables are set (see src/MAKE/Makefile.serial):
 
-   CC =            g++
-   LINK =          g++
-   MPI_INC =       -I../STUBS
-   MPI_PATH =      -L../STUBS
-   MPI_LIB =       -lmpi_stubs
+      .. code-block:: make
 
-You also need to build the STUBS library for your platform before making
-LAMMPS itself.  A ``make serial`` build does this for you automatically,
-otherwise, type ``make mpi-stubs`` from the src directory, or ``make``
-from the ``src/STUBS`` dir.  If the build fails, you may need to edit
-the ``STUBS/Makefile`` for your platform.  The stubs library does not
-provide MPI/IO functions required by some LAMMPS packages,
-e.g. ``MPIIO`` or ``USER-LB``, and thus is not compatible with those
-packages.
+         CC =            g++
+         LINK =          g++
+         MPI_INC =       -I../STUBS
+         MPI_PATH =      -L../STUBS
+         MPI_LIB =       -lmpi_stubs
 
-.. note::
+      You also need to build the STUBS library for your platform before
+      making LAMMPS itself.  A ``make serial`` build does this for you
+      automatically, otherwise, type ``make mpi-stubs`` from the src
+      directory, or ``make`` from the ``src/STUBS`` dir.  If the build
+      fails, you may need to edit the ``STUBS/Makefile`` for your
+      platform.  The stubs library does not provide MPI/IO functions
+      required by some LAMMPS packages, e.g. ``MPIIO`` or ``USER-LB``,
+      and thus is not compatible with those packages.
 
-   The file ``src/STUBS/mpi.c`` provides a CPU timer function called
-   ``MPI_Wtime()`` that calls ``gettimeofday()``.  If your operating system
-   does not support ``gettimeofday()``, you will need to insert code to
-   call another timer.  Note that the ANSI-standard function ``clock()``
-   rolls over after an hour or so, and is therefore insufficient for
-   timing long LAMMPS simulations.
+      .. note::
 
-**MPI and OpenMP support info**\ :
+         The file ``src/STUBS/mpi.c`` provides a CPU timer function
+         called ``MPI_Wtime()`` that calls ``gettimeofday()``.  If your
+         operating system does not support ``gettimeofday()``, you will
+         need to insert code to call another timer.  Note that the
+         ANSI-standard function ``clock()`` rolls over after an hour or
+         so, and is therefore insufficient for timing long LAMMPS
+         simulations.
+
+MPI and OpenMP support in LAMMPS
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 If you are installing MPI yourself to build a parallel LAMMPS
 executable, we recommend either MPICH or OpenMPI which are regularly
@@ -115,12 +121,12 @@ self-installed MPICH or OpenMPI, so you should study the provided
 documentation to find out how to build and link with it.
 
 The majority of OpenMP (threading) support in LAMMPS is provided by the
-``USER-OMP`` package; see the :doc:`Speed omp <Speed_omp>` doc page for
-details. The ``USER-INTEL`` package also includes OpenMP threading (it
-is compatible with ``USER-OMP`` and will usually fall back on styles
-from that package, if a ``USER-INTEL`` does not exist) and adds
-vectorization support when compiled with compatible compilers, in
-particular the Intel compilers on top of OpenMP. Also, the ``KOKKOS``
+``USER-OMP`` package; see the :doc:`Speed_omp`
+page for details. The ``USER-INTEL`` package also includes OpenMP
+threading (it is compatible with ``USER-OMP`` and will usually fall
+back on styles from that package, if a ``USER-INTEL`` does not exist)
+and adds vectorization support when compiled with compatible compilers,
+in particular the Intel compilers on top of OpenMP. Also, the ``KOKKOS``
 package can be compiled to include OpenMP threading.
 
 In addition, there are a few commands in LAMMPS that have native OpenMP
@@ -145,18 +151,19 @@ please refer to its documentation.
 
 .. _default-none-issues:
 
-**OpenMP Compiler compatibility info**\ :
+OpenMP Compiler compatibility
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Some compilers do not fully support the ``default(none)`` directive
-and others (e.g. GCC version 9 and beyond, Clang version 10 and later)
-may implement strict OpenMP 4.0 and later semantics, which are incompatible
+Some compilers do not fully support the ``default(none)`` directive and
+others (e.g. GCC version 9 and beyond, Clang version 10 and later) may
+implement strict OpenMP 4.0 and later semantics, which are incompatible
 with the OpenMP 3.1 semantics used in LAMMPS for maximal compatibility
 with compiler versions in use.  If compilation with OpenMP enabled fails
 because of your compiler requiring strict OpenMP 4.0 semantic, you can
-change the behavior by adding ``-D LAMMPS_OMP_COMPAT=4`` to the ``LMP_INC``
-variable in your makefile, or add it to the command line while configuring
-with CMake. CMake will detect the suitable setting for the GNU, Clang,
-and Intel compilers.
+change the behavior by adding ``-D LAMMPS_OMP_COMPAT=4`` to the
+``LMP_INC`` variable in your makefile, or add it to the command line
+while configuring with CMake. CMake will detect the suitable setting for
+the GNU, Clang, and Intel compilers.
 
 ----------
 
@@ -185,132 +192,139 @@ for their compile/link environments, you can often access different
 compilers by simply loading the appropriate module before building
 LAMMPS.
 
-**CMake build**\ :
+.. tabs::
 
-By default CMake will use a compiler it finds according to internal
-preferences and it will add optimization flags appropriate to that
-compiler and any :doc:`accelerator packages <Speed_packages>` you have
-included in the build.
+   .. tab:: CMake 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:
+      By default CMake will use the compiler it finds according to
+      internal preferences and it will add optimization flags
+      appropriate to that compiler and any :doc:`accelerator packages
+      <Speed_packages>` you have included in the build.  CMake will
+      check if the detected or selected compiler is compatible with the
+      C++ support requirements of LAMMPS and stop with an error, if this
+      is not the case.
 
-.. code-block:: bash
+      You can tell CMake to look for a specific compiler with setting
+      CMake 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:
 
-   -D CMAKE_CXX_COMPILER=name            # name of C++ compiler
-   -D CMAKE_C_COMPILER=name              # name of C compiler
-   -D CMAKE_Fortran_COMPILER=name        # name of Fortran compiler
+      .. code-block:: bash
 
-   -D CMAKE_CXX_FLAGS=string             # flags to use with C++ compiler
-   -D CMAKE_C_FLAGS=string               # flags to use with C compiler
-   -D CMAKE_Fortran_FLAGS=string         # flags to use with Fortran compiler
+         -D CMAKE_CXX_COMPILER=name            # name of C++ compiler
+         -D CMAKE_C_COMPILER=name              # name of C compiler
+         -D CMAKE_Fortran_COMPILER=name        # name of Fortran compiler
 
-A few example command lines are:
+         -D CMAKE_CXX_FLAGS=string             # flags to use with C++ compiler
+         -D CMAKE_C_FLAGS=string               # flags to use with C compiler
+         -D CMAKE_Fortran_FLAGS=string         # flags to use with Fortran compiler
 
-.. code-block:: bash
+      A few example command lines are:
 
-   # Building with GNU Compilers:
-   cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
-   # Building with Intel Compilers:
-   cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
-   # Building with LLVM/Clang Compilers:
-   cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
+      .. code-block:: bash
 
-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 
+         # Building with GNU Compilers:
+         cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
+         # Building with Intel Compilers:
+         cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
+         # Building with LLVM/Clang Compilers:
+         cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
 
-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=``.
+      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 compiler
+      toolchain to the Intel compilers.
 
-.. note::
+      In addition you can set ``CMAKE_TUNE_FLAGS`` to specifically add
+      compiler flags to tune for optimal performance on given hosts. By
+      default this variable is empty.
 
-   When the cmake command completes, it prints a summary to the screen
-   which compilers it is using and what flags and settings will be used
-   for the  compilation.  Note that if the top-level compiler is mpicxx,
-   it is simply a wrapper on a real compiler.  The underlying compiler
-   info is what CMake will try to determine and report.  You should check
-   to confirm you are using the compiler and optimization flags you want.
+      .. note::
 
-**Makefile.machine settings for traditional make**\ :
+         When the cmake command completes, it prints a summary to the
+         screen which compilers it is using and what flags and settings
+         will be used for the compilation.  Note that if the top-level
+         compiler is mpicxx, it is simply a wrapper on a real compiler.
+         The underlying compiler info is what CMake will try to
+         determine and report.  You should check to confirm you are
+         using the compiler and optimization flags you want.
 
-The "compiler/linker settings" section of a Makefile.machine lists
-compiler and linker settings for your C++ compiler, including
-optimization flags.  For a parallel build it is recommended to use
-``mpicxx`` or ``mpiCC``, since these compiler wrappers will include a
-variety of settings appropriate for your MPI installation and thus
-avoiding the guesswork of finding the right flags.
+   .. tab:: Makefile.machine settings for traditional make
 
-Parallel build (see ``src/MAKE/Makefile.mpi``):
+      The "compiler/linker settings" section of a Makefile.machine lists
+      compiler and linker settings for your C++ compiler, including
+      optimization flags.  For a parallel build it is recommended to use
+      ``mpicxx`` or ``mpiCC``, since these compiler wrappers will
+      include a variety of settings appropriate for your MPI
+      installation and thus avoiding the guesswork of finding the right
+      flags.
 
-.. code-block:: bash
+      Parallel build (see ``src/MAKE/Makefile.mpi``):
 
-   CC =            mpicxx
-   CCFLAGS =       -g -O3
-   LINK =          mpicxx
-   LINKFLAGS =     -g -O
+      .. code-block:: bash
 
-Serial build with GNU gcc (see ``src/MAKE/Makefile.serial``):
+         CC =            mpicxx
+         CCFLAGS =       -g -O3
+         LINK =          mpicxx
+         LINKFLAGS =     -g -O
 
-.. code-block:: make
+      Serial build with GNU gcc (see ``src/MAKE/Makefile.serial``):
 
-   CC =            g++
-   CCFLAGS =       -g -O3
-   LINK =          g++
-   LINKFLAGS =     -g -O
+      .. code-block:: make
 
+         CC =            g++
+         CCFLAGS =       -g -O3
+         LINK =          g++
+         LINKFLAGS =     -g -O
 
-.. note::
+      .. note::
 
-   If compilation stops with a message like the following:
+         If compilation stops with a message like the following:
 
-   .. code-block::
+         .. code-block::
 
-      g++ -g -O3  -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64    -I../STUBS     -c ../main.cpp
-      In file included from ../pointers.h:24:0,
-                 from ../input.h:17,
-                 from ../main.cpp:16:
-      ../lmptype.h:34:2: error: #error LAMMPS requires a C++11 (or later) compliant compiler. Enable C++11 compatibility or upgrade the compiler.
+            g++ -g -O3  -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64    -I../STUBS     -c ../main.cpp
+            In file included from ../pointers.h:24:0,
+                       from ../input.h:17,
+                       from ../main.cpp:16:
+            ../lmptype.h:34:2: error: #error LAMMPS requires a C++11 (or later) compliant compiler. Enable C++11 compatibility or upgrade the compiler.
 
-   then you have either an unsupported (old) compiler or you have to
-   turn on C++11 mode.  The latter applies to GCC 4.8.x shipped with
-   RHEL 7.x and CentOS 7.x.  For those compilers, you need to add the
-   ``-std=c++11`` flag.  Otherwise, you would have to install a newer
-   compiler that supports C++11; either as a binary package or through
-   compiling from source.
+         then you have either an unsupported (old) compiler or you have
+         to turn on C++11 mode.  The latter applies to GCC 4.8.x shipped
+         with RHEL 7.x and CentOS 7.x.  For those compilers, you need to
+         add the ``-std=c++11`` flag.  Otherwise, you would have to
+         install a newer compiler that supports C++11; either as a
+         binary package or through compiling from source.
 
-If you build LAMMPS with any :doc:`accelerator packages
-<Speed_packages>` included, there may be specific optimization flags
-that are either required or recommended to enable required features and
-to achieve optimal performance.  You need to include these in the
-CCFLAGS and LINKFLAGS settings above.  For details, see the individual
-package doc pages listed on the :doc:`Speed packages <Speed_packages>`
-doc page.  Or examine these files in the src/MAKE/OPTIONS directory.
-They correspond to each of the 5 accelerator packages and their hardware
-variants:
+         If you build LAMMPS with any :doc:`Speed_packages` included,
+         there may be specific compiler or linker flags that are either
+         required or recommended to enable required features and to
+         achieve optimal performance.  You need to include these in the
+         CCFLAGS and LINKFLAGS settings above.  For details, see the
+         individual package doc pages listed on the
+         :doc:`Speed_packages` page.  Or examine these files in the
+         src/MAKE/OPTIONS directory.  They correspond to each of the 5
+         accelerator packages and their hardware variants:
 
-.. code-block:: bash
+         .. code-block:: bash
 
-   Makefile.opt                   # OPT package
-   Makefile.omp                   # USER-OMP package
-   Makefile.intel_cpu             # USER-INTEL package for CPUs
-   Makefile.intel_coprocessor     # USER-INTEL package for KNLs
-   Makefile.gpu                   # GPU package
-   Makefile.kokkos_cuda_mpi       # KOKKOS package for GPUs
-   Makefile.kokkos_omp            # KOKKOS package for CPUs (OpenMP)
-   Makefile.kokkos_phi            # KOKKOS package for KNLs (OpenMP)
+            Makefile.opt                   # OPT package
+            Makefile.omp                   # USER-OMP package
+            Makefile.intel_cpu             # USER-INTEL package for CPUs
+            Makefile.intel_coprocessor     # USER-INTEL package for KNLs
+            Makefile.gpu                   # GPU package
+            Makefile.kokkos_cuda_mpi       # KOKKOS package for GPUs
+            Makefile.kokkos_omp            # KOKKOS package for CPUs (OpenMP)
+            Makefile.kokkos_phi            # KOKKOS package for KNLs (OpenMP)
 
 ----------
 
@@ -329,50 +343,56 @@ page for more info on coupling LAMMPS to other codes.  See the
 :doc:`Python <Python_head>` doc page for more info on wrapping and
 running LAMMPS from Python via its library interface.
 
-**CMake build**\ :
+.. tabs::
 
-For CMake builds, you can select through setting CMake variables between
-building a shared or a static LAMMPS library and what kind of suffix is
-added to them (in case you want to concurrently install multiple variants
-of binaries with different settings). If none are set, defaults are applied.
+   .. tab:: CMake build
 
-.. code-block:: bash
+      For CMake builds, you can select through setting CMake variables
+      between building a shared or a static LAMMPS library and what kind
+      of suffix is added to them (in case you want to concurrently
+      install multiple variants of binaries with different settings). If
+      none are set, defaults are applied.
 
-   -D BUILD_SHARED_LIBS=value   # yes or no (default)
-   -D LAMMPS_MACHINE=name       # name = mpi, serial, mybox, titan, laptop, etc
-                                # no default value
+      .. code-block:: bash
 
-The compilation will always produce a LAMMPS library and an executable
-linked to it.  By default this will be a static library named
-``liblammps.a`` and an executable named ``lmp`` Setting
-``BUILD_SHARED_LIBS=yes`` will instead produce a shared library called
-``liblammps.so`` (or ``liblammps.dylib`` or ``liblammps.dll`` depending
-on the platform) If ``LAMMPS_MACHINE=name`` is set in addition, the name
-of the generated libraries will be changed to either
-``liblammps_name.a`` or ``liblammps_name.so``\ , respectively and the
-executable will be called ``lmp_name``.
+         -D BUILD_SHARED_LIBS=value   # yes or no (default)
+         -D LAMMPS_MACHINE=name       # name = mpi, serial, mybox, titan, laptop, etc
+                                      # no default value
 
-**Traditional make**\ :
+      The compilation will always produce a LAMMPS library and an
+      executable linked to it.  By default this will be a static library
+      named ``liblammps.a`` and an executable named ``lmp`` Setting
+      ``BUILD_SHARED_LIBS=yes`` will instead produce a shared library
+      called ``liblammps.so`` (or ``liblammps.dylib`` or
+      ``liblammps.dll`` depending on the platform) If
+      ``LAMMPS_MACHINE=name`` is set in addition, the name of the
+      generated libraries will be changed to either ``liblammps_name.a``
+      or ``liblammps_name.so``\ , respectively and the executable will
+      be called ``lmp_name``.
 
-With the traditional makefile based build process, the choice of
-the generated executable or library depends on the "mode" setting.
-Several options are available and ``mode=static`` is the default.
+   .. tab:: Traditional make
 
-.. code-block:: bash
+      With the traditional makefile based build process, the choice of
+      the generated executable or library depends on the "mode" setting.
+      Several options are available and ``mode=static`` is the default.
 
-   make machine               # build LAMMPS executable lmp_machine
-   make mode=static machine   # same as "make machine"
-   make mode=shared machine   # build LAMMPS shared lib liblammps_machine.so instead
+      .. code-block:: bash
 
-The "static" build will generate a static library called
-``liblammps_machine.a`` and an executable named ``lmp_machine``\ , while
-the "shared" build will generate a shared library
-``liblammps_machine.so`` instead and ``lmp_machine`` will be linked to
-it.  The build step will also create generic soft links, named
-``liblammps.a`` and ``liblammps.so``\ , which point to the specific
-``liblammps_machine.a/so`` files.
+         make machine               # build LAMMPS executable lmp_machine
+         make mode=static machine   # same as "make machine"
+         make mode=shared machine   # build LAMMPS shared lib liblammps_machine.so instead
 
-**CMake and make info**\ :
+      The "static" build will generate a static library called
+      ``liblammps_machine.a`` and an executable named ``lmp_machine``\ ,
+      while the "shared" build will generate a shared library
+      ``liblammps_machine.so`` instead and ``lmp_machine`` will be
+      linked to it.  The build step will also create generic soft links,
+      named ``liblammps.a`` and ``liblammps.so``\ , which point to the
+      specific ``liblammps_machine.a/so`` files.
+
+
+Additional information
+^^^^^^^^^^^^^^^^^^^^^^
 
 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
@@ -418,7 +438,7 @@ recommended to ensure the integrity of the system software installation.
 
 .. _debug:
 
-Excluding or removing debug support
+Including or removing debug support
 -----------------------------------
 
 By default the compilation settings will include the *-g* flag which
@@ -460,9 +480,10 @@ python packages are installed into that virtual environment via the pip
 tool.  The actual translation is then done via make commands.
 
 .. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
-.. _sphinx: https://sphinx-doc.org
+.. _sphinx: https://www.sphinx-doc.org
 
-**Documentation make option**\ :
+Documentation makefile options
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The following make commands can be issued in the doc folder of the
 LAMMPS source distribution.
@@ -470,7 +491,7 @@ LAMMPS source distribution.
 .. code-block:: bash
 
   make html          # create HTML doc pages in html directory
-  make pdf           # create Developer.pdf and Manual.pdf in this directory
+  make pdf           # create Manual.pdf in this directory
   make fetch         # fetch HTML and PDF files from LAMMPS web site
   make clean         # remove all intermediate files
   make clean-all     # reset the entire doc build environment
@@ -489,14 +510,16 @@ 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 options
+^^^^^^^^^^^^^^^^^^^
 
-It is also possible to create the HTML version of the manual within
-the :doc:`CMake build directory <Build_cmake>`.  The reason for this
-option is to include the installation of the HTML manual pages into
-the "install" step when installing LAMMPS after the CMake build via
-``make install``.  The documentation build is included in the default
-build target, but can also be requested independently with ``make doc``.
+It is also possible to create the HTML version (and only the HTML
+version) of the manual within the :doc:`CMake build directory
+<Build_cmake>`.  The reason for this option is to include the
+installation of the HTML manual pages into the "install" step when
+installing LAMMPS after the CMake build via ``make install``.  The
+documentation build is included in the default build target, but can
+also be requested independently with ``make doc``.
 
 .. code-block:: bash
 
@@ -512,25 +535,27 @@ Build LAMMPS tools
 Some tools described in :doc:`Auxiliary tools <Tools>` can be built directly
 using CMake or Make.
 
-**CMake build3**\ :
+.. tabs::
 
-.. code-block:: bash
+   .. tab:: CMake build
 
-   -D BUILD_TOOLS=value       # yes or no (default)
+      .. code-block:: bash
 
-The generated binaries will also become part of the LAMMPS installation
-(see below).
+         -D BUILD_TOOLS=value       # yes or no (default)
 
-**Traditional make**\ :
+      The generated binaries will also become part of the LAMMPS installation
+      (see below).
 
-.. code-block:: bash
+   .. tab:: Traditional make
 
-   cd lammps/tools
-   make all              # build all binaries of tools
-   make binary2txt       # build only binary2txt tool
-   make chain            # build only chain tool
-   make micelle2d        # build only micelle2d tool
-   make thermo_extract   # build only thermo_extract tool
+      .. code-block:: bash
+
+         cd lammps/tools
+         make all              # build all binaries of tools
+         make binary2txt       # build only binary2txt tool
+         make chain            # build only chain tool
+         make micelle2d        # build only micelle2d tool
+         make thermo_extract   # build only thermo_extract tool
 
 ----------
 
@@ -545,16 +570,19 @@ 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**\ :
+.. tabs::
 
-.. code-block:: bash
+   .. tab:: CMake build
 
-   cmake -D CMAKE_INSTALL_PREFIX=path [options ...] ../cmake
-   make                        # perform make after CMake command
-   make install                # perform the installation into prefix
+      .. code-block:: bash
 
-**Traditional make**\ :
+         cmake -D CMAKE_INSTALL_PREFIX=path [options ...] ../cmake
+         make                        # perform make after CMake command
+         make install                # perform the installation into prefix
 
-There is no "install" option in the ``src/Makefile`` for LAMMPS.  If
-you wish to do this you will need to first build LAMMPS, then manually
-copy the desired LAMMPS files to the appropriate system directories.
+   .. tab:: Traditional make
+
+      There is no "install" option in the ``src/Makefile`` for LAMMPS.
+      If you wish to do this you will need to first build LAMMPS, then
+      manually copy the desired LAMMPS files to the appropriate system
+      directories.

doc/src/Build_cmake.rst

@@ -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
 
@@ -27,83 +28,425 @@ Another way of doing this without reconfiguration is calling make with variable
 
 ----------
 
+.. _iwyu_processing:
+
+Report missing and unneeded '#include' statements
+-------------------------------------------------
+
+The conventions for how and when to use and order include statements in
+LAMMPS are `documented in a separate file <https://github.com/lammps/lammps/blob/master/doc/include-file-conventions.md>`_
+(also included in the source code distribution).  To assist with following
+these conventions one can use the `Include What You Use tool <https://include-what-you-use.org/>`_.
+This is still under development and for large and complex projects like LAMMPS
+there are some false positives, so suggested changes need to be verified manually.
+It is recommended to use at least version 0.14, which has much fewer incorrect
+reports than earlier versions.
+
+The necessary steps to generate the report can be enabled via a
+CMake variable:
+
+.. code-block:: bash
+
+   -D ENABLE_IWYU=value    # value = no (default) or yes
+
+This will check if the required binary (include-what-you-use or iwyu)
+and python script script (iwyu-tool or iwyu_tool or iwyu_tool.py) can
+be found in the path.  The analysis can then be started with:
+
+.. code-block:: bash
+
+   make iwyu
+
+This may first run some compilation, as the analysis is dependent
+on recording all commands required to do the compilation.
+
+----------
+
 .. _sanitizer:
 
 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>`_
+ - `memory leaks <https://clang.llvm.org/docs/AddressSanitizer.html#memory-leak-detection>`_
  - `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).  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 `PyYAML <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
+             :scale: 25%
+
+          Top of the overview page
+
+        - .. figure:: JPG/coverage-overview-manybody.png
+             :scale: 25%
+
+          Styles with good coverage
+
+        - .. figure:: JPG/coverage-file-top.png
+             :scale: 25%
+
+          Top of individual source page
+
+        - .. figure:: JPG/coverage-file-branches.png
+             :scale: 25%
+
+          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

@@ -1,14 +1,14 @@
 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.
+C-style API for using LAMMPS as a library.  See the
+:doc:`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
+The :doc:`Build_basics` page explains how to build
 LAMMPS as either a shared or static library.  This results in a file
 in the compilation folder called ``liblammps.a`` or ``liblammps_<name>.a``
 in case of building a static library.  In case of a shared library
@@ -31,51 +31,55 @@ 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*\ :
+.. tabs::
 
-This assumes that LAMMPS has been configured without setting a
-``LAMMPS_MACHINE`` name, installed with "make install", and the
-``PKG_CONFIG_PATH`` environment variable has been updated to include the
-``liblammps.pc`` file installed into the configured destination folder.
-The commands to compile and link a coupled executable are then:
+   .. tab:: CMake build
 
-.. code-block:: bash
+      This assumes that LAMMPS has been configured without setting a
+      ``LAMMPS_MACHINE`` name, installed with "make install", and the
+      ``PKG_CONFIG_PATH`` environment variable has been updated to
+      include the ``liblammps.pc`` file installed into the configured
+      destination folder.  The commands to compile and link a coupled
+      executable are then:
 
-   mpicc -c -O $(pkgconf liblammps --cflags) caller.c
-   mpicxx -o caller caller.o -$(pkgconf liblammps --libs)
+      .. code-block:: bash
 
-*Traditional make*\ :
+         mpicc -c -O $(pkgconf liblammps --cflags) caller.c
+         mpicxx -o caller caller.o -$(pkgconf liblammps --libs)
 
-This assumes that LAMMPS has been compiled in the folder
-``${HOME}/lammps/src`` with "make mpi". The commands to compile and link
-a coupled executable are then:
+   .. tab:: Traditional make
 
-.. code-block:: bash
+      This assumes that LAMMPS has been compiled in the folder
+      ``${HOME}/lammps/src`` with "make mpi". The commands to compile
+      and link a coupled executable are then:
 
-   mpicc -c -O -I${HOME}/lammps/src caller.c
-   mpicxx -o caller caller.o -L${HOME}/lammps/src -llammps_mpi
+      .. code-block:: bash
 
-The *-I* argument is the path to the location of the ``library.h``
-header file containing the interface to the LAMMPS C-style library
-interface.  The *-L* argument is the path to where the ``liblammps_mpi.a``
-file is located.  The *-llammps_mpi* argument is shorthand for telling the
-compiler to link the file ``liblammps_mpi.a``.  If LAMMPS has been
-built as a shared library, then the linker will use ``liblammps_mpi.so``
-instead.  If both files are available, the linker will usually prefer
-the shared library.  In case of a shared library, you may need to update
-the ``LD_LIBRARY_PATH`` environment variable or running the ``caller``
-executable will fail since it cannot find the shared library at runtime.
+         mpicc -c -O -I${HOME}/lammps/src caller.c
+         mpicxx -o caller caller.o -L${HOME}/lammps/src -llammps_mpi
+
+      The *-I* argument is the path to the location of the ``library.h``
+      header file containing the interface to the LAMMPS C-style library
+      interface.  The *-L* argument is the path to where the
+      ``liblammps_mpi.a`` file is located.  The *-llammps_mpi* argument
+      is shorthand for telling the compiler to link the file
+      ``liblammps_mpi.a``.  If LAMMPS has been built as a shared
+      library, then the linker will use ``liblammps_mpi.so`` instead.
+      If both files are available, the linker will usually prefer the
+      shared library.  In case of a shared library, you may need to
+      update the ``LD_LIBRARY_PATH`` environment variable or running the
+      ``caller`` executable will fail since it cannot find the shared
+      library at runtime.
 
 However, it is only as simple as shown above for the case of a plain
 LAMMPS library without any optional packages that depend on libraries
@@ -83,65 +87,65 @@ 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*\ :
+.. tabs::
 
-When using CMake, additional libraries with sources in the lib folder
-are built, but not included in ``liblammps.a`` and (currently) not
-installed with "make install" and not included in the *pkgconfig*
-configuration file.  They can be found in the top level build folder,
-but you have to determine the necessary link flags manually.  It is
-therefore recommended to either use the traditional make procedure to
-build and link with a static library or build and link with a shared
-library instead.
+   .. tab:: CMake build
 
-.. TODO: this needs to be updated to reflect that latest CMake changes after they are complete.
+      When using CMake, additional libraries with sources in the lib
+      folder are built, but not included in ``liblammps.a`` and
+      (currently) not installed with ``make install`` and not included
+      in the ``pkgconfig`` configuration file.  They can be found in the
+      top level build folder, but you have to determine the necessary
+      link flags manually.  It is therefore recommended to either use
+      the traditional make procedure to build and link with a static
+      library or build and link with a shared library instead.
 
-*Traditional make*\ :
+   .. tab:: Traditional make
 
-After you have compiled a static LAMMPS library using the conventional
-build system for example with "make mode=static serial". And you also
-have installed the ``POEMS`` package after building its bundled library
-in ``lib/poems``. Then the commands to build and link the coupled executable
-change to:
+      After you have compiled a static LAMMPS library using the
+      conventional build system for example with "make mode=static
+      serial". And you also have installed the ``POEMS`` package after
+      building its bundled library in ``lib/poems``. Then the commands
+      to build and link the coupled executable change to:
 
-.. code-block:: bash
+      .. code-block:: bash
 
-   gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
-   g++ -o caller caller.o -L${HOME}/lammps/lib/poems \
-     -L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src -llammps_serial -lpoems -lmpi_stubs
+         gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
+         g++ -o caller caller.o -L${HOME}/lammps/lib/poems \
+                      -L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src \
+                      -llammps_serial -lpoems -lmpi_stubs
 
-Note, that you need to link with "g++" instead of "gcc", since the
-LAMMPS library is C++ code.  You can display the currently applied
-settings for building LAMMPS for the "serial" machine target by using
-the command:
+      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
+      .. code-block:: bash
 
-   make mode=print serial
+         make mode=print serial
 
-Which should output something like:
+      Which should output something like:
 
-.. code-block:: bash
+      .. code-block:: bash
 
-   # Compiler: 
-   CXX=g++
-   # Linker: 
-   LD=g++
-   # Compilation: 
-   CXXFLAGS=-g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -I${HOME}/compile/lammps/lib/poems -I${HOME}/compile/lammps/src/STUBS
-   # Linking: 
-   LDFLAGS=-g -O
-   # Libraries: 
-   LDLIBS=-L${HOME}/compile/lammps/src -llammps_serial -L${HOME}/compile/lammps/lib/poems -L${HOME}/compile/lammps/src/STUBS -lpoems -lmpi_stubs
+         # Compiler:
+         CXX=g++
+         # Linker:
+         LD=g++
+         # Compilation:
+         CXXFLAGS=-g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -I${HOME}/compile/lammps/lib/poems -I${HOME}/compile/lammps/src/STUBS
+         # Linking:
+         LDFLAGS=-g -O
+         # Libraries:
+         LDLIBS=-L${HOME}/compile/lammps/src -llammps_serial -L${HOME}/compile/lammps/lib/poems -L${HOME}/compile/lammps/src/STUBS -lpoems -lmpi_stubs
 
-From this you can gather the necessary paths and flags.  With
-makefiles for other *machine* configurations you need to do the
-equivalent and replace "serial" with the corresponding *machine* name
-of the makefile.
+      From this you can gather the necessary paths and flags.  With
+      makefiles for other *machine* configurations you need to do the
+      equivalent and replace "serial" with the corresponding "machine"
+      name of the makefile.
 
-----------
-
-**Link with LAMMPS as a shared library**\ :
+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
@@ -151,33 +155,36 @@ 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*\ :
+.. tabs::
 
-The commands with a shared LAMMPS library compiled with the CMake
-build process are the same as for the static library.
+   .. tab:: CMake build
 
-.. code-block:: bash
+      The commands with a shared LAMMPS library compiled with the CMake
+      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)
+      .. code-block:: bash
 
-*Traditional make*\ :
+         mpicc -c -O $(pkgconf liblammps --cflags) caller.c
+         mpicxx -o caller caller.o -$(pkgconf --libs)
 
-The commands with a shared LAMMPS library compiled with the
-traditional make build using "make mode=shared serial" becomes:
+   .. tab:: Traditional make
 
-.. code-block:: bash
+      The commands with a shared LAMMPS library compiled with the
+      traditional make build using ``make mode=shared serial`` becomes:
 
-   gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
-   g++ -o caller caller.o -L${HOME}/lammps/src -llammps_serial
+      .. code-block:: bash
 
-*Locating liblammps.so at runtime*\ :
+         gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
+         g++ -o caller caller.o -L${HOME}/lammps/src -llammps_serial
 
-However, now the ``liblammps.so`` file is required at runtime and needs
-to be in a folder, where the shared linker program of the operating
-system can find it.  This would be either a folder like ``/usr/local/lib64``
-or ``${HOME}/.local/lib64`` or a folder pointed to by the ``LD_LIBRARY_PATH``
-environment variable. You can type
+Locating liblammps.so at runtime
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Unlike with a static link, now the ``liblammps.so`` file is required at
+runtime and needs to be in a folder, where the shared linker program of
+the operating system can find it.  This would be either a folder like
+``/usr/local/lib64`` or ``${HOME}/.local/lib64`` or a folder pointed to
+by the ``LD_LIBRARY_PATH`` environment variable. You can type
 
 .. code-block:: bash
 
@@ -185,9 +192,10 @@ environment variable. You can type
 
 to see what directories are in that list.
 
-Or you can add the LAMMPS src directory (or the directory you performed
-a CMake style build in) to your ``LD_LIBRARY_PATH``, so that the current
-version of the shared library is always available to programs that use it.
+Or you can add the LAMMPS src directory or the directory you performed a
+CMake style build in to your ``LD_LIBRARY_PATH`` environment variable,
+so that the current version of the shared library is always available to
+programs that use it.
 
 For the Bourne or Korn shells (/bin/sh, /bin/ksh, /bin/bash etc.), you
 would add something like this to your ``${HOME}/.profile`` file:
@@ -231,29 +239,3 @@ 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_make.rst

@@ -37,7 +37,7 @@ enable (or "install") them first, as discussed on the :doc:`Build
 package <Build_package>` doc page.  If a packages requires (provided or
 external) libraries, you must configure and build those libraries
 **before** building LAMMPS itself and especially **before** enabling
-such a package with ``make yes-<package>``.  Building :doc:`LAMMPS with
+such a package with ``make yes-<package>``.  :doc:`Building LAMMPS with
 CMake <Build_cmake>` can automate much of this for many types of
 machines, especially workstations, desktops, and laptops, so we suggest
 you try it first when building LAMMPS in those cases.

doc/src/Build_package.rst

@@ -45,94 +45,99 @@ packages:
 The mechanism for including packages is simple but different for CMake
 versus make.
 
-**CMake build**\ :
+.. tabs::
 
-.. code-block:: csh
+   .. tab:: CMake build
 
-   -D PKG_NAME=value          # yes or no (default)
+      .. code-block:: csh
 
-Examples:
+         -D PKG_NAME=value          # yes or no (default)
 
-.. code-block:: csh
+      Examples:
 
-   -D PKG_MANYBODY=yes
-   -D PKG_USER-INTEL=yes
+      .. code-block:: csh
 
-All standard and user packages are included the same way.  Note that
-USER packages have a hyphen between USER and the rest of the package
-name, not an underscore.
+         -D PKG_MANYBODY=yes
+         -D PKG_USER-INTEL=yes
 
-See the shortcut section below for how to install many packages at
-once with CMake.
+      All standard and user packages are included the same way.  Note
+      that USER packages have a hyphen between USER and the rest of the
+      package name, not an underscore.
+
+      See the shortcut section below for how to install many packages at
+      once with CMake.
+
+      .. note::
+
+         If you switch between building with CMake and make builds, no
+         packages in the src directory can be installed when you 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.
+
+   .. tab:: Traditional make
+
+      .. code-block:: bash
+
+         cd lammps/src
+         make ps                    # check which packages are currently installed
+         make yes-name              # install a package with name
+         make no-name               # un-install a package with name
+         make mpi                   # build LAMMPS with whatever packages are now installed
+
+      Examples:
+
+      .. code-block:: bash
+
+         make no-rigid
+         make yes-user-intel
+
+      All standard and user packages are included the same way.
+
+      See the shortcut section below for how to install many packages at
+      once with make.
+
+      .. note::
+
+         You must always re-build LAMMPS (via make) after installing or
+         un-installing a package, for the action to take effect. The
+         included dependency tracking will make certain only files that
+         are required to be rebuilt are recompiled.
+
+      .. note::
+
+         You cannot install or un-install packages and build LAMMPS in a
+         single make command with multiple targets, e.g. ``make
+         yes-colloid mpi``.  This is because the make procedure creates
+         a list of source files that will be out-of-date for the build
+         if the package configuration changes within the same command.
+         You can include or exclude multiple packages in a single make
+         command, e.g. ``make yes-colloid no-manybody``.
+
+
+Information for both build systems
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Almost all packages can be included or excluded in a LAMMPS build,
+independent of the other packages.  However, some packages include files
+derived from files in other packages.  LAMMPS checks for this and does
+the right thing.  Individual files are only included if their
+dependencies are already included.  Likewise, if a package is excluded,
+other files dependent on that package are also excluded.
 
 .. note::
 
-   If you toggle back and forth between building with CMake vs
-   make, no packages in the src directory can be installed when you
-   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**\ :
-
-.. code-block:: bash
-
-   cd lammps/src
-   make ps                    # check which packages are currently installed
-   make yes-name              # install a package with name
-   make no-name               # un-install a package with name
-   make mpi                   # build LAMMPS with whatever packages are now installed
-
-Examples:
-
-.. code-block:: bash
-
-   make no-rigid
-   make yes-user-intel
-
-All standard and user packages are included the same way.
-
-See the shortcut section below for how to install many packages at
-once with make.
-
-.. note::
-
-   You must always re-build LAMMPS (via make) after installing or
-   un-installing a package, for the action to take effect.
-
-.. note::
-
-   You cannot install or un-install packages and build LAMMPS in a
-   single make command with multiple targets, e.g. make yes-colloid mpi.
-   This is because the make procedure creates a list of source files that
-   will be out-of-date for the build if the package configuration changes
-   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**\ :
-
-Any package can be included or excluded in a LAMMPS build, independent
-of all other packages.  However, some packages include files derived
-from files in other packages.  LAMMPS checks for this and does the
-right thing.  Individual files are only included if their dependencies
-are already included.  Likewise, if a package is excluded, other files
-dependent on that package are also excluded.
-
-When you download a LAMMPS tarball or download LAMMPS source files
-from the git repository, no packages are pre-installed in the
-src directory.
-
-.. note::
-
-   Prior to Aug 2018, if you downloaded a tarball, 3 packages
-   (KSPACE, MANYBODY, MOLECULE) were pre-installed in the src directory.
-   That is no longer the case, so that CMake will build as-is without the
-   need to un-install those packages.
+   By default no package is installed.  Prior to August 2018, however,
+   if you downloaded a tarball, 3 packages (KSPACE, MANYBODY, MOLECULE)
+   were pre-installed via the traditional make procedure in the ``src``
+   directory.  That is no longer the case, so that CMake will build
+   as-is without needing to un-install those packages.
 
 ----------
 
 .. _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 +153,14 @@ 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 +170,8 @@ 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 +191,8 @@ 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

@@ -6,7 +6,7 @@ explain how to do this for building both with CMake and make.
 
 * :ref:`C++11 standard compliance <cxx11>` when building all of LAMMPS
 * :ref:`FFT library <fft>` for use with the :doc:`kspace_style pppm <kspace_style>` command
-* :ref:`Size of LAMMPS data types <size>`
+* :ref:`Size of LAMMPS integer types <size>`
 * :ref:`Read or write compressed files <gzip>`
 * :ref:`Output of JPG and PNG files <graphics>` via the :doc:`dump image <dump_image>` command
 * :ref:`Output of movie files <graphics>` via the :doc:`dump_movie <dump_image>` command
@@ -44,67 +44,71 @@ 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**\ :
+.. tabs::
 
-.. code-block:: bash
+   .. tab:: CMake build
 
-   -D FFT=value              # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
-   -D FFT_SINGLE=value       # yes or no (default), no = double precision
-   -D FFT_PACK=value         # array (default) or pointer or memcpy
+      .. code-block:: bash
 
-.. note::
+         -D FFT=value              # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
+         -D FFT_SINGLE=value       # yes or no (default), no = double precision
+         -D FFT_PACK=value         # array (default) or pointer or memcpy
 
-   The values for the FFT variable must be in upper-case.  This is
-   an exception to the rule that all CMake variables can be specified
-   with lower-case values.
+      .. note::
 
-Usually these settings are all that is needed.  If FFTW3 is selected,
-then CMake will try to detect, if threaded FFTW libraries are available
-and enable them by default.  This setting is independent of whether
-OpenMP threads are enabled and a packages like KOKKOS or USER-OMP is
-used.  If CMake cannot detect the FFT library, you can set these variables
-to assist:
+         The values for the FFT variable must be in upper-case.  This is
+         an exception to the rule that all CMake variables can be specified
+         with lower-case values.
 
-.. code-block:: bash
+      Usually these settings are all that is needed.  If FFTW3 is
+      selected, then CMake will try to detect, if threaded FFTW
+      libraries are available and enable them by default.  This setting
+      is independent of whether OpenMP threads are enabled and a
+      packages like KOKKOS or USER-OMP is used.  If CMake cannot detect
+      the FFT library, you can set these variables to assist:
 
-   -D FFTW3_INCLUDE_DIRS=path  # path to FFTW3 include files
-   -D FFTW3_LIBRARIES=path     # path to FFTW3 libraries
-   -D FFT_FFTW_THREADS=on      # enable using threaded FFTW3 libraries
-   -D MKL_INCLUDE_DIRS=path    # ditto for Intel MKL library
-   -D FFT_MKL_THREADS=on       # enable using threaded FFTs with MKL libraries
-   -D MKL_LIBRARIES=path
+      .. code-block:: bash
 
-**Makefile.machine settings**\ :
+         -D FFTW3_INCLUDE_DIR=path   # path to FFTW3 include files
+         -D FFTW3_LIBRARY=path       # path to FFTW3 libraries
+         -D FFT_FFTW_THREADS=on      # enable using threaded FFTW3 libraries
+         -D MKL_INCLUDE_DIR=path     # ditto for Intel MKL library
+         -D FFT_MKL_THREADS=on       # enable using threaded FFTs with MKL libraries
+         -D MKL_LIBRARY=path         # path to MKL libraries
 
-.. code-block:: make
+   .. tab:: Traditional make
 
-   FFT_INC = -DFFT_FFTW3         # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
-                                 # default is KISS if not specified
-   FFT_INC = -DFFT_SINGLE        # do not specify for double precision
-   FFT_INC = -DFFT_FFTW_THREADS  # enable using threaded FFTW3 libraries
-   FFT_INC = -DFFT_MKL_THREADS   # enable using threaded FFTs with MKL libraries
-   FFT_INC = -DFFT_PACK_ARRAY    # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
+      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.
 
-# default is FFT_PACK_ARRAY if not specified
+      .. code-block:: make
 
-.. code-block:: make
+         FFT_INC = -DFFT_FFTW3         # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
+                                       # default is KISS if not specified
+         FFT_INC = -DFFT_SINGLE        # do not specify for double precision
+         FFT_INC = -DFFT_FFTW_THREADS  # enable using threaded FFTW3 libraries
+         FFT_INC = -DFFT_MKL_THREADS   # enable using threaded FFTs with MKL libraries
+         FFT_INC = -DFFT_PACK_ARRAY    # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
+                                       # default is FFT_PACK_ARRAY if not specified
 
-   FFT_INC =       -I/usr/local/include
-   FFT_PATH =      -L/usr/local/lib
-   FFT_LIB =       -lfftw3             # FFTW3 double precision
-   FFT_LIB =       -lfftw3 -lfftw3_omp # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
-   FFT_LIB =       -lfftw3 -lfftw3f    # FFTW3 single precision
-   FFT_LIB =       -lmkl_intel_lp64 -lmkl_sequential -lmkl_core   # MKL with Intel compiler, serial interface
-   FFT_LIB =       -lmkl_gf_lp64 -lmkl_sequential -lmkl_core      # MKL with GNU compiler, serial interface
-   FFT_LIB =       -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core # MKL with Intel compiler, threaded interface
-   FFT_LIB =       -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core      # MKL with GNU compiler, threaded interface
-   FFT_LIB =       -lmkl_rt            # MKL with automatic runtime selection of interface libs
+      .. code-block:: make
 
-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.
+         FFT_INC =       -I/usr/local/include
+         FFT_PATH =      -L/usr/local/lib
+         FFT_LIB =       -lfftw3             # FFTW3 double precision
+         FFT_LIB =       -lfftw3 -lfftw3_omp # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
+         FFT_LIB =       -lfftw3 -lfftw3f    # FFTW3 single precision
+         FFT_LIB =       -lmkl_intel_lp64 -lmkl_sequential -lmkl_core   # MKL with Intel compiler, serial interface
+         FFT_LIB =       -lmkl_gf_lp64 -lmkl_sequential -lmkl_core      # MKL with GNU compiler, serial interface
+         FFT_LIB =       -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core # MKL with Intel compiler, threaded interface
+         FFT_LIB =       -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core      # MKL with GNU compiler, threaded interface
+         FFT_LIB =       -lmkl_rt            # MKL with automatic runtime selection of interface libs
 
-**CMake and make info**\ :
+      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.
 
 The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS
 distribution.  It is portable across all platforms.  Depending on the size
@@ -116,7 +120,8 @@ per-timestep CPU cost, FFTs are only a portion of long-range
 Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
 communication can be costly).  A breakdown of these timings is printed
 to the screen at the end of a run when using the
-:doc:`kspace_style pppm <kspace_style>` command. The :doc:`Run output <Run_output>`
+:doc:`kspace_style pppm <kspace_style>` command. The
+:doc:`Screen and logfile output <Run_output>`
 doc page gives more details.  A more detailed (and time consuming)
 report of the FFT performance is generated with the
 :doc:`kspace_modify fftbench yes <kspace_modify>` command.
@@ -127,7 +132,7 @@ 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.
@@ -169,70 +174,104 @@ ARRAY mode.
 
 .. _size:
 
-Size of LAMMPS data types
-------------------------------------
+Size of LAMMPS integer types and size limits
+--------------------------------------------
 
-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.
+This has an impact on the size of a system that can be simulated
+or how large counters can become before "rolling over".
+The default setting of "smallbig" is almost always adequate.
 
-**CMake variable**\ :
+.. tabs::
 
-.. code-block:: bash
+   .. tab:: CMake build
 
-   -D LAMMPS_SIZES=value   # smallbig (default) or bigbig or smallsmall
+      With CMake the choice of integer types is made via setting a
+      variable during configuration.
 
-**Makefile.machine setting**\ :
+      .. code-block:: bash
 
-.. code-block:: make
+         -D LAMMPS_SIZES=value   # smallbig (default) or bigbig or smallsmall
 
-   LMP_INC = -DLAMMPS_SMALLBIG    # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL
+      If the variable is not set explicitly, "smallbig" is used.
 
-The default setting is ``-DLAMMPS_SMALLBIG`` if nothing is specified
+   .. tab:: Traditional build
 
-**CMake and make info**\ :
+      If you want a setting different from the default, you need to edit the
+      ``LMP_INC`` variable setting your machine Makefile.
 
-The default "smallbig" setting allows for simulations with:
+      .. code-block:: make
 
-* total atom count = 2\^63 atoms (about 9e18)
-* total timesteps = 2\^63 (about 9e18)
-* atom IDs = 2\^31 (about 2 billion)
-* image flags = roll over at 512
+         LMP_INC = -DLAMMPS_SMALLBIG    # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL
 
-The "bigbig" setting increases the latter two limits.  It allows for:
+      The default setting is ``-DLAMMPS_SMALLBIG`` if nothing is specified
 
-* total atom count = 2\^63 atoms (about 9e18)
-* total timesteps = 2\^63 (about 9e18)
-* atom IDs = 2\^63 (about 9e18)
-* image flags = roll over at about 1 million (2\^20)
+LAMMPS system size restrictions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-The "smallsmall" setting is only needed if your machine does not
-support 8-byte integers.  It allows for:
+.. list-table::
+   :header-rows: 1
+   :widths: auto
+   :align: center
 
-* total atom count = 2\^31 atoms (about 2 billion)
-* total timesteps = 2\^31 (about 2 billion)
-* atom IDs = 2\^31 (about 2 billion)
-* image flags = roll over at 512 (2\^9)
+   * -
+     - smallbig
+     - bigbig
+     - smallsmall
+   * - Total atom count
+     - :math:`2^{63}` atoms (= :math:`9.223 \cdot 10^{18}`)
+     - :math:`2^{63}` atoms (= :math:`9.223 \cdot 10^{18}`)
+     - :math:`2^{31}` atoms (= :math:`2.147 \cdot 10^9`)
+   * - Total timesteps
+     - :math:`2^{63}` steps (= :math:`9.223 \cdot 10^{18}`)
+     - :math:`2^{63}` steps (= :math:`9.223 \cdot 10^{18}`)
+     - :math:`2^{31}` steps (= :math:`2.147 \cdot 10^9`)
+   * - Atom ID values
+     - :math:`1 \le i \le 2^{31} (= 2.147 \cdot 10^9)`
+     - :math:`1 \le i \le 2^{63} (= 9.223 \cdot 10^{18})`
+     - :math:`1 \le i \le 2^{31} (= 2.147 \cdot 10^9)`
+   * - Image flag values
+     - :math:`-512 \le i \le 511`
+     - :math:`- 1\,048\,576 \le i \le 1\,048\,575`
+     - :math:`-512 \le i \le 511`
+
+The "bigbig" setting increases the size of image flags and atom IDs over
+"smallbig" and the "smallsmall" setting is only needed if your machine
+does not support 64-bit integers or incurs performance penalties when
+using them.
+
+These are limits for the core of the LAMMPS code, specific features or
+some styles may impose additional limits.  The :ref:`USER-ATC
+<PKG-USER-ATC>` package cannot be compiled with the "bigbig" setting.
+Also, there are limitations when using the library interface where some
+functions with known issues have been replaced by dummy calls printing a
+corresponding error message rather than crashing randomly or corrupting
+data.
 
 Atom IDs are not required for atomic systems which do not store bond
 topology information, though IDs are enabled by default.  The
 :doc:`atom_modify id no <atom_modify>` command will turn them off.  Atom
 IDs are required for molecular systems with bond topology (bonds,
-angles, dihedrals, etc).  Thus if you model a molecular system with
-more than 2 billion atoms, you need the "bigbig" setting.
+angles, dihedrals, etc).  Similarly, some force or compute or fix styles
+require atom IDs.  Thus if you model a molecular system or use one of
+those styles with more than 2 billion atoms, you need the "bigbig"
+setting.
 
-Image flags store 3 values per atom which count the number of times an
-atom has moved through the periodic box in each dimension.  See the
-:doc:`dump <dump>` doc page for a discussion.  If an atom moves through
-the periodic box more than this limit, the value will "roll over",
-e.g. from 511 to -512, which can cause diagnostics like the
-mean-squared displacement, as calculated by the :doc:`compute msd <compute_msd>` command, to be faulty.
+Regardless of the total system size limits, the maximum number of atoms
+per MPI rank (local + ghost atoms) is limited to 2 billion for atomic
+systems and 500 million for systems with bonds (the additional
+restriction is due to using the 2 upper bits of the local atom index
+in neighbor lists for storing special bonds info).
+
+Image flags store 3 values per atom in a single integer which count the
+number of times an atom has moved through the periodic box in each
+dimension.  See the :doc:`dump <dump>` doc page for a discussion.  If an
+atom moves through the periodic box more than this limit, the value will
+"roll over", e.g. from 511 to -512, which can cause diagnostics like the
+mean-squared displacement, as calculated by the :doc:`compute msd
+<compute_msd>` command, to be faulty.
 
-Note that the USER-ATC package and the USER-INTEL package are currently
-not compatible with the "bigbig" setting. Also, there are limitations
-when using the library interface. Some functions with known issues
-have been replaced by dummy calls printing a corresponding error rather
-than crashing randomly or corrupting data.
 
 Also note that the GPU package requires its lib/gpu library to be
 compiled with the same size setting, or the link will fail.  A CMake
@@ -251,51 +290,51 @@ 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**\ :
+.. tabs::
 
-.. code-block:: bash
+   .. tab:: CMake build
 
-   -D WITH_JPEG=value      # yes or no
-                           # default = yes if CMake finds JPEG files, else no
-   -D WITH_PNG=value       # yes or no
-                           # default = yes if CMake finds PNG and ZLIB files, else no
-   -D WITH_FFMPEG=value    # yes or no
-                           # default = yes if CMake can find ffmpeg, else no
+      .. code-block:: bash
 
-Usually these settings are all that is needed.  If CMake cannot find
-the graphics header, library, executable files, you can set these
-variables:
+         -D WITH_JPEG=value      # yes or no
+                                 # default = yes if CMake finds JPEG files, else no
+         -D WITH_PNG=value       # yes or no
+                                 # default = yes if CMake finds PNG and ZLIB files, else no
+         -D WITH_FFMPEG=value    # yes or no
+                                 # default = yes if CMake can find ffmpeg, else no
 
-.. code-block:: bash
+      Usually these settings are all that is needed.  If CMake cannot
+      find the graphics header, library, executable files, you can set
+      these variables:
 
-   -D JPEG_INCLUDE_DIR=path    # path to jpeglib.h header file
-   -D JPEG_LIBRARIES=path      # path to libjpeg.a (.so) file
-   -D PNG_INCLUDE_DIR=path     # path to png.h header file
-   -D PNG_LIBRARIES=path       # path to libpng.a (.so) file
-   -D ZLIB_INCLUDE_DIR=path    # path to zlib.h header file
-   -D ZLIB_LIBRARIES=path      # path to libz.a (.so) file
-   -D FFMPEG_EXECUTABLE=path   # path to ffmpeg executable
+      .. code-block:: bash
 
-**Makefile.machine settings**\ :
+         -D JPEG_INCLUDE_DIR=path    # path to jpeglib.h header file
+         -D JPEG_LIBRARY=path        # path to libjpeg.a (.so) file
+         -D PNG_INCLUDE_DIR=path     # path to png.h header file
+         -D PNG_LIBRARY=path         # path to libpng.a (.so) file
+         -D ZLIB_INCLUDE_DIR=path    # path to zlib.h header file
+         -D ZLIB_LIBRARY=path        # path to libz.a (.so) file
+         -D FFMPEG_EXECUTABLE=path   # path to ffmpeg executable
 
-.. code-block:: make
+   .. tab:: Traditional make
 
-   LMP_INC = -DLAMMPS_JPEG
-   LMP_INC = -DLAMMPS_PNG
-   LMP_INC = -DLAMMPS_FFMPEG
+      .. code-block:: make
 
-   JPG_INC = -I/usr/local/include   # path to jpeglib.h, png.h, zlib.h header files if make cannot find them
-   JPG_PATH = -L/usr/lib            # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them
-   JPG_LIB = -ljpeg -lpng -lz       # library names
+         LMP_INC = -DLAMMPS_JPEG
+         LMP_INC = -DLAMMPS_PNG
+         LMP_INC = -DLAMMPS_FFMPEG
 
-As with CMake, you do not need to set ``JPG_INC`` or ``JPG_PATH``,
-if make can find the graphics header and library files.  You must
-specify ``JPG_LIB``
-with a list of graphics libraries to include in the link.  You must
-insure ffmpeg is in a directory where LAMMPS can find it at runtime,
-that is a directory in your PATH environment variable.
+         JPG_INC = -I/usr/local/include   # path to jpeglib.h, png.h, zlib.h header files if make cannot find them
+         JPG_PATH = -L/usr/lib            # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them
+         JPG_LIB = -ljpeg -lpng -lz       # library names
 
-**CMake and make info**\ :
+      As with CMake, you do not need to set ``JPG_INC`` or ``JPG_PATH``,
+      if make can find the graphics header and library files.  You must
+      specify ``JPG_LIB`` with a list of graphics libraries to include
+      in the link.  You must insure ffmpeg is in a directory where
+      LAMMPS can find it at runtime, that is a directory in your PATH
+      environment variable.
 
 Using ``ffmpeg`` to output movie files requires that your machine
 supports the "popen" function in the standard runtime library.
@@ -318,34 +357,34 @@ 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**\ :
+.. tabs::
 
-.. code-block:: bash
+   .. tab:: CMake build
 
-   -D WITH_GZIP=value       # yes or no
-                            # default is yes if CMake can find gzip, else no
-   -D GZIP_EXECUTABLE=path  # path to gzip executable if CMake cannot find it
+      .. code-block:: bash
 
-**Makefile.machine setting**\ :
+         -D WITH_GZIP=value       # yes or no
+                                  # default is yes if CMake can find gzip, else no
+         -D GZIP_EXECUTABLE=path  # path to gzip executable if CMake cannot find it
 
-.. code-block:: make
+   .. tab:: Traditional make
 
-   LMP_INC = -DLAMMPS_GZIP
+      .. code-block:: make
 
-**CMake and make info**\ :
+         LMP_INC = -DLAMMPS_GZIP
 
-This option requires that your machine supports the "popen()" function
-in the standard runtime library and that a gzip executable can be
+This option requires that your operating system fully supports the "popen()"
+function in the standard runtime library and that a ``gzip`` executable can be
 found by LAMMPS during a run.
 
 .. note::
 
-   On some clusters with high-speed networks, using the fork()
-   library call (required by popen()) can interfere with the fast
-   communication library and lead to simulations using compressed output
-   or input to hang or crash. For selected operations, compressed file
-   I/O is also available using a compression library instead, which is
-   what the :ref:`COMPRESS package <PKG-COMPRESS>` enables.
+   On some clusters with high-speed networks, using the "fork()" library
+   call (required by "popen()") can interfere with the fast communication
+   library and lead to simulations using compressed output or input to
+   hang or crash. For selected operations, compressed file I/O is also
+   available using a compression library instead, which is what the
+   :ref:`COMPRESS package <PKG-COMPRESS>` enables.
 
 ----------
 
@@ -354,61 +393,66 @@ found by LAMMPS during a run.
 Memory allocation alignment
 ---------------------------------------
 
-This setting enables the use of the posix_memalign() call instead of
-malloc() when LAMMPS allocates large chunks or memory.  This can make
-vector instructions on CPUs more efficient, if dynamically allocated
-memory is aligned on larger-than-default byte boundaries.
-On most current systems, the malloc() implementation returns
+This setting enables the use of the "posix_memalign()" call instead of
+"malloc()" when LAMMPS allocates large chunks or memory.  Vector
+instructions on CPUs may become more efficient, if dynamically allocated
+memory is aligned on larger-than-default byte boundaries.  On most
+current operating systems, the "malloc()" implementation returns
 pointers that are aligned to 16-byte boundaries. Using SSE vector
-instructions efficiently, however, requires memory blocks being
-aligned on 64-byte boundaries.
+instructions efficiently, however, requires memory blocks being aligned
+on 64-byte boundaries.
 
-**CMake variable**\ :
+.. tabs::
 
-.. code-block:: bash
+   .. tab:: CMake build
 
-   -D LAMMPS_MEMALIGN=value            # 0, 8, 16, 32, 64 (default)
+      .. code-block:: bash
 
-Use a ``LAMMPS_MEMALIGN`` value of 0 to disable using posix_memalign()
-and revert to using the malloc() C-library function instead.  When
-compiling LAMMPS for Windows systems, malloc() will always be used
-and this setting ignored.
+         -D LAMMPS_MEMALIGN=value            # 0, 8, 16, 32, 64 (default)
 
-**Makefile.machine setting**\ :
+      Use a ``LAMMPS_MEMALIGN`` value of 0 to disable using
+      "posix_memalign()" and revert to using the "malloc()" C-library
+      function instead.  When compiling LAMMPS for Windows systems,
+      "malloc()" will always be used and this setting is ignored.
 
-.. code-block:: make
+   .. tab:: Traditional make
 
-   LMP_INC = -DLAMMPS_MEMALIGN=value   # 8, 16, 32, 64
+      .. code-block:: make
 
-Do not set ``-DLAMMPS_MEMALIGN``, if you want to have memory allocated
-with the malloc() function call instead. ``-DLAMMPS_MEMALIGN`` **cannot**
-be used on Windows, as it does use different function calls for
-allocating aligned memory, that are not compatible with how LAMMPS
-manages its dynamical memory.
+         LMP_INC = -DLAMMPS_MEMALIGN=value   # 8, 16, 32, 64
+
+      Do not set ``-DLAMMPS_MEMALIGN``, if you want to have memory
+      allocated with the "malloc()" function call
+      instead. ``-DLAMMPS_MEMALIGN`` **cannot** be used on Windows, as
+      Windows different function calls with different semantics for
+      allocating aligned memory, that are not compatible with how LAMMPS
+      manages its dynamical memory.
 
 ----------
 
 .. _longlong:
 
 Workaround for long long integers
-------------------------------------------------
+---------------------------------
 
 If your system or MPI version does not recognize "long long" data
 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**\ :
+.. tabs::
 
-.. code-block:: bash
+   .. tab:: CMake build
 
-   -D LAMMPS_LONGLONG_TO_LONG=value     # yes or no (default)
+      .. code-block:: bash
 
-**Makefile.machine setting**\ :
+         -D LAMMPS_LONGLONG_TO_LONG=value     # yes or no (default)
 
-.. code-block:: make
+   .. tab:: Traditional make
 
-   LMP_INC = -DLAMMPS_LONGLONG_TO_LONG
+      .. code-block:: make
+
+         LMP_INC = -DLAMMPS_LONGLONG_TO_LONG
 
 ----------
 
@@ -420,17 +464,26 @@ 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**\ :
+.. tabs::
 
-.. code-block:: bash
+   .. tab:: CMake build
 
-   -D LAMMPS_EXCEPTIONS=value        # yes or no (default)
+      .. code-block:: bash
 
-**Makefile.machine setting**\ :
+         -D LAMMPS_EXCEPTIONS=value        # yes or no (default)
 
-.. code-block:: make
+   .. tab:: Traditional make
 
-   LMP_INC = -DLAMMPS_EXCEPTIONS
+      .. 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

@@ -79,9 +79,8 @@ 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>`
@@ -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>`

doc/src/Commands_fix.rst

@@ -42,6 +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>`
@@ -95,10 +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>`
@@ -149,6 +149,8 @@ OPT.
    * :doc:`oneway <fix_oneway>`
    * :doc:`orient/bcc <fix_orient>`
    * :doc:`orient/fcc <fix_orient>`
+   * :doc:`orient/eco <fix_orient_eco>`
+   * :doc:`pafi <fix_pafi>`
    * :doc:`phonon <fix_phonon>`
    * :doc:`pimd <fix_pimd>`
    * :doc:`planeforce <fix_planeforce>`
@@ -202,6 +204,8 @@ 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>`
@@ -242,3 +246,4 @@ 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/Commands_removed.rst

@@ -17,6 +17,11 @@ ways through the :doc:`compute chunk/atom <compute_chunk_atom>` command
 and then averaging is done using :doc:`fix ave/chunk <fix_ave_chunk>`.
 Please refer to the :doc:`chunk HOWTO <Howto_chunk>` section for an overview.
 
+Reset_ids command
+-----------------
+
+The reset_ids command has been renamed to :doc:`reset_atom_ids <reset_atom_ids>`.
+
 MEAM package
 ------------
 
@@ -27,7 +32,7 @@ which removes several restrictions (e.g. there can be multiple instances
 in hybrid pair styles) and allows for some optimizations leading
 to better performance.  The new pair style :doc:`meam/c <pair_meamc>` has
 the exact same syntax as the old "meam" pair style and thus pair style
-:doc:`meam <pair_meamc>` is an alias to the new style and backward
+meam is an alias to the new style and backward
 compatibility of old inputs is preserved.
 
 REAX package

doc/src/Developer/.gitignore

@@ -1,3 +0,0 @@
-/developer.aux
-/developer.log
-/developer.toc

doc/src/Developer/classes.fig

@@ -1,198 +0,0 @@
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