fixing merge conflicts

.github/CODEOWNERS

@@ -61,12 +61,14 @@ src/GPU/pair_vashishta_gpu.*        @andeplane
 src/KOKKOS/pair_vashishta_kokkos.*  @andeplane
 src/MANYBODY/pair_vashishta_table.* @andeplane
 src/MANYBODY/pair_atm.*             @sergeylishchuk
+src/MANYBODY/pair_nb3b_screened.*   @flodesani
 src/REPLICA/*_grem.*                @dstelter92
 src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
 src/EXTRA-COMPUTE/compute_born_matrix.* @Bibobu @athomps
 src/MISC/*_tracker.*                @jtclemm
 src/MC/fix_gcmc.*                   @athomps
 src/MC/fix_sgcmc.*                  @athomps
+src/REPLICA/fix_pimd_langevin.*     @Yi-FanLi
 
 # core LAMMPS classes
 src/lammps.*              @sjplimp
@@ -134,6 +136,7 @@ src/timer.*               @akohlmey
 src/utils.*               @akohlmey @rbberger
 src/verlet.*              @sjplimp @stanmoore1
 src/math_eigen_impl.h     @jewettaij
+src/fix_press_langevin.*  @Bibobu
 
 # tools
 tools/coding_standard/* @akohlmey @rbberger
@@ -150,12 +153,12 @@ tools/vim/*           @hammondkd
 unittest/*            @akohlmey
 
 # cmake
-cmake/*               @rbberger
+cmake/*               @akohlmey
 cmake/Modules/LAMMPSInterfacePlugin.cmake @akohlmey
 cmake/Modules/MPI4WIN.cmake @akohlmey
 cmake/Modules/OpenCLLoader.cmake @akohlmey
-cmake/Modules/Packages/COLVARS.cmake @rbberger @giacomofiorin
+cmake/Modules/Packages/COLVARS.cmake @giacomofiorin
-cmake/Modules/Packages/KIM.cmake @rbberger @ellio167
+cmake/Modules/Packages/KIM.cmake @ellio167
 cmake/presets/*.cmake @akohlmey
 
 # python

.github/CONTRIBUTING.md

@@ -1,13 +1,13 @@
 # Contributing to LAMMPS via GitHub
 
-Thank your for considering to contribute to the LAMMPS software project.
+Thank you for considering to contribute to the LAMMPS software project.
 
 The following is a set of guidelines as well as explanations of policies and work flows for contributing to the LAMMPS molecular dynamics software project. These guidelines focus on submitting issues or pull requests on the LAMMPS GitHub project.
 
 Thus please also have a look at:
-* [The guide for submitting new features in the LAMMPS manual](https://www.lammps.org/doc/Modify_contribute.html)
+* [The guide for submitting new features in the LAMMPS manual](https://docs.lammps.org/Modify_contribute.html)
-* [The guide on programming style and requirement in the LAMMPS manual](https://www.lammps.org/doc/Modify_style.html)
+* [The guide on programming style and requirement in the LAMMPS manual](https://docs.lammps.org/Modify_requirements.html)
-* [The GitHub tutorial in the LAMMPS manual](http://lammps.sandia.gov/doc/Howto_github.html)
+* [The GitHub tutorial in the LAMMPS manual](http://docs.lammps.org/Howto_github.html)
 
 ## Table of Contents
 
@@ -27,17 +27,17 @@ __
 
 ## I don't want to read this whole thing I just have a question!
 
-> **Note:** Please do not file an issue to ask a general question about LAMMPS, its features, how to use specific commands, or how perform simulations or analysis in LAMMPS. Instead post your question to either the ['lammps-users' mailing list](https://lammps.sandia.gov/mail.html) or the [LAMMPS Material Science Discourse forum](https://matsci.org/lammps). You do not need to be subscribed to post to the list (but a mailing list subscription avoids having your post delayed until it is approved by a mailing list moderator). Most posts to the mailing list receive a response within less than 24 hours. Before posting to the mailing list, please read the [mailing list guidelines](https://lammps.sandia.gov/guidelines.html). Following those guidelines will help greatly to get a helpful response. Always mention which LAMMPS version you are using. The LAMMPS forum was recently created as part of a larger effort to build a materials science community and have discussions not just about using LAMMPS. Thus the forum may be also used for discussions that would be off-topic for the mailing list. Those will just have to be posted to a more general category.
+> **Note:** Please do not file an issue to ask a general question about LAMMPS, its features, how to use specific commands, or how perform simulations or analysis in LAMMPS. Instead post your question to the [LAMMPS Material Science Discourse forum](https://matsci.org/lammps). Before posting to the forum, please read the general [guidelines](https://www.lammps.org/guidelines.html) and the forum specific [suggestions](https://matsci.org/t/please-read-this-first-guidelines-and-suggestions-for-posting-lammps-questions/49913). Following those guidelines and suggestions will help greatly to get a helpful response.  *Always* mention which LAMMPS version you are using. The MatSci website may be also used for discussions that would be off-topic for the LAMMPS categories. Those will just have to be posted to a different category.
 
 ## How Can I Contribute?
 
 There are several ways how you can actively contribute to the LAMMPS project: you can discuss compiling and using LAMMPS, and solving LAMMPS related problems with other LAMMPS users on the lammps-users mailing list or the forum, you can report bugs or suggest enhancements by creating issues on GitHub (or posting them to the lammps-users mailing list or posting in the LAMMPS Materials Science Discourse forum), and you can contribute by submitting pull requests on GitHub or e-mail your code
-to one of the [LAMMPS core developers](https://lammps.sandia.gov/authors.html). As you may see from the aforementioned developer page, the LAMMPS software package includes the efforts of a very large number of contributors beyond the principal authors and maintainers.
+to one of the [LAMMPS core developers](https://www.lammps.org/authors.html). As you may see from the aforementioned developer page, the LAMMPS software package includes the efforts of a very large number of contributors beyond the principal authors and maintainers.
 
 ### Discussing How To Use LAMMPS
 
 The LAMMPS mailing list is hosted at SourceForge. The mailing list began in 2005, and now includes tens of thousands of messages in thousands of threads. LAMMPS developers try to respond to posted questions in a timely manner, but there are no guarantees. Please consider that people live in different timezone and may not have time to answer e-mails outside of their work hours.
-You can post to list by sending your email to lammps-users at lists.sourceforge.net (no subscription required), but before posting, please read the [mailing list guidelines](https://lammps.sandia.gov/guidelines.html) to maximize your chances to receive a helpful response.
+You can post to list by sending your email to lammps-users at lists.sourceforge.net (no subscription required), but before posting, please read the [mailing list guidelines](https://www.lammps.org/guidelines.html) to maximize your chances to receive a helpful response.
 
 Anyone can browse/search previous questions/answers in the archives. You do not have to subscribe to the list to post questions, receive answers (to your questions), or browse/search the archives. You **do** need to subscribe to the list if you want emails for **all** the posts (as individual messages or in digest form), or to answer questions yourself. Feel free to sign up and help us out! Answering questions from fellow LAMMPS users is a great way to pay back the community for providing you a useful tool for free, and to pass on the advice you have received yourself to others. It improves your karma and helps you understand your own research better.
 
@@ -47,7 +47,7 @@ The LAMMPS Materials Science Discourse forum was created recently to facilitate
 
 ### Reporting Bugs
 
-While developers writing code for LAMMPS are careful to test their code, LAMMPS is such a large and complex software, that it is impossible to test for all combinations of features under all normal and not so normal circumstances. Thus bugs do happen, and if you suspect, that you have encountered one, please try to document it and report it as an [Issue](https://github.com/lammps/lammps/issues) on the LAMMPS GitHub project web page. However, before reporting a bug, you need to check whether this is something that may have already been corrected. The [Latest Features and Bug Fixes in LAMMPS](https://lammps.sandia.gov/bug.html) web page lists all significant changes to LAMMPS over the years. It also tells you what the current latest development version of LAMMPS is, and you should test whether your issue still applies to that version.
+While developers writing code for LAMMPS are careful to test their code, LAMMPS is such a large and complex software, that it is impossible to test for all combinations of features under all normal and not so normal circumstances. Thus bugs do happen, and if you suspect, that you have encountered one, please try to document it and report it as an [Issue](https://github.com/lammps/lammps/issues) on the LAMMPS GitHub project web page. However, before reporting a bug, you need to check whether this is something that may have already been corrected. The [Latest Features and Bug Fixes in LAMMPS](https://www.lammps.org/bug.html) web page lists all significant changes to LAMMPS over the years. It also tells you what the current latest development version of LAMMPS is, and you should test whether your issue still applies to that version.
 
 When you click on the green "New Issue" button, you will be provided with a text field, where you can enter your message. That text field with contain a template with several headlines and some descriptions. Keep the headlines that are relevant to your reported potential bug and replace the descriptions with the information as suggested by the descriptions.
 You can also attach small text files (please add the file name extension `.txt` or it will be rejected), images, or small compressed text files (using gzip, do not use RAR or 7-ZIP or similar tools that are uncommon outside of Windows machines). In many cases, bugs are best illustrated by providing a small input deck (do **not** attach your entire production input, but remove everything that is not required to reproduce the issue, and scale down your system size, that the resulting calculation runs fast and can be run on small desktop quickly).
@@ -65,9 +65,9 @@ To be able to submit an issue on GitHub, you have to register for an account (fo
 
 We encourage users to submit new features or modifications for LAMMPS. Instructions, guidelines, requirements,
 and recommendations are in the following sections of the LAMMPS manual:
-* [The guide for submitting new features in the LAMMPS manual](https://lammps.sandia.gov/doc/Modify_contribute.html)
+* [The guide for submitting new features in the LAMMPS manual](https://docs.lammps.org/Modify_contribute.html)
-* [The guide on programming style and requirement in the LAMMPS manual](https://lammps.sandia.gov/doc/Modify_contribute.html)
+* [The guide on programming style and requirement in the LAMMPS manual](https://docs.lammps.org/Modify_requirements.html)
-* [The GitHub tutorial in the LAMMPS manual](http://lammps.sandia.gov/doc/Howto_github.html)
+* [The GitHub tutorial in the LAMMPS manual](http://docs.lammps.org/Howto_github.html)
 
 
 ## GitHub Workflows
@@ -85,7 +85,7 @@ For bug reports, the next step is that one of the core LAMMPS developers will se
 ### Pull Requests
 
 Pull requests are the **only** way that changes get made to the LAMMPS distribution.  So also the LAMMPS core developers will submit pull requests for their own changes and discuss them on GitHub.  Thus if you submit a pull request it will be treated in a similar fashion. When you submit a pull request you may opt to submit a "Draft" pull request.  That means your changes are visible and will be subject to testing, but reviewers will not be (auto-)assigned and comments will take into account that this is not complete. On the other hand, this is a perfect way to ask the LAMMPS developers for comments on non-obvious changes and get feedback and possible suggestions for improvements or recommendations about what to avoid.
-Immediately after the submission, the LAMMPS continuing integration server at ci.lammps.org will download your submitted branch and perform a number of tests: it will tests whether it compiles cleanly under various conditions, it will also do a check on whether your included documentation translates cleanly and run some unit tests and other checks. Whether these tests are successful or fail will be recorded.  If a test fails, please inspect the corresponding output on the CI server and take the necessary steps, if needed, so that the code can compile cleanly again.  The test will be re-run each time the pull request is updated with a push to the remote branch on GitHub.  If you are unsure about what you need to change, ask a question in the discussion area of the pull request.
+Immediately after the submission, the LAMMPS continuing integration server at https://ci.lammps.org will download your submitted branch and perform a number of tests: it will tests whether it compiles cleanly under various conditions, it will also do a check on whether your included documentation translates cleanly and run some unit tests and other checks. Whether these tests are successful or fail will be recorded.  If a test fails, please inspect the corresponding output on the CI server and take the necessary steps, if needed, so that the code can compile cleanly again.  The test will be re-run each time the pull request is updated with a push to the remote branch on GitHub.  If you are unsure about what you need to change, ask a question in the discussion area of the pull request.
 Next a LAMMPS core developer will self-assign and do an overall technical assessment of the submission.  If you submitted a draft pull request, this will not happen unless you mark it "ready for review".  If you are not yet invited as a LAMMPS collaborator, and your contribution seems significant, you may also receive an invitation for collaboration on the LAMMPS repository.  As part of the assessment, the pull request will be categorized with labels. There are two special labels: `needs_work` (indicates that work from the submitter of the pull request is needed) and `work_in_progress` (indicates, that the assigned LAMMPS developer will make changes, if not done by the contributor who made the submit). 
 You may also receive comments and suggestions on the overall submission or specific details and on occasion specific requests for changes as part of the review. If permitted, also additional changes may be pushed into your pull request branch or a pull request may be filed in your LAMMPS fork on GitHub to include those changes.
 The LAMMPS developer may then decide to assign the pull request to another developer (e.g. when that developer is more knowledgeable about the submitted feature or enhancement or has written the modified code). It may also happen, that additional developers are requested to provide a review and approve the changes. For submissions, that may change the general behavior of LAMMPS, or where a possibility of unwanted side effects exists, additional tests may be requested by the assigned developer.

.github/workflows/codeql-analysis.yml

@@ -25,12 +25,12 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 2
 
     - name: Setup Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
 

.github/workflows/compile-msvc.yml

@@ -19,12 +19,12 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 2
 
     - name: Select Python version
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.11'
 

.github/workflows/coverity.yml

@@ -16,7 +16,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 2
 
@@ -59,16 +59,13 @@ jobs:
         -D BUILD_SHARED_LIBS=on \
         -D LAMMPS_SIZES=SMALLBIG \
         -D LAMMPS_EXCEPTIONS=off \
-        -D PKG_MESSAGE=on \
-        -D PKG_MPIIO=on \
         -D PKG_ATC=on \
         -D PKG_AWPMD=on \
-        -D PKG_BOCS=on \
-        -D PKG_EFF=on \
         -D PKG_H5MD=on \
         -D PKG_INTEL=on \
         -D PKG_LATBOLTZ=on \
         -D PKG_MANIFOLD=on \
+        -D PKG_MDI=on \
         -D PKG_MGPT=on \
         -D PKG_ML-PACE=on \
         -D PKG_ML-RANN=on \
@@ -77,7 +74,6 @@ jobs:
         -D PKG_PTM=on \
         -D PKG_QTB=on \
         -D PKG_SMTBQ=on \
-        -D PKG_TALLY=on \
         ../cmake
 
     - name: Run Coverity Scan

.github/workflows/unittest-macos.yml

@@ -21,7 +21,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 2
 

.gitignore

@@ -57,3 +57,6 @@ out/x86
 out/x64
 src/Makefile.package-e
 src/Makefile.package.settings-e
+/cmake/build/x64-Debug-Clang
+/install/x64-GUI-MSVC
+/install

bench/in.chain

@@ -1,25 +1,25 @@
 # FENE beadspring benchmark
 
-units		lj
+units           lj
-atom_style	bond
+atom_style      bond
 special_bonds   fene
 
-read_data	data.chain
+read_data       data.chain
 
-neighbor	0.4 bin
+neighbor        0.4 bin
-neigh_modify	every 1 delay 1
+neigh_modify    every 1 delay 1
 
 bond_style      fene
-bond_coeff	1 30.0 1.5 1.0 1.0
+bond_coeff      1 30.0 1.5 1.0 1.0
 
-pair_style	lj/cut 1.12
+pair_style      lj/cut 1.12
-pair_modify	shift yes
+pair_modify     shift yes
-pair_coeff	1 1 1.0 1.0 1.12
+pair_coeff      1 1 1.0 1.0 1.12
 
-fix		1 all nve
+fix             1 all nve
-fix		2 all langevin 1.0 1.0 10.0 904297
+fix             2 all langevin 1.0 1.0 10.0 904297
 
 thermo          100
-timestep	0.012
+timestep        0.012
 
-run		100
+run             100

bench/in.chain.scaled

@@ -1,32 +1,32 @@
 # FENE beadspring benchmark
 
-variable	x index 1
+variable        x index 1
-variable	y index 1
+variable        y index 1
-variable	z index 1
+variable        z index 1
 
-units		lj
+units           lj
-atom_style	bond
+atom_style      bond
-atom_modify	map hash
+atom_modify     map hash
 special_bonds   fene
 
-read_data	data.chain
+read_data       data.chain
 
-replicate	$x $y $z
+replicate       $x $y $z
 
-neighbor	0.4 bin
+neighbor        0.4 bin
-neigh_modify	every 1 delay 1
+neigh_modify    every 1 delay 1
 
 bond_style      fene
-bond_coeff	1 30.0 1.5 1.0 1.0
+bond_coeff      1 30.0 1.5 1.0 1.0
 
-pair_style	lj/cut 1.12
+pair_style      lj/cut 1.12
-pair_modify	shift yes
+pair_modify     shift yes
-pair_coeff	1 1 1.0 1.0 1.12
+pair_coeff      1 1 1.0 1.0 1.12
 
-fix		1 all nve
+fix             1 all nve
-fix		2 all langevin 1.0 1.0 10.0 904297
+fix             2 all langevin 1.0 1.0 10.0 904297
 
 thermo          100
-timestep	0.012
+timestep        0.012
 
-run		100
+run             100

bench/in.chute

@@ -1,33 +1,33 @@
 # LAMMPS benchmark of granular flow
 # chute flow of 32000 atoms with frozen base at 26 degrees
 
-units		lj
+units           lj
-atom_style	sphere
+atom_style      sphere
-boundary	p p fs
+boundary        p p fs
-newton		off
+newton          off
-comm_modify	vel yes
+comm_modify     vel yes
 
-read_data	data.chute
+read_data       data.chute
 
-pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
+pair_style      gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
-pair_coeff	* *
+pair_coeff      * *
 
-neighbor	0.1 bin
+neighbor        0.1 bin
-neigh_modify	every 1 delay 0
+neigh_modify    every 1 delay 0
 
-timestep	0.0001
+timestep        0.0001
 
-group		bottom type 2
+group           bottom type 2
-group		active subtract all bottom
+group           active subtract all bottom
-neigh_modify	exclude group bottom bottom
+neigh_modify    exclude group bottom bottom
 
-fix		1 all gravity 1.0 chute 26.0
+fix             1 all gravity 1.0 chute 26.0
-fix		2 bottom freeze
+fix             2 bottom freeze
-fix		3 active nve/sphere
+fix             3 active nve/sphere
 
-compute		1 all erotate/sphere
+compute         1 all erotate/sphere
-thermo_style	custom step atoms ke c_1 vol
+thermo_style    custom step atoms ke c_1 vol
-thermo_modify	norm no
+thermo_modify   norm no
-thermo		100
+thermo          100
 
-run		100
+run             100

bench/in.chute.scaled

@@ -1,38 +1,38 @@
 # LAMMPS benchmark of granular flow
 # chute flow of 32000 atoms with frozen base at 26 degrees
 
-variable	x index 1
+variable        x index 1
-variable	y index 1
+variable        y index 1
 
-units		lj
+units           lj
-atom_style	sphere
+atom_style      sphere
-boundary	p p fs
+boundary        p p fs
-newton		off
+newton          off
-comm_modify	vel yes
+comm_modify     vel yes
 
-read_data	data.chute
+read_data       data.chute
 
-replicate	$x $y 1
+replicate       $x $y 1
 
-pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
+pair_style      gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
-pair_coeff	* *
+pair_coeff      * *
 
-neighbor	0.1 bin
+neighbor        0.1 bin
-neigh_modify	every 1 delay 0
+neigh_modify    every 1 delay 0
 
-timestep	0.0001
+timestep        0.0001
 
-group		bottom type 2
+group           bottom type 2
-group		active subtract all bottom
+group           active subtract all bottom
-neigh_modify	exclude group bottom bottom
+neigh_modify    exclude group bottom bottom
 
-fix		1 all gravity 1.0 chute 26.0
+fix             1 all gravity 1.0 chute 26.0
-fix		2 bottom freeze
+fix             2 bottom freeze
-fix		3 active nve/sphere
+fix             3 active nve/sphere
 
-compute		1 all erotate/sphere
+compute         1 all erotate/sphere
-thermo_style	custom step atoms ke c_1 vol
+thermo_style    custom step atoms ke c_1 vol
-thermo_modify	norm no
+thermo_modify   norm no
-thermo		100
+thermo          100
 
-run		100
+run             100

bench/in.eam

@@ -1,32 +1,32 @@
 # bulk Cu lattice
 
-variable	x index 1
+variable        x index 1
-variable	y index 1
+variable        y index 1
-variable	z index 1
+variable        z index 1
 
-variable	xx equal 20*$x
+variable        xx equal 20*$x
-variable	yy equal 20*$y
+variable        yy equal 20*$y
-variable	zz equal 20*$z
+variable        zz equal 20*$z
 
-units		metal
+units           metal
-atom_style	atomic
+atom_style      atomic
 
-lattice		fcc 3.615
+lattice         fcc 3.615
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region          box block 0 ${xx} 0 ${yy} 0 ${zz}
-create_box	1 box
+create_box      1 box
-create_atoms	1 box
+create_atoms    1 box
 
-pair_style	eam
+pair_style      eam
-pair_coeff	1 1 Cu_u3.eam
+pair_coeff      1 1 Cu_u3.eam
 
-velocity	all create 1600.0 376847 loop geom
+velocity        all create 1600.0 376847 loop geom
 
-neighbor	1.0 bin
+neighbor        1.0 bin
 neigh_modify    every 1 delay 5 check yes
 
-fix		1 all nve
+fix             1 all nve
 
-timestep	0.005
+timestep        0.005
-thermo		50
+thermo          50
 
-run		100
+run             100

bench/in.lj

@@ -1,30 +1,30 @@
 # 3d Lennard-Jones melt
 
-variable	x index 1
+variable        x index 1
-variable	y index 1
+variable        y index 1
-variable	z index 1
+variable        z index 1
 
-variable	xx equal 20*$x
+variable        xx equal 20*$x
-variable	yy equal 20*$y
+variable        yy equal 20*$y
-variable	zz equal 20*$z
+variable        zz equal 20*$z
 
-units		lj
+units           lj
-atom_style	atomic
+atom_style      atomic
 
-lattice		fcc 0.8442
+lattice         fcc 0.8442
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region          box block 0 ${xx} 0 ${yy} 0 ${zz}
-create_box	1 box
+create_box      1 box
-create_atoms	1 box
+create_atoms    1 box
-mass		1 1.0
+mass            1 1.0
 
-velocity	all create 1.44 87287 loop geom
+velocity        all create 1.44 87287 loop geom
 
-pair_style	lj/cut 2.5
+pair_style      lj/cut 2.5
-pair_coeff	1 1 1.0 1.0 2.5
+pair_coeff      1 1 1.0 1.0 2.5
 
-neighbor	0.3 bin
+neighbor        0.3 bin
-neigh_modify	delay 0 every 20 check no
+neigh_modify    delay 0 every 20 check no
 
-fix		1 all nve
+fix             1 all nve
 
-run		100
+run             100

bench/in.rhodo

@@ -16,7 +16,7 @@ read_data       data.rhodo
 
 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
+                z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
 
 special_bonds   charmm
 
@@ -24,4 +24,4 @@ thermo          50
 thermo_style    multi
 timestep        2.0
 
-run		100
+run             100

bench/in.rhodo.scaled

@@ -1,14 +1,14 @@
 # Rhodopsin model
 
-variable	x index 1
+variable        x index 1
-variable	y index 1
+variable        y index 1
-variable	z index 1
+variable        z index 1
 
 units           real
 neigh_modify    delay 5 every 1
 
 atom_style      full
-atom_modify	map hash
+atom_modify     map hash
 bond_style      harmonic
 angle_style     charmm
 dihedral_style  charmm
@@ -19,11 +19,11 @@ kspace_style    pppm 1e-4
 
 read_data       data.rhodo
 
-replicate	$x $y $z
+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
+                z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
 
 special_bonds   charmm
 
@@ -31,4 +31,4 @@ thermo          50
 thermo_style    multi
 timestep        2.0
 
-run		100
+run             100

cmake/CMakeLists.jpeg

@@ -1,615 +0,0 @@
-cmake_minimum_required(VERSION 3.10)
-# When using CMake 3.4 and later, don't export symbols from executables unless
-# the CMAKE_ENABLE_EXPORTS variable is set.
-if(POLICY CMP0065)
-  cmake_policy(SET CMP0065 NEW)
-endif()
-if (POLICY CMP0077)
-  cmake_policy(SET CMP0077 NEW)
-endif()
-if(CMAKE_EXECUTABLE_SUFFIX)
-  set(CMAKE_EXECUTABLE_SUFFIX_TMP ${CMAKE_EXECUTABLE_SUFFIX})
-endif()
-
-project(libjpeg-turbo C)
-set(VERSION 2.1.3)
-set(COPYRIGHT_YEAR "1991-2022")
-string(REPLACE "." ";" VERSION_TRIPLET ${VERSION})
-list(GET VERSION_TRIPLET 0 VERSION_MAJOR)
-list(GET VERSION_TRIPLET 1 VERSION_MINOR)
-list(GET VERSION_TRIPLET 2 VERSION_REVISION)
-function(pad_number NUMBER OUTPUT_LEN)
-  string(LENGTH "${${NUMBER}}" INPUT_LEN)
-  if(INPUT_LEN LESS OUTPUT_LEN)
-    math(EXPR ZEROES "${OUTPUT_LEN} - ${INPUT_LEN} - 1")
-    set(NUM ${${NUMBER}})
-    foreach(C RANGE ${ZEROES})
-      set(NUM "0${NUM}")
-    endforeach()
-    set(${NUMBER} ${NUM} PARENT_SCOPE)
-  endif()
-endfunction()
-pad_number(VERSION_MINOR 3)
-pad_number(VERSION_REVISION 3)
-set(LIBJPEG_TURBO_VERSION_NUMBER ${VERSION_MAJOR}${VERSION_MINOR}${VERSION_REVISION})
-
-# CMake 3.14 and later sets CMAKE_MACOSX_BUNDLE to TRUE by default when
-# CMAKE_SYSTEM_NAME is iOS, tvOS, or watchOS, which breaks the libjpeg-turbo
-# build.  (Specifically, when CMAKE_MACOSX_BUNDLE is TRUE, executables for
-# Apple platforms are built as application bundles, which causes CMake to
-# complain that our install() directives for executables do not specify a
-# BUNDLE DESTINATION.  Even if CMake did not complain, building executables as
-# application bundles would break our iOS packages.)
-set(CMAKE_MACOSX_BUNDLE FALSE)
-
-string(TIMESTAMP DEFAULT_BUILD "%Y%m%d")
-set(BUILD ${DEFAULT_BUILD} CACHE STRING "Build string (default: ${DEFAULT_BUILD})")
-
-# NOTE: On Windows, this does nothing except when using MinGW or Cygwin.
-# CMAKE_BUILD_TYPE has no meaning in Visual Studio, and it always defaults to
-# Debug when using NMake.
-if(NOT CMAKE_BUILD_TYPE)
-  set(CMAKE_BUILD_TYPE Release)
-endif()
-message(STATUS "CMAKE_BUILD_TYPE = ${CMAKE_BUILD_TYPE}")
-
-message(STATUS "VERSION = ${VERSION}, BUILD = ${BUILD}")
-
-include(cmakescripts/PackageInfo.cmake)
-
-# Detect CPU type and whether we're building 64-bit or 32-bit code
-math(EXPR BITS "${CMAKE_SIZEOF_VOID_P} * 8")
-string(TOLOWER ${CMAKE_SYSTEM_PROCESSOR} CMAKE_SYSTEM_PROCESSOR_LC)
-set(COUNT 1)
-foreach(ARCH ${CMAKE_OSX_ARCHITECTURES})
-  if(COUNT GREATER 1)
-    message(FATAL_ERROR "The libjpeg-turbo build system does not support multiple values in CMAKE_OSX_ARCHITECTURES.")
-  endif()
-  math(EXPR COUNT "${COUNT}+1")
-endforeach()
-if(CMAKE_SYSTEM_PROCESSOR_LC MATCHES "x86_64" OR
-  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "amd64" OR
-  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "i[0-9]86" OR
-  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "x86" OR
-  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "ia32")
-  if(BITS EQUAL 64 OR CMAKE_C_COMPILER_ABI MATCHES "ELF X32")
-    set(CPU_TYPE x86_64)
-  else()
-    set(CPU_TYPE i386)
-  endif()
-  if(NOT CMAKE_SYSTEM_PROCESSOR STREQUAL ${CPU_TYPE})
-    set(CMAKE_SYSTEM_PROCESSOR ${CPU_TYPE})
-  endif()
-elseif(CMAKE_SYSTEM_PROCESSOR_LC STREQUAL "aarch64" OR
-  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "^arm")
-  if(BITS EQUAL 64)
-    set(CPU_TYPE arm64)
-  else()
-    set(CPU_TYPE arm)
-  endif()
-elseif(CMAKE_SYSTEM_PROCESSOR_LC MATCHES "^ppc" OR
-  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "^powerpc")
-  set(CPU_TYPE powerpc)
-else()
-  set(CPU_TYPE ${CMAKE_SYSTEM_PROCESSOR_LC})
-endif()
-if(CMAKE_OSX_ARCHITECTURES MATCHES "x86_64" OR
-  CMAKE_OSX_ARCHITECTURES MATCHES "arm64" OR
-  CMAKE_OSX_ARCHITECTURES MATCHES "i386")
-  set(CPU_TYPE ${CMAKE_OSX_ARCHITECTURES})
-endif()
-if(CMAKE_OSX_ARCHITECTURES MATCHES "ppc")
-  set(CPU_TYPE powerpc)
-endif()
-if(MSVC_IDE AND CMAKE_GENERATOR_PLATFORM MATCHES "arm64")
-  set(CPU_TYPE arm64)
-endif()
-
-message(STATUS "${BITS}-bit build (${CPU_TYPE})")
-
-macro(report_directory var)
-  if(CMAKE_INSTALL_${var} STREQUAL CMAKE_INSTALL_FULL_${var})
-    message(STATUS "CMAKE_INSTALL_${var} = ${CMAKE_INSTALL_${var}}")
-  else()
-    message(STATUS "CMAKE_INSTALL_${var} = ${CMAKE_INSTALL_${var}} (${CMAKE_INSTALL_FULL_${var}})")
-  endif()
-  mark_as_advanced(CLEAR CMAKE_INSTALL_${var})
-endmacro()
-
-set(DIRLIST "BINDIR;DATAROOTDIR;DOCDIR;INCLUDEDIR;LIBDIR")
-if(UNIX)
-  list(APPEND DIRLIST "MANDIR")
-endif()
-foreach(dir ${DIRLIST})
-  report_directory(${dir})
-endforeach()
-
-
-###############################################################################
-# CONFIGURATION OPTIONS
-###############################################################################
-
-macro(boolean_number var)
-  if(${var})
-    set(${var} 1 ${ARGN})
-  else()
-    set(${var} 0 ${ARGN})
-  endif()
-endmacro()
-
-option(ENABLE_SHARED "Build shared libraries" FALSE)
-boolean_number(ENABLE_SHARED)
-option(ENABLE_STATIC "Build static libraries" TRUE)
-boolean_number(ENABLE_STATIC)
-option(REQUIRE_SIMD "Generate a fatal error if SIMD extensions are not available for this platform (default is to fall back to a non-SIMD build)" FALSE)
-boolean_number(REQUIRE_SIMD)
-option(WITH_12BIT "Encode/decode JPEG images with 12-bit samples (implies WITH_ARITH_DEC=0 WITH_ARITH_ENC=0 WITH_JAVA=0 WITH_SIMD=0 WITH_TURBOJPEG=0 )" FALSE)
-boolean_number(WITH_12BIT)
-option(WITH_ARITH_DEC "Include arithmetic decoding support when emulating the libjpeg v6b API/ABI" TRUE)
-boolean_number(WITH_ARITH_DEC)
-option(WITH_ARITH_ENC "Include arithmetic encoding support when emulating the libjpeg v6b API/ABI" TRUE)
-boolean_number(WITH_ARITH_ENC)
-if(CMAKE_C_COMPILER_ABI MATCHES "ELF X32")
-  set(WITH_JAVA 0)
-else()
-  option(WITH_JAVA "Build Java wrapper for the TurboJPEG API library (implies ENABLE_SHARED=1)" FALSE)
-  boolean_number(WITH_JAVA)
-endif()
-option(WITH_JPEG7 "Emulate libjpeg v7 API/ABI (this makes ${CMAKE_PROJECT_NAME} backward-incompatible with libjpeg v6b)" FALSE)
-boolean_number(WITH_JPEG7)
-option(WITH_JPEG8 "Emulate libjpeg v8 API/ABI (this makes ${CMAKE_PROJECT_NAME} backward-incompatible with libjpeg v6b)" FALSE)
-boolean_number(WITH_JPEG8)
-option(WITH_MEM_SRCDST "Include in-memory source/destination manager functions when emulating the libjpeg v6b or v7 API/ABI" TRUE)
-boolean_number(WITH_MEM_SRCDST)
-option(WITH_SIMD "Include SIMD extensions, if available for this platform" FALSE)
-boolean_number(WITH_SIMD)
-option(WITH_TURBOJPEG "Include the TurboJPEG API library and associated test programs" FALSE)
-boolean_number(WITH_TURBOJPEG)
-option(WITH_FUZZ "Build fuzz targets" FALSE)
-
-macro(report_option var desc)
-  if(${var})
-    message(STATUS "${desc} enabled (${var} = ${${var}})")
-  else()
-    message(STATUS "${desc} disabled (${var} = ${${var}})")
-  endif()
-endmacro()
-
-if(WITH_JAVA)
-  set(ENABLE_SHARED 1)
-endif()
-
-# Explicitly setting CMAKE_POSITION_INDEPENDENT_CODE=FALSE disables PIC for all
-# targets, which will cause the shared library builds to fail.  Thus, if shared
-# libraries are enabled and CMAKE_POSITION_INDEPENDENT_CODE is explicitly set
-# to FALSE, we need to unset it, thus restoring the default behavior
-# (automatically using PIC for shared library targets.)
-if(DEFINED CMAKE_POSITION_INDEPENDENT_CODE AND
-  NOT CMAKE_POSITION_INDEPENDENT_CODE AND ENABLE_SHARED)
-  unset(CMAKE_POSITION_INDEPENDENT_CODE CACHE)
-endif()
-
-report_option(ENABLE_SHARED "Shared libraries")
-report_option(ENABLE_STATIC "Static libraries")
-
-if(ENABLE_SHARED)
-  set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR})
-endif()
-
-if(WITH_JPEG8 OR WITH_JPEG7)
-  set(WITH_ARITH_ENC 1)
-  set(WITH_ARITH_DEC 1)
-endif()
-if(WITH_JPEG8)
-  set(WITH_MEM_SRCDST 0)
-endif()
-
-if(WITH_12BIT)
-  set(WITH_ARITH_DEC 0)
-  set(WITH_ARITH_ENC 0)
-  set(WITH_JAVA 0)
-  set(WITH_SIMD 0)
-  set(WITH_TURBOJPEG 0)
-  set(BITS_IN_JSAMPLE 12)
-else()
-  set(BITS_IN_JSAMPLE 8)
-endif()
-report_option(WITH_12BIT "12-bit JPEG support")
-
-if(WITH_ARITH_DEC)
-  set(D_ARITH_CODING_SUPPORTED 1)
-endif()
-if(NOT WITH_12BIT)
-  report_option(WITH_ARITH_DEC "Arithmetic decoding support")
-endif()
-
-if(WITH_ARITH_ENC)
-  set(C_ARITH_CODING_SUPPORTED 1)
-endif()
-if(NOT WITH_12BIT)
-  report_option(WITH_ARITH_ENC "Arithmetic encoding support")
-endif()
-
-if(NOT WITH_12BIT)
-  report_option(WITH_TURBOJPEG "TurboJPEG API library")
-  report_option(WITH_JAVA "TurboJPEG Java wrapper")
-endif()
-
-if(WITH_MEM_SRCDST)
-  set(MEM_SRCDST_SUPPORTED 1)
-  set(MEM_SRCDST_FUNCTIONS "global:  jpeg_mem_dest;  jpeg_mem_src;")
-endif()
-if(NOT WITH_JPEG8)
-  report_option(WITH_MEM_SRCDST "In-memory source/destination managers")
-endif()
-
-set(SO_AGE 2)
-if(WITH_MEM_SRCDST)
-  set(SO_AGE 3)
-endif()
-
-if(WITH_JPEG8)
-  set(JPEG_LIB_VERSION 80)
-elseif(WITH_JPEG7)
-  set(JPEG_LIB_VERSION 70)
-else()
-  set(JPEG_LIB_VERSION 62)
-endif()
-
-math(EXPR JPEG_LIB_VERSION_DIV10 "${JPEG_LIB_VERSION} / 10")
-math(EXPR JPEG_LIB_VERSION_MOD10 "${JPEG_LIB_VERSION} % 10")
-if(JPEG_LIB_VERSION STREQUAL "62")
-  set(DEFAULT_SO_MAJOR_VERSION ${JPEG_LIB_VERSION})
-else()
-  set(DEFAULT_SO_MAJOR_VERSION ${JPEG_LIB_VERSION_DIV10})
-endif()
-if(JPEG_LIB_VERSION STREQUAL "80")
-  set(DEFAULT_SO_MINOR_VERSION 2)
-else()
-  set(DEFAULT_SO_MINOR_VERSION 0)
-endif()
-
-# This causes SO_MAJOR_VERSION/SO_MINOR_VERSION to reset to defaults if
-# WITH_JPEG7 or WITH_JPEG8 has changed.
-if((DEFINED WITH_JPEG7_INT AND NOT WITH_JPEG7 EQUAL WITH_JPEG7_INT) OR
-  (DEFINED WITH_JPEG8_INT AND NOT WITH_JPEG8 EQUAL WITH_JPEG8_INT))
-  set(FORCE_SO_VERSION "FORCE")
-endif()
-set(WITH_JPEG7_INT ${WITH_JPEG7} CACHE INTERNAL "")
-set(WITH_JPEG8_INT ${WITH_JPEG8} CACHE INTERNAL "")
-
-set(SO_MAJOR_VERSION ${DEFAULT_SO_MAJOR_VERSION} CACHE STRING
-  "Major version of the libjpeg API shared library (default: ${DEFAULT_SO_MAJOR_VERSION})"
-  ${FORCE_SO_VERSION})
-set(SO_MINOR_VERSION ${DEFAULT_SO_MINOR_VERSION} CACHE STRING
-  "Minor version of the libjpeg API shared library (default: ${DEFAULT_SO_MINOR_VERSION})"
-  ${FORCE_SO_VERSION})
-
-set(JPEG_LIB_VERSION_DECIMAL "${JPEG_LIB_VERSION_DIV10}.${JPEG_LIB_VERSION_MOD10}")
-message(STATUS "Emulating libjpeg API/ABI v${JPEG_LIB_VERSION_DECIMAL} (WITH_JPEG7 = ${WITH_JPEG7}, WITH_JPEG8 = ${WITH_JPEG8})")
-message(STATUS "libjpeg API shared library version = ${SO_MAJOR_VERSION}.${SO_AGE}.${SO_MINOR_VERSION}")
-
-# Because the TurboJPEG API library uses versioned symbols and changes the
-# names of functions whenever they are modified in a backward-incompatible
-# manner, it is always backward-ABI-compatible with itself, so the major and
-# minor SO versions don't change.  However, we increase the middle number (the
-# SO "age") whenever functions are added to the API.
-set(TURBOJPEG_SO_MAJOR_VERSION 0)
-set(TURBOJPEG_SO_AGE 2)
-set(TURBOJPEG_SO_VERSION 0.${TURBOJPEG_SO_AGE}.0)
-
-
-###############################################################################
-# COMPILER SETTINGS
-###############################################################################
-
-if(MSVC)
-  option(WITH_CRT_DLL
-    "Link all ${CMAKE_PROJECT_NAME} libraries and executables with the C run-time DLL (msvcr*.dll) instead of the static C run-time library (libcmt*.lib.)  The default is to use the C run-time DLL only with the libraries and executables that need it."
-    FALSE)
-  if(NOT WITH_CRT_DLL)
-    # Use the static C library for all build types
-    foreach(var CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE
-      CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO)
-      if(${var} MATCHES "/MD")
-        string(REGEX REPLACE "/MD" "/MT" ${var} "${${var}}")
-      endif()
-    endforeach()
-  endif()
-  add_definitions(-D_CRT_NONSTDC_NO_WARNINGS)
-endif()
-
-if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_C_COMPILER_ID STREQUAL "Clang")
-  # Use the maximum optimization level for release builds
-  foreach(var CMAKE_C_FLAGS_RELEASE CMAKE_C_FLAGS_RELWITHDEBINFO)
-    if(${var} MATCHES "-O2")
-      string(REGEX REPLACE "-O2" "-O3" ${var} "${${var}}")
-    endif()
-  endforeach()
-endif()
-
-if(CMAKE_SYSTEM_NAME STREQUAL "SunOS")
-  if(CMAKE_C_COMPILER_ID MATCHES "SunPro")
-    # Use the maximum optimization level for release builds
-    foreach(var CMAKE_C_FLAGS_RELEASE CMAKE_C_FLAGS_RELWITHDEBINFO)
-      if(${var} MATCHES "-xO3")
-        string(REGEX REPLACE "-xO3" "-xO5" ${var} "${${var}}")
-      endif()
-      if(${var} MATCHES "-xO2")
-        string(REGEX REPLACE "-xO2" "-xO5" ${var} "${${var}}")
-      endif()
-    endforeach()
-  endif()
-endif()
-
-string(TOUPPER ${CMAKE_BUILD_TYPE} CMAKE_BUILD_TYPE_UC)
-
-set(EFFECTIVE_C_FLAGS "${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${CMAKE_BUILD_TYPE_UC}}")
-message(STATUS "Compiler flags = ${EFFECTIVE_C_FLAGS}")
-
-set(EFFECTIVE_LD_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS_${CMAKE_BUILD_TYPE_UC}}")
-message(STATUS "Linker flags = ${EFFECTIVE_LD_FLAGS}")
-
-include(CheckCSourceCompiles)
-include(CheckIncludeFiles)
-include(CheckTypeSize)
-
-check_type_size("size_t" SIZE_T)
-check_type_size("unsigned long" UNSIGNED_LONG)
-
-if(SIZE_T EQUAL UNSIGNED_LONG)
-  check_c_source_compiles("int main(int argc, char **argv) { unsigned long a = argc;  return __builtin_ctzl(a); }"
-    HAVE_BUILTIN_CTZL)
-endif()
-if(MSVC)
-  check_include_files("intrin.h" HAVE_INTRIN_H)
-endif()
-
-if(UNIX)
-  if(CMAKE_CROSSCOMPILING)
-    set(RIGHT_SHIFT_IS_UNSIGNED 0)
-  else()
-    include(CheckCSourceRuns)
-    check_c_source_runs("
-      #include <stdio.h>
-      #include <stdlib.h>
-      int is_shifting_signed (long arg) {
-        long res = arg >> 4;
-        if (res == -0x7F7E80CL)
-          return 1; /* right shift is signed */
-        /* see if unsigned-shift hack will fix it. */
-        /* we can't just test exact value since it depends on width of long... */
-        res |= (~0L) << (32-4);
-        if (res == -0x7F7E80CL)
-          return 0; /* right shift is unsigned */
-        printf(\"Right shift isn't acting as I expect it to.\\\\n\");
-        printf(\"I fear the JPEG software will not work at all.\\\\n\\\\n\");
-        return 0; /* try it with unsigned anyway */
-      }
-      int main (void) {
-        exit(is_shifting_signed(-0x7F7E80B1L));
-      }" RIGHT_SHIFT_IS_UNSIGNED)
-  endif()
-endif()
-
-if(MSVC)
-  set(INLINE_OPTIONS "__inline;inline")
-else()
-  set(INLINE_OPTIONS "__inline__;inline")
-endif()
-option(FORCE_INLINE "Force function inlining" TRUE)
-boolean_number(FORCE_INLINE)
-if(FORCE_INLINE)
-  if(MSVC)
-    list(INSERT INLINE_OPTIONS 0 "__forceinline")
-  else()
-    list(INSERT INLINE_OPTIONS 0 "inline __attribute__((always_inline))")
-    list(INSERT INLINE_OPTIONS 0 "__inline__ __attribute__((always_inline))")
-  endif()
-endif()
-foreach(inline ${INLINE_OPTIONS})
-  check_c_source_compiles("${inline} static int foo(void) { return 0; } int main(void) { return foo(); }"
-    INLINE_WORKS)
-  if(INLINE_WORKS)
-    set(INLINE ${inline})
-    break()
-  endif()
-endforeach()
-if(NOT INLINE_WORKS)
-  message(FATAL_ERROR "Could not determine how to inline functions.")
-endif()
-message(STATUS "INLINE = ${INLINE} (FORCE_INLINE = ${FORCE_INLINE})")
-
-if(WITH_TURBOJPEG)
-  if(MSVC)
-    set(THREAD_LOCAL "__declspec(thread)")
-  else()
-    set(THREAD_LOCAL "__thread")
-  endif()
-  check_c_source_compiles("${THREAD_LOCAL} int i;  int main(void) { i = 0;  return i; }" HAVE_THREAD_LOCAL)
-  if(HAVE_THREAD_LOCAL)
-    message(STATUS "THREAD_LOCAL = ${THREAD_LOCAL}")
-  else()
-    message(WARNING "Thread-local storage is not available.  The TurboJPEG API library's global error handler will not be thread-safe.")
-    unset(THREAD_LOCAL)
-  endif()
-endif()
-
-if(UNIX AND NOT APPLE)
-  file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/conftest.map "VERS_1 { global: *; };")
-  set(CMAKE_REQUIRED_FLAGS
-    "-Wl,--version-script,${CMAKE_CURRENT_BINARY_DIR}/conftest.map")
-  check_c_source_compiles("int main(void) { return 0; }" HAVE_VERSION_SCRIPT)
-  set(CMAKE_REQUIRED_FLAGS)
-  file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/conftest.map)
-  if(HAVE_VERSION_SCRIPT)
-    message(STATUS "Linker supports GNU-style version scripts")
-    set(MAPFLAG "-Wl,--version-script,")
-    set(TJMAPFLAG "-Wl,--version-script,")
-  else()
-    message(STATUS "Linker does not support GNU-style version scripts")
-    if(CMAKE_SYSTEM_NAME STREQUAL "SunOS")
-      # The Solaris linker doesn't like our version script for the libjpeg API
-      # library, but the version script for the TurboJPEG API library should
-      # still work.
-      file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/conftest.map
-        "VERS_1 { global: foo;  local: *; }; VERS_2 { global: foo2; } VERS_1;")
-      set(CMAKE_REQUIRED_FLAGS "-Wl,-M,${CMAKE_CURRENT_BINARY_DIR}/conftest.map -shared")
-      check_c_source_compiles("int foo() { return 0; } int foo2() { return 2; }"
-        HAVE_MAPFILE)
-      set(CMAKE_REQUIRED_FLAGS)
-      file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/conftest.map)
-      if(HAVE_MAPFILE)
-        message(STATUS "Linker supports mapfiles")
-        set(TJMAPFLAG "-Wl,-M,")
-      else()
-        message(STATUS "Linker does not support mapfiles")
-      endif()
-    endif()
-  endif()
-endif()
-
-# Generate files
-if(WIN32)
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/win/jconfig.h.in jconfig.h)
-else()
-  configure_file(jconfig.h.in jconfig.h)
-endif()
-configure_file(jconfigint.h.in jconfigint.h)
-configure_file(jversion.h.in jversion.h)
-if(UNIX)
-  configure_file(libjpeg.map.in libjpeg.map)
-endif()
-
-# Include directories and compiler definitions
-include_directories(${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_CURRENT_SOURCE_DIR})
-
-
-###############################################################################
-# TARGETS
-###############################################################################
-
-if(CMAKE_EXECUTABLE_SUFFIX_TMP)
-  set(CMAKE_EXECUTABLE_SUFFIX ${CMAKE_EXECUTABLE_SUFFIX_TMP})
-endif()
-message(STATUS "CMAKE_EXECUTABLE_SUFFIX = ${CMAKE_EXECUTABLE_SUFFIX}")
-
-set(JPEG_SOURCES jcapimin.c jcapistd.c jccoefct.c jccolor.c jcdctmgr.c jchuff.c
-  jcicc.c jcinit.c jcmainct.c jcmarker.c jcmaster.c jcomapi.c jcparam.c
-  jcphuff.c jcprepct.c jcsample.c jctrans.c jdapimin.c jdapistd.c jdatadst.c
-  jdatasrc.c jdcoefct.c jdcolor.c jddctmgr.c jdhuff.c jdicc.c jdinput.c
-  jdmainct.c jdmarker.c jdmaster.c jdmerge.c jdphuff.c jdpostct.c jdsample.c
-  jdtrans.c jerror.c jfdctflt.c jfdctfst.c jfdctint.c jidctflt.c jidctfst.c
-  jidctint.c jidctred.c jquant1.c jquant2.c jutils.c jmemmgr.c jmemnobs.c)
-
-if(WITH_ARITH_ENC OR WITH_ARITH_DEC)
-  set(JPEG_SOURCES ${JPEG_SOURCES} jaricom.c)
-endif()
-
-if(WITH_ARITH_ENC)
-  set(JPEG_SOURCES ${JPEG_SOURCES} jcarith.c)
-endif()
-
-if(WITH_ARITH_DEC)
-  set(JPEG_SOURCES ${JPEG_SOURCES} jdarith.c)
-endif()
-
-if(WITH_SIMD)
-  add_subdirectory(simd)
-  if(NEON_INTRINSICS)
-    add_definitions(-DNEON_INTRINSICS)
-  endif()
-elseif(NOT WITH_12BIT)
-  message(STATUS "SIMD extensions: None (WITH_SIMD = ${WITH_SIMD})")
-endif()
-if(WITH_SIMD)
-  message(STATUS "SIMD extensions: ${CPU_TYPE} (WITH_SIMD = ${WITH_SIMD})")
-  if(MSVC_IDE OR XCODE)
-    set_source_files_properties(${SIMD_OBJS} PROPERTIES GENERATED 1)
-  endif()
-else()
-  add_library(simd OBJECT jsimd_none.c)
-  if(NOT WIN32 AND (CMAKE_POSITION_INDEPENDENT_CODE OR ENABLE_SHARED))
-    set_target_properties(simd PROPERTIES POSITION_INDEPENDENT_CODE 1)
-  endif()
-endif()
-
-if(WITH_JAVA)
-  add_subdirectory(java)
-endif()
-
-if(ENABLE_SHARED)
-  add_subdirectory(sharedlib)
-endif()
-
-if(ENABLE_STATIC)
-  add_library(jpeg-static STATIC ${JPEG_SOURCES} $<TARGET_OBJECTS:simd>
-    ${SIMD_OBJS})
-  if(NOT MSVC)
-    set_target_properties(jpeg-static PROPERTIES OUTPUT_NAME jpeg)
-  endif()
-endif()
-
-if(WITH_TURBOJPEG)
-  if(ENABLE_SHARED)
-    set(TURBOJPEG_SOURCES ${JPEG_SOURCES} $<TARGET_OBJECTS:simd> ${SIMD_OBJS}
-      turbojpeg.c transupp.c jdatadst-tj.c jdatasrc-tj.c rdbmp.c rdppm.c
-      wrbmp.c wrppm.c)
-    set(TJMAPFILE ${CMAKE_CURRENT_SOURCE_DIR}/turbojpeg-mapfile)
-    if(WITH_JAVA)
-      set(TURBOJPEG_SOURCES ${TURBOJPEG_SOURCES} turbojpeg-jni.c)
-      include_directories(${JAVA_INCLUDE_PATH} ${JAVA_INCLUDE_PATH2})
-      set(TJMAPFILE ${CMAKE_CURRENT_SOURCE_DIR}/turbojpeg-mapfile.jni)
-    endif()
-    if(MSVC)
-      configure_file(${CMAKE_SOURCE_DIR}/win/turbojpeg.rc.in
-        ${CMAKE_BINARY_DIR}/win/turbojpeg.rc)
-      set(TURBOJPEG_SOURCES ${TURBOJPEG_SOURCES}
-        ${CMAKE_BINARY_DIR}/win/turbojpeg.rc)
-    endif()
-    add_library(turbojpeg SHARED ${TURBOJPEG_SOURCES})
-    set_property(TARGET turbojpeg PROPERTY COMPILE_FLAGS
-      "-DBMP_SUPPORTED -DPPM_SUPPORTED")
-    if(WIN32)
-      set_target_properties(turbojpeg PROPERTIES DEFINE_SYMBOL DLLDEFINE)
-    endif()
-    if(MINGW)
-      set_target_properties(turbojpeg PROPERTIES LINK_FLAGS -Wl,--kill-at)
-    endif()
-    if(APPLE AND (NOT CMAKE_OSX_DEPLOYMENT_TARGET OR
-                  CMAKE_OSX_DEPLOYMENT_TARGET VERSION_GREATER 10.4))
-      if(NOT CMAKE_SHARED_LIBRARY_RUNTIME_C_FLAG)
-        set(CMAKE_SHARED_LIBRARY_RUNTIME_C_FLAG "-Wl,-rpath,")
-      endif()
-      set_target_properties(turbojpeg PROPERTIES MACOSX_RPATH 1)
-    endif()
-    set_target_properties(turbojpeg PROPERTIES
-      SOVERSION ${TURBOJPEG_SO_MAJOR_VERSION} VERSION ${TURBOJPEG_SO_VERSION})
-    if(TJMAPFLAG)
-      set_target_properties(turbojpeg PROPERTIES
-        LINK_FLAGS "${TJMAPFLAG}${TJMAPFILE}")
-    endif()
-  endif()
-
-  if(ENABLE_STATIC)
-    add_library(turbojpeg-static STATIC ${JPEG_SOURCES} $<TARGET_OBJECTS:simd>
-      ${SIMD_OBJS} turbojpeg.c transupp.c jdatadst-tj.c jdatasrc-tj.c rdbmp.c
-      rdppm.c wrbmp.c wrppm.c)
-    set_property(TARGET turbojpeg-static PROPERTY COMPILE_FLAGS
-      "-DBMP_SUPPORTED -DPPM_SUPPORTED")
-    if(NOT MSVC)
-      set_target_properties(turbojpeg-static PROPERTIES OUTPUT_NAME turbojpeg)
-    endif()
-  endif()
-endif()
-
-if(WIN32)
-  set(USE_SETMODE "-DUSE_SETMODE")
-endif()
-if(WITH_12BIT)
-  set(COMPILE_FLAGS "-DGIF_SUPPORTED -DPPM_SUPPORTED ${USE_SETMODE}")
-else()
-  set(COMPILE_FLAGS "-DBMP_SUPPORTED -DGIF_SUPPORTED -DPPM_SUPPORTED -DTARGA_SUPPORTED ${USE_SETMODE}")
-  set(CJPEG_BMP_SOURCES rdbmp.c rdtarga.c)
-  set(DJPEG_BMP_SOURCES wrbmp.c wrtarga.c)
-endif()

cmake/CMakeLists.png

@@ -1,741 +0,0 @@
-# CMakeLists.txt
-
-# Copyright (C) 2018 Cosmin Truta
-# Copyright (C) 2007,2009-2018 Glenn Randers-Pehrson
-# Written by Christian Ehrlicher, 2007
-# Revised by Roger Lowman, 2009-2010
-# Revised by Clifford Yapp, 2011-2012,2017
-# Revised by Roger Leigh, 2016
-# Revised by Andreas Franek, 2016
-# Revised by Sam Serrels, 2017
-# Revised by Vadim Barkov, 2017
-# Revised by Vicky Pfau, 2018
-# Revised by Cameron Cawley, 2018
-# Revised by Cosmin Truta, 2018
-# Revised by Kyle Bentley, 2018
-
-# This code is released under the libpng license.
-# For conditions of distribution and use, see the disclaimer
-# and license in png.h
-
-cmake_minimum_required(VERSION 3.10)
-cmake_policy(VERSION 3.1)
-# When using CMake 3.4 and later, don't export symbols from executables unless
-# the CMAKE_ENABLE_EXPORTS variable is set.
-if(POLICY CMP0065)
-  cmake_policy(SET CMP0065 NEW)
-endif()
-if (POLICY CMP0077)
-  cmake_policy(SET CMP0077 NEW)
-endif()
-set(CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS ON)
-
-project(libpng C ASM)
-enable_testing()
-
-set(PNGLIB_MAJOR 1)
-set(PNGLIB_MINOR 6)
-set(PNGLIB_RELEASE 37)
-set(PNGLIB_NAME libpng${PNGLIB_MAJOR}${PNGLIB_MINOR})
-set(PNGLIB_VERSION ${PNGLIB_MAJOR}.${PNGLIB_MINOR}.${PNGLIB_RELEASE})
-
-include(GNUInstallDirs)
-
-# needed packages
-
-# Allow users to specify location of Zlib.
-# Useful if zlib is being built alongside this as a sub-project.
-option(PNG_BUILD_ZLIB "Custom zlib Location, else find_package is used" ON)
-
-if(NOT PNG_BUILD_ZLIB)
-  find_package(ZLIB REQUIRED)
-  include_directories(${ZLIB_INCLUDE_DIR})
-endif()
-
-if(UNIX AND NOT APPLE AND NOT BEOS AND NOT HAIKU)
-  find_library(M_LIBRARY m)
-else()
-  # libm is not needed and/or not available
-  set(M_LIBRARY "")
-endif()
-
-# COMMAND LINE OPTIONS
-option(PNG_SHARED "Build shared lib" OFF)
-option(PNG_STATIC "Build static lib" ON)
-option(PNG_TESTS  "Build libpng tests" OFF)
-
-# Many more configuration options could be added here
-option(PNG_FRAMEWORK "Build OS X framework" OFF)
-option(PNG_DEBUG "Build with debug output" OFF)
-option(PNG_HARDWARE_OPTIMIZATIONS "Enable hardware optimizations" OFF)
-
-set(PNG_PREFIX "" CACHE STRING "Prefix to add to the API function names")
-set(DFA_XTRA "" CACHE FILEPATH "File containing extra configuration settings")
-
-if(PNG_HARDWARE_OPTIMIZATIONS)
-
-# set definitions and sources for arm
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "^arm" OR
-  CMAKE_SYSTEM_PROCESSOR MATCHES "^aarch64")
-  set(PNG_ARM_NEON_POSSIBLE_VALUES check on off)
-  set(PNG_ARM_NEON "check" CACHE STRING "Enable ARM NEON optimizations:
-     check: (default) use internal checking code;
-     off: disable the optimizations;
-     on: turn on unconditionally.")
-  set_property(CACHE PNG_ARM_NEON PROPERTY STRINGS
-     ${PNG_ARM_NEON_POSSIBLE_VALUES})
-  list(FIND PNG_ARM_NEON_POSSIBLE_VALUES ${PNG_ARM_NEON} index)
-  if(index EQUAL -1)
-    message(FATAL_ERROR
-            "PNG_ARM_NEON must be one of [${PNG_ARM_NEON_POSSIBLE_VALUES}]")
-  elseif(NOT ${PNG_ARM_NEON} STREQUAL "off")
-    set(libpng_arm_sources
-      arm/arm_init.c
-      arm/filter_neon.S
-      arm/filter_neon_intrinsics.c
-      arm/palette_neon_intrinsics.c)
-
-    if(${PNG_ARM_NEON} STREQUAL "on")
-      add_definitions(-DPNG_ARM_NEON_OPT=2)
-    elseif(${PNG_ARM_NEON} STREQUAL "check")
-      add_definitions(-DPNG_ARM_NEON_CHECK_SUPPORTED)
-    endif()
-  else()
-    add_definitions(-DPNG_ARM_NEON_OPT=0)
-  endif()
-endif()
-
-# set definitions and sources for powerpc
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "^powerpc*" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "^ppc64*")
-  set(PNG_POWERPC_VSX_POSSIBLE_VALUES on off)
-  set(PNG_POWERPC_VSX "on" CACHE STRING "Enable POWERPC VSX optimizations:
-     off: disable the optimizations.")
-  set_property(CACHE PNG_POWERPC_VSX PROPERTY STRINGS
-     ${PNG_POWERPC_VSX_POSSIBLE_VALUES})
-  list(FIND PNG_POWERPC_VSX_POSSIBLE_VALUES ${PNG_POWERPC_VSX} index)
-  if(index EQUAL -1)
-    message(FATAL_ERROR
-            "PNG_POWERPC_VSX must be one of [${PNG_POWERPC_VSX_POSSIBLE_VALUES}]")
-  elseif(NOT ${PNG_POWERPC_VSX} STREQUAL "off")
-    set(libpng_powerpc_sources
-      powerpc/powerpc_init.c
-      powerpc/filter_vsx_intrinsics.c)
-    if(${PNG_POWERPC_VSX} STREQUAL "on")
-      add_definitions(-DPNG_POWERPC_VSX_OPT=2)
-    endif()
-  else()
-    add_definitions(-DPNG_POWERPC_VSX_OPT=0)
-  endif()
-endif()
-
-# set definitions and sources for intel
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "^i?86" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "^x86_64*")
-  set(PNG_INTEL_SSE_POSSIBLE_VALUES on off)
-  set(PNG_INTEL_SSE "on" CACHE STRING "Enable INTEL_SSE optimizations:
-     off: disable the optimizations")
-  set_property(CACHE PNG_INTEL_SSE PROPERTY STRINGS
-     ${PNG_INTEL_SSE_POSSIBLE_VALUES})
-  list(FIND PNG_INTEL_SSE_POSSIBLE_VALUES ${PNG_INTEL_SSE} index)
-  if(index EQUAL -1)
-    message(FATAL_ERROR
-            "PNG_INTEL_SSE must be one of [${PNG_INTEL_SSE_POSSIBLE_VALUES}]")
-  elseif(NOT ${PNG_INTEL_SSE} STREQUAL "off")
-    set(libpng_intel_sources
-      intel/intel_init.c
-      intel/filter_sse2_intrinsics.c)
-    if(${PNG_INTEL_SSE} STREQUAL "on")
-      add_definitions(-DPNG_INTEL_SSE_OPT=1)
-    endif()
-  else()
-    add_definitions(-DPNG_INTEL_SSE_OPT=0)
-  endif()
-endif()
-
-# set definitions and sources for MIPS
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "mipsel*" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "mips64el*")
-  set(PNG_MIPS_MSA_POSSIBLE_VALUES on off)
-  set(PNG_MIPS_MSA "on" CACHE STRING "Enable MIPS_MSA optimizations:
-     off: disable the optimizations")
-  set_property(CACHE PNG_MIPS_MSA PROPERTY STRINGS
-     ${PNG_MIPS_MSA_POSSIBLE_VALUES})
-  list(FIND PNG_MIPS_MSA_POSSIBLE_VALUES ${PNG_MIPS_MSA} index)
-  if(index EQUAL -1)
-    message(FATAL_ERROR
-            "PNG_MIPS_MSA must be one of [${PNG_MIPS_MSA_POSSIBLE_VALUES}]")
-  elseif(NOT ${PNG_MIPS_MSA} STREQUAL "off")
-    set(libpng_mips_sources
-      mips/mips_init.c
-      mips/filter_msa_intrinsics.c)
-    if(${PNG_MIPS_MSA} STREQUAL "on")
-      add_definitions(-DPNG_MIPS_MSA_OPT=2)
-    endif()
-  else()
-    add_definitions(-DPNG_MIPS_MSA_OPT=0)
-  endif()
-endif()
-
-else(PNG_HARDWARE_OPTIMIZATIONS)
-
-# set definitions and sources for arm
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "^arm" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "^aarch64")
-  add_definitions(-DPNG_ARM_NEON_OPT=0)
-endif()
-
-# set definitions and sources for powerpc
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "^powerpc*" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "^ppc64*")
-  add_definitions(-DPNG_POWERPC_VSX_OPT=0)
-endif()
-
-# set definitions and sources for intel
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "^i?86" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "^x86_64*")
-  add_definitions(-DPNG_INTEL_SSE_OPT=0)
-endif()
-
-# set definitions and sources for MIPS
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "mipsel*" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "mips64el*")
-  add_definitions(-DPNG_MIPS_MSA_OPT=0)
-endif()
-
-endif(PNG_HARDWARE_OPTIMIZATIONS)
-
-# SET LIBNAME
-set(PNG_LIB_NAME png${PNGLIB_MAJOR}${PNGLIB_MINOR})
-
-# to distinguish between debug and release lib
-set(CMAKE_DEBUG_POSTFIX "d")
-
-include(CheckCSourceCompiles)
-option(ld-version-script "Enable linker version script" ON)
-if(ld-version-script AND NOT APPLE)
-  # Check if LD supports linker scripts.
-  file(WRITE "${CMAKE_CURRENT_BINARY_DIR}/conftest.map" "VERS_1 {
-        global: sym;
-        local: *;
-};
-
-VERS_2 {
-        global: sym2;
-                main;
-} VERS_1;
-")
-  set(CMAKE_REQUIRED_FLAGS_SAVE ${CMAKE_REQUIRED_FLAGS})
-  set(CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS} "-Wl,--version-script='${CMAKE_CURRENT_BINARY_DIR}/conftest.map'")
-  check_c_source_compiles("void sym(void) {}
-void sym2(void) {}
-int main(void) {return 0;}
-" HAVE_LD_VERSION_SCRIPT)
-  if(NOT HAVE_LD_VERSION_SCRIPT)
-    set(CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS_SAVE} "-Wl,-M -Wl,${CMAKE_CURRENT_BINARY_DIR}/conftest.map")
-  check_c_source_compiles("void sym(void) {}
-void sym2(void) {}
-int main(void) {return 0;}
-" HAVE_SOLARIS_LD_VERSION_SCRIPT)
-  endif()
-  set(CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS_SAVE})
-  file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/conftest.map")
-endif()
-
-# Find symbol prefix.  Likely obsolete and unnecessary with recent
-# toolchains (it's not done in many other projects).
-function(symbol_prefix)
-  set(SYMBOL_PREFIX)
-
-  execute_process(COMMAND "${CMAKE_C_COMPILER}" "-E" "-"
-                  INPUT_FILE /dev/null
-                  OUTPUT_VARIABLE OUT
-                  RESULT_VARIABLE STATUS)
-
-  if(CPP_FAIL)
-    message(WARNING "Failed to run the C preprocessor")
-  endif()
-
-  string(REPLACE "\n" ";" OUT "${OUT}")
-  foreach(line ${OUT})
-    string(REGEX MATCH "^PREFIX=" found_match "${line}")
-    if(found_match)
-      string(REGEX REPLACE "^PREFIX=(.*\)" "\\1" prefix "${line}")
-      string(REGEX MATCH "__USER_LABEL_PREFIX__" found_match "${prefix}")
-      if(found_match)
-        string(REGEX REPLACE "(.*)__USER_LABEL_PREFIX__(.*)" "\\1\\2" prefix "${prefix}")
-      endif()
-      set(SYMBOL_PREFIX "${prefix}")
-    endif()
-  endforeach()
-
-  message(STATUS "Symbol prefix: ${SYMBOL_PREFIX}")
-  set(SYMBOL_PREFIX "${SYMBOL_PREFIX}" PARENT_SCOPE)
-endfunction()
-
-if(UNIX)
-  symbol_prefix()
-endif()
-
-find_program(AWK NAMES gawk awk)
-
-include_directories(${CMAKE_CURRENT_BINARY_DIR})
-
-if(NOT AWK OR ANDROID)
-  # No awk available to generate sources; use pre-built pnglibconf.h
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/scripts/pnglibconf.h.prebuilt
-                 ${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h)
-  add_custom_target(genfiles) # Dummy
-else()
-  include(CMakeParseArguments)
-  # Generate .chk from .out with awk
-  # generate_chk(INPUT inputfile OUTPUT outputfile [DEPENDS dep1 [dep2...]])
-  function(generate_chk)
-    set(options)
-    set(oneValueArgs INPUT OUTPUT)
-    set(multiValueArgs DEPENDS)
-    cmake_parse_arguments(_GC "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
-    if(NOT _GC_INPUT)
-      message(FATAL_ERROR "generate_chk: Missing INPUT argument")
-    endif()
-    if(NOT _GC_OUTPUT)
-      message(FATAL_ERROR "generate_chk: Missing OUTPUT argument")
-    endif()
-
-    add_custom_command(OUTPUT "${_GC_OUTPUT}"
-                       COMMAND "${CMAKE_COMMAND}"
-                               "-DINPUT=${_GC_INPUT}"
-                               "-DOUTPUT=${_GC_OUTPUT}"
-                               -P "${CMAKE_CURRENT_BINARY_DIR}/scripts/genchk.cmake"
-                       DEPENDS "${_GC_INPUT}" ${_GC_DEPENDS}
-                       WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
-  endfunction()
-
-  # Generate .out from .c with awk
-  # generate_out(INPUT inputfile OUTPUT outputfile [DEPENDS dep1 [dep2...]])
-  function(generate_out)
-    set(options)
-    set(oneValueArgs INPUT OUTPUT)
-    set(multiValueArgs DEPENDS)
-    cmake_parse_arguments(_GO "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
-    if(NOT _GO_INPUT)
-      message(FATAL_ERROR "generate_out: Missing INPUT argument")
-    endif()
-    if(NOT _GO_OUTPUT)
-      message(FATAL_ERROR "generate_out: Missing OUTPUT argument")
-    endif()
-
-    add_custom_command(OUTPUT "${_GO_OUTPUT}"
-                       COMMAND "${CMAKE_COMMAND}"
-                               "-DINPUT=${_GO_INPUT}"
-                               "-DOUTPUT=${_GO_OUTPUT}"
-                               -P "${CMAKE_CURRENT_BINARY_DIR}/scripts/genout.cmake"
-                       DEPENDS "${_GO_INPUT}" ${_GO_DEPENDS}
-                       WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
-  endfunction()
-
-  # Generate specific source file with awk
-  # generate_source(OUTPUT outputfile [DEPENDS dep1 [dep2...]])
-  function(generate_source)
-    set(options)
-    set(oneValueArgs OUTPUT)
-    set(multiValueArgs DEPENDS)
-    cmake_parse_arguments(_GSO "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
-    if(NOT _GSO_OUTPUT)
-      message(FATAL_ERROR "generate_source: Missing OUTPUT argument")
-    endif()
-
-    add_custom_command(OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/${_GSO_OUTPUT}"
-                       COMMAND "${CMAKE_COMMAND}"
-                               "-DOUTPUT=${_GSO_OUTPUT}"
-                               -P "${CMAKE_CURRENT_BINARY_DIR}/scripts/gensrc.cmake"
-                       DEPENDS ${_GSO_DEPENDS}
-                       WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
-  endfunction()
-
-  # Copy file
-  function(generate_copy source destination)
-    add_custom_command(OUTPUT "${destination}"
-                       COMMAND "${CMAKE_COMMAND}" -E remove "${destination}"
-                       COMMAND "${CMAKE_COMMAND}" -E copy "${source}"
-                                                          "${destination}"
-                       DEPENDS "${source}")
-  endfunction()
-
-  # Generate scripts/pnglibconf.h
-  generate_source(OUTPUT "scripts/pnglibconf.c"
-                  DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/scripts/pnglibconf.dfa"
-                          "${CMAKE_CURRENT_SOURCE_DIR}/scripts/options.awk"
-                          "${CMAKE_CURRENT_SOURCE_DIR}/pngconf.h")
-
-  # Generate pnglibconf.c
-  generate_source(OUTPUT "pnglibconf.c"
-                  DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/scripts/pnglibconf.dfa"
-                          "${CMAKE_CURRENT_SOURCE_DIR}/scripts/options.awk"
-                          "${CMAKE_CURRENT_SOURCE_DIR}/pngconf.h")
-
-  if(PNG_PREFIX)
-    set(PNGLIBCONF_H_EXTRA_DEPENDS
-        "${CMAKE_CURRENT_BINARY_DIR}/scripts/prefix.out"
-        "${CMAKE_CURRENT_SOURCE_DIR}/scripts/macro.lst")
-    set(PNGPREFIX_H_EXTRA_DEPENDS
-        "${CMAKE_CURRENT_BINARY_DIR}/scripts/intprefix.out")
-  endif()
-
-  generate_out(INPUT "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.c"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.out")
-
-  # Generate pnglibconf.h
-  generate_source(OUTPUT "pnglibconf.h"
-                  DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.out"
-                          ${PNGLIBCONF_H_EXTRA_DEPENDS})
-
-  generate_out(INPUT "${CMAKE_CURRENT_SOURCE_DIR}/scripts/intprefix.c"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/intprefix.out"
-               DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h")
-
-  generate_out(INPUT "${CMAKE_CURRENT_SOURCE_DIR}/scripts/prefix.c"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/prefix.out"
-               DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/png.h"
-                       "${CMAKE_CURRENT_SOURCE_DIR}/pngconf.h"
-                       "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.out")
-
-  # Generate pngprefix.h
-  generate_source(OUTPUT "pngprefix.h"
-                  DEPENDS ${PNGPREFIX_H_EXTRA_DEPENDS})
-
-  generate_out(INPUT "${CMAKE_CURRENT_SOURCE_DIR}/scripts/sym.c"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/sym.out"
-               DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h")
-
-  generate_out(INPUT "${CMAKE_CURRENT_SOURCE_DIR}/scripts/symbols.c"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.out"
-               DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/png.h"
-                       "${CMAKE_CURRENT_SOURCE_DIR}/pngconf.h"
-                       "${CMAKE_CURRENT_SOURCE_DIR}/scripts/pnglibconf.h.prebuilt")
-
-  generate_out(INPUT "${CMAKE_CURRENT_SOURCE_DIR}/scripts/vers.c"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/vers.out"
-               DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/png.h"
-                       "${CMAKE_CURRENT_SOURCE_DIR}/pngconf.h"
-                       "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h")
-
-  generate_chk(INPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.out"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.chk"
-               DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/scripts/checksym.awk"
-                       "${CMAKE_CURRENT_SOURCE_DIR}/scripts/symbols.def")
-
-  add_custom_target(symbol-check DEPENDS
-                    "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.chk")
-
-  generate_copy("${CMAKE_CURRENT_BINARY_DIR}/scripts/sym.out"
-                "${CMAKE_CURRENT_BINARY_DIR}/libpng.sym")
-  generate_copy("${CMAKE_CURRENT_BINARY_DIR}/scripts/vers.out"
-                "${CMAKE_CURRENT_BINARY_DIR}/libpng.vers")
-
-  add_custom_target(genvers DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/libpng.vers")
-  add_custom_target(gensym DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/libpng.sym")
-
-  add_custom_target("genprebuilt"
-                    COMMAND "${CMAKE_COMMAND}"
-                            "-DOUTPUT=scripts/pnglibconf.h.prebuilt"
-                            -P "${CMAKE_CURRENT_BINARY_DIR}/scripts/gensrc.cmake"
-                    WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
-
-  # A single target handles generation of all generated files.  If
-  # they are depended upon separately by multiple targets, this
-  # confuses parallel make (it would require a separate top-level
-  # target for each file to track the dependencies properly).
-  add_custom_target(genfiles DEPENDS
-    "${CMAKE_CURRENT_BINARY_DIR}/libpng.sym"
-    "${CMAKE_CURRENT_BINARY_DIR}/libpng.vers"
-    "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.c"
-    "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h"
-    "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.out"
-    "${CMAKE_CURRENT_BINARY_DIR}/pngprefix.h"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/intprefix.out"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/pnglibconf.c"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/prefix.out"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/sym.out"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.chk"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.out"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/vers.out")
-endif(NOT AWK OR ANDROID)
-
-# OUR SOURCES
-set(libpng_public_hdrs
-  png.h
-  pngconf.h
-  "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h"
-)
-set(libpng_private_hdrs
-  pngpriv.h
-  pngdebug.h
-  pnginfo.h
-  pngstruct.h
-)
-if(AWK AND NOT ANDROID)
-  list(APPEND libpng_private_hdrs "${CMAKE_CURRENT_BINARY_DIR}/pngprefix.h")
-endif()
-set(libpng_sources
-  ${libpng_public_hdrs}
-  ${libpng_private_hdrs}
-  png.c
-  pngerror.c
-  pngget.c
-  pngmem.c
-  pngpread.c
-  pngread.c
-  pngrio.c
-  pngrtran.c
-  pngrutil.c
-  pngset.c
-  pngtrans.c
-  pngwio.c
-  pngwrite.c
-  pngwtran.c
-  pngwutil.c
-  ${libpng_arm_sources}
-  ${libpng_intel_sources}
-  ${libpng_mips_sources}
-  ${libpng_powerpc_sources}
-)
-set(pngtest_sources
-  pngtest.c
-)
-set(pngvalid_sources
-  contrib/libtests/pngvalid.c
-)
-set(pngstest_sources
-  contrib/libtests/pngstest.c
-)
-set(pngunknown_sources
-  contrib/libtests/pngunknown.c
-)
-set(pngimage_sources
-  contrib/libtests/pngimage.c
-)
-set(pngfix_sources
-  contrib/tools/pngfix.c
-)
-set(png_fix_itxt_sources
-  contrib/tools/png-fix-itxt.c
-)
-
-if(MSVC)
-  add_definitions(-D_CRT_SECURE_NO_DEPRECATE)
-endif()
-
-if(PNG_DEBUG)
-  add_definitions(-DPNG_DEBUG)
-endif()
-
-# NOW BUILD OUR TARGET
-include_directories(${CMAKE_CURRENT_SOURCE_DIR} ${ZLIB_INCLUDE_DIR})
-
-unset(PNG_LIB_TARGETS)
-
-if(PNG_STATIC)
-  # does not work without changing name
-  set(PNG_LIB_NAME_STATIC png_static)
-  add_library(png_static STATIC ${libpng_sources})
-  add_dependencies(png_static genfiles)
-  # MSVC doesn't use a different file extension for shared vs. static
-  # libs.  We are able to change OUTPUT_NAME to remove the _static
-  # for all other platforms.
-  if(NOT MSVC)
-    set_target_properties(png_static PROPERTIES
-      OUTPUT_NAME "${PNG_LIB_NAME}"
-      CLEAN_DIRECT_OUTPUT 1)
-  else()
-    set_target_properties(png_static PROPERTIES
-      OUTPUT_NAME "${PNG_LIB_NAME}_static"
-      CLEAN_DIRECT_OUTPUT 1)
-  endif()
-  list(APPEND PNG_LIB_TARGETS png_static)
-  if(MSVC)
-    # msvc does not append 'lib' - do it here to have consistent name
-    set_target_properties(png_static PROPERTIES PREFIX "lib")
-  endif()
-  target_link_libraries(png_static ${M_LIBRARY})
-endif()
-
-if(NOT PNG_LIB_TARGETS)
-  message(SEND_ERROR
-    "No library variant selected to build. "
-    "Please enable at least one of the following options: "
-    "PNG_STATIC, PNG_SHARED, PNG_FRAMEWORK")
-endif()
-
-# Set a variable with CMake code which:
-# Creates a symlink from src to dest (if possible) or alternatively
-# copies if different.
-include(CMakeParseArguments)
-
-function(create_symlink DEST_FILE)
-
-  cmake_parse_arguments(S "" "FILE;TARGET" "" ${ARGN})
-
-  if(NOT S_TARGET AND NOT S_FILE)
-    message(FATAL_ERROR "create_symlink: Missing TARGET or FILE argument")
-  endif()
-
-  if(S_TARGET AND S_FILE)
-    message(FATAL_ERROR "create_symlink: Both source file ${S_FILE} and build target ${S_TARGET} arguments are present; can only have one.")
-  endif()
-
-  if(S_FILE)
-    # If we don't need to symlink something that's coming from a build target,
-    # we can go ahead and symlink/copy at configure time.
-    if(CMAKE_HOST_WIN32 AND NOT CYGWIN)
-      execute_process(
-        COMMAND "${CMAKE_COMMAND}" -E copy_if_different ${S_FILE} ${DEST_FILE}
-        WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
-    else()
-      execute_process(
-        COMMAND ${CMAKE_COMMAND} -E create_symlink ${S_FILE} ${DEST_FILE}
-        WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
-    endif()
-  endif()
-
-  if(S_TARGET)
-    # We need to use generator expressions, which can be a bit tricky, so for
-    # simplicity make the symlink a POST_BUILD step and use the TARGET
-    # signature of add_custom_command.
-    if(CMAKE_HOST_WIN32 AND NOT CYGWIN)
-      add_custom_command(TARGET ${S_TARGET} POST_BUILD
-        COMMAND "${CMAKE_COMMAND}" -E copy_if_different $<TARGET_LINKER_FILE_NAME:${S_TARGET}> $<TARGET_LINKER_FILE_DIR:${S_TARGET}>/${DEST_FILE})
-    else()
-      add_custom_command(TARGET ${S_TARGET} POST_BUILD
-        COMMAND "${CMAKE_COMMAND}" -E create_symlink $<TARGET_LINKER_FILE_NAME:${S_TARGET}> $<TARGET_LINKER_FILE_DIR:${S_TARGET}>/${DEST_FILE})
-    endif()
-  endif()
-
-endfunction()
-
-# Create source generation scripts.
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/scripts/genchk.cmake.in
-               ${CMAKE_CURRENT_BINARY_DIR}/scripts/genchk.cmake @ONLY)
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/scripts/genout.cmake.in
-               ${CMAKE_CURRENT_BINARY_DIR}/scripts/genout.cmake @ONLY)
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/scripts/gensrc.cmake.in
-               ${CMAKE_CURRENT_BINARY_DIR}/scripts/gensrc.cmake @ONLY)
-
-# libpng is a library so default to 'lib'
-if(NOT DEFINED CMAKE_INSTALL_LIBDIR)
-  set(CMAKE_INSTALL_LIBDIR lib)
-endif()
-
-# CREATE PKGCONFIG FILES
-# We use the same files like ./configure, so we have to set its vars.
-# Only do this on Windows for Cygwin - the files don't make much sense outside
-# of a UNIX look-alike.
-if(NOT WIN32 OR CYGWIN OR MINGW)
-  set(prefix      ${CMAKE_INSTALL_PREFIX})
-  set(exec_prefix ${CMAKE_INSTALL_PREFIX})
-  set(libdir      ${CMAKE_INSTALL_FULL_LIBDIR})
-  set(includedir  ${CMAKE_INSTALL_FULL_INCLUDEDIR})
-  set(LIBS        "-lz -lm")
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libpng.pc.in
-    ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}.pc @ONLY)
-  create_symlink(libpng.pc FILE ${PNGLIB_NAME}.pc)
-
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libpng-config.in
-    ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}-config @ONLY)
-  create_symlink(libpng-config FILE ${PNGLIB_NAME}-config)
-endif()
-
-# SET UP LINKS
-if(PNG_SHARED)
-  set_target_properties(png PROPERTIES
-#   VERSION 16.${PNGLIB_RELEASE}.1.6.37
-    VERSION 16.${PNGLIB_RELEASE}.0
-    SOVERSION 16
-    CLEAN_DIRECT_OUTPUT 1)
-endif()
-
-# INSTALL
-if(NOT SKIP_INSTALL_LIBRARIES AND NOT SKIP_INSTALL_ALL)
-  install(TARGETS ${PNG_LIB_TARGETS}
-          EXPORT libpng
-          RUNTIME DESTINATION bin
-          LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-          ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
-          FRAMEWORK DESTINATION ${CMAKE_INSTALL_LIBDIR})
-
-  if(PNG_SHARED)
-    # Create a symlink for libpng.dll.a => libpng16.dll.a on Cygwin
-    if(CYGWIN OR MINGW)
-      create_symlink(libpng${CMAKE_IMPORT_LIBRARY_SUFFIX} TARGET png)
-      install(FILES $<TARGET_LINKER_FILE_DIR:png>/libpng${CMAKE_IMPORT_LIBRARY_SUFFIX}
-              DESTINATION ${CMAKE_INSTALL_LIBDIR})
-    endif()
-
-    if(NOT WIN32)
-      create_symlink(libpng${CMAKE_SHARED_LIBRARY_SUFFIX} TARGET png)
-      install(FILES $<TARGET_LINKER_FILE_DIR:png>/libpng${CMAKE_SHARED_LIBRARY_SUFFIX}
-              DESTINATION ${CMAKE_INSTALL_LIBDIR})
-    endif()
-  endif()
-
-  if(PNG_STATIC)
-    if(NOT WIN32 OR CYGWIN OR MINGW)
-      create_symlink(libpng${CMAKE_STATIC_LIBRARY_SUFFIX} TARGET png_static)
-      install(FILES $<TARGET_LINKER_FILE_DIR:png_static>/libpng${CMAKE_STATIC_LIBRARY_SUFFIX}
-              DESTINATION ${CMAKE_INSTALL_LIBDIR})
-    endif()
-  endif()
-endif()
-
-if(NOT SKIP_INSTALL_HEADERS AND NOT SKIP_INSTALL_ALL)
-  install(FILES ${libpng_public_hdrs} DESTINATION include)
-  install(FILES ${libpng_public_hdrs} DESTINATION include/${PNGLIB_NAME})
-endif()
-if(NOT SKIP_INSTALL_EXECUTABLES AND NOT SKIP_INSTALL_ALL)
-  if(NOT WIN32 OR CYGWIN OR MINGW)
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/libpng-config DESTINATION bin)
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}-config DESTINATION bin)
-  endif()
-endif()
-
-if(NOT SKIP_INSTALL_PROGRAMS AND NOT SKIP_INSTALL_ALL)
-  install(TARGETS ${PNG_BIN_TARGETS}
-          RUNTIME DESTINATION bin)
-endif()
-
-if(NOT SKIP_INSTALL_FILES AND NOT SKIP_INSTALL_ALL)
-  # Install man pages
-  if(NOT PNG_MAN_DIR)
-    set(PNG_MAN_DIR "share/man")
-  endif()
-  install(FILES libpng.3 libpngpf.3 DESTINATION ${PNG_MAN_DIR}/man3)
-  install(FILES png.5 DESTINATION ${PNG_MAN_DIR}/man5)
-  # Install pkg-config files
-  if(NOT CMAKE_HOST_WIN32 OR CYGWIN OR MINGW)
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libpng.pc
-            DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/libpng-config
-            DESTINATION bin)
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}.pc
-            DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}-config
-            DESTINATION bin)
-  endif()
-endif()
-
-# Create an export file that CMake users can include() to import our targets.
-if(NOT SKIP_INSTALL_EXPORT AND NOT SKIP_INSTALL_ALL)
-  install(EXPORT libpng DESTINATION lib/libpng FILE lib${PNG_LIB_NAME}.cmake)
-endif()
-
-# what's with libpng-manual.txt and all the extra files?
-
-# UNINSTALL
-# do we need this?
-
-# DIST
-# do we need this?
-
-# to create msvc import lib for mingw compiled shared lib
-# pexports libpng.dll > libpng.def
-# lib /def:libpng.def /machine:x86

cmake/CMakeLists.txt

@@ -1,8 +1,8 @@
+# -*- CMake -*- master configuration file for building LAMMPS
 ########################################
 # CMake build system
 # This file is part of LAMMPS
-# Created by Christoph Junghans and Richard Berger
+cmake_minimum_required(VERSION 3.16)
-cmake_minimum_required(VERSION 3.10)
 ########################################
 # set policy to silence warnings about ignoring <PackageName>_ROOT but use it
 if(POLICY CMP0074)
@@ -12,22 +12,11 @@ endif()
 if(POLICY CMP0075)
   cmake_policy(SET CMP0075 NEW)
 endif()
-# set policy to silence warnings about missing executable permissions in
-# pythonx.y-config when cross-compiling. review occasionally if it may be set to NEW
-if(POLICY CMP0109)
-  cmake_policy(SET CMP0109 OLD)
-endif()
 # set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
 if(POLICY CMP0135)
   cmake_policy(SET CMP0135 OLD)
 endif()
-########################################
+
-# Use CONFIGURE_DEPENDS as option for file(GLOB...) when available
-if(CMAKE_VERSION VERSION_LESS 3.12)
-  unset(CONFIGURE_DEPENDS)
-else()
-  set(CONFIGURE_DEPENDS CONFIGURE_DEPENDS)
-endif()
 ########################################
 
 project(lammps CXX)
@@ -116,7 +105,7 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
     if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
       set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
     else()
-      set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=2196")
+      set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=11074 -diag-disable=11076 -diag-disable=2196")
     endif()
   endif()
 endif()
@@ -136,15 +125,15 @@ if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL
   set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT} -Xcudafe --diag_suppress=unrecognized_pragma")
 endif()
 
-# we require C++11 without extensions. Kokkos requires at least C++14 (currently)
+# we require C++11 without extensions. Kokkos requires at least C++17 (currently)
 if(NOT CMAKE_CXX_STANDARD)
   set(CMAKE_CXX_STANDARD 11)
 endif()
 if(CMAKE_CXX_STANDARD LESS 11)
   message(FATAL_ERROR "C++ standard must be set to at least 11")
 endif()
-if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 14))
+if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 17))
-  set(CMAKE_CXX_STANDARD 14)
+  set(CMAKE_CXX_STANDARD 17)
 endif()
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
@@ -155,6 +144,7 @@ if(MSVC)
     add_compile_options(/Zc:__cplusplus)
     add_compile_options(/wd4244)
     add_compile_options(/wd4267)
+    add_compile_options(/wd4250)
     add_compile_options(/EHsc)
   endif()
   add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
@@ -168,17 +158,20 @@ endif()
 ########################################################################
 # User input options                                                   #
 ########################################################################
-# set path to python interpreter and thus enforcing python version when
+# backward compatibility with CMake before 3.12 and older LAMMPS documentation
-# in a virtual environment and PYTHON_EXECUTABLE is not set on command line
+if (PYTHON_EXECUTABLE)
-if(DEFINED ENV{VIRTUAL_ENV} AND NOT PYTHON_EXECUTABLE)
-  if(CMAKE_HOST_SYSTEM_NAME STREQUAL "Windows")
-    set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/Scripts/python.exe")
-  else()
-    set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/bin/python")
-  endif()
   set(Python_EXECUTABLE "${PYTHON_EXECUTABLE}")
+endif()
+# set path to python interpreter and thus enforcing python version when
+# in a virtual environment and Python_EXECUTABLE is not set on command line
+if(DEFINED ENV{VIRTUAL_ENV} AND NOT Python_EXECUTABLE)
+  if(CMAKE_HOST_SYSTEM_NAME STREQUAL "Windows")
+    set(Python_EXECUTABLE "$ENV{VIRTUAL_ENV}/Scripts/python.exe")
+  else()
+    set(Python_EXECUTABLE "$ENV{VIRTUAL_ENV}/bin/python")
+  endif()
   message(STATUS "Running in virtual environment: $ENV{VIRTUAL_ENV}\n"
-    "   Setting Python interpreter to: ${PYTHON_EXECUTABLE}")
+    "   Setting Python interpreter to: ${Python_EXECUTABLE}")
 endif()
 
 set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically")
@@ -192,6 +185,7 @@ option(BUILD_SHARED_LIBS "Build shared library" OFF)
 option(CMAKE_POSITION_INDEPENDENT_CODE "Create object compatible with shared libraries" ON)
 option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
 option(BUILD_LAMMPS_SHELL "Build and install the LAMMPS shell" OFF)
+option(BUILD_LAMMPS_GUI "Build and install the LAMMPS GUI" OFF)
 
 # Support using clang-tidy for C++ files with selected options
 set(ENABLE_CLANG_TIDY OFF CACHE BOOL "Include clang-tidy processing when compiling")
@@ -202,8 +196,8 @@ else()
 endif()
 
 include(GNUInstallDirs)
-file(GLOB ALL_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
+file(GLOB ALL_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
-file(GLOB MAIN_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/main.cpp)
+file(GLOB MAIN_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/main.cpp)
 list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})
 add_library(lammps ${ALL_SOURCES})
 
@@ -257,7 +251,6 @@ set(STANDARD_PACKAGES
   KIM
   KSPACE
   LATBOLTZ
-  LATTE
   LEPTON
   MACHDYN
   MANIFOLD
@@ -278,8 +271,6 @@ set(STANDARD_PACKAGES
   MOFFF
   MOLECULE
   MOLFILE
-  MPIIO
-  MSCG
   NETCDF
   ORIENT
   PERI
@@ -386,15 +377,9 @@ 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)" ${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(ML-IAP ML-SNAP)
-pkg_depends(MPIIO MPI)
 pkg_depends(ATC MANYBODY)
 pkg_depends(LATBOLTZ MPI)
 pkg_depends(SCAFACOS MPI)
@@ -405,6 +390,7 @@ pkg_depends(CG-DNA MOLECULE)
 pkg_depends(CG-DNA ASPHERE)
 pkg_depends(ELECTRODE KSPACE)
 pkg_depends(EXTRA-MOLECULE MOLECULE)
+pkg_depends(MESONT MOLECULE)
 
 # detect if we may enable OpenMP support by default
 set(BUILD_OMP_DEFAULT OFF)
@@ -442,14 +428,26 @@ if(BUILD_OMP)
   target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX)
 endif()
 
-if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_LATTE OR PKG_ELECTRODE OR PKG_RHEO)
+# lower C++ standard for fmtlib sources when using Intel classic compiler
+if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_STANDARD GREATER_EQUAL 17)
+    AND (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 2021.10))
+  message(STATUS "Lowering C++ standard for compiling fmtlib sources with Intel Classic compiler")
+  get_filename_component(LMP_UTILS_SRC "${LAMMPS_SOURCE_DIR}/utils.cpp" ABSOLUTE)
+  get_filename_component(LMP_VARIABLE_SRC "${LAMMPS_SOURCE_DIR}/variable.cpp" ABSOLUTE)
+  get_filename_component(FMT_FORMAT_SRC "${LAMMPS_SOURCE_DIR}/fmtlib_format.cpp" ABSOLUTE)
+  get_filename_component(FMT_OS_SRC "${LAMMPS_SOURCE_DIR}/fmtlib_os.cpp" ABSOLUTE)
+  set_source_files_properties("${FMT_FORMAT_SRC}" "${FMT_OS_SRC}" "${LMP_VARIABLE_SRC}" "${LMP_UTILS_SRC}"
+          PROPERTIES COMPILE_OPTIONS "-std=c++14")
+endif()
+
+if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_TOOLS OR PKG_RHEO)
   enable_language(C)
   if (NOT USE_INTERNAL_LINALG)
     find_package(LAPACK)
     find_package(BLAS)
   endif()
   if(NOT LAPACK_FOUND OR NOT BLAS_FOUND OR USE_INTERNAL_LINALG)
-    file(GLOB LINALG_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.cpp)
+    file(GLOB LINALG_SOURCES CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.cpp)
     add_library(linalg STATIC ${LINALG_SOURCES})
     set_target_properties(linalg PROPERTIES OUTPUT_NAME lammps_linalg${LAMMPS_MACHINE})
     set(BLAS_LIBRARIES "$<TARGET_FILE:linalg>")
@@ -467,12 +465,7 @@ 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_link_libraries(lammps PRIVATE JPEG::JPEG)
-    target_include_directories(lammps PRIVATE ${JPEG_INCLUDE_DIRS})
-    target_link_libraries(lammps PRIVATE ${JPEG_LIBRARIES})
-  else()
-    target_link_libraries(lammps PRIVATE JPEG::JPEG)
-  endif()
 endif()
 
 find_package(PNG QUIET)
@@ -522,7 +515,7 @@ else()
 endif()
 
 foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
-        PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM LATTE MSCG COMPRESS ML-PACE LEPTON)
+        PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()
@@ -584,8 +577,8 @@ endforeach()
 foreach(PKG ${STANDARD_PACKAGES})
   set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
 
-  file(GLOB ${PKG}_SOURCES ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
+  file(GLOB ${PKG}_SOURCES CONFIGURE_DEPENDS ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
-  file(GLOB ${PKG}_HEADERS ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.h)
+  file(GLOB ${PKG}_HEADERS CONFIGURE_DEPENDS ${${PKG}_SOURCES_DIR}/[^.]*.h)
 
   # check for package files in src directory due to old make system
   DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
@@ -601,19 +594,12 @@ foreach(PKG ${STANDARD_PACKAGES})
   RegisterPackages(${${PKG}_SOURCES_DIR})
 endforeach()
 
-# packages that need defines set
-foreach(PKG MPIIO)
-  if(PKG_${PKG})
-    target_compile_definitions(lammps PRIVATE -DLMP_${PKG})
-  endif()
-endforeach()
-
 # dedicated check for entire contents of accelerator packages
 foreach(PKG ${SUFFIX_PACKAGES})
   set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
 
-  file(GLOB ${PKG}_SOURCES ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
+  file(GLOB ${PKG}_SOURCES CONFIGURE_DEPENDS ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
-  file(GLOB ${PKG}_HEADERS ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.h)
+  file(GLOB ${PKG}_HEADERS CONFIGURE_DEPENDS ${${PKG}_SOURCES_DIR}/[^.]*.h)
 
   # check for package files in src directory due to old make system
   DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
@@ -627,7 +613,7 @@ endforeach()
 foreach(PKG_LIB POEMS ATC AWPMD H5MD)
   if(PKG_${PKG_LIB})
     string(TOLOWER "${PKG_LIB}" PKG_LIB)
-    file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${CONFIGURE_DEPENDS}
+    file(GLOB_RECURSE ${PKG_LIB}_SOURCES CONFIGURE_DEPENDS
       ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
     add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
     set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE})
@@ -797,9 +783,11 @@ include(Tools)
 include(Documentation)
 
 ###############################################################################
-# Install potential and force field files in data directory
+# Install bench, potential and force field files in data directory
 ###############################################################################
-set(LAMMPS_INSTALL_DATADIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps)
+set(LAMMPS_INSTALL_DATADIR ${CMAKE_INSTALL_DATADIR}/lammps)
+
+install(DIRECTORY ${LAMMPS_DIR}/bench DESTINATION ${LAMMPS_INSTALL_DATADIR})
 install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_DATADIR})
 if(BUILD_TOOLS)
   install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files DESTINATION ${LAMMPS_INSTALL_DATADIR})
@@ -820,20 +808,8 @@ install(
 # This is primarily for people that only want to use the Python wrapper.
 ###############################################################################
 if(BUILD_SHARED_LIBS)
-  if(CMAKE_VERSION VERSION_LESS 3.12)
+  # backward compatibility
-    # adjust so we find Python 3 versions before Python 2 on old systems with old CMake
+  find_package(Python COMPONENTS Interpreter)
-    set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
-    find_package(PythonInterp) # Deprecated since version 3.12
-    if(PYTHONINTERP_FOUND)
-      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
-    endif()
-  else()
-    # backward compatibility
-    if(PYTHON_EXECUTABLE)
-      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
-    endif()
-    find_package(Python COMPONENTS Interpreter)
-  endif()
   if(BUILD_IS_MULTI_CONFIG)
     set(MY_BUILD_DIR ${CMAKE_BINARY_DIR}/$<CONFIG>)
   else()
@@ -843,7 +819,7 @@ if(BUILD_SHARED_LIBS)
   if(Python_EXECUTABLE)
     add_custom_target(
       install-python ${Python_EXECUTABLE} ${LAMMPS_PYTHON_DIR}/install.py -p ${LAMMPS_PYTHON_DIR}/lammps
-              -l ${LIBLAMMPS_SHARED_BINARY} -w ${MY_BUILD_DIR}
+      -l ${LIBLAMMPS_SHARED_BINARY} -w ${MY_BUILD_DIR} -v ${LAMMPS_SOURCE_DIR}/version.h
       COMMENT "Installing LAMMPS Python module")
   else()
     add_custom_target(
@@ -892,13 +868,23 @@ else()
 endif()
 include(FeatureSummary)
 feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND)
+if(GIT_FOUND AND EXISTS ${LAMMPS_DIR}/.git)
+  execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty=-modified --always
+    OUTPUT_VARIABLE GIT_DESCRIBE
+    ERROR_QUIET
+    WORKING_DIRECTORY ${LAMMPS_DIR}
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+endif()
 message(STATUS "<<< Build configuration >>>
-   LAMMPS Version:   ${PROJECT_VERSION}
+   LAMMPS Version:   ${PROJECT_VERSION} ${GIT_DESCRIBE}
    Operating System: ${CMAKE_SYSTEM_NAME} ${CMAKE_LINUX_DISTRO} ${CMAKE_DISTRO_VERSION}
    CMake Version:    ${CMAKE_VERSION}
    Build type:       ${LAMMPS_BUILD_TYPE}
    Install path:     ${CMAKE_INSTALL_PREFIX}
    Generator:        ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}")
+if(CMAKE_CROSSCOMPILING)
+  message(STATUS "Cross compiling on ${CMAKE_HOST_SYSTEM}")
+endif()
 ###############################################################################
 # Print package summary
 ###############################################################################
@@ -942,11 +928,9 @@ 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)
-  get_target_property(OPTIONS lammps LINK_OPTIONS)
+if(OPTIONS)
-  if(OPTIONS)
+  message(STATUS "Linker options:   ${OPTIONS}")
-    message(STATUS "Linker options:   ${OPTIONS}")
-  endif()
 endif()
 if(CMAKE_EXE_LINKER_FLAGS)
   message(STATUS "Executable linker flags: ${CMAKE_EXE_LINKER_FLAGS}")
@@ -988,33 +972,53 @@ if(PKG_KOKKOS)
   endif()
 endif()
 if(PKG_KSPACE)
-  message(STATUS "<<< FFT settings >>>
+  if (LMP_HEFFTE)
--- Primary FFT lib:  ${FFT}")
+    message(STATUS "<<< FFT settings >>>
-  if(FFT_SINGLE)
+-- Primary FFT lib:  heFFTe")
-    message(STATUS "Using single precision FFTs")
+    if (HEFFTE_BACKEND)
-  else()
+      message(STATUS "heFFTe backend:  ${HEFFTE_BACKEND}")
-    message(STATUS "Using double precision FFTs")
-  endif()
-  if(FFT_FFTW_THREADS OR FFT_MKL_THREADS)
-    message(STATUS "Using threaded FFTs")
-  else()
-    message(STATUS "Using non-threaded FFTs")
-  endif()
-  if(PKG_KOKKOS)
-    if(Kokkos_ENABLE_CUDA)
-      if(FFT STREQUAL "KISS")
-        message(STATUS "Kokkos FFT: KISS")
-      else()
-        message(STATUS "Kokkos FFT: cuFFT")
-      endif()
-    elseif(Kokkos_ENABLE_HIP)
-      if(FFT STREQUAL "KISS")
-        message(STATUS "Kokkos FFT: KISS")
-      else()
-        message(STATUS "Kokkos FFT: hipFFT")
-      endif()
     else()
-      message(STATUS "Kokkos FFT: ${FFT}")
+      message(STATUS "heFFTe backend:  stock (builtin FFT implementation, tested for corrected but not optimized for production)")
+    endif()
+    if(FFT_SINGLE)
+      message(STATUS "Using single precision FFTs")
+    else()
+      message(STATUS "Using double precision FFTs")
+    endif()
+  else()
+    message(STATUS "<<< FFT settings >>>
+-- Primary FFT lib:  ${FFT}")
+    if(FFT_SINGLE)
+      message(STATUS "Using single precision FFTs")
+    else()
+      message(STATUS "Using double precision FFTs")
+    endif()
+    if(FFT_FFTW_THREADS OR FFT_MKL_THREADS)
+      message(STATUS "Using threaded FFTs")
+    else()
+      message(STATUS "Using non-threaded FFTs")
+    endif()
+    if (FFT_HEFFTE)
+      message(STATUS "Using distributed algorithms from heFTTe")
+    else()
+      message(STATUS "Using builtin distributed algorithms")
+    endif()
+    if(PKG_KOKKOS)
+      if(Kokkos_ENABLE_CUDA)
+        if(FFT STREQUAL "KISS")
+          message(STATUS "Kokkos FFT: KISS")
+        else()
+          message(STATUS "Kokkos FFT: cuFFT")
+        endif()
+      elseif(Kokkos_ENABLE_HIP)
+        if(FFT STREQUAL "KISS")
+          message(STATUS "Kokkos FFT: KISS")
+        else()
+          message(STATUS "Kokkos FFT: hipFFT")
+        endif()
+      else()
+        message(STATUS "Kokkos FFT: ${FFT}")
+      endif()
     endif()
   endif()
 endif()
@@ -1027,6 +1031,14 @@ endif()
 if(BUILD_LAMMPS_SHELL)
   message(STATUS "<<< Building LAMMPS Shell >>>")
 endif()
+if(BUILD_LAMMPS_GUI)
+  message(STATUS "<<< Building LAMMPS GUI >>>")
+  if(LAMMPS_GUI_USE_PLUGIN)
+    message(STATUS "Loading LAMMPS library as plugin at run time")
+  else()
+    message(STATUS "Linking LAMMPS library at compile time")
+  endif()
+endif()
 if(ENABLE_TESTING)
   message(STATUS "<<< Building Unit Tests >>>")
   if(ENABLE_COVERAGE)

cmake/CMakeLists.zlib

@@ -1,195 +0,0 @@
-cmake_minimum_required(VERSION 3.10)
-# When using CMake 3.4 and later, don't export symbols from executables unless
-# the CMAKE_ENABLE_EXPORTS variable is set.
-if(POLICY CMP0065)
-  cmake_policy(SET CMP0065 NEW)
-endif()
-if (POLICY CMP0077)
-  cmake_policy(SET CMP0077 NEW)
-endif()
-set(CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS ON)
-
-project(zlib C)
-
-set(VERSION "1.2.11")
-
-option(ASM686 "Enable building i686 assembly implementation" OFF)
-option(AMD64 "Enable building amd64 assembly implementation" OFF)
-
-set(INSTALL_BIN_DIR "${CMAKE_INSTALL_PREFIX}/bin" CACHE PATH "Installation directory for executables")
-set(INSTALL_LIB_DIR "${CMAKE_INSTALL_PREFIX}/lib" CACHE PATH "Installation directory for libraries")
-set(INSTALL_INC_DIR "${CMAKE_INSTALL_PREFIX}/include" CACHE PATH "Installation directory for headers")
-set(INSTALL_MAN_DIR "${CMAKE_INSTALL_PREFIX}/share/man" CACHE PATH "Installation directory for manual pages")
-set(INSTALL_PKGCONFIG_DIR "${CMAKE_INSTALL_PREFIX}/share/pkgconfig" CACHE PATH "Installation directory for pkgconfig (.pc) files")
-
-include(CheckTypeSize)
-include(CheckFunctionExists)
-include(CheckIncludeFile)
-include(CheckCSourceCompiles)
-
-check_include_file(sys/types.h HAVE_SYS_TYPES_H)
-check_include_file(stdint.h    HAVE_STDINT_H)
-check_include_file(stddef.h    HAVE_STDDEF_H)
-
-#
-# Check to see if we have large file support
-#
-set(CMAKE_REQUIRED_DEFINITIONS -D_LARGEFILE64_SOURCE=1)
-# We add these other definitions here because CheckTypeSize.cmake
-# in CMake 2.4.x does not automatically do so and we want
-# compatibility with CMake 2.4.x.
-if(HAVE_SYS_TYPES_H)
-    list(APPEND CMAKE_REQUIRED_DEFINITIONS -DHAVE_SYS_TYPES_H)
-endif()
-if(HAVE_STDINT_H)
-    list(APPEND CMAKE_REQUIRED_DEFINITIONS -DHAVE_STDINT_H)
-endif()
-if(HAVE_STDDEF_H)
-    list(APPEND CMAKE_REQUIRED_DEFINITIONS -DHAVE_STDDEF_H)
-endif()
-check_type_size(off64_t OFF64_T)
-check_type_size(off64_t OFF64_T)
-if(HAVE_OFF64_T)
-   add_definitions(-D_LARGEFILE64_SOURCE=1)
-endif()
-set(CMAKE_REQUIRED_DEFINITIONS) # clear variable
-
-#
-# Check for fseeko
-#
-check_function_exists(fseeko HAVE_FSEEKO)
-if(NOT HAVE_FSEEKO)
-    add_definitions(-DNO_FSEEKO)
-endif()
-
-#
-# Check for unistd.h
-#
-check_include_file(unistd.h Z_HAVE_UNISTD_H)
-
-if(MSVC)
-    set(CMAKE_DEBUG_POSTFIX "d")
-    add_definitions(-D_CRT_SECURE_NO_DEPRECATE)
-    add_definitions(-D_CRT_NONSTDC_NO_DEPRECATE)
-    include_directories(${CMAKE_CURRENT_SOURCE_DIR})
-endif()
-
-if(NOT CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_CURRENT_BINARY_DIR)
-    # If we're doing an out of source build and the user has a zconf.h
-    # in their source tree...
-    if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h)
-        file(RENAME ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h.included)
-  endif()
-endif()
-
-set(ZLIB_PC ${CMAKE_CURRENT_BINARY_DIR}/zlib.pc)
-configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/zlib.pc.cmakein
-		${ZLIB_PC} @ONLY)
-configure_file(	${CMAKE_CURRENT_SOURCE_DIR}/zconf.h.cmakein
-		${CMAKE_CURRENT_BINARY_DIR}/zconf.h @ONLY)
-include_directories(${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_SOURCE_DIR})
-
-
-#============================================================================
-# zlib
-#============================================================================
-
-set(ZLIB_PUBLIC_HDRS
-    ${CMAKE_CURRENT_BINARY_DIR}/zconf.h
-    zlib.h
-)
-set(ZLIB_PRIVATE_HDRS
-    crc32.h
-    deflate.h
-    gzguts.h
-    inffast.h
-    inffixed.h
-    inflate.h
-    inftrees.h
-    trees.h
-    zutil.h
-)
-set(ZLIB_SRCS
-    adler32.c
-    compress.c
-    crc32.c
-    deflate.c
-    gzclose.c
-    gzlib.c
-    gzread.c
-    gzwrite.c
-    inflate.c
-    infback.c
-    inftrees.c
-    inffast.c
-    trees.c
-    uncompr.c
-    zutil.c
-)
-
-if(NOT MINGW)
-    set(ZLIB_DLL_SRCS
-        win32/zlib1.rc # If present will override custom build rule below.
-    )
-endif()
-
-if(CMAKE_COMPILER_IS_GNUCC)
-    if(ASM686)
-        set(ZLIB_ASMS contrib/asm686/match.S)
-    elseif (AMD64)
-        set(ZLIB_ASMS contrib/amd64/amd64-match.S)
-    endif ()
-
-	if(ZLIB_ASMS)
-		add_definitions(-DASMV)
-		set_source_files_properties(${ZLIB_ASMS} PROPERTIES LANGUAGE C COMPILE_FLAGS -DNO_UNDERLINE)
-	endif()
-endif()
-
-if(MSVC)
-    if(ASM686)
-		ENABLE_LANGUAGE(ASM_MASM)
-        set(ZLIB_ASMS
-			contrib/masmx86/inffas32.asm
-			contrib/masmx86/match686.asm
-		)
-    elseif (AMD64)
-		ENABLE_LANGUAGE(ASM_MASM)
-        set(ZLIB_ASMS
-			contrib/masmx64/gvmat64.asm
-			contrib/masmx64/inffasx64.asm
-		)
-    endif()
-
-	if(ZLIB_ASMS)
-		add_definitions(-DASMV -DASMINF)
-	endif()
-endif()
-
-# parse the full version number from zlib.h and include in ZLIB_FULL_VERSION
-file(READ ${CMAKE_CURRENT_SOURCE_DIR}/zlib.h _zlib_h_contents)
-string(REGEX REPLACE ".*#define[ \t]+ZLIB_VERSION[ \t]+\"([-0-9A-Za-z.]+)\".*"
-    "\\1" ZLIB_FULL_VERSION ${_zlib_h_contents})
-
-if(MINGW)
-    # This gets us DLL resource information when compiling on MinGW.
-    if(NOT CMAKE_RC_COMPILER)
-        set(CMAKE_RC_COMPILER windres.exe)
-    endif()
-
-    add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/zlib1rc.obj
-                       COMMAND ${CMAKE_RC_COMPILER}
-                            -D GCC_WINDRES
-                            -I ${CMAKE_CURRENT_SOURCE_DIR}
-                            -I ${CMAKE_CURRENT_BINARY_DIR}
-                            -o ${CMAKE_CURRENT_BINARY_DIR}/zlib1rc.obj
-                            -i ${CMAKE_CURRENT_SOURCE_DIR}/win32/zlib1.rc)
-    set(ZLIB_DLL_SRCS ${CMAKE_CURRENT_BINARY_DIR}/zlib1rc.obj)
-endif(MINGW)
-
-add_library(zlibstatic STATIC ${ZLIB_SRCS} ${ZLIB_ASMS} ${ZLIB_PUBLIC_HDRS} ${ZLIB_PRIVATE_HDRS})
-
-if(UNIX)
-    # On unix-like platforms the library is almost always called libz
-   set_target_properties(zlibstatic PROPERTIES OUTPUT_NAME z)
-endif()

cmake/CMakeSettings.json

@@ -63,6 +63,11 @@
           "name": "ENABLE_TESTING",
           "value": "True",
           "type": "BOOL"
+        },
+        {
+          "name": "BUILD_LAMMPS_GUI",
+          "value": "False",
+          "type": "BOOL"
         }
       ]
     },
@@ -303,6 +308,54 @@
           "type": "STRING"
         }
       ]
+    },
+    {
+      "name": "x64-GUI-MSVC",
+      "generator": "Ninja",
+      "configurationType": "Release",
+      "buildRoot": "${workspaceRoot}\\build\\${name}",
+      "installRoot": "${workspaceRoot}\\install\\${name}",
+      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -D QT_DIR=C:\\Qt\\5.15.2\\msvc2019_64\\lib\\cmake\\Qt5  -D Qt5_DIR=C:\\Qt\\5.15.2\\msvc2019_64\\lib\\cmake\\Qt5",
+      "buildCommandArgs": "",
+      "ctestCommandArgs": "-V",
+      "inheritEnvironments": [ "msvc_x64_x64" ],
+      "variables": [
+        {
+          "name": "BUILD_SHARED_LIBS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "BUILD_TOOLS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "LAMMPS_EXCEPTIONS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "ENABLE_TESTING",
+          "value": "False",
+          "type": "BOOL"
+        },
+        {
+          "name": "BUILD_MPI",
+          "value": "False",
+          "type": "BOOL"
+        },
+        {
+          "name": "WITH_PNG",
+          "value": "False",
+          "type": "BOOL"
+        },
+        {
+          "name": "BUILD_LAMMPS_GUI",
+          "value": "True",
+          "type": "BOOL"
+        }
+      ]
     }
   ]
 }

cmake/Modules/CodingStandard.cmake

@@ -1,15 +1,11 @@
-if(CMAKE_VERSION VERSION_LESS 3.12)
+# use default (or custom) Python executable, if version is sufficient
-    find_package(PythonInterp 3.5 QUIET) # Deprecated since version 3.12
+if(Python_VERSION VERSION_GREATER_EQUAL 3.6)
-    if(PYTHONINTERP_FOUND)
+  set(Python3_EXECUTABLE ${Python_EXECUTABLE})
-        set(Python3_EXECUTABLE ${PYTHON_EXECUTABLE})
-        set(Python3_VERSION ${PYTHON_VERSION_STRING})
-    endif()
-else()
-    find_package(Python3 COMPONENTS Interpreter QUIET)
 endif()
+find_package(Python3 COMPONENTS Interpreter)
 
 if(Python3_EXECUTABLE)
-    if(Python3_VERSION VERSION_GREATER_EQUAL 3.5)
+    if(Python3_VERSION VERSION_GREATER_EQUAL 3.6)
         add_custom_target(
           check-whitespace
           ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .

cmake/Modules/DetectHIPInstallation.cmake

@@ -0,0 +1,16 @@
+if(NOT DEFINED HIP_PATH)
+    if(NOT DEFINED ENV{HIP_PATH})
+        message(FATAL_ERROR "HIP support requires HIP_PATH to be defined.\n"
+        "Either pass the HIP_PATH as a CMake option via -DHIP_PATH=... or set the HIP_PATH environment variable.")
+    else()
+        set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to HIP installation")
+    endif()
+endif()
+if(NOT DEFINED ROCM_PATH)
+    if(NOT DEFINED ENV{ROCM_PATH})
+        set(ROCM_PATH "/opt/rocm" CACHE PATH "Path to ROCm installation")
+    else()
+        set(ROCM_PATH $ENV{ROCM_PATH} CACHE PATH "Path to ROCm installation")
+    endif()
+endif()
+list(APPEND CMAKE_PREFIX_PATH ${HIP_PATH} ${ROCM_PATH})

cmake/Modules/Documentation.cmake

@@ -4,21 +4,19 @@
 option(BUILD_DOC "Build LAMMPS HTML documentation" OFF)
 
 if(BUILD_DOC)
-  # Sphinx 3.x requires at least Python 3.5
+  # Current Sphinx versions require at least Python 3.8
-  if(CMAKE_VERSION VERSION_LESS 3.12)
+  # use default (or custom) Python executable, if version is sufficient
-    find_package(PythonInterp 3.5 REQUIRED)
+  if(Python_VERSION VERSION_GREATER_EQUAL 3.8)
-    set(VIRTUALENV ${PYTHON_EXECUTABLE} -m venv)
+    set(Python3_EXECUTABLE ${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 venv)
   endif()
+  find_package(Python3 REQUIRED COMPONENTS Interpreter)
+  if(Python3_VERSION VERSION_LESS 3.8)
+    message(FATAL_ERROR "Python 3.8 and up is required to build the HTML documentation")
+  endif()
+  set(VIRTUALENV ${Python3_EXECUTABLE} -m venv)
+
   find_package(Doxygen 1.8.10 REQUIRED)
-
+  file(GLOB DOC_SOURCES CONFIGURE_DEPENDS ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
-  file(GLOB DOC_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
-
 
   add_custom_command(
     OUTPUT docenv
@@ -76,7 +74,7 @@ if(BUILD_DOC)
       message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
     endif()
     execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
-    file(GLOB MATHJAX_VERSION_DIR ${CONFIGURE_DEPENDS} ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
+    file(GLOB MATHJAX_VERSION_DIR CONFIGURE_DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
     execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax)
   endif()
 

cmake/Modules/FindClangFormat.cmake

@@ -1,5 +1,7 @@
 # Find clang-format
 find_program(ClangFormat_EXECUTABLE NAMES clang-format
+                                          clang-format-17.0
+                                          clang-format-16.0
                                           clang-format-15.0
                                           clang-format-14.0
                                           clang-format-13.0
@@ -19,7 +21,7 @@ if(ClangFormat_EXECUTABLE)
                   OUTPUT_VARIABLE clang_format_version
                   ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
 
-  if(clang_format_version MATCHES "^(Ubuntu |)clang-format version .*")
+  if(clang_format_version MATCHES "^(Ubuntu |Debian |)clang-format version .*")
     # Arch Linux output:
     # clang-format version 10.0.0
     #
@@ -32,9 +34,15 @@ if(ClangFormat_EXECUTABLE)
     # Ubuntu 22.04 LTS output:
     # Ubuntu clang-format version 14.0.0-1ubuntu1
     #
+    # Debian 11 output:
+    # Debian clang-format version 11.0.1-2
+    #
+    # Debian 12 output:
+    # Debian clang-format version 14.0.6
+    #
     # Fedora 36 output:
     # clang-format version 14.0.5 (Fedora 14.0.5-1.fc36)
-    string(REGEX REPLACE "^(Ubuntu |)clang-format version ([0-9.]+).*"
+    string(REGEX REPLACE "^(Ubuntu |Debian |)clang-format version ([0-9.]+).*"
                          "\\2"
                          ClangFormat_VERSION
                          "${clang_format_version}")

cmake/Modules/FindCythonize.cmake

@@ -7,15 +7,7 @@
 # adapted from https://github.com/cmarshall108/cython-cmake-example/blob/master/cmake/FindCython.cmake
 #=============================================================================
 
-if(CMAKE_VERSION VERSION_LESS 3.12)
+find_package(Python 3.6 COMPONENTS Interpreter QUIET)
-    set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
-    find_package(PythonInterp 3.6 QUIET) # Deprecated since version 3.12
-    if(PYTHONINTERP_FOUND)
-        set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
-    endif()
-else()
-    find_package(Python 3.6 COMPONENTS Interpreter QUIET)
-endif()
 
 # Use the Cython executable that lives next to the Python executable
 # if it is a local installation.

cmake/Modules/LAMMPSInterfacePlugin.cmake

@@ -28,9 +28,8 @@ if(MSVC)
     add_compile_options(/Zc:__cplusplus)
     add_compile_options(/wd4244)
     add_compile_options(/wd4267)
-    if(LAMMPS_EXCEPTIONS)
+    add_compile_options(/wd4250)
-      add_compile_options(/EHsc)
+    add_compile_options(/EHsc)
-    endif()
   endif()
   add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
 endif()
@@ -65,7 +64,7 @@ endfunction(validate_option)
 
 # helper function for getting the most recently modified file or folder from a glob pattern
 function(get_newest_file path variable)
-  file(GLOB _dirs ${CONFIGURE_DEPENDS} ${path})
+  file(GLOB _dirs CONFIGURE_DEPENDS ${path})
   set(_besttime 2000-01-01T00:00:00)
   set(_bestfile "<unknown>")
   foreach(_dir ${_dirs})

cmake/Modules/LAMMPSUtils.cmake

@@ -41,7 +41,7 @@ endfunction()
 
 # helper function for getting the most recently modified file or folder from a glob pattern
 function(get_newest_file path variable)
-  file(GLOB _dirs ${CONFIGURE_DEPENDS} ${path})
+  file(GLOB _dirs CONFIGURE_DEPENDS ${path})
   set(_besttime 2000-01-01T00:00:00)
   set(_bestfile "<unknown>")
   foreach(_dir ${_dirs})
@@ -80,20 +80,20 @@ endfunction()
 
 function(check_for_autogen_files source_dir)
     message(STATUS "Running check for auto-generated files from make-based build system")
-    file(GLOB SRC_AUTOGEN_FILES ${CONFIGURE_DEPENDS} ${source_dir}/style_*.h)
+    file(GLOB SRC_AUTOGEN_FILES CONFIGURE_DEPENDS ${source_dir}/style_*.h)
-    file(GLOB SRC_AUTOGEN_PACKAGES ${CONFIGURE_DEPENDS} ${source_dir}/packages_*.h)
+    file(GLOB SRC_AUTOGEN_PACKAGES CONFIGURE_DEPENDS ${source_dir}/packages_*.h)
     list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/lmpinstalledpkgs.h ${source_dir}/lmpgitversion.h)
-    list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/mliap_model_python_couple.h ${source_dir}/mliap_model_python_couple.cpp)
+    list(APPEND SRC_AUTOGEN_FILES ${source_dir}/mliap_model_python_couple.h ${source_dir}/mliap_model_python_couple.cpp)
     foreach(_SRC ${SRC_AUTOGEN_FILES})
       get_filename_component(FILENAME "${_SRC}" NAME)
       if(EXISTS ${source_dir}/${FILENAME})
         message(FATAL_ERROR "\n########################################################################\n"
-                              "Found header file(s) generated by the make-based build system\n"
+                            "Found header file ${source_dir}/${FILENAME} generated by the make-based build system\n"
-                              "\n"
+                            "\n"
-                              "Please run\n"
+                            "Please run\n"
-                              "make -C ${source_dir} purge\n"
+                            "make -C ${source_dir} purge\n"
-                              "to remove\n"
+                            "to remove\n"
-                              "########################################################################")
+                            "########################################################################")
       endif()
     endforeach()
 endfunction()
@@ -152,7 +152,7 @@ endfunction(FetchPotentials)
 # set CMAKE_LINUX_DISTRO and CMAKE_DISTRO_VERSION on Linux
 if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (EXISTS /etc/os-release))
   file(STRINGS /etc/os-release distro REGEX "^NAME=")
-  string(REGEX REPLACE "NAME=\"?([^\"]*)\"?" "\\1" distro "${distro}")
+  string(REGEX REPLACE "NAME=\"?([^ ]+).*\"?" "\\1" distro "${distro}")
   file(STRINGS /etc/os-release disversion REGEX "^VERSION_ID=")
   string(REGEX REPLACE "VERSION_ID=\"?([^\"]*)\"?" "\\1" disversion "${disversion}")
   set(CMAKE_LINUX_DISTRO ${distro})

cmake/Modules/Packages/COLVARS.cmake

@@ -1,6 +1,6 @@
 set(COLVARS_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars)
 
-file(GLOB COLVARS_SOURCES ${CONFIGURE_DEPENDS} ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
+file(GLOB COLVARS_SOURCES CONFIGURE_DEPENDS ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
 
 option(COLVARS_DEBUG "Enable debugging messages for Colvars (quite verbose)" OFF)
 

cmake/Modules/Packages/GPU.cmake

@@ -39,7 +39,7 @@ if (PKG_AMOEBA)
               ${GPU_SOURCES_DIR}/amoeba_convolution_gpu.cpp)
 endif()
 
-file(GLOB GPU_LIB_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
+file(GLOB GPU_LIB_SOURCES CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
 file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
 
 if(GPU_API STREQUAL "CUDA")
@@ -64,11 +64,13 @@ if(GPU_API STREQUAL "CUDA")
     endif()
     set(GPU_CUDA_MPS_FLAGS "-DCUDA_MPS_SUPPORT")
   endif()
+  option(CUDA_BUILD_MULTIARCH "Enable building CUDA kernels for all supported GPU architectures" ON)
+  mark_as_advanced(GPU_BUILD_MULTIARCH)
 
   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 ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h)
+  file(GLOB GPU_LIB_OLD_CUBIN_HEADERS CONFIGURE_DEPENDS ${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"
@@ -78,79 +80,81 @@ if(GPU_API STREQUAL "CUDA")
       "########################################################################")
   endif()
 
-  file(GLOB GPU_LIB_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
+  file(GLOB GPU_LIB_CU CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
   list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
 
   cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
 
   if(CUDPP_OPT)
     cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
-    file(GLOB GPU_LIB_CUDPP_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
+    file(GLOB GPU_LIB_CUDPP_SOURCES CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
-    file(GLOB GPU_LIB_CUDPP_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
+    file(GLOB GPU_LIB_CUDPP_CU CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
   endif()
 
   # build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
   # --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
   set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH}")
 
-  # apply the following to build "fat" CUDA binaries only for known CUDA toolkits since version 8.0
+  if(CUDA_BUILD_MULTIARCH)
-  # only the Kepler achitecture and beyond is supported
+    # apply the following to build "fat" CUDA binaries only for known CUDA toolkits since version 8.0
-  # comparison chart according to: https://en.wikipedia.org/wiki/CUDA#GPUs_supported
+    # only the Kepler achitecture and beyond is supported
-  if(CUDA_VERSION VERSION_LESS 8.0)
+    # comparison chart according to: https://en.wikipedia.org/wiki/CUDA#GPUs_supported
-    message(FATAL_ERROR "CUDA Toolkit version 8.0 or later is required")
+    if(CUDA_VERSION VERSION_LESS 8.0)
-  elseif(CUDA_VERSION VERSION_GREATER_EQUAL "13.0")
+      message(FATAL_ERROR "CUDA Toolkit version 8.0 or later is required")
-    message(WARNING "Untested CUDA Toolkit version ${CUDA_VERSION}. Use at your own risk")
+    elseif(CUDA_VERSION VERSION_GREATER_EQUAL "13.0")
-    set(GPU_CUDA_GENCODE "-arch=all")
+      message(WARNING "Untested CUDA Toolkit version ${CUDA_VERSION}. Use at your own risk")
-  elseif(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
+      set(GPU_CUDA_GENCODE "-arch=all")
-    set(GPU_CUDA_GENCODE "-arch=all")
+    elseif(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
-  else()
+      set(GPU_CUDA_GENCODE "-arch=all")
-    # Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
+    else()
-    if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
+      # Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] ")
+      if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
-    endif()
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] ")
-    # Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11
+      endif()
-    if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
+      # Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_35,code=[sm_35,compute_35]")
+      if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
-    endif()
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_35,code=[sm_35,compute_35]")
-    # Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
+      endif()
-    if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
+      # Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
-      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")
-    endif()
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")
-    # Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
+      endif()
-    if(CUDA_VERSION VERSION_GREATER_EQUAL "8.0")
+      # Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
-      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")
-    endif()
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")
-    # Volta (GPU Arch 7.0) is supported by CUDA 9 and later
+      endif()
-    if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
+      # Volta (GPU Arch 7.0) is supported by CUDA 9 and later
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
-    endif()
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")
-    # Turing (GPU Arch 7.5) is supported by CUDA 10 and later
+      endif()
-    if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
+      # Turing (GPU Arch 7.5) is supported by CUDA 10 and later
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
-    endif()
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
-    # Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
+      endif()
-    if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
+      # Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
-    endif()
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
-    # Ampere (GPU Arch 8.6) is supported by CUDA 11.1 and later
+      endif()
-    if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
+      # Ampere (GPU Arch 8.6) is supported by CUDA 11.1 and later
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
-    endif()
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
-    # Lovelace (GPU Arch 8.9) is supported by CUDA 11.8 and later
+      endif()
-    if(CUDA_VERSION VERSION_GREATER_EQUAL "11.8")
+      # Lovelace (GPU Arch 8.9) is supported by CUDA 11.8 and later
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "11.8")
-    endif()
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
-    # Hopper (GPU Arch 9.0) is supported by CUDA 12.0 and later
+      endif()
-    if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
+      # Hopper (GPU Arch 9.0) is supported by CUDA 12.0 and later
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
+      endif()
     endif()
   endif()
 
   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} -DLAMMPS_${LAMMPS_SIZES})
+          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -allow-unsupported-compiler -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
 
   cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
-          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
+          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -allow-unsupported-compiler -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
 
   foreach(CU_OBJ ${GPU_GEN_OBJS})
     get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
@@ -201,7 +205,7 @@ elseif(GPU_API STREQUAL "OPENCL")
   include(OpenCLUtils)
   set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
 
-  file(GLOB GPU_LIB_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
+  file(GLOB GPU_LIB_CU CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
   list(REMOVE_ITEM GPU_LIB_CU
     ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu
     ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu
@@ -256,22 +260,7 @@ elseif(GPU_API STREQUAL "OPENCL")
   add_dependencies(ocl_get_devices OpenCL::OpenCL)
 
 elseif(GPU_API STREQUAL "HIP")
-  if(NOT DEFINED HIP_PATH)
+  include(DetectHIPInstallation)
-      if(NOT DEFINED ENV{HIP_PATH})
-          message(FATAL_ERROR "GPU_API=HIP requires HIP_PATH to be defined.\n"
-          "Either pass the HIP_PATH as a CMake option via -DHIP_PATH=... or set the HIP_PATH environment variable.")
-      else()
-          set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to HIP installation")
-      endif()
-  endif()
-  if(NOT DEFINED ROCM_PATH)
-      if(NOT DEFINED ENV{ROCM_PATH})
-          set(ROCM_PATH "/opt/rocm" CACHE PATH "Path to ROCm installation")
-      else()
-          set(ROCM_PATH $ENV{ROCM_PATH} CACHE PATH "Path to ROCm installation")
-      endif()
-  endif()
-  list(APPEND CMAKE_PREFIX_PATH ${HIP_PATH} ${ROCM_PATH})
   find_package(hip REQUIRED)
   option(HIP_USE_DEVICE_SORT "Use GPU sorting" ON)
 
@@ -346,7 +335,7 @@ elseif(GPU_API STREQUAL "HIP")
     endif()
   endif()
 
-  file(GLOB GPU_LIB_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
+  file(GLOB GPU_LIB_CU CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
   list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
 
   set(GPU_LIB_CU_HIP "")

cmake/Modules/Packages/KIM.cmake

@@ -1,12 +1,7 @@
 set(KIM-API_MIN_VERSION 2.1.3)
 find_package(CURL)
 if(CURL_FOUND)
-  if(CMAKE_VERSION VERSION_LESS 3.12)
+  target_link_libraries(lammps PRIVATE CURL::libcurl)
-    target_include_directories(lammps PRIVATE ${CURL_INCLUDE_DIRS})
-    target_link_libraries(lammps PRIVATE ${CURL_LIBRARIES})
-  else()
-    target_link_libraries(lammps PRIVATE CURL::libcurl)
-  endif()
   target_compile_definitions(lammps PRIVATE -DLMP_KIM_CURL)
   set(LMP_DEBUG_CURL OFF CACHE STRING "Set libcurl verbose mode on/off. If on, it displays a lot of verbose information about its operations.")
   mark_as_advanced(LMP_DEBUG_CURL)
@@ -19,7 +14,7 @@ if(CURL_FOUND)
     target_compile_definitions(lammps PRIVATE -DLMP_NO_SSL_CHECK)
   endif()
 endif()
-set(KIM_EXTRA_UNITTESTS OFF CACHE STRING "Set extra unit tests verbose mode on/off. If on, extra tests are included.")
+option(KIM_EXTRA_UNITTESTS "Enable extra unit tests for the KIM package." OFF)
 mark_as_advanced(KIM_EXTRA_UNITTESTS)
 find_package(PkgConfig QUIET)
 set(DOWNLOAD_KIM_DEFAULT ON)

cmake/Modules/Packages/KOKKOS.cmake

@@ -1,7 +1,8 @@
 ########################################################################
-# As of version 3.3.0 Kokkos requires C++14
+# As of version 4.0.0 Kokkos requires C++17
-if(CMAKE_CXX_STANDARD LESS 14)
+if(CMAKE_CXX_STANDARD LESS 17)
-  message(FATAL_ERROR "The KOKKOS package requires the C++ standard to be set to at least C++14")
+  message(FATAL_ERROR "The KOKKOS package requires the C++ standard to
+be set to at least C++17")
 endif()
 
 ########################################################################
@@ -16,8 +17,8 @@ if(Kokkos_ENABLE_OPENMP)
   if(NOT BUILD_OMP)
     message(FATAL_ERROR "Must enable BUILD_OMP with Kokkos_ENABLE_OPENMP")
   else()
-    # NVHPC does not seem to provide a detectable OpenMP version, but is far beyond version 3.1
+    # NVHPC/(AMD)Clang does not seem to provide a detectable OpenMP version, but is far beyond version 3.1
-    if((OpenMP_CXX_VERSION VERSION_LESS 3.1) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC"))
+    if((OpenMP_CXX_VERSION VERSION_LESS 3.1) AND NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
       message(FATAL_ERROR "Compiler must support OpenMP 3.1 or later with Kokkos_ENABLE_OPENMP")
     endif()
   endif()
@@ -49,8 +50,8 @@ if(DOWNLOAD_KOKKOS)
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
   include(ExternalProject)
-  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.7.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.2.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "f140e02b826223b1045207d9bc10d404" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  set(KOKKOS_MD5 "731647b61a4233f568d583702e9cd6d1" CACHE STRING "MD5 checksum of KOKKOS tarball")
   mark_as_advanced(KOKKOS_URL)
   mark_as_advanced(KOKKOS_MD5)
   GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@@ -75,7 +76,7 @@ if(DOWNLOAD_KOKKOS)
   add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
   add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 3.7.01 REQUIRED CONFIG)
+  find_package(Kokkos 4.2.00 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
 else()
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
@@ -88,7 +89,7 @@ else()
   if(CMAKE_REQUEST_PIC)
     set(CMAKE_POSITION_INDEPENDENT_CODE ON)
   endif()
-  add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
+  add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR} EXCLUDE_FROM_ALL)
 
   set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
                           ${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
@@ -121,6 +122,11 @@ set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
 
+# fix wall/gran has been refactored in an incompatible way. Use old version of base class for now
+if(PKG_GRANULAR)
+  list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/fix_wall_gran_old.cpp)
+endif()
+
 if(PKG_KSPACE)
   list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/fft3d_kokkos.cpp
                                  ${KOKKOS_PKG_SOURCES_DIR}/grid3d_kokkos.cpp
@@ -132,8 +138,10 @@ if(PKG_KSPACE)
     endif()
   elseif(Kokkos_ENABLE_HIP)
     if(NOT (FFT STREQUAL "KISS"))
+      include(DetectHIPInstallation)
+      find_package(hipfft REQUIRED)
       target_compile_definitions(lammps PRIVATE -DFFT_HIPFFT)
-      target_link_libraries(lammps PRIVATE hipfft)
+      target_link_libraries(lammps PRIVATE hip::hipfft)
     endif()
   endif()
 endif()
@@ -148,7 +156,7 @@ if(PKG_ML-IAP)
 
   # Add KOKKOS version of ML-IAP Python coupling if non-KOKKOS version is included
   if(MLIAP_ENABLE_PYTHON AND Cythonize_EXECUTABLE)
-    file(GLOB MLIAP_KOKKOS_CYTHON_SRC ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/KOKKOS/*.pyx)
+    file(GLOB MLIAP_KOKKOS_CYTHON_SRC CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/KOKKOS/*.pyx)
     foreach(MLIAP_CYTHON_FILE ${MLIAP_KOKKOS_CYTHON_SRC})
       get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_FILE} NAME_WE)
       add_custom_command(OUTPUT  ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h

cmake/Modules/Packages/KSPACE.cmake

@@ -46,6 +46,42 @@ else()
   target_compile_definitions(lammps PRIVATE -DFFT_KISS)
 endif()
 
+option(FFT_USE_HEFFTE  "Use heFFTe as the distributed FFT engine, overrides the FFT option."  OFF)
+if(FFT_USE_HEFFTE)
+  # if FFT_HEFFTE is enabled, switch the builtin FFT engine with Heffte
+  set(FFT_HEFFTE_BACKEND_VALUES FFTW MKL)
+  set(FFT_HEFFTE_BACKEND "" CACHE STRING "Select heFFTe backend, e.g., FFTW or MKL")
+  set_property(CACHE FFT_HEFFTE_BACKEND PROPERTY STRINGS ${FFT_HEFFTE_BACKEND_VALUES})
+
+  if(FFT_HEFFTE_BACKEND STREQUAL "FFTW") # respect the backend choice, FFTW or MKL
+    set(HEFFTE_COMPONENTS "FFTW")
+    set(Heffte_ENABLE_FFTW "ON" CACHE BOOL "Enables FFTW backend for heFFTe")
+  elseif(FFT_HEFFTE_BACKEND STREQUAL "MKL")
+    set(HEFFTE_COMPONENTS "MKL")
+    set(Heffte_ENABLE_MKL "ON" CACHE BOOL "Enables MKL backend for heFFTe")
+  else()
+    message(WARNING "FFT_HEFFTE_BACKEND not selected, defaulting to the builtin 'stock' backend, which is intended for testing and is not optimized for production runs")
+  endif()
+
+  find_package(Heffte 2.4.0 QUIET COMPONENTS ${HEFFTE_COMPONENTS})
+  if (NOT Heffte_FOUND) # download and build
+    include(FetchContent)
+    FetchContent_Declare(HEFFTE_PROJECT # using v2.4.0
+      URL  "https://github.com/icl-utk-edu/heffte/archive/refs/tags/v2.4.0.tar.gz"
+      URL_HASH SHA256=02310fb4f9688df02f7181667e61c3adb7e38baf79611d80919d47452ff7881d
+      )
+    FetchContent_Populate(HEFFTE_PROJECT)
+    add_subdirectory(${heffte_project_SOURCE_DIR} ${heffte_project_BINARY_DIR})
+    set_target_properties(lmp PROPERTIES INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+    set_target_properties(lammps PROPERTIES INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+    add_library(Heffte::Heffte INTERFACE IMPORTED GLOBAL)
+    target_link_libraries(Heffte::Heffte INTERFACE Heffte)
+  endif()
+
+  target_compile_definitions(lammps PRIVATE -DFFT_HEFFTE "-DFFT_HEFFTE_${FFT_HEFFTE_BACKEND}")
+  target_link_libraries(lammps PRIVATE Heffte::Heffte)
+endif()
+
 set(FFT_PACK "array" CACHE STRING "Optimization for FFT")
 set(FFT_PACK_VALUES array pointer memcpy)
 set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES})

cmake/Modules/Packages/LATTE.cmake

@@ -1,54 +0,0 @@
-enable_language(Fortran)
-
-# using lammps in a super-build setting
-if(TARGET LATTE::latte)
-  target_link_libraries(lammps PRIVATE LATTE::latte)
-  return()
-endif()
-
-find_package(LATTE 1.2.2 CONFIG)
-if(LATTE_FOUND)
-  set(DOWNLOAD_LATTE_DEFAULT OFF)
-else()
-  set(DOWNLOAD_LATTE_DEFAULT ON)
-endif()
-option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
-if(DOWNLOAD_LATTE)
-  message(STATUS "LATTE download requested - we will build our own")
-  set(LATTE_URL "https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz" CACHE STRING "URL for LATTE tarball")
-  set(LATTE_MD5 "820e73a457ced178c08c71389a385de7" CACHE STRING "MD5 checksum of LATTE tarball")
-  mark_as_advanced(LATTE_URL)
-  mark_as_advanced(LATTE_MD5)
-  GetFallbackURL(LATTE_URL LATTE_FALLBACK)
-
-  # CMake cannot pass BLAS or LAPACK library variable to external project if they are a list
-  list(LENGTH BLAS_LIBRARIES} NUM_BLAS)
-  list(LENGTH LAPACK_LIBRARIES NUM_LAPACK)
-  if((NUM_BLAS GREATER 1) OR (NUM_LAPACK GREATER 1) AND NOT USE_INTERNAL_LINALG)
-    message(FATAL_ERROR "Cannot compile downloaded LATTE library due to a technical limitation. "
-                        "Try to configure LAMMPS with '-D USE_INTERNAL_LINALG=on' added as a workaround.")
-  endif()
-
-  include(ExternalProject)
-  ExternalProject_Add(latte_build
-    URL     ${LATTE_URL} ${LATTE_FALLBACK}
-    URL_MD5 ${LATTE_MD5}
-    SOURCE_SUBDIR cmake
-    CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} -DCMAKE_INSTALL_LIBDIR=lib
-    -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
-    -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=${CMAKE_Fortran_FLAGS}
-    -DCMAKE_Fortran_FLAGS_${BTYPE}=${CMAKE_Fortran_FLAGS_${BTYPE}} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-    -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM} -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
-    BUILD_BYPRODUCTS <INSTALL_DIR>/lib/liblatte.a
-  )
-  ExternalProject_get_property(latte_build INSTALL_DIR)
-  add_library(LAMMPS::LATTE UNKNOWN IMPORTED)
-  set_target_properties(LAMMPS::LATTE PROPERTIES
-    IMPORTED_LOCATION "${INSTALL_DIR}/lib/liblatte.a"
-    INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
-  target_link_libraries(lammps PRIVATE LAMMPS::LATTE)
-  add_dependencies(LAMMPS::LATTE latte_build)
-else()
-  find_package(LATTE 1.2.2 REQUIRED CONFIG)
-  target_link_libraries(lammps PRIVATE LATTE::latte)
-endif()

cmake/Modules/Packages/LEPTON.cmake

@@ -4,7 +4,7 @@ if(LEPTON_SOURCE_DIR)
 endif()
 set(LEPTON_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/lepton)
 
-file(GLOB LEPTON_SOURCES ${CONFIGURE_DEPENDS} ${LEPTON_SOURCE_DIR}/src/[^.]*.cpp)
+file(GLOB LEPTON_SOURCES CONFIGURE_DEPENDS ${LEPTON_SOURCE_DIR}/src/[^.]*.cpp)
 
 if((CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "amd64") OR
    (CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "AMD64") OR
@@ -15,7 +15,7 @@ else()
 endif()
 
 if(LEPTON_ENABLE_JIT)
-  file(GLOB ASMJIT_SOURCES ${CONFIGURE_DEPENDS} ${LEPTON_SOURCE_DIR}/asmjit/*/[^.]*.cpp)
+  file(GLOB ASMJIT_SOURCES CONFIGURE_DEPENDS ${LEPTON_SOURCE_DIR}/asmjit/*/[^.]*.cpp)
 endif()
 
 add_library(lepton STATIC ${LEPTON_SOURCES} ${ASMJIT_SOURCES})

cmake/Modules/Packages/MDI.cmake

@@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
 
 if(DOWNLOAD_MDI)
   message(STATUS "MDI download requested - we will build our own")
-  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.12.tar.gz" CACHE STRING "URL for MDI tarball")
+  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.16.tar.gz" CACHE STRING "URL for MDI tarball")
-  set(MDI_MD5 "7a222353ae8e03961d5365e6cd48baee" CACHE STRING "MD5 checksum for MDI tarball")
+  set(MDI_MD5 "407db44e2d79447ab5c1233af1965f65" CACHE STRING "MD5 checksum for MDI tarball")
   mark_as_advanced(MDI_URL)
   mark_as_advanced(MDI_MD5)
   GetFallbackURL(MDI_URL MDI_FALLBACK)
@@ -26,29 +26,9 @@ if(DOWNLOAD_MDI)
 
   # detect if we have python development support and thus can enable python plugins
   set(MDI_USE_PYTHON_PLUGINS OFF)
-  if(CMAKE_VERSION VERSION_LESS 3.12)
+  find_package(Python QUIET COMPONENTS Development)
-    if(NOT PYTHON_VERSION_STRING)
+  if(Python_Development_FOUND)
-      set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
+    set(MDI_USE_PYTHON_PLUGINS ON)
-      # search for interpreter first, so we have a consistent library
-      find_package(PythonInterp) # Deprecated since version 3.12
-      if(PYTHONINTERP_FOUND)
-        set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
-      endif()
-    endif()
-    # search for the library matching the selected interpreter
-    set(Python_ADDITIONAL_VERSIONS ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR})
-    find_package(PythonLibs QUIET) # Deprecated since version 3.12
-    if(PYTHONLIBS_FOUND)
-      if(NOT (PYTHON_VERSION_STRING STREQUAL PYTHONLIBS_VERSION_STRING))
-        message(FATAL_ERROR "Python Library version ${PYTHONLIBS_VERSION_STRING} does not match Interpreter version ${PYTHON_VERSION_STRING}")
-      endif()
-      set(MDI_USE_PYTHON_PLUGINS ON)
-    endif()
-  else()
-    find_package(Python QUIET COMPONENTS Development)
-    if(Python_Development_FOUND)
-      set(MDI_USE_PYTHON_PLUGINS ON)
-    endif()
   endif()
   # python plugins are not supported and thus must be always off on Windows
   if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
@@ -102,13 +82,9 @@ if(DOWNLOAD_MDI)
   # if compiling with python plugins we need
   # to add python libraries as dependency.
   if(MDI_USE_PYTHON_PLUGINS)
-    if(CMAKE_VERSION VERSION_LESS 3.12)
+    list(APPEND MDI_DEP_LIBS Python::Python)
-      list(APPEND MDI_DEP_LIBS ${PYTHON_LIBRARIES})
-    else()
-      list(APPEND MDI_DEP_LIBS Python::Python)
-    endif()
-
   endif()
+
   # need to add support for dlopen/dlsym, except when compiling for Windows.
   if(NOT (CMAKE_SYSTEM_NAME STREQUAL "Windows"))
     list(APPEND MDI_DEP_LIBS "${CMAKE_DL_LIBS}")

cmake/Modules/Packages/ML-IAP.cmake

@@ -2,12 +2,7 @@
 set(MLIAP_ENABLE_PYTHON_DEFAULT OFF)
 if(PKG_PYTHON)
   find_package(Cythonize QUIET)
-  if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.14)
+  find_package(Python COMPONENTS NumPy QUIET)
-    find_package(Python COMPONENTS NumPy QUIET)
-  else()
-    # assume we have NumPy
-    set(Python_NumPy_FOUND ON)
-  endif()
   if(Cythonize_FOUND AND Python_NumPy_FOUND)
     set(MLIAP_ENABLE_PYTHON_DEFAULT ON)
   endif()
@@ -17,24 +12,16 @@ option(MLIAP_ENABLE_PYTHON "Build ML-IAP package with Python support" ${MLIAP_EN
 
 if(MLIAP_ENABLE_PYTHON)
   find_package(Cythonize REQUIRED)
-  if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.14)
+  find_package(Python COMPONENTS NumPy REQUIRED)
-    find_package(Python COMPONENTS NumPy REQUIRED)
-  endif()
   if(NOT PKG_PYTHON)
     message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP")
   endif()
-  if(CMAKE_VERSION VERSION_LESS 3.12)
+  if(Python_VERSION VERSION_LESS 3.6)
-    if(PYTHONLIBS_VERSION_STRING VERSION_LESS 3.6)
+    message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later")
-      message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later")
-    endif()
-  else()
-    if(Python_VERSION VERSION_LESS 3.6)
-      message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later")
-    endif()
   endif()
 
   set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
-  file(GLOB MLIAP_CYTHON_SRC ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)
+  file(GLOB MLIAP_CYTHON_SRC CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)
   file(MAKE_DIRECTORY ${MLIAP_BINARY_DIR})
   foreach(MLIAP_CYTHON_FILE ${MLIAP_CYTHON_SRC})
     get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_FILE} NAME_WE)

cmake/Modules/Packages/ML-PACE.cmake

@@ -1,33 +1,40 @@
-set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.01.3.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.11.25.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
 
-set(PACELIB_MD5 "4f0b3b5b14456fe9a73b447de3765caa" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
+set(PACELIB_MD5 "b45de9a633f42ed65422567e3ce56f9f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
 mark_as_advanced(PACELIB_URL)
 mark_as_advanced(PACELIB_MD5)
 GetFallbackURL(PACELIB_URL PACELIB_FALLBACK)
 
-# download library sources to build folder
+# LOCAL_ML-PACE points to top-level dir with local lammps-user-pace repo,
-if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
+# to make it easier to check local build without going through the public github releases
-  file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
+if(LOCAL_ML-PACE)
-endif()
+ set(lib-pace "${LOCAL_ML-PACE}")
-if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
-  message(STATUS "Downloading ${PACELIB_URL}")
-  file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz STATUS DL_STATUS SHOW_PROGRESS)
-  file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
-  if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}"))
-    message(WARNING "Download from primary URL ${PACELIB_URL} failed\nTrying fallback URL ${PACELIB_FALLBACK}")
-    file(DOWNLOAD ${PACELIB_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5} SHOW_PROGRESS)
-  endif()
 else()
-  message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
+  # download library sources to build folder
-endif()
+  if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
+    file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
+  endif()
+  if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
+    message(STATUS "Downloading ${PACELIB_URL}")
+    file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz STATUS DL_STATUS SHOW_PROGRESS)
+    file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
+    if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}"))
+      message(WARNING "Download from primary URL ${PACELIB_URL} failed\nTrying fallback URL ${PACELIB_FALLBACK}")
+      file(DOWNLOAD ${PACELIB_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5} SHOW_PROGRESS)
+    endif()
+  else()
+    message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
+  endif()
 
-# uncompress downloaded sources
+
-execute_process(
+  # uncompress downloaded sources
-  COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
+  execute_process(
-  COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
+    COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
-  WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+    COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
-)
+    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
-get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
+  )
+  get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
+endif()
 
 add_subdirectory(${lib-pace} build-pace)
 set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})

cmake/Modules/Packages/MSCG.cmake

@@ -1,28 +0,0 @@
-find_package(GSL REQUIRED)
-find_package(MSCG QUIET)
-if(MSGC_FOUND)
-  set(DOWNLOAD_MSCG_DEFAULT OFF)
-else()
-  set(DOWNLOAD_MSCG_DEFAULT ON)
-endif()
-option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
-if(DOWNLOAD_MSCG)
-  set(MSCG_URL "https://github.com/uchicago-voth/MSCG-release/archive/491270a73539e3f6951e76f7dbe84e258b3ebb45.tar.gz" CACHE STRING "URL for MSCG tarball")
-  set(MSCG_MD5 "7ea50748fba5c3a372e0266bd31d2f11" CACHE STRING "MD5 checksum of MSCG tarball")
-  mark_as_advanced(MSCG_URL)
-  mark_as_advanced(MSCG_MD5)
-
-  include(ExternalCMakeProject)
-  ExternalCMakeProject(mscg ${MSCG_URL} ${MSCG_MD5} MSCG-release src/CMake "")
-
-  # set include and link library
-  target_include_directories(lammps PRIVATE "${CMAKE_BINARY_DIR}/_deps/mscg-src/src")
-  target_link_libraries(lammps PRIVATE mscg)
-else()
-  find_package(MSCG)
-  if(NOT MSCG_FOUND)
-    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()
-target_link_libraries(lammps PRIVATE GSL::gsl ${LAPACK_LIBRARIES})

cmake/Modules/Packages/PLUMED.cmake

@@ -1,106 +1,169 @@
-set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")
+# Plumed2 support for PLUMED package
-set(PLUMED_MODE_VALUES static shared runtime)
-set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})
-validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
-string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
 
-set(PLUMED_LINK_LIBS)
+if(BUILD_MPI)
-if(PLUMED_MODE STREQUAL "STATIC")
+  set(PLUMED_CONFIG_MPI "--enable-mpi")
-  find_package(LAPACK REQUIRED)
+  set(PLUMED_CONFIG_CC  ${CMAKE_MPI_C_COMPILER})
-  find_package(BLAS REQUIRED)
+  set(PLUMED_CONFIG_CXX  ${CMAKE_MPI_CXX_COMPILER})
-  find_package(GSL REQUIRED)
+  set(PLUMED_CONFIG_CPP "-I ${MPI_CXX_INCLUDE_PATH}")
-  list(APPEND PLUMED_LINK_LIBS ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} GSL::gsl)
+  set(PLUMED_CONFIG_LIB "${MPI_CXX_LIBRARIES}")
-  find_package(ZLIB QUIET)
+  set(PLUMED_CONFIG_DEP "mpi4win_build")
-  if(ZLIB_FOUND)
+else()
-    list(APPEND PLUMED_LINK_LIBS ZLIB::ZLIB)
+  set(PLUMED_CONFIG_MPI "--disable-mpi")
-  endif()
+  set(PLUMED_CONFIG_CC  ${CMAKE_C_COMPILER})
-  find_package(FFTW3 QUIET)
+  set(PLUMED_CONFIG_CXX  ${CMAKE_CXX_COMPILER})
-  if(FFTW3_FOUND)
+  set(PLUMED_CONFIG_CPP "")
-    list(APPEND PLUMED_LINK_LIBS FFTW3::FFTW3)
+  set(PLUMED_CONFIG_LIB "")
-  endif()
+  set(PLUMED_CONFIG_DEP "")
+endif()
+if(BUILD_OMP)
+  set(PLUMED_CONFIG_OMP "--enable-openmp")
+else()
+  set(PLUMED_CONFIG_OMP "--disable-openmp")
 endif()
 
-find_package(PkgConfig QUIET)
+set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.2/plumed-src-2.8.2.tgz"
-set(DOWNLOAD_PLUMED_DEFAULT ON)
+  CACHE STRING "URL for PLUMED tarball")
-if(PKG_CONFIG_FOUND)
+set(PLUMED_MD5 "599092b6a0aa6fff992612537ad98994" CACHE STRING "MD5 checksum of PLUMED tarball")
-  pkg_check_modules(PLUMED QUIET plumed)
-  if(PLUMED_FOUND)
-    set(DOWNLOAD_PLUMED_DEFAULT OFF)
-  endif()
-endif()
 
-option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT})
+mark_as_advanced(PLUMED_URL)
-if(DOWNLOAD_PLUMED)
+mark_as_advanced(PLUMED_MD5)
-  if(BUILD_MPI)
+GetFallbackURL(PLUMED_URL PLUMED_FALLBACK)
-    set(PLUMED_CONFIG_MPI "--enable-mpi")
+
-    set(PLUMED_CONFIG_CC  ${CMAKE_MPI_C_COMPILER})
+if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (CMAKE_CROSSCOMPILING))
-    set(PLUMED_CONFIG_CXX  ${CMAKE_MPI_CXX_COMPILER})
+  if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+    set(CROSS_CONFIGURE mingw64-configure)
+  elseif(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86")
+    set(CROSS_CONFIGURE mingw32-configure)
   else()
-    set(PLUMED_CONFIG_MPI "--disable-mpi")
+    message(FATAL_ERROR "Unsupported target system: ${CMAKE_SYSTEM_NAME}/${CMAKE_SYSTEM_PROCESSOR}")
-    set(PLUMED_CONFIG_CC  ${CMAKE_C_COMPILER})
-    set(PLUMED_CONFIG_CXX  ${CMAKE_CXX_COMPILER})
   endif()
-  if(BUILD_OMP)
+  message(STATUS "Downloading and cross-compiling Plumed2 for ${CMAKE_SYSTEM_NAME}/${CMAKE_SYSTEM_PROCESSOR} with ${CROSS_CONFIGURE}")
-    set(PLUMED_CONFIG_OMP "--enable-openmp")
-  else()
-    set(PLUMED_CONFIG_OMP "--disable-openmp")
-  endif()
-  message(STATUS "PLUMED download requested - we will build our own")
-  if(PLUMED_MODE STREQUAL "STATIC")
-    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX}")
-  elseif(PLUMED_MODE STREQUAL "SHARED")
-    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX};<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
-  elseif(PLUMED_MODE STREQUAL "RUNTIME")
-    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_PREFIX}")
-  endif()
-
-  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.2/plumed-src-2.8.2.tgz" CACHE STRING "URL for PLUMED tarball")
-  set(PLUMED_MD5 "599092b6a0aa6fff992612537ad98994" CACHE STRING "MD5 checksum of PLUMED tarball")
-
-  mark_as_advanced(PLUMED_URL)
-  mark_as_advanced(PLUMED_MD5)
-  GetFallbackURL(PLUMED_URL PLUMED_FALLBACK)
-
   include(ExternalProject)
   ExternalProject_Add(plumed_build
     URL     ${PLUMED_URL} ${PLUMED_FALLBACK}
     URL_MD5 ${PLUMED_MD5}
     BUILD_IN_SOURCE 1
-    CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
+    CONFIGURE_COMMAND ${CROSS_CONFIGURE} --disable-shared --disable-bsymbolic
+                                         --disable-python --enable-cxx=11
+                                         --enable-modules=-adjmat:+crystallization:-dimred:+drr:+eds:-fisst:+funnel:+logmfd:+manyrestraints:+maze:+opes:+multicolvar:-pamm:-piv:+s2cm:-sasa:-ves
+                                         ${PLUMED_CONFIG_OMP}
+                                         ${PLUMED_CONFIG_MPI}
+                                         CXX=${PLUMED_CONFIG_CXX}
+                                         CC=${PLUMED_CONFIG_CC}
+                                         CPPFLAGS=${PLUMED_CONFIG_CPP}
+                                         LIBS=${PLUMED_CONFIG_LIB}
+    INSTALL_COMMAND ""
+    BUILD_BYPRODUCTS "<SOURCE_DIR>/src/lib/install/libplumed.a" "<SOURCE_DIR>/src/lib/install/plumed.exe"
+    DEPENDS "${PLUMED_MPI_CONFIG_DEP}"
+  )
+  ExternalProject_Get_Property(plumed_build SOURCE_DIR)
+  set(PLUMED_BUILD_DIR ${SOURCE_DIR})
+  set(PLUMED_INSTALL_DIR ${PLUMED_BUILD_DIR}/src/lib/install)
+  file(MAKE_DIRECTORY ${PLUMED_BUILD_DIR}/src/include)
+
+  add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
+  add_dependencies(LAMMPS::PLUMED plumed_build)
+  set_target_properties(LAMMPS::PLUMED PROPERTIES
+    IMPORTED_LOCATION "${PLUMED_INSTALL_DIR}/libplumed.a"
+    INTERFACE_LINK_LIBRARIES "-Wl,--image-base -Wl,0x10000000 -lfftw3 -lz  -fstack-protector -lssp -fopenmp"
+    INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_BUILD_DIR}/src/include")
+
+  add_custom_target(plumed_copy ALL ${CMAKE_COMMAND} -E rm -rf ${CMAKE_BINARY_DIR}/plumed.exe ${CMAKE_BINARY_DIR}/plumed_patches
+    COMMAND ${CMAKE_COMMAND} -E copy ${PLUMED_INSTALL_DIR}/plumed.exe ${CMAKE_BINARY_DIR}/plumed.exe
+    COMMAND ${CMAKE_COMMAND} -E copy_directory ${PLUMED_BUILD_DIR}/patches ${CMAKE_BINARY_DIR}/patches
+    BYPRODUCTS ${CMAKE_BINARY_DIR}/plumed.exe ${CMAKE_BINARY_DIR}/patches
+    DEPENDS plumed_build
+    COMMENT "Copying Plumed files"
+  )
+
+else()
+
+  set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")
+  set(PLUMED_MODE_VALUES static shared runtime)
+  set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})
+  validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
+  string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
+
+  set(PLUMED_LINK_LIBS)
+  if(PLUMED_MODE STREQUAL "STATIC")
+    find_package(LAPACK REQUIRED)
+    find_package(BLAS REQUIRED)
+    find_package(GSL REQUIRED)
+    list(APPEND PLUMED_LINK_LIBS ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} GSL::gsl)
+    find_package(ZLIB QUIET)
+    if(ZLIB_FOUND)
+      list(APPEND PLUMED_LINK_LIBS ZLIB::ZLIB)
+    endif()
+    find_package(FFTW3 QUIET)
+    if(FFTW3_FOUND)
+      list(APPEND PLUMED_LINK_LIBS FFTW3::FFTW3)
+    endif()
+  endif()
+
+  find_package(PkgConfig QUIET)
+  set(DOWNLOAD_PLUMED_DEFAULT ON)
+  if(PKG_CONFIG_FOUND)
+    pkg_check_modules(PLUMED QUIET plumed)
+    if(PLUMED_FOUND)
+      set(DOWNLOAD_PLUMED_DEFAULT OFF)
+    endif()
+  endif()
+
+  option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT})
+  if(DOWNLOAD_PLUMED)
+    message(STATUS "PLUMED download requested - we will build our own")
+    if(PLUMED_MODE STREQUAL "STATIC")
+      set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX}")
+    elseif(PLUMED_MODE STREQUAL "SHARED")
+      set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX};<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+    elseif(PLUMED_MODE STREQUAL "RUNTIME")
+      set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_PREFIX}")
+    endif()
+
+    include(ExternalProject)
+    ExternalProject_Add(plumed_build
+      URL     ${PLUMED_URL} ${PLUMED_FALLBACK}
+      URL_MD5 ${PLUMED_MD5}
+      BUILD_IN_SOURCE 1
+      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
                                              ${CONFIGURE_REQUEST_PIC}
                                              --enable-modules=all
+                                             --enable-cxx=11
+                                             --disable-python
                                              ${PLUMED_CONFIG_MPI}
                                              ${PLUMED_CONFIG_OMP}
                                              CXX=${PLUMED_CONFIG_CXX}
                                              CC=${PLUMED_CONFIG_CC}
-    BUILD_BYPRODUCTS ${PLUMED_BUILD_BYPRODUCTS}
+      BUILD_BYPRODUCTS ${PLUMED_BUILD_BYPRODUCTS}
-  )
+    )
-  ExternalProject_get_property(plumed_build INSTALL_DIR)
+    ExternalProject_get_property(plumed_build INSTALL_DIR)
-  add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
+    add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
-  add_dependencies(LAMMPS::PLUMED plumed_build)
+    add_dependencies(LAMMPS::PLUMED plumed_build)
-  if(PLUMED_MODE STREQUAL "STATIC")
+    if(PLUMED_MODE STREQUAL "STATIC")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
+      set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
-  elseif(PLUMED_MODE STREQUAL "SHARED")
+    elseif(PLUMED_MODE STREQUAL "SHARED")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}")
+      set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}")
-  elseif(PLUMED_MODE STREQUAL "RUNTIME")
+    elseif(PLUMED_MODE STREQUAL "RUNTIME")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+      set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${CMAKE_DL_LIBS}")
+      set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${CMAKE_DL_LIBS}")
+    endif()
+    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
+    file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
+  else()
+    find_package(PkgConfig REQUIRED)
+    pkg_check_modules(PLUMED REQUIRED plumed)
+    add_library(LAMMPS::PLUMED INTERFACE IMPORTED)
+    if(PLUMED_MODE STREQUAL "STATIC")
+      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
+    elseif(PLUMED_MODE STREQUAL "SHARED")
+      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
+    elseif(PLUMED_MODE STREQUAL "RUNTIME")
+      set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
+    endif()
+    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_INCLUDE_DIRS}")
   endif()
-  set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
-  file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
-else()
-  find_package(PkgConfig REQUIRED)
-  pkg_check_modules(PLUMED REQUIRED plumed)
-  add_library(LAMMPS::PLUMED INTERFACE IMPORTED)
-  if(PLUMED_MODE STREQUAL "STATIC")
-    include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
-  elseif(PLUMED_MODE STREQUAL "SHARED")
-    include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
-  elseif(PLUMED_MODE STREQUAL "RUNTIME")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
-    include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
-  endif()
-  set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")
-  set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_INCLUDE_DIRS}")
 endif()
+
 target_link_libraries(lammps PRIVATE LAMMPS::PLUMED)

cmake/Modules/Packages/PYTHON.cmake

@@ -1,29 +1,11 @@
-if(CMAKE_VERSION VERSION_LESS 3.12)
+
-  if(NOT PYTHON_VERSION_STRING)
+if(NOT Python_INTERPRETER)
-    set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
+  # backward compatibility with CMake before 3.12 and older LAMMPS documentation
-    # search for interpreter first, so we have a consistent library
+  if(PYTHON_EXECUTABLE)
-    find_package(PythonInterp) # Deprecated since version 3.12
+    set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
-    if(PYTHONINTERP_FOUND)
-      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
-    endif()
   endif()
-  # search for the library matching the selected interpreter
+  find_package(Python COMPONENTS Interpreter)
-  set(Python_ADDITIONAL_VERSIONS ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR})
-  find_package(PythonLibs REQUIRED) # Deprecated since version 3.12
-  if(NOT (PYTHON_VERSION_STRING STREQUAL PYTHONLIBS_VERSION_STRING))
-    message(FATAL_ERROR "Python Library version ${PYTHONLIBS_VERSION_STRING} does not match Interpreter version ${PYTHON_VERSION_STRING}")
-  endif()
-  target_include_directories(lammps PRIVATE ${PYTHON_INCLUDE_DIRS})
-  target_link_libraries(lammps PRIVATE ${PYTHON_LIBRARIES})
-else()
-  if(NOT Python_INTERPRETER)
-    # backward compatibility
-    if(PYTHON_EXECUTABLE)
-      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
-    endif()
-    find_package(Python COMPONENTS Interpreter)
-  endif()
-  find_package(Python REQUIRED COMPONENTS Interpreter Development)
-  target_link_libraries(lammps PRIVATE Python::Python)
 endif()
+find_package(Python REQUIRED COMPONENTS Interpreter Development)
+target_link_libraries(lammps PRIVATE Python::Python)
 target_compile_definitions(lammps PRIVATE -DLMP_PYTHON)

cmake/Modules/StyleHeaderUtils.cmake

@@ -1,5 +1,5 @@
 function(FindStyleHeaders path style_class file_pattern headers)
-    file(GLOB files ${CONFIGURE_DEPENDS} "${path}/${file_pattern}*.h")
+    file(GLOB files CONFIGURE_DEPENDS "${path}/${file_pattern}*.h")
     get_property(hlist GLOBAL PROPERTY ${headers})
 
     foreach(file_name ${files})
@@ -187,7 +187,7 @@ endfunction(DetectBuildSystemConflict)
 
 
 function(FindPackagesHeaders path style_class file_pattern headers)
-    file(GLOB files ${CONFIGURE_DEPENDS} "${path}/${file_pattern}*.h")
+    file(GLOB files CONFIGURE_DEPENDS "${path}/${file_pattern}*.h")
     get_property(plist GLOBAL PROPERTY ${headers})
 
     foreach(file_name ${files})

cmake/Modules/Testing.cmake

@@ -6,7 +6,7 @@ if(ENABLE_TESTING)
   find_program(VALGRIND_BINARY NAMES valgrind)
   # generate custom suppression file
   file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "\n")
-  file(GLOB VALGRIND_SUPPRESSION_FILES ${CONFIGURE_DEPENDS} ${LAMMPS_TOOLS_DIR}/valgrind/[^.]*.supp)
+  file(GLOB VALGRIND_SUPPRESSION_FILES CONFIGURE_DEPENDS ${LAMMPS_TOOLS_DIR}/valgrind/[^.]*.supp)
   foreach(SUPP ${VALGRIND_SUPPRESSION_FILES})
     file(READ ${SUPP} SUPPRESSIONS)
     file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "${SUPPRESSIONS}")
@@ -18,29 +18,33 @@ if(ENABLE_TESTING)
 
   # we need to build and link a LOT of tester executables, so it is worth checking if
   # a faster linker is available. requires GNU or Clang compiler, newer CMake.
-  # also only verified with Fedora Linux > 30 and Ubuntu <= 18.04 (Ubuntu 20.04 fails)
+  # also only verified with Fedora Linux > 30 and Ubuntu 18.04 or 22.04+(Ubuntu 20.04 fails)
-  if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
+  if((CMAKE_SYSTEM_NAME STREQUAL "Linux")
-      AND ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
+      AND ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
-        OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
+    if(((CMAKE_LINUX_DISTRO STREQUAL "Ubuntu") AND
-    if(((CMAKE_LINUX_DISTRO STREQUAL "Ubuntu") AND (CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04))
+          ((CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04) OR (CMAKE_DISTRO_VERSION VERSION_GREATER_EQUAL 22.04)))
         OR ((CMAKE_LINUX_DISTRO STREQUAL "Fedora") AND (CMAKE_DISTRO_VERSION VERSION_GREATER 30)))
       include(CheckCXXCompilerFlag)
       set(CMAKE_CUSTOM_LINKER_DEFAULT default)
+      check_cxx_compiler_flag(-fuse-ld=mold HAVE_MOLD_LINKER_FLAG)
       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_MOLD_LINKER_BIN ld.mold)
       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)
+      if(HAVE_MOLD_LINKER_FLAG AND HAVE_MOLD_LINKER_BIN)
+        set(CMAKE_CUSTOM_LINKER_DEFAULT mold)
+      elseif(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_VALUES mold 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)")
+      set(CMAKE_CUSTOM_LINKER ${CMAKE_CUSTOM_LINKER_DEFAULT} CACHE STRING "Choose a custom linker for faster linking (mold, lld, gold, bfd, default)")
       validate_option(CMAKE_CUSTOM_LINKER CMAKE_CUSTOM_LINKER_VALUES)
       mark_as_advanced(CMAKE_CUSTOM_LINKER)
       if(NOT "${CMAKE_CUSTOM_LINKER}" STREQUAL "default")
@@ -62,16 +66,8 @@ 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)
+    target_compile_options(lammps PUBLIC --coverage)
-      if(CMAKE_CXX_FLAGS)
+    target_link_options(lammps PUBLIC --coverage)
-        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()
 
@@ -114,16 +110,8 @@ 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 (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
-    if(CMAKE_VERSION VERSION_LESS 3.13)
+    target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
-      if(CMAKE_CXX_FLAGS)
+    target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
-        set(CMAKE_CXX_FLAGS "${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")

cmake/Modules/Tools.cmake

@@ -26,21 +26,24 @@ if(BUILD_TOOLS)
 
   enable_language(C)
   get_filename_component(MSI2LMP_SOURCE_DIR ${LAMMPS_TOOLS_DIR}/msi2lmp/src ABSOLUTE)
-  file(GLOB MSI2LMP_SOURCES ${CONFIGURE_DEPENDS} ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
+  file(GLOB MSI2LMP_SOURCES CONFIGURE_DEPENDS ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
   add_executable(msi2lmp ${MSI2LMP_SOURCES})
   if(STANDARD_MATH_LIB)
     target_link_libraries(msi2lmp PRIVATE ${STANDARD_MATH_LIB})
   endif()
   install(TARGETS msi2lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
   install(FILES ${LAMMPS_DOC_DIR}/msi2lmp.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
+
+  add_subdirectory(${LAMMPS_TOOLS_DIR}/phonon ${CMAKE_BINARY_DIR}/phana_build)
 endif()
 
+find_package(PkgConfig QUIET)
 if(BUILD_LAMMPS_SHELL)
+  if(NOT PkgConfig_FOUND)
+    message(FATAL_ERROR "Must have pkg-config installed for building LAMMPS shell")
+  endif()
   find_package(PkgConfig REQUIRED)
   pkg_check_modules(READLINE IMPORTED_TARGET REQUIRED readline)
-  if(NOT LAMMPS_EXCEPTIONS)
-    message(WARNING "The LAMMPS shell needs LAMMPS_EXCEPTIONS enabled for full functionality")
-  endif()
 
   # include resource compiler to embed icons into the executable on Windows
   if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
@@ -65,4 +68,8 @@ if(BUILD_LAMMPS_SHELL)
   install(FILES ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.desktop DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/applications/)
 endif()
 
-
+if(BUILD_LAMMPS_GUI)
+  get_filename_component(LAMMPS_GUI_DIR ${LAMMPS_SOURCE_DIR}/../tools/lammps-gui ABSOLUTE)
+  get_filename_component(LAMMPS_GUI_BIN ${CMAKE_BINARY_DIR}/lammps-gui-build ABSOLUTE)
+  add_subdirectory(${LAMMPS_GUI_DIR} ${LAMMPS_GUI_BIN})
+endif()

cmake/packaging/MacOSXBundleInfo.plist.in

@@ -0,0 +1,34 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict>
+	<key>CFBundleDevelopmentRegion</key>
+	<string>en-US</string>
+	<key>CFBundleExecutable</key>
+	<string>${MACOSX_BUNDLE_EXECUTABLE_NAME}</string>
+        <key>CFBundleDisplayName</key>
+        <string>The LAMMPS Molecular Dynamics Software</string>
+	<key>CFBundleIconFile</key>
+	<string>lammps</string>
+	<key>CFBundleIdentifier</key>
+	<string>org.lammps.gui</string>
+	<key>CFBundleInfoDictionaryVersion</key>
+	<string>6.0</string>
+	<key>CFBundleLongVersionString</key>
+	<string>${MACOSX_BUNDLE_LONG_VERSION_STRING}</string>
+	<key>CFBundleName</key>
+	<string>LAMMPS_GUI</string>
+	<key>CFBundlePackageType</key>
+	<string>APPL</string>
+	<key>CFBundleShortVersionString</key>
+	<string>${MACOSX_BUNDLE_SHORT_VERSION_STRING}</string>
+	<key>CFBundleSignature</key>
+	<string>????</string>
+	<key>CFBundleVersion</key>
+	<string>${MACOSX_BUNDLE_BUNDLE_VERSION}</string>
+	<key>CSResourcesFileMapped</key>
+	<true/>
+	<key>NSHumanReadableCopyright</key>
+	<string>${MACOSX_BUNDLE_COPYRIGHT}</string>
+</dict>
+</plist>

cmake/packaging/README.macos

@@ -0,0 +1,69 @@
+LAMMPS and LAMMPS GUI universal binaries for macOS (arm64/x86_64)
+=================================================================
+
+This package provides universal binaries of LAMMPS and LAMMPS GUI that should
+run on macOS systems running running macOS version 11 (Big Sur) or newer.  Note
+the binaries are compiled without MPI support and contain a compatible subset
+of the available packages.
+
+The following individual commands are included:
+binary2txt lammps-gui lmp msi2lmp phana stl_bin2txt
+
+After copying the LAMMPS_GUI folder into your Applications folder, please follow
+these steps:
+
+1. Open the Terminal app
+
+2. Type the following command and press ENTER:
+
+   open ~/.zprofile
+
+   This will open a text editor for modifying the .zprofile file in your home
+   directory.
+
+3. Add the following lines to the end of the file, save it, and close the editor
+
+   LAMMPS_INSTALL_DIR=/Applications/LAMMPS_GUI.app/Contents
+   LAMMPS_POTENTIALS=${LAMMPS_INSTALL_DIR}/share/lammps/potentials
+   LAMMPS_BENCH_DIR=${LAMMPS_INSTALL_DIR}/share/lammps/bench
+   MSI2LMP_LIBRARY=${LAMMPS_INSTALL_DIR}/share/lammps/frc_files
+   PATH=${LAMMPS_INSTALL_DIR}/bin:$PATH
+   export LAMMPS_POTENTIALS LAMMPS_BENCH_DIR PATH
+
+4. In your existing terminal, type the following command make the settings active
+
+   source ~/.zprofile
+
+   Note, you don't have to type this in new terminals, since they will apply
+   the changes from .zprofile automatically.
+
+   Note: the above assumes you use the default shell (zsh) that comes with
+   MacOS. If you customized MacOS to use a different shell, you'll need to
+   modify that shell's init file (.cshrc, .bashrc, etc.) instead with
+   appropiate commands to modify the same environment variables.
+
+5. Try running LAMMPS (which might fail, see step 7)
+
+   lmp -in ${LAMMPS_BENCH_DIR}/in.lj
+
+6. Try running the LAMMPS GUI
+
+   lammps-gui ${LAMMPS_BENCH_DIR}/in.rhodo
+
+   Depending on the size and resolution of your screen, the fonts may be too
+   small to read. This can be adjusted by setting the environment variable
+   QT_FONT_DPI. The default value would be 72, so to increase the fonts by a
+   third, one can add to the .zprofile file the line
+
+   export QT_FONT_DPI=96
+
+   and reload as shown above.
+
+7. Give permission to execute the commands (lmp, lammps-gui, msi2lmp, binary2txt, phana, stl_bin2txt)
+
+   MacOS will likely block the initial run of the executables, since they were
+   downloaded from the internet and are missing a known signature from an
+   identified developer. Go to "Settings" and search for "Security settings".
+   It should display a message that an executable like "lmp" was blocked. Press
+   "Open anyway", which might prompt you for your admin credentials. Afterwards
+   "lmp" and the other executables should work as expected.

cmake/packaging/build_linux_tgz.sh

@@ -0,0 +1,77 @@
+#!/bin/bash
+
+APP_NAME=lammps-gui
+DESTDIR=${PWD}/../LAMMPS_GUI
+
+echo "Delete old files, if they exist"
+rm -rf ${DESTDIR} ../LAMMPS_GUI-Linux-amd64.tar.gz
+
+echo "Create staging area for deployment and populate"
+DESTDIR=${DESTDIR} cmake --install .  --prefix "/"
+
+echo "Remove debug info"
+for s in ${DESTDIR}/bin/* ${DESTDIR}/lib/liblammps*
+do \
+        test -f $s && strip --strip-debug $s
+done
+
+echo "Remove libc, gcc, and X11 related shared libs"
+rm -f ${DESTDIR}/lib/ld*.so ${DESTDIR}/lib/ld*.so.[0-9]
+rm -f ${DESTDIR}/lib/lib{c,dl,rt,m,pthread}.so.?
+rm -f ${DESTDIR}/lib/lib{c,dl,rt,m,pthread}-[0-9].[0-9]*.so
+rm -f ${DESTDIR}/lib/libX* ${DESTDIR}/lib/libxcb*
+rm -f ${DESTDIR}/lib/libgcc_s*
+rm -f ${DESTDIR}/lib/libstdc++*
+
+# get qt dir
+QTDIR=$(ldd ${DESTDIR}/bin/lammps-gui | grep libQt5Core | sed -e 's/^.*=> *//' -e 's/libQt5Core.so.*$/qt5/')
+cat > ${DESTDIR}/bin/qt.conf <<EOF
+[Paths]
+Plugins = ../qt5plugins
+EOF
+
+# platform plugin
+mkdir -p ${DESTDIR}/qt5plugins/platforms
+cp ${QTDIR}/plugins/platforms/libqxcb.so ${DESTDIR}/qt5plugins/platforms
+
+# get platform plugin dependencies
+QTDEPS=$(LD_LIBRARY_PATH=${DESTDIR}/lib ldd ${QTDIR}/plugins/platforms/libqxcb.so | grep -v ${DESTDIR} | grep libQt5 | sed -e 's/^.*=> *//' -e 's/\(libQt5.*.so.*\) .*$/\1/')
+for dep in ${QTDEPS}
+do \
+    cp ${dep} ${DESTDIR}/lib
+done
+
+echo "Add additional plugins for Qt"
+for dir in styles imageformats
+do \
+    cp -r  ${QTDIR}/plugins/${dir} ${DESTDIR}/qt5plugins/
+done
+
+# get imageplugin dependencies
+for s in ${DESTDIR}/qt5plugins/imageformats/*.so
+do \
+    QTDEPS=$(LD_LIBRARY_PATH=${DESTDIR}/lib ldd $s | grep -v ${DESTDIR} | grep -E '(libQt5|jpeg)' | sed -e 's/^.*=> *//' -e 's/\(lib.*.so.*\) .*$/\1/')
+    for dep in ${QTDEPS}
+    do \
+        cp ${dep} ${DESTDIR}/lib
+    done
+done
+
+echo "Set up wrapper script"
+MYDIR=$(dirname "$0")
+cp ${MYDIR}/linux_wrapper.sh ${DESTDIR}/bin
+for s in ${DESTDIR}/bin/*
+do \
+        EXE=$(basename $s)
+        test ${EXE} = linux_wrapper.sh && continue
+        test ${EXE} = qt.conf && continue
+        ln -s bin/linux_wrapper.sh ${DESTDIR}/${EXE}
+done
+
+pushd ..
+tar -czvvf LAMMPS_GUI-Linux-amd64.tar.gz LAMMPS_GUI
+popd
+
+echo "Cleanup dir"
+rm -r ${DESTDIR}
+exit 0

cmake/packaging/build_macos_dmg.sh

@@ -0,0 +1,111 @@
+#!/bin/bash
+
+APP_NAME=lammps-gui
+
+echo "Delete old files, if they exist"
+rm -f ${APP_NAME}.dmg ${APP_NAME}-rw.dmg LAMMPS_GUI-macOS-multiarch.dmg
+
+echo "Create initial dmg file with macdeployqt"
+macdeployqt  lammps-gui.app -dmg
+echo "Create writable dmg file"
+hdiutil convert ${APP_NAME}.dmg -format UDRW -o ${APP_NAME}-rw.dmg
+
+echo "Mount writeable DMG file in read-write mode. Keep track of device and volume names"
+DEVICE=$(hdiutil attach -readwrite -noverify ${APP_NAME}-rw.dmg | grep '^/dev/' | sed 1q | awk '{print $1}')
+VOLUME=$(df | grep ${DEVICE} | sed -e 's/^.*\(\/Volumes\/\)/\1/')
+sleep 2
+
+echo "Create link to Application folder and move README and background image files"
+
+pushd "${VOLUME}"
+ln -s /Applications .
+mv  ${APP_NAME}.app/Contents/Resources/README.txt .
+mkdir  .background
+mv ${APP_NAME}.app/Contents/Resources/LAMMPS_DMG_Background.png .background/background.png
+mv ${APP_NAME}.app LAMMPS_GUI.app
+cd LAMMPS_GUI.app/Contents
+
+echo "Attach icons to LAMMPS console and GUI executables"
+echo "read 'icns' (-16455) \"Resources/lammps.icns\";" > icon.rsrc
+Rez -a icon.rsrc -o bin/lmp
+SetFile -a C bin/lmp
+Rez -a icon.rsrc -o MacOS/lammps-gui
+SetFile -a C MacOS/lammps-gui
+rm icon.rsrc
+popd
+
+echo 'Tell the Finder to resize the window, set the background,'
+echo 'change the icon size, place the icons in the right position, etc.'
+echo '
+    tell application "Finder"
+    tell disk "'${APP_NAME}'"
+
+      -- wait for the image to finish mounting
+      set open_attempts to 0
+      repeat while open_attempts < 4
+        try
+          open
+            delay 1
+            set open_attempts to 5
+          close
+        on error errStr number errorNumber
+          set open_attempts to open_attempts + 1
+          delay 10
+        end try
+      end repeat
+      delay 5
+
+      -- open the image the first time and save a .DS_Store
+      -- just the background and icon setup
+      open
+        set current view of container window to icon view
+        set theViewOptions to the icon view options of container window
+        set background picture of theViewOptions to file ".background:background.png"
+        set arrangement of theViewOptions to not arranged
+        set icon size of theViewOptions to 64
+        delay 5
+      close
+
+      -- next set up the position of the app and Applications symlink
+      -- plus hide all window decorations
+      open
+        update without registering applications
+        tell container window
+          set sidebar width to 0
+          set statusbar visible to false
+          set toolbar visible to false
+          set the bounds to { 100, 40, 868, 640 }
+          set position of item "'LAMMPS_GUI'.app" to { 190, 216 }
+          set position of item "Applications" to { 576, 216 }
+          set position of item "README.txt" to { 190, 400 }
+        end tell
+        update without registering applications
+        delay 5
+      close
+
+      -- one last open and close to check the results
+      open
+        delay 5
+      close
+    end tell
+    delay 1
+  end tell
+' | osascript
+
+sync
+
+echo "Unmount modified disk image and convert to compressed read-only image"
+hdiutil detach "${DEVICE}"
+hdiutil convert "${APP_NAME}-rw.dmg" -format UDZO -o "LAMMPS_GUI-macOS-multiarch.dmg"
+
+echo "Attach icon to .dmg file"
+echo "read 'icns' (-16455) \"lammps-gui.app/Contents/Resources/lammps.icns\";" > icon.rsrc
+Rez -a icon.rsrc -o LAMMPS_GUI-macOS-multiarch.dmg
+SetFile -a C LAMMPS_GUI-macOS-multiarch.dmg
+rm icon.rsrc
+
+echo "Delete temporary disk images"
+rm -f "${APP_NAME}-rw.dmg"
+rm -f "${APP_NAME}.dmg"
+
+exit 0

cmake/packaging/build_windows_cross_zip.sh

@@ -0,0 +1,64 @@
+#!/bin/bash
+
+APP_NAME=lammps-gui
+DESTDIR=${PWD}/LAMMPS_GUI
+SYSROOT="$1"
+
+echo "Delete old files, if they exist"
+rm -rvf ${DESTDIR}/LAMMPS_GUI ${DESTDIR}/LAMMPS-Win10-amd64.zip
+
+echo "Create staging area for deployment and populate"
+DESTDIR=${DESTDIR} cmake --install .  --prefix "/"
+
+# no static libs needed
+rm -rvf ${DESTDIR}/lib
+# but the LAMMPS lib
+
+echo "Copying required DLL files"
+for dll in $(objdump -p *.exe *.dll | sed -n -e '/DLL Name:/s/^.*DLL Name: *//p' | sort | uniq)
+do \
+    doskip=0
+    for skip in ADVAPI32 CFGMGR32 GDI32 KERNEL32 MPR NETAPI32 PSAPI SHELL32 USER32 USERENV UxTheme VERSION WS2_32 WSOCK32 d3d11 dwmapi liblammps msvcrt_ole32
+    do \
+        test ${dll} = ${skip}.dll && doskip=1
+    done
+    test ${doskip} -eq 1 && continue
+    test -f ${DESTDIR}/bin/${dll} || cp -v ${SYSROOT}/bin/${dll} ${DESTDIR}/bin
+done
+
+echo "Copy required Qt plugins"
+mkdir -p ${DESTDIR}/qt5plugins
+for plugin in imageformats platforms styles
+do \
+    cp -r ${SYSROOT}/lib/qt5/plugins/${plugin} ${DESTDIR}/qt5plugins/
+done
+
+echo "Check dependencies of DLL files"
+for dll in $(objdump -p ${DESTDIR}/bin/*.dll ${DESTDIR}/qt5plugins/*/*.dll | sed -n -e '/DLL Name:/s/^.*DLL Name: *//p' | sort | uniq)
+do \
+    doskip=0
+    for skip in ADVAPI32 CFGMGR32 GDI32 KERNEL32 MPR NETAPI32 PSAPI SHELL32 USER32 USERENV UxTheme VERSION WS2_32 WSOCK32 d3d11 dwmapi liblammps msvcrt_ole32
+    do \
+        test ${dll} = ${skip}.dll && doskip=1
+    done
+    test ${doskip} -eq 1 && continue
+    test -f ${DESTDIR}/bin/${dll} || cp -v ${SYSROOT}/bin/${dll} ${DESTDIR}/bin
+done
+
+for dll in $(objdump -p ${DESTDIR}/bin/*.dll ${DESTDIR}/qt5plugins/*/*.dll | sed -n -e '/DLL Name:/s/^.*DLL Name: *//p' | sort | uniq)
+do \
+    doskip=0
+    for skip in ADVAPI32 CFGMGR32 GDI32 KERNEL32 MPR NETAPI32 PSAPI SHELL32 USER32 USERENV UxTheme VERSION WS2_32 WSOCK32 d3d11 dwmapi liblammps msvcrt_ole32
+    do \
+        test ${dll} = ${skip}.dll && doskip=1
+    done
+    test ${doskip} -eq 1 && continue
+    test -f ${DESTDIR}/bin/${dll} || cp -v ${SYSROOT}/bin/${dll} ${DESTDIR}/bin
+done
+
+cat > ${DESTDIR}/bin/qt.conf <<EOF
+[Paths]
+Plugins = ../qt5plugins
+EOF
+zip -9rvD LAMMPS-Win10-amd64.zip LAMMPS_GUI
+

cmake/packaging/build_windows_vs.cmake

@@ -0,0 +1,35 @@
+# CMake script to be run post installation to build zipped package
+
+# clean up old zipfile and deployment tree
+file(REMOVE LAMMPS_GUI-Win10-amd64.zip)
+file(REMOVE_RECURSE LAMMPS_GUI)
+file(RENAME ${INSTNAME} LAMMPS_GUI)
+
+# move all executables and dlls to main folder and delete bin folder
+file(GLOB BINFILES LIST_DIRECTORIES FALSE LAMMPS_GUI/bin/*.exe LAMMPS_GUI/bin/*.dll)
+foreach(bin ${BINFILES})
+  get_filename_component(exe ${bin} NAME)
+  file(RENAME ${bin} LAMMPS_GUI/${exe})
+endforeach()
+file(REMOVE_RECURSE LAMMPS_GUI/bin)
+
+# create qt.conf so Qt will find its plugins
+file(WRITE LAMMPS_GUI/qt.conf "[Paths]\r\nPlugins = qt5plugins\r\n")
+
+# initialize environment and then run windeployqt to populate folder with missing dependencies and Qt plugins
+file(WRITE qtdeploy.bat "@ECHO OFF\r\nset VSCMD_DEBUG=0\r\nCALL ${VC_INIT} x64\r\nset PATH=${QT5_BIN_DIR};%PATH%\r\nwindeployqt --plugindir LAMMPS_GUI/qt5plugins --release  LAMMPS_GUI/lammps-gui.exe --no-quick-import --no-webkit2 --no-translations --no-system-d3d-compiler --no-angle --no-opengl-sw\r\n")
+execute_process(COMMAND cmd.exe /c qtdeploy.bat COMMAND_ECHO STDERR)
+file(REMOVE qtdeploy.bat)
+
+# download and uncompress static FFMpeg and gzip binaries
+file(DOWNLOAD "https://download.lammps.org/thirdparty/ffmpeg-gzip.zip" ffmpeg-gzip.zip)
+file(WRITE unpackzip.ps1 "Expand-Archive -Path ffmpeg-gzip.zip -DestinationPath LAMMPS_GUI")
+execute_process(COMMAND powershell -ExecutionPolicy Bypass -File unpackzip.ps1)
+file(REMOVE unpackzip.ps1)
+file(REMOVE ffmpeg-gzip.zip)
+
+# create zip archive
+file(WRITE makearchive.ps1 "Compress-Archive -Path LAMMPS_GUI -CompressionLevel Optimal -DestinationPath LAMMPS_GUI-Win10-amd64.zip")
+execute_process(COMMAND powershell -ExecutionPolicy Bypass -File makearchive.ps1)
+file(REMOVE makearchive.ps1)
+file(REMOVE_RECURSE LAMMPS_GUI)

cmake/packaging/linux_wrapper.sh

@@ -0,0 +1,18 @@
+#!/bin/sh
+# wrapper for bundled executables
+
+# reset locale to avoid problems with decimal numbers
+export LC_ALL=C
+
+BASEDIR=$(dirname "$0")
+EXENAME=$(basename "$0")
+
+# append to LD_LIBRARY_PATH to prefer local (newer) libs
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${BASEDIR}/lib
+
+# set some environment variables for LAMMPS etc.
+LAMMPS_POTENTIALS=${BASEDIR}/share/lammps/potentials
+MSI2LMP_LIBRARY=${BASEDIR}/share/lammps/frc_files
+export LD_LIBRARY_PATH LAMMPS_POTENTIALS MSI2LMP_LIBRARY
+
+exec "${BASEDIR}/bin/${EXENAME}" "$@"

cmake/packaging/png2iconset.sh

@@ -0,0 +1,30 @@
+#!/bin/sh
+
+if [ $# != 2 ]
+then
+   echo "usage: $0 <pngfile> <iconset name>"
+   exit 1
+fi
+
+png="$1"
+ico="$2"
+
+if [ ! -f ${png} ]
+then
+   echo "PNG Image $1 not found"
+fi
+
+rm -rf ${ico}.iconset
+mkdir ${ico}.iconset
+sips -z   16   16 ${png} --out ${ico}.iconset/icon_16x16.png
+sips -z   32   32 ${png} --out ${ico}.iconset/icon_16x16@2x.png
+sips -z   32   32 ${png} --out ${ico}.iconset/icon_32x32.png
+sips -z   64   64 ${png} --out ${ico}.iconset/icon_32x32@2x.png
+sips -z  128  128 ${png} --out ${ico}.iconset/icon_128x128.png
+sips -z  256  256 ${png} --out ${ico}.iconset/icon_128x128@2x.png
+sips -z  256  256 ${png} --out ${ico}.iconset/icon_256x256.png
+sips -z  512  512 ${png} --out ${ico}.iconset/icon_256x256@2x.png
+sips -z  512  512 ${png} --out ${ico}.iconset/icon_512x512.png
+sips -z 1024 1024 ${png} --out ${ico}.iconset/icon_512x512@2x.png
+iconutil -c icns ${ico}.iconset
+rm -rf ${ico}.iconset

cmake/presets/all_off.cmake

@@ -43,7 +43,6 @@ set(ALL_PACKAGES
   KOKKOS
   KSPACE
   LATBOLTZ
-  LATTE
   LEPTON
   MACHDYN
   MANIFOLD
@@ -64,8 +63,6 @@ set(ALL_PACKAGES
   MOFFF
   MOLECULE
   MOLFILE
-  MPIIO
-  MSCG
   NETCDF
   OPENMP
   OPT

cmake/presets/all_on.cmake

@@ -45,7 +45,6 @@ set(ALL_PACKAGES
   KOKKOS
   KSPACE
   LATBOLTZ
-  LATTE
   LEPTON
   MACHDYN
   MANIFOLD
@@ -66,8 +65,6 @@ set(ALL_PACKAGES
   MOFFF
   MOLECULE
   MOLFILE
-  MPIIO
-  MSCG
   NETCDF
   OPENMP
   OPT

cmake/presets/download.cmake

@@ -1,16 +1,14 @@
 # Preset that turns on packages with automatic downloads of sources or potentials.
 # Compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time.
 
-set(ALL_PACKAGES KIM LATTE MSCG VORONOI PLUMED SCAFACOS MACHDYN MESONT MDI ML-PACE)
+set(ALL_PACKAGES KIM MSCG VORONOI PLUMED SCAFACOS MACHDYN MESONT MDI ML-PACE)
 
 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_MDI ON CACHE BOOL "" FORCE)
-set(DOWNLOAD_MSCG ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_PACE ON CACHE BOOL "" FORCE)

cmake/presets/gpu-cuda.cmake

@@ -0,0 +1,11 @@
+# preset that enables GPU and selects CUDA API
+
+set(PKG_GPU ON CACHE BOOL "Build GPU package" FORCE)
+set(GPU_API "cuda" CACHE STRING "APU used by GPU package" FORCE)
+set(GPU_PREC "mixed" CACHE STRING "" FORCE)
+
+set(CUDA_NVCC_FLAGS "-allow-unsupported-compiler" CACHE STRING "" FORCE)
+set(CUDA_NVCC_FLAGS_DEBUG "-allow-unsupported-compiler" CACHE STRING "" FORCE)
+set(CUDA_NVCC_FLAGS_MINSIZEREL "-allow-unsupported-compiler" CACHE STRING "" FORCE)
+set(CUDA_NVCC_FLAGS_RELWITHDEBINFO "-allow-unsupported-compiler" CACHE STRING "" FORCE)
+set(CUDA_NVCC_FLAGS_RELEASE "-allow-unsupported-compiler" CACHE STRING "" FORCE)

cmake/presets/kokkos-cuda.cmake

@@ -6,6 +6,8 @@ set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_CUDA   ON CACHE BOOL "" FORCE)
 set(Kokkos_ARCH_PASCAL60 ON CACHE BOOL "" FORCE)
 set(BUILD_OMP ON CACHE BOOL "" FORCE)
+get_filename_component(NVCC_WRAPPER_CMD ${CMAKE_CURRENT_SOURCE_DIR}/../lib/kokkos/bin/nvcc_wrapper ABSOLUTE)
+set(CMAKE_CXX_COMPILER ${NVCC_WRAPPER_CMD} CACHE FILEPATH "" FORCE)
 
 # hide deprecation warnings temporarily for stable release
 set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)

cmake/presets/macos-multiarch.cmake

@@ -0,0 +1,12 @@
+# preset that will build portable multi-arch binaries on macOS without MPI
+
+set(CMAKE_OSX_ARCHITECTURES "arm64;x86_64" CACHE STRING "" FORCE)
+set(CMAKE_OSX_DEPLOYMENT_TARGET 11.0 CACHE STRING "" FORCE)
+set(CMAKE_BUILD_TYPE Release CACHE STRING "" FORCE)
+
+set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
+set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+
+set(BUILD_MPI FALSE CACHE BOOL "" FORCE)

cmake/presets/mingw-cross.cmake

@@ -35,7 +35,6 @@ set(WIN_PACKAGES
   INTEL
   INTERLAYER
   KSPACE
-  LATTE
   LEPTON
   MACHDYN
   MANIFOLD
@@ -84,7 +83,6 @@ endforeach()
 
 # these two packages require a full MPI implementation
 if(BUILD_MPI)
-  set(PKG_MPIIO ON CACHE BOOL "" FORCE)
   set(PKG_LATBOLTZ ON CACHE BOOL "" FORCE)
 endif()
 

cmake/presets/most.cmake

@@ -24,8 +24,8 @@ set(ALL_PACKAGES
   DPD-REACT
   DPD-SMOOTH
   DRUDE
-  ELECTRODE
   EFF
+  ELECTRODE
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX

cmake/presets/nolib.cmake

@@ -12,7 +12,6 @@ set(PACKAGES_WITH_LIB
   KIM
   KOKKOS
   LATBOLTZ
-  LATTE
   LEPTON
   MACHDYN
   MDI
@@ -20,8 +19,6 @@ set(PACKAGES_WITH_LIB
   ML-PACE
   ML-QUIP
   MOLFILE
-  MPIIO
-  MSCG
   NETCDF
   PLUMED
   PYTHON

cmake/presets/windows.cmake

@@ -32,6 +32,7 @@ set(WIN_PACKAGES
   INTERLAYER
   KSPACE
   LEPTON
+  MACHDYN
   MANIFOLD
   MANYBODY
   MC
@@ -45,6 +46,7 @@ set(WIN_PACKAGES
   MOLECULE
   MOLFILE
   OPENMP
+  OPT
   ORIENT
   PERI
   PHONON

doc/Makefile

@@ -63,6 +63,7 @@ help:
 	@echo "  anchor_check  scan for duplicate anchor labels"
 	@echo "  style_check   check for complete and consistent style lists"
 	@echo "  package_check check for complete and consistent package lists"
+	@echo "  role_check    check for misformatted role keywords"
 	@echo "  spelling      spell-check the manual"
 
 # ------------------------------------------
@@ -98,6 +99,7 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
+		env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
 		$(PYTHON) $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
@@ -179,6 +181,7 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
+		env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
 		$(PYTHON) utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
@@ -227,6 +230,7 @@ char_check :
 role_check :
 	@( env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst && exit 1 || : )
 	@( env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst && exit 1 || : )
+	@( env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst && exit 1 || : )
 
 link_check : $(VENV) html
 	@(\

doc/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "8 February 2023" "2023-02-08"
+.TH LAMMPS "1" "21 November 2023" "2023-11-21"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 8 February 2023
+\- Molecular Dynamics Simulator.  Version 21 November 2023
 
 .SH SYNOPSIS
 .B lmp

doc/src/Bibliography.rst

@@ -203,7 +203,7 @@ Bibliography
    A Caro, DA Crowson, M Caro; Phys Rev Lett, 95, 075702 (2005)
 
 **(CasP)**
-   CasP webpage: https://www.helmholtz-berlin.de/people/gregor-schiwietz/casp_en.html
+   CasP webpage: http://www.casp-program.org/
 
 **(Cawkwell2012)**
    A.\  M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86 (17), 174308 (2012).
@@ -562,6 +562,9 @@ Bibliography
 **(Kumar)**
    Kumar and Skinner, J. Phys. Chem. B, 112, 8311 (2008)
 
+**(Lafourcade)**
+  Lafourcade, Maillet, Denoual, Duval, Allera, Goryaeva, and Marinica, `Comp. Mat. Science, 230, 112534 (2023) <https://doi.org/10.1016/j.commatsci.2023.112534>`_
+
 **(Lamoureux and Roux)**
    G.\  Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
 

doc/src/Build_basics.rst

@@ -90,7 +90,7 @@ standard. A more detailed discussion of that is below.
       directory, or ``make`` from the ``src/STUBS`` dir.  If the build
       fails, you may need to edit the ``STUBS/Makefile`` for your
       platform.  The stubs library does not provide MPI/IO functions
-      required by some LAMMPS packages, e.g. ``MPIIO`` or ``LATBOLTZ``,
+      required by some LAMMPS packages, e.g. ``LATBOLTZ``,
       and thus is not compatible with those packages.
 
       .. note::
@@ -129,13 +129,12 @@ in particular the Intel compilers on top of OpenMP. Also, the ``KOKKOS``
 package can be compiled to include OpenMP threading.
 
 In addition, there are a few commands in LAMMPS that have native OpenMP
-support included as well.  These are commands in the ``MPIIO``,
+support included as well.  These are commands in the ``ML-SNAP``,
-``ML-SNAP``, ``DIFFRACTION``, and ``DPD-REACT`` packages.  Furthermore,
+``DIFFRACTION``, and ``DPD-REACT`` packages.  Furthermore, some packages
-some packages support OpenMP threading indirectly through the libraries
+support OpenMP threading indirectly through the libraries they interface
-they interface to: e.g. ``LATTE``, ``KSPACE``, and ``COLVARS``.  See the
+to: e.g. ``KSPACE``, and ``COLVARS``.  See the :doc:`Packages details
-:doc:`Packages details <Packages_details>` page for more info on these
+<Packages_details>` page for more info on these packages, and the pages
-packages, and the pages for their respective commands for OpenMP
+for their respective commands for OpenMP threading info.
-threading info.
 
 For CMake, if you use ``BUILD_OMP=yes``, you can use these packages
 and turn on their native OpenMP support and turn on their native OpenMP
@@ -489,8 +488,9 @@ using CMake or Make.
 
       .. code-block:: bash
 
-         -D BUILD_TOOLS=value         # yes or no (default)
+         -D BUILD_TOOLS=value         # yes or no (default). Build binary2txt, chain.x, micelle2d.x, msi2lmp, phana, stl_bin2txt
-         -D BUILD_LAMMPS_SHELL=value  # yes or no (default)
+         -D BUILD_LAMMPS_SHELL=value  # yes or no (default). Build lammps-shell
+         -D BUILD_LAMMPS_GUI=value    # yes or no (default). Build lammps-gui
 
       The generated binaries will also become part of the LAMMPS installation
       (see below).
@@ -504,7 +504,6 @@ using CMake or Make.
          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
 
          cd lammps/tools/lammps-shell
          make                  # build LAMMPS shell

doc/src/Build_cmake.rst

@@ -16,8 +16,7 @@ environments is on a :doc:`separate page <Howto_cmake>`.
 
 .. note::
 
-   LAMMPS currently requires that CMake version 3.10 or later is available;
+   LAMMPS currently requires that CMake version 3.16 or later is available.
-   version 3.12 or later is preferred.
 
 .. warning::
 
@@ -34,19 +33,18 @@ Advantages of using CMake
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 
 CMake is an alternative to compiling LAMMPS in the traditional way
-through :doc:`(manually customized) makefiles <Build_make>` and a recent
+through :doc:`(manually customized) makefiles <Build_make>`.  Using
-addition to LAMMPS thanks to the efforts of Christoph Junghans (LANL)
+CMake has multiple advantages that are specifically helpful for
-and Richard Berger (Temple U).  Using CMake has multiple advantages that
+people with limited experience in compiling software or for people
-are specifically helpful for people with limited experience in compiling
+that want to modify or extend LAMMPS.
-software or for people that want to modify or extend LAMMPS.
 
 - CMake can detect available hardware, tools, features, and libraries
   and adapt the LAMMPS default build configuration accordingly.
 - CMake can generate files for different build tools and integrated
   development environments (IDE).
 - CMake supports customization of settings with a command line, text
-  mode, or graphical user interface.  No knowledge of file formats or
+  mode, or graphical user interface.  No manual editing of files,
-  complex command line syntax is required.
+  knowledge of file formats or complex command line syntax is required.
 - All enabled components are compiled in a single build operation.
 - Automated dependency tracking for all files and configuration options.
 - Support for true out-of-source compilation. Multiple configurations
@@ -179,13 +177,13 @@ configuration is selected with the *-C* flag:
 
    ctest -C Debug
 
-The CMake scripts in LAMMPS have basic support for being compiled using a
+The CMake scripts in LAMMPS have basic support for being compiled using
-multi-config build system, but not all of it has been ported.  This is in
+a multi-config build system, but not all of it has been ported.  This is
-particular applicable to compiling packages that require additional libraries
+in particular applicable to compiling packages that require additional
-that would be downloaded and compiled by CMake.  The "windows" preset file
+libraries that would be downloaded and compiled by CMake.  The
-tries to keep track of which packages can be compiled natively with the
+``windows.cmake`` preset file tries to keep track of which packages can
-MSVC compilers out-of-the box.  Not all of those external libraries are
+be compiled natively with the MSVC compilers out-of-the box.  Not all of
-portable to Windows, either.
+the external libraries are portable to Windows, either.
 
 
 Installing CMake

doc/src/Build_development.rst

@@ -255,16 +255,18 @@ 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
+suffix. Currently the programs ``test_pair_style``, ``test_bond_style``,
-``test_angle_style`` are implemented.  They will compare forces, energies and
+``test_angle_style``, ``test_dihedral_style``, and
-(global) stress for all atoms after a ``run 0`` calculation and after a
+``test_improper_style`` are implemented.  They will compare forces,
-few steps of MD with :doc:`fix nve <fix_nve>`, each in multiple variants
+energies and (global) stress for all atoms after a ``run 0`` calculation
-with different settings and also for multiple accelerated styles. If a
+and after a few steps of MD with :doc:`fix nve <fix_nve>`, each in
-prerequisite style or package is missing, the individual tests are
+multiple variants with different settings and also for multiple
-skipped.  All tests will be executed on a single MPI process, so using
+accelerated styles. If a prerequisite style or package is missing, the
-the CMake option ``-D BUILD_MPI=off`` can significantly speed up testing,
+individual tests are skipped.  All force style tests will be executed on
-since this will skip the MPI initialization for each test run.
+a single MPI process, so using the CMake option ``-D BUILD_MPI=off`` can
-Below is an example command and output:
+significantly speed up testing, since this will skip the MPI
+initialization for each test run.  Below is an example command and
+output:
 
 .. code-block:: console
 
@@ -416,15 +418,16 @@ 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
+Linux systems).  Alternatives like the ``mold`` linker, the ``lld``
-or the ``gold`` linker available with GNU binutils can speed up this step
+linker of the LLVM project, or the ``gold`` linker available with GNU
-substantially. CMake will by default test if any of the two can be
+binutils can speed up this step substantially (in this order).  CMake
-enabled and use it when ``ENABLE_TESTING`` is active.  It can also be
+will by default test if any of the three can be enabled and use it when
-selected manually through the ``CMAKE_CUSTOM_LINKER`` CMake variable.
+``ENABLE_TESTING`` is active.  It can also be selected manually through
-Allowed values are ``lld``, ``gold``, ``bfd``, or ``default``.  The
+the ``CMAKE_CUSTOM_LINKER`` CMake variable.  Allowed values are
-``default`` option will use the system default linker otherwise, the
+``mold``, ``lld``, ``gold``, ``bfd``, or ``default``.  The ``default``
-linker is chosen explicitly.  This option is only available for the
+option will use the system default linker otherwise, the linker is
-GNU or Clang C++ compiler.
+chosen explicitly.  This option is only available for the GNU or Clang
+C++ compilers.
 
 Tests for other components and utility functions
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -518,11 +521,15 @@ The following options are available.
    make fix-errordocs       # remove error docs in header files
    make check-permissions   # search for files with permissions issues
    make fix-permissions     # correct permissions issues in files
+   make check-docs          # search for several issues in the manual
+   make check-version       # list files with pending release version tags
    make check               # run all check targets from above
 
 These should help to make source and documentation files conforming
 to some the coding style preferences of the LAMMPS developers.
 
+.. _clang-format:
+
 Clang-format support
 --------------------
 

doc/src/Build_extras.rst

@@ -43,7 +43,6 @@ This is the list of packages that may require additional steps.
    * :ref:`INTEL <intel>`
    * :ref:`KIM <kim>`
    * :ref:`KOKKOS <kokkos>`
-   * :ref:`LATTE <latte>`
    * :ref:`LEPTON <lepton>`
    * :ref:`MACHDYN <machdyn>`
    * :ref:`MDI <mdi>`
@@ -53,7 +52,6 @@ This is the list of packages that may require additional steps.
    * :ref:`ML-POD <ml-pod>`
    * :ref:`ML-QUIP <ml-quip>`
    * :ref:`MOLFILE <molfile>`
-   * :ref:`MSCG <mscg>`
    * :ref:`NETCDF <netcdf>`
    * :ref:`OPENMP <openmp>`
    * :ref:`OPT <opt>`
@@ -141,6 +139,8 @@ CMake build
                                 # value = yes or no (default)
    -D CUDA_MPS_SUPPORT=value    # enables some tweaks required to run with active nvidia-cuda-mps daemon
                                 # value = yes or no (default)
+   -D CUDA_BUILD_MULTIARCH=value  # enables building CUDA kernels for all supported GPU architectures
+                                  # value = yes (default) or no
    -D USE_STATIC_OPENCL_LOADER=value  # downloads/includes OpenCL ICD loader library, no local OpenCL headers/libs needed
                                       # value = yes (default) or no
 
@@ -159,41 +159,49 @@ CMake build
 A more detailed list can be found, for example,
 at `Wikipedia's CUDA article <https://en.wikipedia.org/wiki/CUDA#GPUs_supported>`_
 
-CMake can detect which version of the CUDA toolkit is used and thus will try
+CMake can detect which version of the CUDA toolkit is used and thus will
-to include support for **all** major GPU architectures supported by this toolkit.
+try to include support for **all** major GPU architectures supported by
-Thus the GPU_ARCH setting is merely an optimization, to have code for
+this toolkit.  Thus the GPU_ARCH setting is merely an optimization, to
-the preferred GPU architecture directly included rather than having to wait
+have code for the preferred GPU architecture directly included rather
-for the JIT compiler of the CUDA driver to translate it.
+than having to wait for the JIT compiler of the CUDA driver to translate
+it.  This behavior can be turned off (e.g. to speed up compilation) by
+setting :code:`CUDA_ENABLE_MULTIARCH` to :code:`no`.
 
-When compiling for CUDA or HIP with CUDA, version 8.0 or later of the CUDA toolkit
+When compiling for CUDA or HIP with CUDA, version 8.0 or later of the
-is required and a GPU architecture of Kepler or later, which must *also* be
+CUDA toolkit is required and a GPU architecture of Kepler or later,
-supported by the CUDA toolkit in use **and** the CUDA driver in use.
+which must *also* be supported by the CUDA toolkit in use **and** the
-When compiling for OpenCL, OpenCL version 1.2 or later is required and the
+CUDA driver in use.  When compiling for OpenCL, OpenCL version 1.2 or
-GPU must be supported by the GPU driver and OpenCL runtime bundled with the driver.
+later is required and the GPU must be supported by the GPU driver and
+OpenCL runtime bundled with the driver.
 
-When building with CMake, you **must NOT** build the GPU library in ``lib/gpu``
+When building with CMake, you **must NOT** build the GPU library in
-using the traditional build procedure. CMake will detect files generated by that
+``lib/gpu`` using the traditional build procedure. CMake will detect
-process and will terminate with an error and a suggestion for how to remove them.
+files generated by that process and will terminate with an error and a
+suggestion for how to remove them.
 
-If you are compiling for OpenCL, the default setting is to download, build, and
+If you are compiling for OpenCL, the default setting is to download,
-link with a static OpenCL ICD loader library and standard OpenCL headers.  This
+build, and link with a static OpenCL ICD loader library and standard
-way no local OpenCL development headers or library needs to be present and only
+OpenCL headers.  This way no local OpenCL development headers or library
-OpenCL compatible drivers need to be installed to use OpenCL.  If this is not
+needs to be present and only OpenCL compatible drivers need to be
-desired, you can set :code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
+installed to use OpenCL.  If this is not desired, you can set
+:code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
 
-The GPU library has some multi-thread support using OpenMP.  If LAMMPS is built
+The GPU library has some multi-thread support using OpenMP.  If LAMMPS
-with ``-D BUILD_OMP=on`` this will also be enabled.
+is built with ``-D BUILD_OMP=on`` this will also be enabled.
 
-If you are compiling with HIP, note that before running CMake you will have to
+If you are compiling with HIP, note that before running CMake you will
-set appropriate environment variables. Some variables such as
+have to set appropriate environment variables. Some variables such as
-:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc`
+:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are
-and the linker to work correctly.
+necessary for :code:`hipcc` and the linker to work correctly.
 
-Using CHIP-SPV implementation of HIP is now supported. It allows one to run HIP
+.. versionadded:: 3Aug2022
-code on Intel GPUs via the OpenCL or Level Zero backends. To use CHIP-SPV, you must
+
-set :code:`-DHIP_USE_DEVICE_SORT=OFF` in your CMake command line as CHIP-SPV does not
+Using the CHIP-SPV implementation of HIP is supported. It allows one to
-yet support hipCUB. The use of HIP for Intel GPUs is still experimental so you
+run HIP code on Intel GPUs via the OpenCL or Level Zero backends. To use
-should only use this option in preparations to run on Aurora system at ANL.
+CHIP-SPV, you must set :code:`-DHIP_USE_DEVICE_SORT=OFF` in your CMake
+command line as CHIP-SPV does not yet support hipCUB. As of Summer 2022,
+the use of HIP for Intel GPUs is experimental. You should only use this
+option in preparations to run on Aurora system at Argonne.
 
 .. code:: bash
 
@@ -618,18 +626,24 @@ They must be specified in uppercase.
    *  - HOPPER90
       - GPU
       - NVIDIA Hopper generation CC 9.0 GPU
-   *  - VEGA900
+   *  - AMD_GFX906
       - GPU
-      - AMD GPU MI25 GFX900
+      - AMD GPU MI50/MI60
-   *  - VEGA906
+   *  - AMD_GFX908
       - GPU
-      - AMD GPU MI50/MI60 GFX906
+      - AMD GPU MI100
-   *  - VEGA908
+   *  - AMD_GFX90A
       - GPU
-      - AMD GPU MI100 GFX908
+      - AMD GPU MI200
-   *  - VEGA90A
+   *  - AMD_GFX942
       - GPU
-      - AMD GPU MI200 GFX90A
+      - AMD GPU MI300
+   *  - AMD_GFX1030
+      - GPU
+      - AMD GPU V620/W6800
+   *  - AMD_GFX1100
+      - GPU
+      - AMD GPU RX7900XTX
    *  - INTEL_GEN
       - GPU
       - SPIR64-based devices, e.g. Intel GPUs, using JIT
@@ -652,7 +666,7 @@ They must be specified in uppercase.
       - GPU
       - Intel GPU Ponte Vecchio
 
-This list was last updated for version 3.7.1 of the Kokkos library.
+This list was last updated for version 4.2 of the Kokkos library.
 
 .. tabs::
 
@@ -684,20 +698,11 @@ This list was last updated for version 3.7.1 of the Kokkos library.
          -D Kokkos_ARCH_GPUARCH=yes    # GPUARCH = GPU from list above
          -D Kokkos_ENABLE_CUDA=yes
          -D Kokkos_ENABLE_OPENMP=yes
-         -D CMAKE_CXX_COMPILER=wrapper # wrapper = full path to Cuda nvcc wrapper
 
       This will also enable executing FFTs on the GPU, either via the
       internal KISSFFT library, or - by preference - with the cuFFT
       library bundled with the CUDA toolkit, depending on whether CMake
-      can identify its location.  The *wrapper* value for
+      can identify its location.
-      ``CMAKE_CXX_COMPILER`` variable is the path to the CUDA nvcc
-      compiler wrapper provided in the Kokkos library:
-      ``lib/kokkos/bin/nvcc_wrapper``\ .  The setting should include the
-      full path name to the wrapper, e.g.
-
-      .. code-block:: bash
-
-         -D CMAKE_CXX_COMPILER=${HOME}/lammps/lib/kokkos/bin/nvcc_wrapper
 
       For AMD or NVIDIA GPUs using HIP, set these variables:
 
@@ -717,9 +722,10 @@ This list was last updated for version 3.7.1 of the Kokkos library.
       ``cmake/presets`` folder, ``kokkos-serial.cmake``,
       ``kokkos-openmp.cmake``, ``kokkos-cuda.cmake``,
       ``kokkos-hip.cmake``, and ``kokkos-sycl.cmake``.  They will enable
-      the KOKKOS package and enable some hardware choice.  So to compile
+      the KOKKOS package and enable some hardware choices.  For GPU
-      with CUDA device parallelization (for GPUs with CC 5.0 and up)
+      support those preset files must be customized to match the
-      with some common packages enabled, you can do the following:
+      hardware used. So to compile with CUDA device parallelization with
+      some common packages enabled, you can do the following:
 
       .. code-block:: bash
 
@@ -832,63 +838,6 @@ will thus always enable it.
 
 ----------
 
-.. _latte:
-
-LATTE package
--------------------------
-
-To build with this package, you must download and build the LATTE
-library.
-
-.. tabs::
-
-   .. tab:: CMake build
-
-      .. code-block:: bash
-
-         -D DOWNLOAD_LATTE=value      # download LATTE for build, value = no (default) or yes
-         -D LATTE_LIBRARY=path        # LATTE library file (only needed if a custom location)
-         -D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
-                                      #   value = no (default) or yes
-
-      If ``DOWNLOAD_LATTE`` is set, the LATTE library will be downloaded
-      and built inside the CMake build directory.  If the LATTE library
-      is already on your system (in a location CMake cannot find it),
-      ``LATTE_LIBRARY`` is the filename (plus path) of the LATTE library
-      file, not the directory the library file is in.
-
-      The LATTE library requires LAPACK (and BLAS) and CMake can identify
-      their locations and pass that info to the LATTE build script. But
-      on some systems this triggers a (current) limitation of CMake and
-      the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in
-      those cases to use the bundled linear algebra library and work around
-      the limitation.
-
-   .. tab:: Traditional make
-
-      You can download and build the LATTE library manually if you
-      prefer; follow the instructions in ``lib/latte/README``\ .  You
-      can also do it in one step from the ``lammps/src`` dir, using a
-      command like these, which simply invokes the
-      ``lib/latte/Install.py`` script with the specified args:
-
-      .. code-block:: bash
-
-         make lib-latte                        # print help message
-         make lib-latte args="-b"              # download and build in lib/latte/LATTE-master
-         make lib-latte args="-p $HOME/latte"  # use existing LATTE installation in $HOME/latte
-         make lib-latte args="-b -m gfortran"  # download and build in lib/latte and
-                                               #   copy Makefile.lammps.gfortran to Makefile.lammps
-
-      Note that 3 symbolic (soft) links, ``includelink`` and ``liblink``
-      and ``filelink.o``, are created in ``lib/latte`` to point to
-      required folders and files in the LATTE home directory.  When
-      LAMMPS itself is built it will use these links.  You should also
-      check that the ``Makefile.lammps`` file you create is appropriate
-      for the compiler you use on your system to build LATTE.
-
-----------
-
 .. _lepton:
 
 LEPTON package
@@ -938,6 +887,50 @@ included in the LAMMPS source distribution in the ``lib/lepton`` folder.
 
 ----------
 
+.. _machdyn:
+
+MACHDYN package
+-------------------------------
+
+To build with this package, you must download the Eigen3 library.
+Eigen3 is a template library, so you do not need to build it.
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      .. code-block:: bash
+
+         -D DOWNLOAD_EIGEN3            # download Eigen3, value = no (default) or yes
+         -D EIGEN3_INCLUDE_DIR=path    # path to Eigen library (only needed if a custom location)
+
+      If ``DOWNLOAD_EIGEN3`` is set, the Eigen3 library will be
+      downloaded and inside the CMake build directory.  If the Eigen3
+      library is already on your system (in a location where CMake
+      cannot find it), set ``EIGEN3_INCLUDE_DIR`` to the directory the
+      ``Eigen3`` include file is in.
+
+   .. tab:: Traditional make
+
+      You can download the Eigen3 library manually if you prefer; follow
+      the instructions in ``lib/machdyn/README``.  You can also do it in one
+      step from the ``lammps/src`` dir, using a command like these,
+      which simply invokes the ``lib/machdyn/Install.py`` script with the
+      specified args:
+
+      .. code-block:: bash
+
+         make lib-machdyn                         # print help message
+         make lib-machdyn args="-b"               # download to lib/machdyn/eigen3
+         make lib-machdyn args="-p /usr/include/eigen3"    # use existing Eigen installation in /usr/include/eigen3
+
+      Note that a symbolic (soft) link named ``includelink`` is created
+      in ``lib/machdyn`` to point to the Eigen dir.  When LAMMPS builds it
+      will use this link.  You should not need to edit the
+      ``lib/machdyn/Makefile.lammps`` file.
+
+----------
+
 .. _mliap:
 
 ML-IAP package
@@ -988,59 +981,6 @@ Python version 3.6 or later.
 
 ----------
 
-.. _mscg:
-
-MSCG package
------------------------
-
-To build with this package, you must download and build the MS-CG
-library.  Building the MS-CG library requires that the GSL
-(GNU Scientific Library) headers and libraries are installed on your
-machine.  See the ``lib/mscg/README`` and ``MSCG/Install`` files for
-more details.
-
-.. tabs::
-
-   .. tab:: CMake build
-
-      .. code-block:: bash
-
-         -D DOWNLOAD_MSCG=value    # download MSCG for build, value = no (default) or yes
-         -D MSCG_LIBRARY=path      # MSCG library file (only needed if a custom location)
-         -D MSCG_INCLUDE_DIR=path  # MSCG include directory (only needed if a custom location)
-
-      If ``DOWNLOAD_MSCG`` is set, the MSCG library will be downloaded
-      and built inside the CMake build directory.  If the MSCG library
-      is already on your system (in a location CMake cannot find it),
-      ``MSCG_LIBRARY`` is the filename (plus path) of the MSCG library
-      file, not the directory the library file is in.
-      ``MSCG_INCLUDE_DIR`` is the directory the MSCG include file is in.
-
-   .. tab:: Traditional make
-
-      You can download and build the MS-CG library manually if you
-      prefer; follow the instructions in ``lib/mscg/README``\ .  You can
-      also do it in one step from the ``lammps/src`` dir, using a
-      command like these, which simply invokes the
-      ``lib/mscg/Install.py`` script with the specified args:
-
-      .. code-block:: bash
-
-         make lib-mscg             # print help message
-         make lib-mscg args="-b -m serial"   # download and build in lib/mscg/MSCG-release-master
-                                             # with the settings compatible with "make serial"
-         make lib-mscg args="-b -m mpi"      # download and build in lib/mscg/MSCG-release-master
-                                             # with the settings compatible with "make mpi"
-         make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release
-
-      Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``,
-      will be created in ``lib/mscg`` to point to the MS-CG
-      ``src/installation`` dir.  When LAMMPS is built in src it will use
-      these links.  You should not need to edit the
-      ``lib/mscg/Makefile.lammps`` file.
-
-----------
-
 .. _opt:
 
 OPT package
@@ -1116,12 +1056,12 @@ additional details.
 
       .. code-block:: bash
 
-         -D PYTHON_EXECUTABLE=path   # path to Python executable to use
+         -D Python_EXECUTABLE=path   # path to Python executable to use
 
       Without this setting, CMake will guess the default Python version
       on your system.  To use a different Python version, you can either
       create a virtualenv, activate it and then run cmake.  Or you can
-      set the PYTHON_EXECUTABLE variable to specify which Python
+      set the Python_EXECUTABLE variable to specify which Python
       interpreter should be used.  Note note that you will also need to
       have the development headers installed for this version,
       e.g. python2-devel.
@@ -1413,9 +1353,9 @@ This package depends on the KSPACE package.
       KSPACE package so the latter one *must* be enabled.
 
       The ELECTRODE package also requires LAPACK (and BLAS) and CMake
-      can identify their locations and pass that info to the LATTE build
+      can identify their locations and pass that info to the ELECTRODE
-      script.  But on some systems this may cause problems when linking
+      build script.  But on some systems this may cause problems when
-      or the dependency is not desired.  Try enabling
+      linking or the dependency is not desired.  Try enabling
       ``USE_INTERNAL_LINALG`` in those cases to use the bundled linear
       algebra library and work around the limitation.
 
@@ -1536,6 +1476,55 @@ ML-POD package
 
 ----------
 
+.. _ml-quip:
+
+ML-QUIP package
+---------------------------------
+
+To build with this package, you must download and build the QUIP
+library.  It can be obtained from GitHub.  For support of GAP
+potentials, additional files with specific licensing conditions need
+to be downloaded and configured.  The automatic download will from
+within CMake will download the non-commercial use version.
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      .. code-block:: bash
+
+         -D DOWNLOAD_QUIP=value       # download QUIP library for build, value = no (default) or yes
+         -D QUIP_LIBRARY=path         # path to libquip.a (only needed if a custom location)
+         -D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
+                                      #   value = no (default) or yes
+
+      CMake will try to download and build the QUIP library from GitHub,
+      if it is not found on the local machine. This requires to have git
+      installed. It will use the same compilers and flags as used for
+      compiling LAMMPS.  Currently this is only supported for the GNU
+      and the Intel compilers. Set the ``QUIP_LIBRARY`` variable if you
+      want to use a previously compiled and installed QUIP library and
+      CMake cannot find it.
+
+      The QUIP library requires LAPACK (and BLAS) and CMake can identify
+      their locations and pass that info to the QUIP build script. But
+      on some systems this triggers a (current) limitation of CMake and
+      the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in
+      those cases to use the bundled linear algebra library and work around
+      the limitation.
+
+   .. tab:: Traditional make
+
+      The download/build procedure for the QUIP library, described in
+      ``lib/quip/README`` file requires setting two environment
+      variables, ``QUIP_ROOT`` and ``QUIP_ARCH``.  These are accessed by
+      the ``lib/quip/Makefile.lammps`` file which is used when you
+      compile and link LAMMPS with this package.  You should only need
+      to edit ``Makefile.lammps`` if the LAMMPS build can not use its
+      settings to successfully build on your system.
+
+----------
+
 .. _plumed:
 
 PLUMED package
@@ -2057,55 +2046,6 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
 
 ----------
 
-.. _ml-quip:
-
-ML-QUIP package
----------------------------------
-
-To build with this package, you must download and build the QUIP
-library.  It can be obtained from GitHub.  For support of GAP
-potentials, additional files with specific licensing conditions need
-to be downloaded and configured.  The automatic download will from
-within CMake will download the non-commercial use version.
-
-.. tabs::
-
-   .. tab:: CMake build
-
-      .. code-block:: bash
-
-         -D DOWNLOAD_QUIP=value       # download QUIP library for build, value = no (default) or yes
-         -D QUIP_LIBRARY=path         # path to libquip.a (only needed if a custom location)
-         -D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
-                                      #   value = no (default) or yes
-
-      CMake will try to download and build the QUIP library from GitHub,
-      if it is not found on the local machine. This requires to have git
-      installed. It will use the same compilers and flags as used for
-      compiling LAMMPS.  Currently this is only supported for the GNU
-      and the Intel compilers. Set the ``QUIP_LIBRARY`` variable if you
-      want to use a previously compiled and installed QUIP library and
-      CMake cannot find it.
-
-      The QUIP library requires LAPACK (and BLAS) and CMake can identify
-      their locations and pass that info to the QUIP build script. But
-      on some systems this triggers a (current) limitation of CMake and
-      the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in
-      those cases to use the bundled linear algebra library and work around
-      the limitation.
-
-   .. tab:: Traditional make
-
-      The download/build procedure for the QUIP library, described in
-      ``lib/quip/README`` file requires setting two environment
-      variables, ``QUIP_ROOT`` and ``QUIP_ARCH``.  These are accessed by
-      the ``lib/quip/Makefile.lammps`` file which is used when you
-      compile and link LAMMPS with this package.  You should only need
-      to edit ``Makefile.lammps`` if the LAMMPS build can not use its
-      settings to successfully build on your system.
-
-----------
-
 .. _scafacos:
 
 SCAFACOS package
@@ -2153,50 +2093,6 @@ To build with this package, you must download and build the
 
 ----------
 
-.. _machdyn:
-
-MACHDYN package
--------------------------------
-
-To build with this package, you must download the Eigen3 library.
-Eigen3 is a template library, so you do not need to build it.
-
-.. tabs::
-
-   .. tab:: CMake build
-
-      .. code-block:: bash
-
-         -D DOWNLOAD_EIGEN3            # download Eigen3, value = no (default) or yes
-         -D EIGEN3_INCLUDE_DIR=path    # path to Eigen library (only needed if a custom location)
-
-      If ``DOWNLOAD_EIGEN3`` is set, the Eigen3 library will be
-      downloaded and inside the CMake build directory.  If the Eigen3
-      library is already on your system (in a location where CMake
-      cannot find it), set ``EIGEN3_INCLUDE_DIR`` to the directory the
-      ``Eigen3`` include file is in.
-
-   .. tab:: Traditional make
-
-      You can download the Eigen3 library manually if you prefer; follow
-      the instructions in ``lib/smd/README``.  You can also do it in one
-      step from the ``lammps/src`` dir, using a command like these,
-      which simply invokes the ``lib/smd/Install.py`` script with the
-      specified args:
-
-      .. code-block:: bash
-
-         make lib-smd                         # print help message
-         make lib-smd args="-b"               # download to lib/smd/eigen3
-         make lib-smd args="-p /usr/include/eigen3"    # use existing Eigen installation in /usr/include/eigen3
-
-      Note that a symbolic (soft) link named ``includelink`` is created
-      in ``lib/smd`` to point to the Eigen dir.  When LAMMPS builds it
-      will use this link.  You should not need to edit the
-      ``lib/smd/Makefile.lammps`` file.
-
-----------
-
 .. _vtk:
 
 VTK package

doc/src/Build_make.rst

@@ -117,8 +117,8 @@ their settings may become outdated, too:
 
 .. code-block:: bash
 
-   make mac             # build serial LAMMPS on a Mac
+   make mac             # build serial LAMMPS on macOS
-   make mac_mpi         # build parallel LAMMPS on a Mac
+   make mac_mpi         # build parallel LAMMPS on macOS
    make intel_cpu       # build with the INTEL package optimized for CPUs
    make knl             # build with the INTEL package optimized for KNLs
    make opt             # build with the OPT package optimized for CPUs

doc/src/Build_manual.rst

@@ -53,10 +53,10 @@ incorporates programmer documentation extracted from the LAMMPS C++
 sources through the `Doxygen <https://doxygen.nl/>`_ program.  Currently
 the translation to HTML, PDF (via LaTeX), ePUB (for many e-book readers)
 and MOBI (for Amazon Kindle readers) are supported.  For that to work a
-Python 3 interpreter, the ``doxygen`` tools and internet access to
+Python interpreter version 3.8 or later, the ``doxygen`` tools and
-download additional files and tools are required.  This download is
+internet access to download additional files and tools are required.
-usually only required once or after the documentation folder is returned
+This download is usually only required once or after the documentation
-to a pristine state with ``make clean-all``.
+folder is returned to a pristine state with ``make clean-all``.
 
 For the documentation build a python virtual environment is set up in
 the folder ``doc/docenv`` and various python packages are installed into

doc/src/Build_package.rst

@@ -46,7 +46,6 @@ packages:
    * :ref:`INTEL <intel>`
    * :ref:`KIM <kim>`
    * :ref:`KOKKOS <kokkos>`
-   * :ref:`LATTE <latte>`
    * :ref:`LEPTON <lepton>`
    * :ref:`MACHDYN <machdyn>`
    * :ref:`MDI <mdi>`
@@ -56,7 +55,6 @@ packages:
    * :ref:`ML-POD <ml-pod>`
    * :ref:`ML-QUIP <ml-quip>`
    * :ref:`MOLFILE <molfile>`
-   * :ref:`MSCG <mscg>`
    * :ref:`NETCDF <netcdf>`
    * :ref:`OPENMP <openmp>`
    * :ref:`OPT <opt>`
@@ -184,6 +182,7 @@ make a copy of one of them and modify it to suit your needs.
     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
+    cmake -C ../cmake/presets/macos-multiarch.cmake [OPTIONS] ../cmake # compile serial multi-arch binaries on macOS
 
 Presets that have names starting with "windows" are specifically for
 compiling LAMMPS :doc:`natively on Windows <Build_windows>` and

doc/src/Build_settings.rst

@@ -44,6 +44,14 @@ 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.
 
+.. versionadded:: TBD
+
+Alternatively, LAMMPS can use the `heFFTe
+<https://icl-utk-edu.github.io/heffte/>`_ library for the MPI
+communication algorithms, which comes with many optimizations for
+special cases, e.g. leveraging available 2D and 3D FFTs in the back end
+libraries and better pipelining for packing and communication.
+
 .. tabs::
 
    .. tab:: CMake build
@@ -53,6 +61,7 @@ LAMMPS can use them if they are available on your system.
          -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
+         -D FFT_USE_HEFFTE=value   # yes or no (default), yes links to heFFTe
 
       .. note::
 
@@ -76,6 +85,16 @@ LAMMPS can use them if they are available on your system.
          -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
+         -D FFT_HEFFTE_BACKEND=value # FFTW or MKL or empty/undefined for the stock heFFTe back end
+         -D Heffte_ROOT=path         # path to an existing heFFTe installation
+
+      .. note::
+
+         heFFTe comes with a builtin (= stock) back end for FFTs, i.e. a
+         default internal FFT implementation; however, this stock back
+         end is intended for testing purposes only and is not optimized
+         for production runs.
+
 
    .. tab:: Traditional make
 
@@ -111,6 +130,24 @@ LAMMPS can use them if they are available on your system.
       files in its default search path.  You must specify ``FFT_LIB``
       with the appropriate FFT libraries to include in the link.
 
+      Traditional make can also link to heFFTe using an existing installation
+
+      .. code-block:: make
+
+         include <path-to-heffte-installation>/share/heffte/HeffteMakefile.in
+         FFT_INC = -DFFT_HEFFTE -DFFT_HEFFTE_FFTW $(heffte_include)
+         FFT_PATH =
+         FFT_LIB = $(heffte_link) $(heffte_libs)
+
+      The heFFTe install path will contain `HeffteMakefile.in`.
+      which will define the `heffte_` include variables needed to link to heFFTe from
+      an external project using traditional make.
+      The `-DFFT_HEFFTE` is required to switch to using heFFTe, while the optional `-DFFT_HEFFTE_FFTW`
+      selects the desired heFFTe back end, e.g., `-DFFT_HEFFTE_FFTW` or `-DFFT_HEFFTE_MKL`,
+      omitting the variable will default to the `stock` back end.
+      The heFFTe `stock` back end is intended to be used for testing and debugging,
+      but is not performance optimized for large scale production runs.
+
 The `KISS FFT library <https://github.com/mborgerding/kissfft>`_ is
 included in the LAMMPS distribution.  It is portable across all
 platforms.  Depending on the size of the FFTs and the number of
@@ -170,6 +207,16 @@ Depending on the machine, the size of the FFT grid, the number of
 processors used, one option may be slightly faster.  The default is
 ARRAY mode.
 
+When using ``-DFFT_HEFFTE`` CMake will first look for an existing
+install with hints provided by ``-DHeffte_ROOT``, as recommended by the
+CMake standard and note that the name is case sensitive. If CMake cannot
+find a heFFTe installation with the correct back end (e.g., FFTW or
+MKL), it will attempt to download and build the library automatically.
+In this case, LAMMPS CMake will also accept all heFFTe specific
+variables listed in the `heFFTe documentation
+<https://mkstoyanov.bitbucket.io/heffte/md_doxygen_installation.html>`_
+and those variables will be passed into the heFFTe build.
+
 ----------
 
 .. _size:
@@ -459,27 +506,13 @@ those systems:
 .. _exceptions:
 
 Exception handling when using LAMMPS as a library
-------------------------------------------------------------------
+-------------------------------------------------
 
-This setting is useful when external codes drive LAMMPS as a library.
+LAMMPS errors do not kill the calling code, but throw an exception.  In
-With this option enabled, LAMMPS errors do not kill the calling code.
+the C-library interface, the call stack is unwound and control returns
-Instead, the call stack is unwound and control returns to the caller,
+to the caller, e.g. to Python or a code that is coupled to LAMMPS. The
-e.g. to Python. Of course, the calling code has to be set up to
+error status can then be queried.  When using C++ directly, the calling
-*catch* exceptions thrown from within LAMMPS.
+code has to be set up to *catch* exceptions thrown from within LAMMPS.
-
-.. tabs::
-
-   .. tab:: CMake build
-
-      .. code-block:: bash
-
-         -D LAMMPS_EXCEPTIONS=value        # yes or no (default)
-
-   .. tab:: Traditional make
-
-      .. code-block:: make
-
-         LMP_INC = -DLAMMPS_EXCEPTIONS   <other LMP_INC settings>
 
 .. note::
 

doc/src/Commands_compute.rst

@@ -46,6 +46,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`com/chunk <compute_com_chunk>`
    * :doc:`contact/atom <compute_contact_atom>`
    * :doc:`coord/atom (k) <compute_coord_atom>`
+   * :doc:`count/type <compute_count_type>`
    * :doc:`damage/atom <compute_damage_atom>`
    * :doc:`dihedral <compute_dihedral>`
    * :doc:`dihedral/local <compute_dihedral_local>`
@@ -63,7 +64,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`entropy/atom <compute_entropy_atom>`
    * :doc:`erotate/asphere <compute_erotate_asphere>`
    * :doc:`erotate/rigid <compute_erotate_rigid>`
-   * :doc:`erotate/sphere <compute_erotate_sphere>`
+   * :doc:`erotate/sphere (k) <compute_erotate_sphere>`
    * :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>`
    * :doc:`event/displace <compute_event_displace>`
    * :doc:`fabric <compute_fabric>`
@@ -90,6 +91,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`ke/atom/eff <compute_ke_atom_eff>`
    * :doc:`ke/eff <compute_ke_eff>`
    * :doc:`ke/rigid <compute_ke_rigid>`
+   * :doc:`composition/atom (k) <compute_composition_atom>`
    * :doc:`mliap <compute_mliap>`
    * :doc:`momentum <compute_momentum>`
    * :doc:`msd <compute_msd>`
@@ -98,6 +100,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`nbond/atom <compute_nbond_atom>`
    * :doc:`omega/chunk <compute_omega_chunk>`
    * :doc:`orientorder/atom (k) <compute_orientorder_atom>`
+   * :doc:`pace <compute_pace>`
    * :doc:`pair <compute_pair>`
    * :doc:`pair/local <compute_pair_local>`
    * :doc:`pe <compute_pe>`
@@ -113,12 +116,15 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`property/grid <compute_property_grid>`
    * :doc:`property/local <compute_property_local>`
    * :doc:`ptm/atom <compute_ptm_atom>`
+   * :doc:`rattlers/atom <compute_rattlers_atom>`
    * :doc:`rdf <compute_rdf>`
+   * :doc:`reaxff/atom (k) <compute_reaxff_atom>`
    * :doc:`reduce <compute_reduce>`
    * :doc:`reduce/chunk <compute_reduce_chunk>`
    * :doc:`reduce/region <compute_reduce>`
    * :doc:`rigid/local <compute_rigid_local>`
    * :doc:`saed <compute_saed>`
+   * :doc:`slcsa/atom <compute_slcsa_atom>`
    * :doc:`slice <compute_slice>`
    * :doc:`smd/contact/radius <compute_smd_contact_radius>`
    * :doc:`smd/damage <compute_smd_damage>`
@@ -152,11 +158,11 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`sph/t/atom <compute_sph_t_atom>`
    * :doc:`spin <compute_spin>`
    * :doc:`stress/atom <compute_stress_atom>`
-   * :doc:`stress/cartesian <compute_stress_profile>`
+   * :doc:`stress/cartesian <compute_stress_cartesian>`
-   * :doc:`stress/cylinder <compute_stress_profile>`
+   * :doc:`stress/cylinder <compute_stress_curvilinear>`
    * :doc:`stress/mop <compute_stress_mop>`
    * :doc:`stress/mop/profile <compute_stress_mop>`
-   * :doc:`stress/spherical <compute_stress_profile>`
+   * :doc:`stress/spherical <compute_stress_curvilinear>`
    * :doc:`stress/tally <compute_tally>`
    * :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>`
    * :doc:`temp (k) <compute_temp>`

doc/src/Commands_dump.rst

@@ -23,17 +23,14 @@ An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
    * :doc:`atom <dump>`
    * :doc:`atom/adios <dump_adios>`
    * :doc:`atom/gz <dump>`
-   * :doc:`atom/mpiio <dump>`
    * :doc:`atom/zstd <dump>`
    * :doc:`cfg <dump>`
    * :doc:`cfg/gz <dump>`
-   * :doc:`cfg/mpiio <dump>`
    * :doc:`cfg/uef <dump_cfg_uef>`
    * :doc:`cfg/zstd <dump>`
    * :doc:`custom <dump>`
    * :doc:`custom/adios <dump_adios>`
    * :doc:`custom/gz <dump>`
-   * :doc:`custom/mpiio <dump>`
    * :doc:`custom/zstd <dump>`
    * :doc:`dcd <dump>`
    * :doc:`grid <dump>`
@@ -51,7 +48,6 @@ An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
    * :doc:`xtc <dump>`
    * :doc:`xyz <dump>`
    * :doc:`xyz/gz <dump>`
-   * :doc:`xyz/mpiio <dump>`
    * :doc:`xyz/zstd <dump>`
    * :doc:`yaml <dump>`
 

doc/src/Commands_fix.rst

@@ -69,7 +69,7 @@ OPT.
    * :doc:`drude/transform/inverse <fix_drude_transform>`
    * :doc:`dt/reset (k) <fix_dt_reset>`
    * :doc:`edpd/source <fix_dpd_source>`
-   * :doc:`efield <fix_efield>`
+   * :doc:`efield (k) <fix_efield>`
    * :doc:`efield/tip4p <fix_efield>`
    * :doc:`ehex <fix_ehex>`
    * :doc:`electrode/conp (i) <fix_electrode>`
@@ -104,25 +104,25 @@ OPT.
    * :doc:`langevin/drude <fix_langevin_drude>`
    * :doc:`langevin/eff <fix_langevin_eff>`
    * :doc:`langevin/spin <fix_langevin_spin>`
-   * :doc:`latte <fix_latte>`
    * :doc:`lb/fluid <fix_lb_fluid>`
    * :doc:`lb/momentum <fix_lb_momentum>`
    * :doc:`lb/viscous <fix_lb_viscous>`
    * :doc:`lineforce <fix_lineforce>`
    * :doc:`manifoldforce <fix_manifoldforce>`
    * :doc:`mdi/qm <fix_mdi_qm>`
+   * :doc:`mdi/qmmm <fix_mdi_qmmm>`
    * :doc:`meso/move <fix_meso_move>`
    * :doc:`mol/swap <fix_mol_swap>`
    * :doc:`momentum (k) <fix_momentum>`
    * :doc:`momentum/chunk <fix_momentum>`
    * :doc:`move <fix_move>`
-   * :doc:`mscg <fix_mscg>`
    * :doc:`msst <fix_msst>`
    * :doc:`mvv/dpd <fix_mvv_dpd>`
    * :doc:`mvv/edpd <fix_mvv_dpd>`
    * :doc:`mvv/tdpd <fix_mvv_dpd>`
    * :doc:`neb <fix_neb>`
    * :doc:`neb/spin <fix_neb_spin>`
+   * :doc:`nonaffine/displacement <fix_nonaffine_displacement>`
    * :doc:`nph (ko) <fix_nh>`
    * :doc:`nph/asphere (o) <fix_nph_asphere>`
    * :doc:`nph/body <fix_nph_body>`
@@ -171,6 +171,7 @@ OPT.
    * :doc:`pafi <fix_pafi>`
    * :doc:`pair <fix_pair>`
    * :doc:`phonon <fix_phonon>`
+   * :doc:`pimd/langevin <fix_pimd>`
    * :doc:`pimd/nvt <fix_pimd>`
    * :doc:`planeforce <fix_planeforce>`
    * :doc:`plumed <fix_plumed>`
@@ -181,6 +182,7 @@ OPT.
    * :doc:`pour <fix_pour>`
    * :doc:`precession/spin <fix_precession_spin>`
    * :doc:`press/berendsen <fix_press_berendsen>`
+   * :doc:`press/langevin <fix_press_langevin>`
    * :doc:`print <fix_print>`
    * :doc:`propel/self <fix_propel_self>`
    * :doc:`property/atom (k) <fix_property_atom>`
@@ -232,15 +234,15 @@ OPT.
    * :doc:`spring <fix_spring>`
    * :doc:`spring/chunk <fix_spring_chunk>`
    * :doc:`spring/rg <fix_spring_rg>`
-   * :doc:`spring/self <fix_spring_self>`
+   * :doc:`spring/self (k) <fix_spring_self>`
    * :doc:`srd <fix_srd>`
    * :doc:`store/force <fix_store_force>`
    * :doc:`store/state <fix_store_state>`
    * :doc:`tdpd/source <fix_dpd_source>`
-   * :doc:`temp/berendsen <fix_temp_berendsen>`
+   * :doc:`temp/berendsen (k) <fix_temp_berendsen>`
    * :doc:`temp/csld <fix_temp_csvr>`
    * :doc:`temp/csvr <fix_temp_csvr>`
-   * :doc:`temp/rescale <fix_temp_rescale>`
+   * :doc:`temp/rescale (k) <fix_temp_rescale>`
    * :doc:`temp/rescale/eff <fix_temp_rescale_eff>`
    * :doc:`tfmc <fix_tfmc>`
    * :doc:`tgnpt/drude <fix_tgnh_drude>`
@@ -260,7 +262,7 @@ OPT.
    * :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>`
    * :doc:`wall/colloid <fix_wall>`
    * :doc:`wall/ees <fix_wall_ees>`
-   * :doc:`wall/gran <fix_wall_gran>`
+   * :doc:`wall/gran (k) <fix_wall_gran>`
    * :doc:`wall/gran/region <fix_wall_gran_region>`
    * :doc:`wall/harmonic <fix_wall>`
    * :doc:`wall/lj1043 <fix_wall>`

doc/src/Commands_pair.rst

@@ -37,6 +37,7 @@ OPT.
    *
    * :doc:`adp (ko) <pair_adp>`
    * :doc:`agni (o) <pair_agni>`
+   * :doc:`aip/water/2dm (t) <pair_aip_water_2dm>`
    * :doc:`airebo (io) <pair_airebo>`
    * :doc:`airebo/morse (io) <pair_airebo>`
    * :doc:`amoeba (g) <pair_amoeba>`
@@ -55,6 +56,7 @@ OPT.
    * :doc:`born/coul/msm (o) <pair_born>`
    * :doc:`born/coul/wolf (go) <pair_born>`
    * :doc:`born/coul/wolf/cs (g) <pair_cs>`
+   * :doc:`born/gauss <pair_born_gauss>`
    * :doc:`bpm/spring <pair_bpm_spring>`
    * :doc:`brownian (o) <pair_brownian>`
    * :doc:`brownian/poly (o) <pair_brownian>`
@@ -85,7 +87,7 @@ 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 (g) <pair_coul_slater>`
    * :doc:`coul/shield <pair_coul_shield>`
    * :doc:`coul/streitz <pair_coul>`
    * :doc:`coul/tt <pair_coul_tt>`
@@ -108,7 +110,7 @@ OPT.
    * :doc:`eam/he <pair_eam>`
    * :doc:`edip (o) <pair_edip>`
    * :doc:`edip/multi <pair_edip>`
-   * :doc:`edpd <pair_mesodpd>`
+   * :doc:`edpd (g) <pair_mesodpd>`
    * :doc:`eff/cut <pair_eff>`
    * :doc:`eim (o) <pair_eim>`
    * :doc:`exp6/rx (k) <pair_exp6_rx>`
@@ -136,6 +138,7 @@ OPT.
    * :doc:`lennard/mdf <pair_mdf>`
    * :doc:`lepton (o) <pair_lepton>`
    * :doc:`lepton/coul (o) <pair_lepton>`
+   * :doc:`lepton/sphere (o) <pair_lepton>`
    * :doc:`line/lj <pair_line_lj>`
    * :doc:`lj/charmm/coul/charmm (giko) <pair_charmm>`
    * :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`
@@ -155,14 +158,14 @@ OPT.
    * :doc:`lj/cut (gikot) <pair_lj>`
    * :doc:`lj/cut/coul/cut (gko) <pair_lj_cut_coul>`
    * :doc:`lj/cut/coul/cut/dielectric (o) <pair_dielectric>`
-   * :doc:`lj/cut/coul/cut/soft (o) <pair_fep_soft>`
+   * :doc:`lj/cut/coul/cut/soft (go) <pair_fep_soft>`
    * :doc:`lj/cut/coul/debye (gko) <pair_lj_cut_coul>`
    * :doc:`lj/cut/coul/debye/dielectric (o) <pair_dielectric>`
    * :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/dielectric (o) <pair_dielectric>`
-   * :doc:`lj/cut/coul/long/soft (o) <pair_fep_soft>`
+   * :doc:`lj/cut/coul/long/soft (go) <pair_fep_soft>`
    * :doc:`lj/cut/coul/msm (go) <pair_lj_cut_coul>`
    * :doc:`lj/cut/coul/msm/dielectric <pair_dielectric>`
    * :doc:`lj/cut/coul/wolf (o) <pair_lj_cut_coul>`
@@ -170,12 +173,14 @@ OPT.
    * :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/sphere (o) <pair_lj_cut_sphere>`
    * :doc:`lj/cut/thole/long (o) <pair_thole>`
    * :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 (gk) <pair_lj_expand>`
+   * :doc:`lj/expand/sphere (o) <pair_lj_expand_sphere>`
    * :doc:`lj/gromacs (gko) <pair_gromacs>`
    * :doc:`lj/gromacs/coul/gromacs (ko) <pair_gromacs>`
    * :doc:`lj/long/coul/long (iot) <pair_lj_long>`
@@ -197,7 +202,7 @@ OPT.
    * :doc:`lubricate/poly (o) <pair_lubricate>`
    * :doc:`lubricateU <pair_lubricateU>`
    * :doc:`lubricateU/poly <pair_lubricateU>`
-   * :doc:`mdpd <pair_mesodpd>`
+   * :doc:`mdpd (g) <pair_mesodpd>`
    * :doc:`mdpd/rhosum <pair_mesodpd>`
    * :doc:`meam (k) <pair_meam>`
    * :doc:`meam/ms (k) <pair_meam>`
@@ -215,7 +220,8 @@ OPT.
    * :doc:`morse/soft <pair_fep_soft>`
    * :doc:`multi/lucy <pair_multi_lucy>`
    * :doc:`multi/lucy/rx (k) <pair_multi_lucy_rx>`
-   * :doc:`nb3b/harmonic <pair_nb3b_harmonic>`
+   * :doc:`nb3b/harmonic <pair_nb3b>`
+   * :doc:`nb3b/screened <pair_nb3b>`
    * :doc:`nm/cut (o) <pair_nm>`
    * :doc:`nm/cut/coul/cut (o) <pair_nm>`
    * :doc:`nm/cut/coul/long (o) <pair_nm>`
@@ -260,13 +266,13 @@ OPT.
    * :doc:`smd/tri_surface <pair_smd_triangulated_surface>`
    * :doc:`smd/ulsph <pair_smd_ulsph>`
    * :doc:`smtbq <pair_smtbq>`
-   * :doc:`snap (k) <pair_snap>`
+   * :doc:`snap (ik) <pair_snap>`
    * :doc:`soft (go) <pair_soft>`
-   * :doc:`sph/heatconduction <pair_sph_heatconduction>`
+   * :doc:`sph/heatconduction (g) <pair_sph_heatconduction>`
    * :doc:`sph/idealgas <pair_sph_idealgas>`
-   * :doc:`sph/lj <pair_sph_lj>`
+   * :doc:`sph/lj (g) <pair_sph_lj>`
    * :doc:`sph/rhosum <pair_sph_rhosum>`
-   * :doc:`sph/taitwater <pair_sph_taitwater>`
+   * :doc:`sph/taitwater (g) <pair_sph_taitwater>`
    * :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>`
    * :doc:`spin/dipole/cut <pair_spin_dipole>`
    * :doc:`spin/dipole/long <pair_spin_dipole>`
@@ -300,5 +306,5 @@ OPT.
    * :doc:`wf/cut <pair_wf_cut>`
    * :doc:`ylz <pair_ylz>`
    * :doc:`yukawa (gko) <pair_yukawa>`
-   * :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
+   * :doc:`yukawa/colloid (gko) <pair_yukawa_colloid>`
    * :doc:`zbl (gko) <pair_zbl>`

doc/src/Commands_removed.rst

@@ -38,6 +38,20 @@ been folded into the :doc:`reset_atoms <reset_atoms>` command.  If
 present, LAMMPS will replace the commands accordingly and print a
 warning.
 
+LATTE package
+-------------
+
+.. deprecated:: 15Jun2023
+
+The LATTE package with the fix latte command was removed from LAMMPS.
+This functionality has been superseded by :doc:`fix mdi/qm <fix_mdi_qm>`
+and :doc:`fix mdi/qmmm <fix_mdi_qmmm>` from the :ref:`MDI package
+<PKG-MDI>`.  These fixes are compatible with several quantum software
+packages, including LATTE.  See the ``examples/QUANTUM`` dir and the
+:doc:`MDI coupling HOWTO <Howto_mdi>` page.  MDI supports running LAMMPS
+with LATTE as a plugin library (similar to the way fix latte worked), as
+well as on a different set of MPI processors.
+
 MEAM package
 ------------
 
@@ -71,6 +85,35 @@ The same functionality is available through
 :doc:`bond style mesocnt <bond_mesocnt>` and
 :doc:`angle style mesocnt <angle_mesocnt>`.
 
+MPIIO package
+-------------
+
+.. deprecated:: 21Nov2023
+
+The MPIIO package has been removed from LAMMPS since it was unmaintained
+for many years and thus not updated to incorporate required changes that
+had been applied to the corresponding non-MPIIO commands. As a
+consequence the MPIIO commands had become unreliable and sometimes
+crashing LAMMPS or corrupting data.  Similar functionality is available
+through the :ref:`ADIOS package <PKG-ADIOS>` and the :ref:`NETCDF
+package <PKG-NETCDF>`.  Also, the :doc:`dump_modify nfile or dump_modify
+fileper <dump_modify>` keywords may be used for an efficient way of
+writing out dump files when running on large numbers of processors.
+Similarly, the "nfile" and "fileper" keywords exist for restarts:
+see :doc:`restart <restart>`, :doc:`read_restart <read_restart>`,
+:doc:`write_restart <write_restart>`.
+
+
+MSCG package
+------------
+
+.. deprecated:: 21Nov2023
+
+The MSCG package has been removed from LAMMPS since it was unmaintained
+for many years and instead superseded by the `OpenMSCG software
+<https://software.rcc.uchicago.edu/mscg/>`_ of the Voth group at the
+University of Chicago, which can be used independent from LAMMPS.
+
 REAX package
 ------------
 
@@ -83,6 +126,17 @@ syntax compatible with the removed reax pair style, so input files will
 have to be adapted.  The REAXFF package was originally called
 USER-REAXC.
 
+USER-REAXC package
+------------------
+
+.. deprecated:: TBD
+
+The USER-REAXC package has been renamed to :ref:`REAXFF <PKG-REAXFF>`.
+In the process also the pair style and related fixes were renamed to use
+the "reaxff" string instead of "reax/c". For a while LAMMPS was maintaining
+backward compatibility by providing aliases for the styles.  These have
+been removed, so using "reaxff" is now *required*.
+
 USER-CUDA package
 -----------------
 

doc/src/Developer.rst

@@ -13,6 +13,7 @@ of time and requests from the LAMMPS user community.
    Developer_org
    Developer_code_design
    Developer_parallel
+   Developer_atom
    Developer_comm_ops
    Developer_flow
    Developer_write

doc/src/Developer_atom.rst

@@ -0,0 +1,88 @@
+Accessing per-atom data
+-----------------------
+
+This page discusses how per-atom data is managed in LAMMPS, how it can
+be accessed, what communication patters apply, and some of the utility
+functions that exist for a variety of purposes.
+
+
+Owned and ghost atoms
+^^^^^^^^^^^^^^^^^^^^^
+
+As described on the :doc:`parallel partitioning algorithms
+<Developer_par_part>` page, LAMMPS uses a domain decomposition of the
+simulation domain, either in a *brick* or *tiled* manner.  Each MPI
+process *owns* exactly one subdomain and the atoms within it. To compute
+forces for tuples of atoms that are spread across sub-domain boundaries,
+also a "halo" of *ghost* atoms are maintained within a the communication
+cutoff distance of its subdomain.
+
+The total number of atoms is stored in `Atom::natoms` (within any
+typical class this can be referred to at `atom->natoms`. The number of
+*owned* (or "local" atoms) are stored in `Atom::nlocal`; the number of
+*ghost* atoms is stored in `Atom::nghost`.  The sum of `Atom::nlocal`
+over all MPI processes should be `Atom::natoms`. This is by default
+regularly checked by the Thermo class, and if the sum does not match,
+LAMMPS stops with a "lost atoms" error.  For convenience also the
+property `Atom::nmax` is available, this is the maximum of
+`Atom::nlocal + Atom::nghost` across all MPI processes.
+
+Per-atom properties are either managed by the atom style, or individual
+classes.  or as custom arrays by the individual classes. If only access
+to *owned* atoms is needed, they are usually allocated to be of size
+`Atom::nlocal`, otherwise of size `Atom::nmax`. Please note that not all
+per-atom properties are available or updated on *ghost* atoms. For
+example, per-atom velocities are only updated with :doc:`comm_modify vel
+yes <comm_modify>`.
+
+
+Atom indexing
+^^^^^^^^^^^^^
+
+When referring to individual atoms, they may be indexed by their local
+*index*, their index in their `Atom::x` array. This is densely populated
+containing first all *owned* atoms (index < `Atom::nlocal`) and then all
+*ghost* atoms.  The order of atoms in these arrays can change due to
+atoms migrating between between subdomains, atoms being added or
+deleted, or atoms being sorted for better cache efficiency.  Atoms are
+globally uniquely identified by their *atom ID*. There may be multiple
+atoms with the same atom ID present, but only one of them may be an
+*owned* atom.
+
+To find the local *index* of an atom, when the *atom ID* is known, the
+`Atom::map()` function may be used. It will return the local atom index
+or -1. If the returned value is between 0 (inclusive) and `Atom::nlocal`
+(exclusive) it is an *owned* or "local" atom; for larger values the atom
+is present as a ghost atom; for a value of -1, the atom is not present
+on the current subdomain at all.
+
+If multiple atoms with the same tag exist in the same subdomain, they
+can be found via the `Atom::sametag` array. It points to the next atom
+index with the same tag or -1 if there are no more atoms with the same
+tag.  The list will be exhaustive when starting with an index of an
+*owned* atom, since the atom IDs are unique, so there can only be one
+such atom.  Example code to count atoms with same atom ID in subdomain:
+
+.. code-block:: c++
+
+   for (int i = 0; i < atom->nlocal; ++i) {
+     int count = 0;
+     while (sametag[i] >= 0) {
+       i = sametag[i];
+       ++count;
+     }
+     printf("Atom ID: %ld is present %d times\n", atom->tag[i], count);
+   }
+
+Atom class versus AtomVec classes
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The `Atom` class contains all kinds of flags and counters about atoms in
+the system and that includes pointers to **all** per-atom properties
+available for atoms.  However, only a subset of these pointers are
+non-NULL and which those are depends on the atom style.  For each atom
+style there is a corresponding `AtomVecXXX` class derived from the
+`AtomVec` base class, where the XXX indicates the atom style.  This
+`AtomVecXXX` class will update the counters and per-atom pointers if
+atoms are added or removed to the system or migrate between subdomains.
+

doc/src/Developer_grid.rst

@@ -92,8 +92,8 @@ Arguments for these methods can be values returned by the
 *setup_grid()* method (described below), which define the extent of
 the grid cells (owned+ghost) the processor owns.  These 4 methods
 allocate memory for 2d (first two) and 3d (second two) grid data.  The
-two methods that end in "_one" allocate an array which stores a single
+two methods that end in "_offset" allocate an array which stores a single
-value per grid cell.  The two that end in "_multi" allocate an array
+value per grid cell.  The two that end in "_last" allocate an array
 which stores *Nvalues* per grid cell.
 
 .. code-block:: c++

doc/src/Developer_notes.rst

@@ -74,6 +74,8 @@ when converting "12.5", while the ValueTokenizer class will throw an
 :cpp:func:`ValueTokenizer::next_int()
 <LAMMPS_NS::ValueTokenizer::next_int>` is called on the same string.
 
+.. _request-neighbor-list:
+
 Requesting and accessing neighbor lists
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

doc/src/Developer_unittest.rst

@@ -121,7 +121,7 @@ will be suppressed and only a summary printed, but adding
 the '-V' option will then produce output from the tests
 above like the following:
 
-.. code-block::
+.. code-block:: console
 
    [...]
    1: [ RUN      ] Tokenizer.empty_string
@@ -180,19 +180,11 @@ discarded but by setting the verbose flag (via setting the ``TEST_ARGS``
 environment variable, ``TEST_ARGS=-v``) it can be printed and used to
 understand why tests fail unexpectedly.
 
-Another complexity of these tests stems from the need to capture
+The specifics of so-called "death tests", i.e. conditions where LAMMPS
-situations where LAMMPS will stop with an error, i.e. handle so-called
+should fail and throw an exception, are implemented in the
-"death tests".  Here the LAMMPS code will operate differently depending
+``TEST_FAILURE()`` macro. These tests operate by capturing the screen
-on whether it was configured to throw C++ exceptions on errors or call
+output when executing the failing command and then comparing that with a
-either ``exit()`` or ``MPI_Abort()``.  In the latter case, the test code
+provided regular expression string pattern.  Example:
-also needs to detect whether LAMMPS was compiled with the OpenMPI
-library, as OpenMPI is **only** compatible the death test options of the
-GoogleTest library when C++ exceptions are enabled; otherwise those
-"death tests" must be skipped to avoid reporting bogus failures.  The
-specifics of this step are implemented in the ``TEST_FAILURE()``
-macro. These tests operate by capturing the screen output when executing
-the failing command and then comparing that with a provided regular
-expression string pattern.  Example:
 
 .. code-block:: c++
 
@@ -282,9 +274,7 @@ Tests for using the Fortran module are in the ``unittest/fortran``
 folder.  Since they are also using the GoogleTest library, they require
 to also implement test wrappers in C++ that will call fortran functions
 which provide a C function interface through ISO_C_BINDINGS that will in
-turn call the functions in the LAMMPS Fortran module.  This part of the
+turn call the functions in the LAMMPS Fortran module.
-unit tests is incomplete since the Fortran module it is based on is
-incomplete as well.
 
 Tests for the C++-style library interface
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -405,10 +395,10 @@ compare with the reference and also start from the data file.  A final
 check will use multi-cutoff r-RESPA (if supported by the pair style) at
 a 1:1 split and compare to the Verlet results.  These sets of tests are
 run with multiple test fixtures for accelerated styles (OPT, OPENMP,
-INTEL) and for the latter two with 4 OpenMP threads enabled.  For
+INTEL, KOKKOS (OpenMP only)) and for the latter three with 4 OpenMP
-these tests the relative error (epsilon) is lowered by a common factor
+threads enabled.  For these tests the relative error (epsilon) is lowered
-due to the additional numerical noise, but the tests are still comparing
+by a common factor due to the additional numerical noise, but the tests
-to the same reference data.
+are still comparing to the same reference data.
 
 Additional tests will check whether all listed extract keywords are
 supported and have the correct dimensionality and the final set of tests
@@ -442,17 +432,19 @@ The ``test_pair_style`` tester is used with 4 categories of test inputs:
   pair style is defined, but the computation of the pair style contributions
   is disabled.
 
-The ``test_bond_style`` and ``test_angle_style`` are set up in a similar
+The ``test_bond_style``, ``test_angle_style``, ``test_dihedral_style``, and
-fashion and share support functions with the pair style tester.  The final
+``test_improper_style`` tester programs are set up in a similar fashion and
-group of tests in this section is for fix styles that add/manipulate forces
+share support functions with the pair style tester.  The final group of
-and velocities, e.g. for time integration, thermostats and more.
+tests in this section is for fix styles that add/manipulate forces and
+velocities, e.g. for time integration, thermostats and more.
 
-Adding a new test is easiest done by copying and modifying an existing test
+Adding a new test is easiest done by copying and modifying an existing YAML
-for a style that is similar to one to be tested.  The file name should follow
+file for a style that is similar to one to be tested.  The file name should
-the naming conventions described above and after copying the file, the first
+follow the naming conventions described above and after copying the file,
-step is to replace the style names where needed.  The coefficient values
+the first step is to replace the style names where needed.  The coefficient
-do not have to be meaningful, just in a reasonable range for the given system.
+values do not have to be meaningful, just in a reasonable range for the
-It does not matter if some forces are large, for as long as they do not diverge.
+given system.  It does not matter if some forces are large, for as long as
+they do not diverge.
 
 The template input files define a large number of index variables at the top
 that can be modified inside the YAML file to control the behavior.  For example,
@@ -480,7 +472,7 @@ Note that this disables computing the kspace contribution, but still will run
 the setup.  The "gewald" parameter should be set explicitly to speed up the run.
 For styles with long-range electrostatics, typically two tests are added one using
 the (slower) analytic approximation of the erfc() function and the other using
-the tabulated coulomb, to test both code paths. The reference results in the YAML
+the tabulated coulomb, to test both code paths.  The reference results in the YAML
 files then should be compared manually, if they agree well enough within the limits
 of those two approximations.
 
@@ -534,3 +526,102 @@ The ``unittest/tools`` folder contains tests for programs in the
 shell, which are implemented as a python scripts using the ``unittest``
 Python module and launching the tool commands through the ``subprocess``
 Python module.
+
+
+Troubleshooting failed unit tests
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The are by default no unit tests for newly added features (e.g. pair, fix,
+or compute styles) unless your pull request also includes tests for the
+added features.  If you are modifying some features, you may see failures
+for existing tests, if your modifications have some unexpected side effects
+or your changes render the existing text invalid.  If you are adding an
+accelerated version of an existing style, then only tests for INTEL,
+KOKKOS (with OpenMP only), OPENMP, and OPT will be run automatically.
+Tests for the GPU package are time consuming and thus are only run
+*after* a merge, or when a special label, ``gpu_unit_tests`` is added
+to the pull request.  After the test has started, it is often best to
+remove the label since every PR activity will re-trigger the test (that
+is a limitation of triggering a test with a label).  Support for unit
+tests with using KOKKOS with GPU acceleration is currently not supported.
+
+When you see a failed build on GitHub, click on ``Details`` to be taken
+to the corresponding LAMMPS Jenkins CI web page.  Click on the "Exit"
+symbol near the ``Logout`` button on the top right of that page to go to
+the "classic view".  In the classic view, there is a list of the
+individual runs that make up this test run (they are shown but cannot be
+inspected in the default view).  You can click on any of those.
+Clicking on ``Test Result`` will display the list of failed tests. Click
+on the "Status" column to sort the tests based on their Failed or Passed
+status.  Then click on the failed test to expand its output.
+
+For example, the following output snippet shows the failed unit test
+
+.. code-block:: console
+
+   [ RUN      ] PairStyle.gpu
+   /home/builder/workspace/dev/pull_requests/ubuntu_gpu/unit_tests/cmake_gpu_opencl_mixed_smallbig_clang_static/unittest/force-styles/test_main.cpp:63: Failure
+   Expected: (err) <= (epsilon)
+   Actual: 0.00018957912910606503 vs 0.0001
+   Google Test trace:
+   /home/builder/workspace/dev/pull_requests/ubuntu_gpu/unit_tests/cmake_gpu_opencl_mixed_smallbig_clang_static/unittest/force-styles/test_main.cpp:56: EXPECT_FORCES: init_forces (newton off)
+   /home/builder/workspace/dev/pull_requests/ubuntu_gpu/unit_tests/cmake_gpu_opencl_mixed_smallbig_clang_static/unittest/force-styles/test_main.cpp:64: Failure
+   Expected: (err) <= (epsilon)
+   Actual: 0.00022892713393549854 vs 0.0001
+
+The failed assertions provide line numbers in the test source
+(e.g. ``test_main.cpp:56``), from which one can understand what
+specific assertion failed.
+
+Note that the force style engine runs one of a small number of systems
+in a rather off-equilibrium configuration with a few atoms for a few
+steps, writes data and restart files, uses :doc:`the clear command
+<clear>` to reset LAMMPS, and then runs from those files with different
+settings (e.g. newton on/off) and integrators (e.g. verlet vs. respa).
+Beyond potential issues/bugs in the source code, the mismatch between
+the expected and actual values could be that force arrays are not
+properly cleared between multiple run commands or that class members are
+not correctly initialized or written to or read from a data or restart
+file.
+
+While the epsilon (relative precision) for a single, `IEEE 754 compliant
+<https://en.wikipedia.org/wiki/IEEE_754>`_, double precision floating
+point operation is at about 2.2e-16, the achievable precision for the
+tests is lower due to most numbers being sums over intermediate results
+and the non-associativity of floating point math leading to larger
+errors.  In some cases specific properties of the tested style.  As a
+rule of thumb, the test epsilon can often be in the range 5.0e-14 to
+1.0e-13.  But for "noisy" force kernels, e.g. those a larger amount of
+arithmetic operations involving `exp()`, `log()` or `sin()` functions,
+and also due to the effect of compiler optimization or differences
+between compilers or platforms, epsilon may need to be further relaxed,
+sometimes epsilon can be relaxed to 1.0e-12. If interpolation or lookup
+tables are used, epsilon may need to be set to 1.0e-10 or even higher.
+For tests of accelerated styles, the per-test epsilon is multiplied
+by empirical factors that take into account the differences in the order
+of floating point operations or that some or most intermediate operations
+may be done using approximations or with single precision floating point
+math.
+
+To rerun the failed unit test individually, change to the ``build`` directory
+and run the test with verbose output. For example,
+
+.. code-block:: bash
+
+    env TEST_ARGS=-v ctest -R ^MolPairStyle:lj_cut_coul_long -V
+
+``ctest`` with the ``-V`` flag also shows the exact command line
+of the test. One can then use ``gdb --args`` to further debug and
+catch exceptions with the test command, for example,
+
+.. code-block:: bash
+
+    gdb --args /path/to/lammps/build/test_pair_style /path/to/lammps/unittest/force-styles/tests/mol-pair-lj_cut_coul_long.yaml
+
+
+It is recommended to configure the build with ``-D
+BUILD_SHARED_LIBS=on`` and use a custom linker to shorten the build time
+during recompilation.  Installing `ccache` in your development
+environment helps speed up recompilation by caching previous
+compilations and detecting when the same compilation is being done
+again.  Please see :doc:`Build_development` for further details.

doc/src/Developer_updating.rst

@@ -389,7 +389,7 @@ This change is **required** or else the code will not compile.
 Rename of fix STORE/PERATOM to fix STORE/ATOM and change of arguments
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. versionchanged:: TBD
+.. versionchanged:: 28Mar2023
 
 The available functionality of the internal fix to store per-atom
 properties was expanded to enable storing data with ghost atoms and to

doc/src/Developer_write.rst

@@ -6,250 +6,9 @@ be extended by writing new classes that derive from existing
 parent classes in LAMMPS.  Here, some specific coding
 details are provided for writing code for LAMMPS.
 
-Writing a new fix style
-^^^^^^^^^^^^^^^^^^^^^^^
 
-Writing fixes is a flexible way of extending LAMMPS.  Users can
+.. toctree::
-implement many things using fixes:
+   :maxdepth: 1
-
-- changing particles attributes (positions, velocities, forces, etc.). Examples: FixNVE, FixFreeze.
-- reading/writing data. Example: FixRestart.
-- adding or modifying properties due to geometry. Example: FixWall.
-- interacting with other subsystems or external code: Examples: FixTTM, FixExternal, FixLATTE
-- saving information for analysis or future use (previous positions,
-  for instance). Examples: Fix AveTime, FixStoreState.
-
-
-All fixes are derived from the Fix base class and must have a
-constructor with the signature: ``FixPrintVel(class LAMMPS *, int, char **)``.
-
-Every fix must be registered in LAMMPS by writing the following lines
-of code in the header before include guards:
-
-.. code-block:: c++
-
-   #ifdef FIX_CLASS
-   // clang-format off
-   FixStyle(print/vel,FixPrintVel);
-   // clang-format on
-   #else
-   /* the definition of the FixPrintVel class comes here */
-   ...
-   #endif
-
-Where ``print/vel`` is the style name of your fix in the input script and
-``FixPrintVel`` is the name of the class. The header file would be called
-``fix_print_vel.h`` and the implementation file ``fix_print_vel.cpp``.
-These conventions allow LAMMPS to automatically integrate it into the
-executable when compiling and associate your new fix class with the designated
-keyword when it parses the input script.
-
-Let's write a simple fix which will print the average velocity at the end
-of each timestep. First of all, implement a constructor:
-
-.. code-block:: c++
-
-   FixPrintVel::FixPrintVel(LAMMPS *lmp, int narg, char **arg)
-   : Fix(lmp, narg, arg)
-   {
-     if (narg < 4)
-       error->all(FLERR,"Illegal fix print/vel command");
-
-     nevery = utils::inumeric(FLERR,arg[3],false,lmp);
-     if (nevery <= 0)
-       error->all(FLERR,"Illegal fix print/vel command");
-   }
-
-In the constructor you should parse your fix arguments which are
-specified in the script. All fixes have pretty much the same syntax:
-``fix <fix-ID> <fix group> <fix name> <fix arguments ...>``. The
-first 3 parameters are parsed by Fix base class constructor, while
-``<fix arguments>`` should be parsed by you. In our case, we need to
-specify how often we want to print an average velocity. For instance,
-once in 50 timesteps: ``fix 1 print/vel 50``. There is a special variable
-in the Fix class called ``nevery`` which specifies how often the method
-``end_of_step()`` is called. Thus all we need to do is just set it up.
-
-The next method we need to implement is ``setmask()``:
-
-.. code-block:: c++
-
-   int FixPrintVel::setmask()
-   {
-     int mask = 0;
-     mask |= FixConst::END_OF_STEP;
-     return mask;
-   }
-
-Here the user specifies which methods of your fix should be called
-during execution. The constant ``END_OF_STEP`` corresponds to the
-``end_of_step()`` method. The most important available methods that
-are called during a timestep and the order in which they are called
-are shown in the previous section.
-
-.. code-block:: c++
-
-   void FixPrintVel::end_of_step()
-   {
-     // for add3, scale3
-     using namespace MathExtra;
-
-     double** v = atom->v;
-     int nlocal = atom->nlocal;
-     double localAvgVel[4]; // 4th element for particles count
-     memset(localAvgVel, 0, 4 * sizeof(double));
-     for (int particleInd = 0; particleInd < nlocal; ++particleInd) {
-       add3(localAvgVel, v[particleInd], localAvgVel);
-     }
-     localAvgVel[3] = nlocal;
-     double globalAvgVel[4];
-     memset(globalAvgVel, 0, 4 * sizeof(double));
-     MPI_Allreduce(localAvgVel, globalAvgVel, 4, MPI_DOUBLE, MPI_SUM, world);
-     scale3(1.0 / globalAvgVel[3], globalAvgVel);
-     if ((comm->me == 0) && screen) {
-       fmt::print(screen,"{}, {}, {}\n",
-                  globalAvgVel[0], globalAvgVel[1], globalAvgVel[2]);
-     }
-   }
-
-In the code above, we use MathExtra routines defined in
-``math_extra.h``.  There are bunch of math functions to work with
-arrays of doubles as with math vectors.  It is also important to note
-that LAMMPS code should always assume to be run in parallel and that
-atom data is thus distributed across the MPI ranks.  Thus you can
-only process data from local atoms directly and need to use MPI library
-calls to combine or exchange data.  For serial execution, LAMMPS
-comes bundled with the MPI STUBS library that contains the MPI library
-function calls in dummy versions that only work for a single MPI rank.
-
-In this code we use an instance of Atom class. This object is stored
-in the Pointers class (see ``pointers.h``) which is the base class of
-the Fix base class. This object contains references to various class
-instances (the original instances are created and held by the LAMMPS
-class) with all global information about the simulation system.
-Data from the Pointers class is available to all classes inherited from
-it using protected inheritance. Hence when you write you own class,
-which is going to use LAMMPS data, don't forget to inherit from Pointers
-or pass an Pointer to it to all functions that need access. When writing
-fixes we inherit from class Fix which is inherited from Pointers so
-there is no need to inherit from it directly.
-
-The code above computes average velocity for all particles in the
-simulation.  Yet you have one unused parameter in fix call from the
-script: ``group_name``.  This parameter specifies the group of atoms
-used in the fix. So we should compute average for all particles in the
-simulation only if ``group_name == "all"``, but it can be any group.
-The group membership information of an atom is contained in the *mask*
-property of and atom and the bit corresponding to a given group is
-stored in the groupbit variable which is defined in Fix base class:
-
-.. code-block:: c++
-
-   for (int i = 0; i < nlocal; ++i) {
-     if (atom->mask[i] & groupbit) {
-     // Do all job here
-     }
-   }
-
-Class Atom encapsulates atoms positions, velocities, forces, etc. User
-can access them using particle index. Note, that particle indexes are
-usually changed every few timesteps because of neighbor list rebuilds
-and spatial sorting (to improve cache efficiency).
-
-Let us consider another Fix example: We want to have a fix which stores
-atoms position from previous time step in your fix. The local atoms
-indexes may not be valid on the next iteration. In order to handle
-this situation there are several methods which should be implemented:
-
-- ``double memory_usage()``: return how much memory the fix uses (optional)
-- ``void grow_arrays(int)``: do reallocation of the per particle arrays in your fix
-- ``void copy_arrays(int i, int j, int delflag)``: copy i-th per-particle
-  information to j-th. Used when atom sorting is performed. if delflag is set
-  and atom j owns a body, move the body information to atom i.
-- ``void set_arrays(int i)``: sets i-th particle related information to zero
-
-Note, that if your class implements these methods, it must call add calls of
-add_callback and delete_callback to constructor and destructor. Since we want
-to store positions of atoms from previous timestep, we need to add
-``double** xold`` to the header file. Than add allocation code
-to the constructor:
-
-.. code-block:: c++
-
-   FixSavePos::FixSavePos(LAMMPS *lmp, int narg, char **arg), xold(nullptr)
-   {
-   //...
-     memory->create(xold, atom->nmax, 3, "FixSavePos:x");
-     atom->add_callback(0);
-   }
-
-   FixSavePos::~FixSavePos() {
-     atom->delete_callback(id, 0);
-     memory->destroy(xold);
-   }
-
-Implement the aforementioned methods:
-
-.. code-block:: c++
-
-   double FixSavePos::memory_usage()
-   {
-     int nmax = atom->nmax;
-     double bytes = 0.0;
-     bytes += nmax * 3 * sizeof(double);
-     return bytes;
-   }
-
-   void FixSavePos::grow_arrays(int nmax)
-   {
-     memory->grow(xold, nmax, 3, "FixSavePos:xold");
-   }
-
-   void FixSavePos::copy_arrays(int i, int j, int delflag)
-   {
-     memcpy(xold[j], xold[i], sizeof(double) * 3);
-   }
-
-   void FixSavePos::set_arrays(int i)
-   {
-     memset(xold[i], 0, sizeof(double) * 3);
-   }
-
-   int FixSavePos::pack_exchange(int i, double *buf)
-   {
-     int m = 0;
-     buf[m++] = xold[i][0];
-     buf[m++] = xold[i][1];
-     buf[m++] = xold[i][2];
-
-     return m;
-   }
-
-   int FixSavePos::unpack_exchange(int nlocal, double *buf)
-   {
-     int m = 0;
-     xold[nlocal][0] = buf[m++];
-     xold[nlocal][1] = buf[m++];
-     xold[nlocal][2] = buf[m++];
-
-     return m;
-   }
-
-Now, a little bit about memory allocation. We use the Memory class which
-is just a bunch of template functions for allocating 1D and 2D
-arrays. So you need to add include ``memory.h`` to have access to them.
-
-Finally, if you need to write/read some global information used in
-your fix to the restart file, you might do it by setting flag
-``restart_global = 1`` in the constructor and implementing methods void
-``write_restart(FILE *fp)`` and ``void restart(char *buf)``.
-If, in addition, you want to write the per-atom property to restart
-files additional settings and functions are needed:
-
-- a fix flag indicating this needs to be set ``restart_peratom = 1;``
-- ``atom->add_callback()`` and ``atom->delete_callback()`` must be called
-  a second time with the final argument set to 1 instead of 0 (indicating
-  restart processing instead of per-atom data memory management).
-- the functions ``void pack_restart(int i, double *buf)`` and
-  ``void unpack_restart(int nlocal, int nth)`` need to be implemented
 
+   Developer_write_pair
+   Developer_write_fix

doc/src/Developer_write_fix.rst

@@ -0,0 +1,245 @@
+Writing a new fix style
+^^^^^^^^^^^^^^^^^^^^^^^
+
+Writing fix styles is a flexible way of extending LAMMPS.  Users can
+implement many things using fixes.  Some fix styles are only used
+internally to support compute styles or pair styles:
+
+- change particles attributes (positions, velocities, forces, etc.). Examples: ``FixNVE``, ``FixFreeze``.
+- read or write data.  Example: ``FixRestart``.
+- adding or modifying properties due to geometry. Example: ``FixWall``.
+- interacting with other subsystems or external code: Examples: ``FixTTM``, ``FixExternal``, ``FixMDI``
+- saving information for analysis or future use (previous positions,
+  for instance). Examples: ``FixAveTime``, ``FixStoreState``.
+
+All fixes are derived from the ``Fix`` base class and must have a
+constructor with the signature: ``FixPrintVel(class LAMMPS *, int, char **)``.
+
+Every fix must be registered in LAMMPS by writing the following lines
+of code in the header before include guards:
+
+.. code-block:: c++
+
+   #ifdef FIX_CLASS
+   // clang-format off
+   FixStyle(print/vel,FixPrintVel);
+   // clang-format on
+   #else
+   /* the definition of the FixPrintVel class comes here */
+   ...
+   #endif
+
+Where ``print/vel`` is the style name of your fix in the input script and
+``FixPrintVel`` is the name of the class. The header file would be called
+``fix_print_vel.h`` and the implementation file ``fix_print_vel.cpp``.
+These conventions allow LAMMPS to automatically integrate it into the
+executable when compiling and associate your new fix class with the designated
+keyword when it parses the input script.
+
+Let's write a simple fix which will print the average velocity at the end
+of each timestep. First of all, implement a constructor:
+
+.. code-block:: c++
+
+   FixPrintVel::FixPrintVel(LAMMPS *lmp, int narg, char **arg)
+   : Fix(lmp, narg, arg)
+   {
+     if (narg < 4) utils::missing_cmd_args(FLERR, "fix print/vel", error);
+
+     nevery = utils::inumeric(FLERR,arg[3],false,lmp);
+     if (nevery <= 0)
+       error->all(FLERR,"Illegal fix print/vel nevery value: {}", nevery);
+   }
+
+In the constructor you should parse the fix arguments which are
+specified in the script.  All fixes have pretty much the same syntax:
+``fix <fix-ID> <fix group> <fix name> <fix arguments ...>``. The first 3
+parameters are parsed by Fix base class constructor, while ``<fix
+arguments>`` should be parsed by you.  In our case, we need to specify
+how often we want to print an average velocity. For instance, once in 50
+timesteps: ``fix 1 print/vel 50``. There is a special variable in the
+Fix class called ``nevery`` which specifies how often the method
+``end_of_step()`` is called.  Thus all we need to do is just set it up.
+
+The next method we need to implement is ``setmask()``:
+
+.. code-block:: c++
+
+   int FixPrintVel::setmask()
+   {
+     int mask = 0;
+     mask |= FixConst::END_OF_STEP;
+     return mask;
+   }
+
+Here the we specify which methods of the fix should be called during
+:doc:`execution of a timestep <Developer_flow>`.  The constant
+``END_OF_STEP`` corresponds to the ``end_of_step()`` method. The most
+important available methods that are called during a timestep.
+
+.. code-block:: c++
+
+   void FixPrintVel::end_of_step()
+   {
+     // for add3, scale3
+     using namespace MathExtra;
+
+     double** v = atom->v;
+     int nlocal = atom->nlocal;
+     double localAvgVel[4]; // 4th element for particles count
+     memset(localAvgVel, 0, 4 * sizeof(double));
+     for (int particleInd = 0; particleInd < nlocal; ++particleInd) {
+       add3(localAvgVel, v[particleInd], localAvgVel);
+     }
+     localAvgVel[3] = nlocal;
+     double globalAvgVel[4];
+     memset(globalAvgVel, 0, 4 * sizeof(double));
+     MPI_Allreduce(localAvgVel, globalAvgVel, 4, MPI_DOUBLE, MPI_SUM, world);
+     scale3(1.0 / globalAvgVel[3], globalAvgVel);
+     if ((comm->me == 0) && screen) {
+       fmt::print(screen,"{}, {}, {}\n",
+                  globalAvgVel[0], globalAvgVel[1], globalAvgVel[2]);
+     }
+   }
+
+In the code above, we use MathExtra routines defined in
+``math_extra.h``.  There are bunch of math functions to work with
+arrays of doubles as with math vectors.  It is also important to note
+that LAMMPS code should always assume to be run in parallel and that
+atom data is thus distributed across the MPI ranks.  Thus you can
+only process data from local atoms directly and need to use MPI library
+calls to combine or exchange data.  For serial execution, LAMMPS
+comes bundled with the MPI STUBS library that contains the MPI library
+function calls in dummy versions that only work for a single MPI rank.
+
+In this code we use an instance of Atom class. This object is stored
+in the Pointers class (see ``pointers.h``) which is the base class of
+the Fix base class. This object contains references to various class
+instances (the original instances are created and held by the LAMMPS
+class) with all global information about the simulation system.
+Data from the Pointers class is available to all classes inherited from
+it using protected inheritance. Hence when you write you own class,
+which is going to use LAMMPS data, don't forget to inherit from Pointers
+or pass a Pointer to it to all functions that need access. When writing
+fixes we inherit from class Fix which is inherited from Pointers so
+there is no need to inherit from it directly.
+
+The code above computes average velocity for all particles in the
+simulation.  Yet you have one unused parameter in fix call from the
+script: ``group_name``.  This parameter specifies the group of atoms
+used in the fix. So we should compute average for all particles in the
+simulation only if ``group_name == "all"``, but it can be any group.
+The group membership information of an atom is contained in the *mask*
+property of an atom and the bit corresponding to a given group is
+stored in the groupbit variable which is defined in Fix base class:
+
+.. code-block:: c++
+
+   for (int i = 0; i < nlocal; ++i) {
+     if (atom->mask[i] & groupbit) {
+     // Do all job here
+     }
+   }
+
+Class Atom encapsulates atoms positions, velocities, forces, etc. Users
+can access them using particle index. Note, that particle indexes are
+usually changed every few timesteps because of neighbor list rebuilds
+and spatial sorting (to improve cache efficiency).
+
+Let us consider another Fix example: We want to have a fix which stores
+atoms position from the previous time step in your fix. The local atoms
+indexes may not be valid on the next iteration. In order to handle
+this situation there are several methods which should be implemented:
+
+- ``double memory_usage()``: return how much memory the fix uses (optional)
+- ``void grow_arrays(int)``: do reallocation of the per-particle arrays in your fix
+- ``void copy_arrays(int i, int j, int delflag)``: copy i-th per-particle
+  information to j-th. Used when atom sorting is performed. if delflag is set
+  and atom j owns a body, move the body information to atom i.
+- ``void set_arrays(int i)``: sets i-th particle related information to zero
+
+Note, that if your class implements these methods, it must add calls of
+add_callback and delete_callback to the constructor and destructor. Since we want
+to store positions of atoms from the previous timestep, we need to add
+``double** xold`` to the header file. Than add allocation code
+to the constructor:
+
+.. code-block:: c++
+
+   FixSavePos::FixSavePos(LAMMPS *lmp, int narg, char **arg), xold(nullptr)
+   {
+   //...
+     memory->create(xold, atom->nmax, 3, "FixSavePos:x");
+     atom->add_callback(0);
+   }
+
+   FixSavePos::~FixSavePos() {
+     atom->delete_callback(id, 0);
+     memory->destroy(xold);
+   }
+
+Implement the aforementioned methods:
+
+.. code-block:: c++
+
+   double FixSavePos::memory_usage()
+   {
+     int nmax = atom->nmax;
+     double bytes = 0.0;
+     bytes += nmax * 3 * sizeof(double);
+     return bytes;
+   }
+
+   void FixSavePos::grow_arrays(int nmax)
+   {
+     memory->grow(xold, nmax, 3, "FixSavePos:xold");
+   }
+
+   void FixSavePos::copy_arrays(int i, int j, int delflag)
+   {
+     memcpy(xold[j], xold[i], sizeof(double) * 3);
+   }
+
+   void FixSavePos::set_arrays(int i)
+   {
+     memset(xold[i], 0, sizeof(double) * 3);
+   }
+
+   int FixSavePos::pack_exchange(int i, double *buf)
+   {
+     int m = 0;
+     buf[m++] = xold[i][0];
+     buf[m++] = xold[i][1];
+     buf[m++] = xold[i][2];
+
+     return m;
+   }
+
+   int FixSavePos::unpack_exchange(int nlocal, double *buf)
+   {
+     int m = 0;
+     xold[nlocal][0] = buf[m++];
+     xold[nlocal][1] = buf[m++];
+     xold[nlocal][2] = buf[m++];
+
+     return m;
+   }
+
+Now, a little bit about memory allocation. We use the Memory class which
+is just a bunch of template functions for allocating 1D and 2D
+arrays. So you need to add include ``memory.h`` to have access to them.
+
+Finally, if you need to write/read some global information used in
+your fix to the restart file, you might do it by setting flag
+``restart_global = 1`` in the constructor and implementing methods void
+``write_restart(FILE *fp)`` and ``void restart(char *buf)``.
+If, in addition, you want to write the per-atom property to restart
+files additional settings and functions are needed:
+
+- a fix flag indicating this needs to be set ``restart_peratom = 1;``
+- ``atom->add_callback()`` and ``atom->delete_callback()`` must be called
+  a second time with the final argument set to 1 instead of 0 (indicating
+  restart processing instead of per-atom data memory management).
+- the functions ``void pack_restart(int i, double *buf)`` and
+  ``void unpack_restart(int nlocal, int nth)`` need to be implemented
+

doc/src/Errors_messages.rst

@@ -7148,9 +7148,6 @@ keyword to allow for additional bonds to be formed
 *Read_dump xyz fields do not have consistent scaling/wrapping*
    Self-explanatory.
 
-*Reading from MPI-IO filename when MPIIO package is not installed*
-   Self-explanatory.
-
 *Reax_defs.h setting for NATDEF is too small*
    Edit the setting in the ReaxFF library and re-compile the
    library and re-build LAMMPS.
@@ -8489,9 +8486,6 @@ keyword to allow for additional bonds to be formed
    The write_restart command cannot be used before a read_data,
    read_restart, or create_box command.
 
-*Writing to MPI-IO filename when MPIIO package is not installed*
-   Self-explanatory.
-
 *Zero length rotation vector with displace_atoms*
    Self-explanatory.
 

doc/src/Examples.rst

@@ -94,8 +94,6 @@ Lowercase directories
 +-------------+------------------------------------------------------------------+
 | kim         | use of potentials from the `OpenKIM Repository <openkim_>`_      |
 +-------------+------------------------------------------------------------------+
-| latte       | examples for using fix latte for DFTB via the LATTE library      |
-+-------------+------------------------------------------------------------------+
 | mdi         | use of the MDI package and MolSSI MDI code coupling library      |
 +-------------+------------------------------------------------------------------+
 | meam        | MEAM test for SiC and shear (same as shear examples)             |
@@ -106,8 +104,6 @@ Lowercase directories
 +-------------+------------------------------------------------------------------+
 | min         | energy minimization of 2d LJ melt                                |
 +-------------+------------------------------------------------------------------+
-| mscg        | parameterize a multi-scale coarse-graining (MSCG) model          |
-+-------------+------------------------------------------------------------------+
 | msst        | MSST shock dynamics                                              |
 +-------------+------------------------------------------------------------------+
 | multi       | multi neighboring for systems with large interaction disparities |

doc/src/Fortran.rst

@@ -56,17 +56,6 @@ C++ in the ``examples/COUPLE/simple`` folder of the LAMMPS distribution.
    and Ubuntu 18.04 LTS and not compatible.  Either newer compilers
    need to be installed or the Linux updated.
 
-.. versionchanged:: 8Feb2023
-
-.. note::
-
-   A contributed Fortran interface is available in the
-   ``examples/COUPLE/fortran2`` folder.  However, since the completion
-   of the :f:mod:`LIBLAMMPS` module, this interface is now deprecated,
-   no longer actively maintained and will likely be removed in the
-   future.  Please see the ``README`` file in that folder for more
-   information about it and how to contact its author and maintainer.
-
 ----------
 
 Creating or deleting a LAMMPS object
@@ -203,40 +192,62 @@ Below is an example demonstrating some of the possible uses.
 
 .. code-block:: fortran
 
-  PROGRAM testprop
+   PROGRAM testprop
-    USE LIBLAMMPS
+     USE LIBLAMMPS
-    USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int64_t
+     USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int64_t, c_int
-    USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT
+     USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT
-    TYPE(lammps) :: lmp
+     TYPE(lammps) :: lmp
-    INTEGER(KIND=c_int64_t), POINTER :: natoms
+     INTEGER(KIND=c_int64_t), POINTER :: natoms, ntimestep, bval
-    REAL(KIND=c_double), POINTER :: dt
+     REAL(KIND=c_double), POINTER :: dt, dval
-    INTEGER(KIND=c_int64_t), POINTER :: ntimestep
+     INTEGER(KIND=c_int), POINTER :: nfield, typ, ival
-    REAL(KIND=c_double) :: pe, ke
+     INTEGER(KIND=c_int) :: i
+     CHARACTER(LEN=11) :: key
+     REAL(KIND=c_double) :: pe, ke
 
-    lmp = lammps()
+     lmp = lammps()
-    CALL lmp%file('in.sysinit')
+     CALL lmp%file('in.sysinit')
-    natoms = lmp%extract_global('natoms')
+     natoms = lmp%extract_global('natoms')
-    WRITE(OUTPUT_UNIT,'(A,I0,A)') 'Running a simulation with ', natoms, ' atoms'
+     WRITE(OUTPUT_UNIT,'(A,I0,A)') 'Running a simulation with ', natoms, ' atoms'
-    WRITE(OUTPUT_UNIT,'(I0,A,I0,A,I0,A)') lmp%extract_setting('nlocal'), &
+     WRITE(OUTPUT_UNIT,'(I0,A,I0,A,I0,A)') lmp%extract_setting('nlocal'), &
-        ' local and ', lmp%extract_setting('nghost'), ' ghost atoms. ', &
+         ' local and ', lmp%extract_setting('nghost'), ' ghost atoms. ', &
-        lmp%extract_setting('ntypes'), ' atom types'
+         lmp%extract_setting('ntypes'), ' atom types'
 
-    CALL lmp%command('run 2 post no')
+     CALL lmp%command('run 2 post no')
-    dt = lmp%extract_global('dt')
-    ntimestep = lmp%extract_global('ntimestep')
-    WRITE(OUTPUT_UNIT,'(A,I0,A,F4.1,A)') 'At step: ', ntimestep, &
-        '  Changing timestep from', dt, ' to 0.5'
-    dt = 0.5_c_double
-    CALL lmp%command('run 2 post no')
 
-    WRITE(OUTPUT_UNIT,'(A,I0)') 'At step: ', ntimestep
+     ntimestep = lmp%last_thermo('step', 0)
-    pe = lmp%get_thermo('pe')
+     nfield = lmp%last_thermo('num', 0)
-    ke = lmp%get_thermo('ke')
+     WRITE(OUTPUT_UNIT,'(A,I0,A,I0)') 'Last thermo output on step: ', ntimestep, &
-    PRINT*, 'PE = ', pe
+         ',  number of fields: ', nfield
-    PRINT*, 'KE = ', ke
+     DO i=1, nfield
+         key = lmp%last_thermo('keyword',i)
+         typ = lmp%last_thermo('type',i)
+         IF (typ == lmp%dtype%i32) THEN
+             ival = lmp%last_thermo('data',i)
+             WRITE(OUTPUT_UNIT,*) key, ':', ival
+         ELSE IF (typ == lmp%dtype%i64) THEN
+             bval = lmp%last_thermo('data',i)
+             WRITE(OUTPUT_UNIT,*) key, ':', bval
+         ELSE IF (typ == lmp%dtype%r64) THEN
+             dval = lmp%last_thermo('data',i)
+             WRITE(OUTPUT_UNIT,*) key, ':', dval
+         END IF
+     END DO
 
-    CALL lmp%close(.TRUE.)
+     dt = lmp%extract_global('dt')
-  END PROGRAM testprop
+     ntimestep = lmp%extract_global('ntimestep')
+     WRITE(OUTPUT_UNIT,'(A,I0,A,F4.1,A)') 'At step: ', ntimestep, &
+         '  Changing timestep from', dt, ' to 0.5'
+     dt = 0.5_c_double
+     CALL lmp%command('run 2 post no')
+
+     WRITE(OUTPUT_UNIT,'(A,I0)') 'At step: ', ntimestep
+     pe = lmp%get_thermo('pe')
+     ke = lmp%get_thermo('ke')
+     WRITE(OUTPUT_UNIT,*) 'PE = ', pe
+     WRITE(OUTPUT_UNIT,*) 'KE = ', ke
+
+     CALL lmp%close(.TRUE.)
+   END PROGRAM testprop
 
 ---------------
 
@@ -262,6 +273,8 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
    :ftype style: type(lammps_style)
    :f type: derived type to access lammps type constants
    :ftype type: type(lammps_type)
+   :f dtype: derived type to access lammps data type constants
+   :ftype dtype: type(lammps_dtype)
    :f close: :f:subr:`close`
    :ftype close: subroutine
    :f subroutine error: :f:subr:`error`
@@ -278,6 +291,8 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
    :ftype get_natoms: function
    :f get_thermo: :f:func:`get_thermo`
    :ftype get_thermo: function
+   :f last_thermo: :f:func:`last_thermo`
+   :ftype last_thermo: function
    :f extract_box: :f:subr:`extract_box`
    :ftype extract_box: subroutine
    :f reset_box: :f:subr:`reset_box`
@@ -587,6 +602,96 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
 --------
 
+.. f:function:: last_thermo(what, index)
+
+   This function will call :cpp:func:`lammps_last_thermo` and returns
+   either a string or a pointer to a cached copy of LAMMPS last thermodynamic
+   output, depending on the data requested through *what*.  Note that *index*
+   uses 1-based indexing to access thermo output columns.
+
+   .. versionadded:: 15Jun2023
+
+   Note that this function actually does not return a value, but rather
+   associates the pointer on the left side of the assignment to point to
+   internal LAMMPS data (with the exception of string data, which are
+   copied and returned as ordinary Fortran strings).  Pointers must be
+   of the correct data type to point to said data (typically
+   ``INTEGER(c_int)``, ``INTEGER(c_int64_t)``, or ``REAL(c_double)``).
+   The pointer being associated with LAMMPS data is type-checked at
+   run-time via an overloaded assignment operator.  The pointers
+   returned by this function point to temporary, read-only data that may
+   be overwritten at any time, so their target values need to be copied
+   to local storage if they are supposed to persist.
+
+   For example,
+
+   .. code-block:: fortran
+
+      PROGRAM thermo
+        USE LIBLAMMPS
+        USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int64_t, c_int
+        TYPE(lammps) :: lmp
+        INTEGER(KIND=c_int64_t), POINTER :: ntimestep, bval
+        REAL(KIND=c_double), POINTER :: dval
+        INTEGER(KIND=c_int), POINTER :: nfield, typ, ival
+        INTEGER(KIND=c_int) :: i
+        CHARACTER(LEN=11) :: key
+
+        lmp = lammps()
+        CALL lmp%file('in.sysinit')
+
+        ntimestep = lmp%last_thermo('step', 0)
+        nfield = lmp%last_thermo('num', 0)
+        PRINT*, 'Last thermo output on step: ', ntimestep, '  Number of fields: ', nfield
+        DO i=1, nfield
+            key = lmp%last_thermo('keyword',i)
+            typ = lmp%last_thermo('type',i)
+            IF (typ == lmp%dtype%i32) THEN
+                ival = lmp%last_thermo('data',i)
+                PRINT*, key, ':', ival
+            ELSE IF (typ == lmp%dtype%i64) THEN
+                bval = lmp%last_thermo('data',i)
+                PRINT*, key, ':', bval
+            ELSE IF (typ == lmp%dtype%r64) THEN
+                dval = lmp%last_thermo('data',i)
+                PRINT*, key, ':', dval
+            END IF
+        END DO
+        CALL lmp%close(.TRUE.)
+      END PROGRAM thermo
+
+   would extract the last timestep where thermo output was done and the number
+   of columns it printed.  Then it loops over the columns to print out column
+   header keywords and the corresponding data.
+
+   .. note::
+
+      If :f:func:`last_thermo` returns a string, the string must have a length
+      greater than or equal to the length of the string (not including the
+      terminal ``NULL`` character) that LAMMPS returns. If the variable's
+      length is too short, the string will be truncated.  As usual in Fortran,
+      strings are padded with spaces at the end.  If you use an allocatable
+      string, the string **must be allocated** prior to calling this function.
+
+   :p character(len=\*) what: string with the name of the thermo keyword
+   :p integer(c_int) index: 1-based column index
+   :to: :cpp:func:`lammps_last_thermo`
+   :r pointer [polymorphic]: pointer to LAMMPS data. The left-hand side of the
+    assignment should be either a string (if expecting string data) or a
+    C-compatible pointer (e.g., ``INTEGER(c_int), POINTER :: nlocal``) to the
+    extracted property.
+
+   .. warning::
+
+       Modifying the data in the location pointed to by the returned pointer
+       may lead to inconsistent internal data and thus may cause failures,
+       crashes, or bogus simulations.  In general, it is much better
+       to use a LAMMPS input command that sets or changes these parameters.
+       Using an input command will take care of all side effects and necessary
+       updates of settings derived from such settings.
+
+--------
+
 .. f:subroutine:: extract_box([boxlo][, boxhi][, xy][, yz][, xz][, pflags][, boxflag])
 
    This subroutine will call :cpp:func:`lammps_extract_box`. All
@@ -764,13 +869,14 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
    .. note::
 
-      If :f:func:`extract_global` returns a string, the string must have length
+      If :f:func:`extract_global` returns a string, the string must have
-      greater than or equal to the length of the string (not including the
+      a length greater than or equal to the length of the string (not
-      terminal ``NULL`` character) that LAMMPS returns. If the variable's
+      including the terminal ``NULL`` character) that LAMMPS returns. If
-      length is too short, the string will be truncated. As usual in Fortran,
+      the variable's length is too short, the string will be
-      strings are padded with spaces at the end. If you use an allocatable
+      truncated. As usual in Fortran, strings are padded with spaces at
-      string, the string **must be allocated** prior to calling this function,
+      the end. If you use an allocatable string, the string **must be
-      but you can automatically reallocate it to the correct length after the
+      allocated** prior to calling this function, but you can
+      automatically reallocate it to the correct length after the
       function returns, viz.,
 
       .. code-block :: fortran
@@ -2172,19 +2278,13 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
    .. versionadded:: 3Nov2022
 
-   In case of an error, LAMMPS will either abort or throw a C++ exception.
+   When using the library interface, the library interface functions
-   The latter has to be :ref:`enabled at compile time <exceptions>`.
+   will "catch" exceptions, and then the error status can be checked by
-   This function checks if exceptions were enabled.
+   calling :f:func:`has_error`.  The most recent error message can be
-
+   retrieved via :f:func:`get_last_error_message`.  This allows to
-   When using the library interface with C++ exceptions enabled, the library
+   restart a calculation or delete and recreate the LAMMPS instance when
-   interface functions will "catch" them, and the error status can then be
+   a C++ exception occurs.  One application of using exceptions this way
-   checked by calling :f:func:`has_error`. The most recent error message can be
+   is the :ref:`lammps_shell`.
-   retrieved via :f:func:`get_last_error_message`.
-   This can allow one to restart a calculation or delete and recreate
-   the LAMMPS instance when a C++ exception occurs.  One application
-   of using exceptions this way is the :ref:`lammps_shell`.  If C++
-   exceptions are disabled and an error happens during a call to
-   LAMMPS or the Fortran API, the application will terminate.
 
    :to: :cpp:func:`lammps_config_has_exceptions`
    :r has_exceptions:
@@ -2938,14 +3038,6 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    This function can be used to query if an error inside of LAMMPS
    has thrown a :ref:`C++ exception <exceptions>`.
 
-   .. note::
-
-      This function will always report "no error" when the LAMMPS library
-      has been compiled without ``-DLAMMPS_EXCEPTIONS``, which turns fatal
-      errors aborting LAMMPS into C++ exceptions. You can use the library
-      function :cpp:func:`lammps_config_has_exceptions` to check if this is
-      the case.
-
    :to: :cpp:func:`lammps_has_error`
    :r has_error: ``.TRUE.`` if there is an error.
    :rtype has_error: logical
@@ -2968,13 +3060,6 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    would happen only in a single MPI rank and thus may not be recoverable, as
    other MPI ranks may be waiting on the failing MPI rank(s) to send messages.
 
-   .. note::
-
-      This function will do nothing when the LAMMPS library has been
-      compiled without ``-DLAMMPS_EXCEPTIONS``, which turns errors aborting
-      LAMMPS into C++ exceptions.  You can use the function
-      :f:func:`config_has_exceptions` to check whether this is the case.
-
    :p character(len=\*) buffer: string buffer to copy the error message into
    :o integer(c_int) status [optional]: 1 when all ranks had the error,
     2 on a single-rank error.

doc/src/Howto.rst

@@ -23,7 +23,6 @@ General howto
    Howto_library
    Howto_couple
    Howto_mdi
-   Howto_bpm
    Howto_broken_bonds
 
 Settings howto
@@ -83,6 +82,7 @@ Packages howto
    Howto_spherical
    Howto_granular
    Howto_body
+   Howto_bpm
    Howto_polarizable
    Howto_coreshell
    Howto_drude
@@ -101,6 +101,8 @@ Tutorials howto
 
    Howto_cmake
    Howto_github
+   Howto_lammps_gui
+   Howto_moltemplate
    Howto_pylammps
    Howto_wsl
 

doc/src/Howto_2d.rst

@@ -13,9 +13,9 @@ box with a single z plane of atoms - e.g.
 
 .. code-block:: LAMMPS
 
-   create box 1 -10 10 -10 10 -0.25 0.25
+   create_box 1 -10 10 -10 10 -0.25 0.25
 
-If using the :doc:`read data <read_data>` command to read in a file of
+If using the :doc:`read_data <read_data>` command to read in a file of
 atom coordinates, set the "zlo zhi" values to be finite but narrow,
 similar to the create_box command settings just described.  For each
 atom in the file, assign a z coordinate so it falls inside the

doc/src/Howto_body.rst

@@ -170,9 +170,9 @@ with this body style to compute body/body and body/non-body interactions.
 The *rounded/polygon* body style represents body particles as a 2d
 polygon with a variable number of N vertices.  This style can only be
 used for 2d models; see the :doc:`boundary <boundary>` command.  See the
-"pair_style body/rounded/polygon" page for a diagram of two
+:doc:`pair_style body/rounded/polygon <pair_body_rounded_polygon>` page for
-squares with rounded circles at the vertices.  Special cases for N = 1
+a diagram of two squares with rounded circles at the vertices.  Special cases
-(circle) and N = 2 (rod with rounded ends) can also be specified.
+for N = 1 (circle) and N = 2 (rod with rounded ends) can also be specified.
 
 One use of this body style is for 2d discrete element models, as
 described in :ref:`Fraige <body-Fraige>`.
@@ -335,7 +335,7 @@ faces are listed, so that M = 6 + 3\*N + 1.
 The integer line has three values: number of vertices (N), number of
 edges (E) and number of faces (F). The floating point line(s) list 6
 moments of inertia followed by the coordinates of the N vertices (x1
-to zN) as 3N values, followed by 2N vertex indices corresponding to
+to zN) as 3N values, followed by 2E vertex indices corresponding to
 the end points of the E edges, then 4\*F vertex indices defining F
 faces.  The last value is the diameter value = the rounded diameter of
 the sphere that surrounds each vertex. The diameter value can be

doc/src/Howto_bpm.rst

@@ -79,9 +79,9 @@ As bonds can be broken between neighbor list builds, the
 bond styles. There are two possible settings which determine how pair
 interactions work between bonded particles.  First, one can overlay
 pair forces with bond forces such that all bonded particles also
-feel pair interactions. This can be accomplished by using the *overlay/pair*
+feel pair interactions. This can be accomplished by setting the *overlay/pair*
-keyword present in all bpm bond styles and by using the following special
+keyword present in all bpm bond styles to *yes* and requires using the
-bond settings
+following special bond settings
 
    .. code-block:: LAMMPS
 
@@ -107,7 +107,17 @@ bond lists is expensive.  By setting the lj weight for 1-2 bonds to
 zero, this turns off pairwise interactions.  Even though there are no
 charges in BPM models, setting a nonzero coul weight for 1-2 bonds
 ensures all bonded neighbors are still included in the neighbor list
-in case bonds break between neighbor list builds.
+in case bonds break between neighbor list builds. If bond breakage is
+disabled during a simulation run by setting the *break* keyword to *no*,
+a zero coul weight for 1-2 bonds can be used to exclude bonded atoms
+from the neighbor list builds
+
+   .. code-block:: LAMMPS
+
+      special_bonds lj 0 1 1 coul 0 1 1
+
+This can be useful for post-processing, or to determine pair interaction
+properties between distinct bonded particles.
 
 To monitor the fracture of bonds in the system, all BPM bond styles
 have the ability to record instances of bond breakage to output using

doc/src/Howto_broken_bonds.rst

@@ -1,48 +1,56 @@
 Broken Bonds
 ============
 
-Typically, bond interactions persist for the duration of a simulation in
+Typically, molecular bond interactions persist for the duration of a
-LAMMPS. However, there are some exceptions that allow for bonds to
+simulation in LAMMPS.  However, some commands break bonds dynamically,
-break, including the :doc:`quartic bond style <bond_quartic>` and the
+including the following:
-bond styles in the :doc:`BPM package <Howto_bpm>` which contains the
-:doc:`bpm/spring <bond_bpm_spring>` and :doc:`bpm/rotational
-<bond_bpm_rotational>` bond styles. In these cases, a bond can be broken
-if it is stretched beyond a user-defined threshold.  LAMMPS accomplishes
-this by setting the bond type to 0, such that the bond force is no
-longer computed.
 
-Users are normally able to weight the contribution of pair forces to atoms
+* :doc:`bond_style quartic <bond_quartic>`
-that are bonded using the :doc:`special_bonds command <special_bonds>`.
+* :doc:`fix bond/break <fix_bond_break>`
-When bonds break, this is not always the case. For the quartic bond style,
+* :doc:`fix bond/react <fix_bond_react>`
-pair forces are always turned off between bonded particles. LAMMPS does
+* :doc:`BPM package <Howto_bpm>` bond styles
-this via a computational sleight-of-hand. It subtracts the pairwise
-interaction as part of the bond computation. When the bond breaks, the
-subtraction stops.  For this to work, the pairwise interaction must always
-be computed by the :doc:`pair_style <pair_style>` command, whether the bond
-is broken or not.  This means that :doc:`special_bonds <special_bonds>` must
-be set to 1,1,1. After the bond breaks, the pairwise interaction between the
-two atoms is turned on, since they are no longer bonded.
 
-In the BPM package, one can either turn off all pair interactions between
+A bond can break if it is stretched beyond a user-defined threshold or
-bonded particles or leave them on, overlaying pair forces on top of bond
+more generally if other criteria are met.
-forces. To remove pair forces, the special bond list is dynamically
-updated. More details can be found on the :doc:`Howto BPM <Howto_bpm>`
-page.
 
-Bonds can also be broken by fixes which change bond topology, including
+For the quartic bond style, when a bond is broken its bond type is set
-:doc:`fix bond/break <fix_bond_break>` and
+to 0 to effectively break it and pairwise forces between the two atoms
-:doc:`fix bond/react <fix_bond_react>`. These fixes will automatically
+in the broken bond are "turned on".  Angles, dihedrals, etc cannot be
-trigger a rebuild of the neighbor list and update special bond data structures
+defined for a system when :doc:`bond_style quartic <bond_quartic>` is
-when bonds are broken.
+used.
 
-Note that when bonds are dumped to a file via the :doc:`dump local <dump>` command, bonds with type 0 are not included.  The
+Similarly, bond styles in the BPM package are also incompatible with
-:doc:`delete_bonds <delete_bonds>` command can also be used to query the
+angles, dihedrals, etc. and when a bond breaks its type is set to zero.
-status of broken bonds or permanently delete them, e.g.:
+However, in the BPM package one can either turn off all pair interactions
+between bonded particles or leave them on, overlaying pair forces on
+top of bond forces. To remove pair forces, the special bond list is
+dynamically updated.  More details can be found on the :doc:`Howto BPM
+<Howto_bpm>` page.
+
+The :doc:`fix bond/break <fix_bond_break>` and :doc:`fix bond/react
+<fix_bond_react>` commands allow breaking of bonds within a molecular
+topology with may also define angles, dihedrals, etc.  These commands
+update internal topology data structures to remove broken bonds, as
+well as the appropriate angle, dihedral, etc interactions which
+include the bond.  They also trigger a rebuild of the neighbor list
+when this occurs, to turn on the appropriate pairwise forces.
+
+Note that when bonds are dumped to a file via the :doc:`dump local
+<dump>` command, bonds with type 0 are not included.
+
+The :doc:`delete_bonds <delete_bonds>` command can be used to query
+the status of broken bonds with type = 0 or permanently delete them,
+e.g.:
 
 .. code-block:: LAMMPS
 
    delete_bonds all stats
    delete_bonds all bond 0 remove
 
-The compute :doc:`nbond/atom <compute_nbond_atom>` can also be used
+The compute :doc:`count/type <compute_count_type>` command tallies the
-to tally the current number of bonds per atom, excluding broken bonds.
+current number of bonds (or angles, etc) for each bond (angle, etc)
+type.  It also tallies broken bonds with type = 0.
+
+The compute :doc:`nbond/atom <compute_nbond_atom>` command tallies the
+current number of bonds each atom is part of, excluding broken bonds
+with type = 0.

doc/src/Howto_cmake.rst

@@ -1,11 +1,11 @@
-Using CMake with LAMMPS tutorial
+Using CMake with LAMMPS
-================================
+=======================
 
 The support for building LAMMPS with CMake is a recent addition to
 LAMMPS thanks to the efforts of Christoph Junghans (LANL) and Richard
-Berger (Temple U).  One of the key strengths of CMake is that it is not
+Berger (LANL).  One of the key strengths of CMake is that it is not
-tied to a specific platform or build system and thus generate the files
+tied to a specific platform or build system. Instead it generates the
-necessary to build and develop for different build systems and on
+files necessary to build and develop for different build systems and on
 different platforms.  Note, that this applies to the build system itself
 not the LAMMPS code. In other words, without additional porting effort,
 it is not possible - for example - to compile LAMMPS with Visual C++ on
@@ -14,7 +14,7 @@ necessary to program LAMMPS as a project in integrated development
 environments (IDE) like Eclipse, Visual Studio, QtCreator, Xcode,
 CodeBlocks, Kate and others.
 
-A second important feature of CMake is, that it can detect and validate
+A second important feature of CMake is that it can detect and validate
 available libraries, optimal settings, available support tools and so
 on, so that by default LAMMPS will take advantage of available tools
 without requiring to provide the details about how to enable/integrate
@@ -32,8 +32,8 @@ program ``cmake`` (or ``cmake3``), a text mode interactive user
 interface (TUI) program ``ccmake`` (or ``ccmake3``), or a graphical user
 interface (GUI) program ``cmake-gui``.  All of them are portable
 software available on all supported platforms and can be used
-interchangeably.  The minimum supported CMake version is 3.10 (3.12 or
+interchangeably.  As of LAMMPS version 2 August 2023, the minimum
-later is recommended).
+required CMake version is 3.16.
 
 All details about features and settings for CMake are in the `CMake
 online documentation <https://cmake.org/documentation/>`_. We focus
@@ -43,11 +43,20 @@ Prerequisites
 -------------
 
 This tutorial assumes that you are operating in a command-line environment
-using a shell like Bash.
+using a shell like Bash or Zsh.
 
-- Linux: any Terminal window will work
+- Linux: any Terminal window will work or text console
-- macOS: launch the Terminal application.
+- macOS: launch the Terminal application
-- Windows 10: install and run the :doc:`Windows Subsystem for Linux <Howto_wsl>`
+- Windows 10 or 11: install and run the :doc:`Windows Subsystem for Linux <Howto_wsl>`
+- other Unix-like operating systems like FreeBSD
+
+.. note::
+
+   It is also possible to use CMake on Windows 10 or 11 through either the Microsoft
+   Visual Studio IDE with the bundled CMake or from the Windows command prompt using
+   a separately installed CMake package, both using the native Microsoft Visual C++
+   compilers and (optionally) the Microsoft MPI SDK.  This tutorial, however, only
+   covers unix-like command line interfaces.
 
 We also assume that you have downloaded and unpacked a recent LAMMPS source code package
 or used Git to create a clone of the LAMMPS sources on your compilation machine.
@@ -338,8 +347,6 @@ Some common LAMMPS specific variables
      - common compiler flags, for optimization or instrumentation (default:)
    * - ``LAMMPS_MACHINE``
      - when set to ``name`` the LAMMPS executable and library will be called ``lmp_name`` and ``liblammps_name.a``
-   * - ``LAMMPS_EXCEPTIONS``
-     - when set to ``on`` errors will throw a C++ exception instead of aborting (default: ``off``)
    * - ``FFT``
      - select which FFT library to use: ``FFTW3``, ``MKL``, ``KISS`` (default, unless FFTW3 is found)
    * - ``FFT_SINGLE``
@@ -412,9 +419,9 @@ interface (``ccmake`` or ``cmake-gui``).
 
    Using a preset to select a compiler package (``clang.cmake``,
    ``gcc.cmake``, ``intel.cmake``, ``oneapi.cmake``, or ``pgi.cmake``)
-   are an exception to the mechanism of updating the configuration incrementally,
+   are an exception to the mechanism of updating the configuration
-   as they will trigger a reset of cached internal CMake settings and thus
+   incrementally, as they will trigger a reset of cached internal CMake
-   reset settings to their default values.
+   settings and thus reset settings to their default values.
 
 Compilation and build targets
 -----------------------------

doc/src/Howto_couple.rst

@@ -12,16 +12,16 @@ LAMMPS can be coupled to other codes in at least 4 different ways.  Each
 has advantages and disadvantages, which you will have to think about in
 the context of your application.
 
-1. Define a new :doc:`fix <fix>` command that calls the other code.  In
+1. Define a new :doc:`fix <fix>` or :doc:`compute <compute>` command
-   this scenario, LAMMPS is the driver code.  During timestepping, the
+   that calls the other code.  In this scenario, LAMMPS is the driver
-   fix is invoked, and can make library calls to the other code, which
+   code.  During timestepping, the fix or compute is invoked, and can
-   has been linked to LAMMPS as a library.  This is the way the
+   make library calls to the other code, which has been linked to LAMMPS
-   :ref:`LATTE <PKG-LATTE>` package, which performs density-functional
+   as a library.  This is the way the :ref:`VORONOI <PKG-VORONOI>`
-   tight-binding calculations using the `LATTE software
+   package, which computes Voronoi tesselations using the `Voro++
-   <https://github.com/lanl/LATTE>`_ to compute forces, is interfaced to
+   library <http://math.lbl.gov/voro++>`_, is interfaced to LAMMPS.  See
-   LAMMPS.  See the :doc:`fix latte <fix_latte>` command for more
+   the :doc:`compute voronoi <compute_voronoi_atom>` command for more
    details.  Also see the :doc:`Modify <Modify>` pages for information
-   on how to add a new fix to LAMMPS.
+   on how to add a new fix or compute to LAMMPS.
 
 .. spacer
 

doc/src/Howto_lammps_gui.rst

@@ -0,0 +1,700 @@
+Using the LAMMPS GUI
+====================
+
+This document describes **LAMMPS GUI version 1.5**.
+
+-----
+
+LAMMPS GUI is a graphical text editor customized for editing LAMMPS
+input files that is linked to the :ref:`LAMMPS library <lammps_c_api>`
+and thus can run LAMMPS directly using the contents of the editor's text
+buffer as input.  It can retrieve and display information from LAMMPS
+while it is running, display visualizations created with the :doc:`dump
+image command <dump_image>`, and is adapted specifically for editing
+LAMMPS input files through text completion and reformatting, and linking
+to the online LAMMPS documentation for known LAMMPS commands and styles.
+
+.. note::
+
+   Pre-compiled, ready-to-use LAMMPS GUI executables for Linux (Ubuntu
+   20.04LTS or later and compatible), macOS (version 11 aka Big Sur or
+   later), and Windows (version 10 or later) :ref:`are available
+   <lammps_gui_install>` for download.  They may be linked to a
+   development version of LAMMPS in case they need features not yet
+   available in a released version. Serial LAMMPS executables of the
+   same LAMMPS version are included as well.  The source code for the
+   LAMMPS GUI is included in the LAMMPS source code and can be found in
+   the ``tools/lammps-gui`` folder.  It can be compiled alongside LAMMPS
+   when :doc:`compiling with CMake <Build_cmake>`.
+
+LAMMPS GUI tries to provide an experience similar to what people
+traditionally would do to run LAMMPS using a command line window:
+
+- editing inputs with a text editor
+- run LAMMPS on the input with selected command line flags
+- and then use or extract data from the created files and visualize it
+
+That procedure is quite effective for people proficient in using the
+command line, as that allows them to use tools for the individual steps
+which they are most comfortable with.  It is often required when running
+LAMMPS on high-performance computing facilities.
+
+The main benefit of using the LAMMPS GUI application instead is that
+many basic tasks can be done directly from the GUI without switching to
+a text console window or using external programs, let alone writing
+scripts to extract data from the generated output.  It also integrates
+well with graphical desktop environments.
+
+LAMMPS GUI thus makes it easier for beginners to get started running
+simple LAMMPS simulations.  It is very suitable for tutorials on LAMMPS
+since you only need to learn how to use a single program for most tasks
+and thus time can be saved and people can focus on learning LAMMPS.  It
+is also designed to keep the barrier low when you decide to switch to a
+full featured, standalone programming editor and more sophisticated
+visualization and analysis tools and run LAMMPS from a command line.
+
+The following text provides a detailed tour of the features and
+functionality of the LAMMPS GUI.
+
+Suggestions for new features and reports of bugs are always welcome.
+You can use the :doc:`the same channels as for LAMMPS itself
+<Errors_bugs>` for that purpose.
+
+-----
+
+Main window
+-----------
+
+When LAMMPS GUI starts, it will show a main window with either an
+empty buffer or the contents of a loaded file. In the latter case it
+may look like the following:
+
+.. image:: JPG/lammps-gui-main.png
+   :align: center
+   :scale: 50%
+
+There is the typical menu bar at the top, then the main editor buffer,
+and a status bar at the bottom.  The input file contents are shown
+with line numbers on the left and the input is colored according to
+the LAMMPS input file syntax.  The status bar shows the status of
+LAMMPS execution on the left (e.g. "Ready." when idle) and the current
+working directory on the right.  The name of the current file in the
+buffer is shown in the window title; the word `*modified*` is added if
+the buffer edits have not yet saved to a file.  The size of the main
+window will be stored when exiting and restored when starting again.
+
+Opening Files
+^^^^^^^^^^^^^
+
+The LAMMPS GUI application will try to open the first command line
+argument as a LAMMPS input script, further arguments are ignored.
+When no argument is given, LAMMPS GUI will start with an empty buffer.
+Files can also be opened via the ``File`` menu or by drag-and-drop of
+a file from a graphical file manager into the editor window.  Only one
+file can be open at a time, so opening a new file with a filled buffer
+will close the buffer.  If the buffer has unsaved modifications, you
+will be asked to either cancel the operation, discard the changes, or
+save them.
+
+Running LAMMPS
+^^^^^^^^^^^^^^
+
+From within the LAMMPS GUI main window LAMMPS can be started either from
+the ``Run`` menu using the ``Run LAMMPS from Editor Buffer`` entry, by
+the keyboard shortcut `Ctrl-Enter` (`Command-Enter` on macOS), or by
+clicking on the green "Run" button in the status bar.  All of these
+operations will cause LAMMPS to process the entire input script, which
+may contain multiple :doc:`run <run>` or :doc:`minimize <minimize>`
+commands.
+
+LAMMPS runs in a separate thread, so the GUI stays responsive and is
+able to interact with the running calculation and access data it
+produces.  It is important to note that running LAMMPS this way is
+using the contents of the input buffer for the run (via the
+:cpp:func:`lammps_commands_string()` function of the LAMMPS C-library
+interface), and **not** the original file it was read from.  Thus, if
+there are unsaved changes in the buffer, they *will* be used.  As an
+alternative, it is also possible to run LAMMPS by reading the contents
+of a file from the ``Run LAMMPS from File`` menu entry or with
+`Ctrl-Shift-Enter`.  This option may be required in some rare cases
+where the input uses some functionality that is not compatible with
+running LAMMPS from a string buffer.  For consistency, any unsaved
+changes in the buffer must be either saved to the file or undone
+before LAMMPS can be run from a file.
+
+.. image:: JPG/lammps-gui-running.png
+   :align: center
+   :scale: 75%
+
+While LAMMPS is running, the contents of the status bar change.  On
+the left side there is a text indicating that LAMMPS is running, which
+will also show the number of active threads, if thread-parallel
+acceleration was selected in the ``Preferences`` dialog.  On the right
+side, a progress bar is shown that displays the estimated progress for
+the current :doc:`run command <run>`.
+
+Also, the line number of the currently executed command will be
+highlighted in green.
+
+.. image:: JPG/lammps-gui-run-highlight.png
+   :align: center
+   :scale: 75%
+
+If an error occurs (in the example below the command :doc:`label
+<label>` was incorrectly capitalized as "Label"), an error message
+dialog will be shown and the line of the input which triggered the
+error will be highlighted.  The state of LAMMPS in the status bar will
+be set to "Failed." instead of "Ready."
+
+.. image:: JPG/lammps-gui-run-error.png
+   :align: center
+   :scale: 75%
+
+Up to three additional windows will open during a run:
+
+- a log window with the captured screen output
+- a chart window with a line graph created from the thermodynamic output of the run
+- a slide show window with images created by a :doc:`dump image command <dump_image>`
+
+More information on those windows and how to adjust their behavior and
+contents is given below.
+
+An active LAMMPS run can be stopped cleanly by using either the ``Stop
+LAMMPS`` entry in the ``Run`` menu, the keyboard shortcut `Ctrl-/`
+(`Command-/` on macOS), or by clicking on the red button in the status
+bar.  This will cause the running LAMMPS process to complete the current
+timestep (or iteration for energy minimization) and then complete the
+processing of the buffer while skipping all run or minimize commands.
+This is equivalent to the input script command :doc:`timer timeout 0
+<timer>` and is implemented by calling the
+:cpp:func:`lammps_force_timeout()` function of the LAMMPS C-library
+interface.  Please see the corresponding documentation pages to
+understand the implications of this operation.
+
+Log Window
+----------
+
+By default, when starting a run, a "Log Window" will open that displays
+the current screen output of the LAMMPS calculation, that would normally
+be seen in the command line window, as shown below.
+
+.. image:: JPG/lammps-gui-log.png
+   :align: center
+   :scale: 50%
+
+LAMMPS GUI captures the screen output as it is generated and updates
+the log window regularly during a run.
+
+By default, the log window will be replaced each time a run is started.
+The runs are counted and the run number for the current run is displayed
+in the window title.  It is possible to change the behavior of LAMMPS
+GUI in the preferences dialog to create a *new* log window for every run
+or to not show the current log window.  It is also possible to show or
+hide the *current* log window from the ``View`` menu.
+
+The text in the log window is read-only and cannot be modified, but
+keyboard shortcuts to select and copy all or parts of the text can be
+used to transfer text to another program. Also, the keyboard shortcut
+`Ctrl-S` (`Command-S` on macOS) is available to save the log buffer to a
+file.  The "Select All" and "Copy" functions, as well as a "Save Log to
+File" option are also available from a context menu by clicking with the
+right mouse button into the log window text area.
+
+Chart Window
+------------
+
+By default, when starting a run, a "Chart Window" will open that
+displays a plot of thermodynamic output of the LAMMPS calculation as
+shown below.
+
+.. image:: JPG/lammps-gui-chart.png
+   :align: center
+   :scale: 50%
+
+The drop down menu on the top right allows selection of different
+properties that are computed and written to thermo output.  Only one
+property can be shown at a time.  The plots will be updated with new
+data as the run progresses, so they can be used to visually monitor the
+evolution of available properties.  The window title will show the
+current run number that this chart window corresponds to.  Same as
+explained for the log window above, by default, the chart window will
+be replaced on each new run, but the behavior can be changed in the
+preferences dialog.
+
+From the ``File`` menu on the top left, it is possible to save an image
+of the currently displayed plot or export the data in either plain text
+columns (for use by plotting tools like `gnuplot
+<http://www.gnuplot.info/>`_ or `grace
+<https://plasma-gate.weizmann.ac.il/Grace/>`_), or as CSV data which can
+be imported for further processing with Microsoft Excel or `pandas
+<https://pandas.pydata.org/>`_
+
+Thermo output data from successive run commands in the input script will
+be combined into a single data set unless the format, number, or names
+of output columns are changed with a :doc:`thermo_style <thermo_style>`
+or a :doc:`thermo_modify <thermo_modify>` command, or the current time
+step is reset with :doc:`reset_timestep <reset_timestep>`, or if a
+:doc:`clear <clear>` command is issued.
+
+Image Slide Show
+----------------
+
+By default, if the LAMMPS input contains a :doc:`dump image
+<dump_image>` command, a "Slide Show" window will open which loads and
+displays the images created by LAMMPS as they are written.
+
+.. image:: JPG/lammps-gui-slideshow.png
+   :align: center
+   :scale: 50%
+
+The various buttons at the bottom right of the window allow single
+stepping through the sequence of images or playing an animation (as a
+continuous loop or once from first to last).  It is also possible to
+zoom in or zoom out of the displayed images, and to export the slide
+show animation to a movie file, if `ffmpeg <https://ffmpeg.org/>`_ is
+installed.
+
+Variable Info
+-------------
+
+During a run, it may be of interest to monitor the value of input script
+variables, for example to monitor the progress of loops.  This can be
+done by enabling the "Variables Window" in the ``View`` menu or by using
+the `Ctrl-Shift-W` keyboard shortcut.  This will show info similar to
+the :doc:`info variables <info>` command in a separate window as shown
+below.
+
+.. image:: JPG/lammps-gui-variable-info.png
+   :align: center
+   :scale: 75%
+
+Like the log and chart windows, its content is continuously updated
+during a run.  It will show "(none)" if there are no variables
+defined.  Note that it is also possible to *set* :doc:`index style
+variables <variable>`, that would normally be set via command line
+flags, via the "Set Variables..." dialog from the ``Run`` menu.
+LAMMPS GUI will automatically set the variable "gui_run" to the
+current value of the run counter.  That way it would be possible
+to automatically record a log for each run attempt by using the
+command
+
+.. code-block:: LAMMPS
+
+   log logfile-${gui_run}.txt
+
+at the beginning of an input file. That would record logs to files
+``logfile-1.txt``, ``logfile-2.txt``, and so on for successive runs.
+
+Viewing Snapshot Images
+-----------------------
+
+By selecting the ``Create Image`` entry in the ``Run`` menu, or by
+hitting the `Ctrl-I` (`Command-I` on macOS) keyboard shortcut, or by
+clicking on the "palette" button in the status bar, LAMMPS GUI will send
+a custom :doc:`write_dump image <dump_image>` command to LAMMPS and read
+the resulting snapshot image with the current state of the system into
+an image viewer window.  This functionality is not available *during* an
+ongoing run.  When LAMMPS is not yet initialized, LAMMPS GUI will try to
+identify the line with the first run or minimize command and execute all
+command up to that line from the input buffer and then add a "run 0"
+command.  This will initialize the system so an image of the initial
+state of the system can be rendered.  If there was an error, the
+snapshot image viewer will not appear.
+
+When possible, LAMMPS GUI will try to detect which elements the atoms
+correspond to (via their mass) and then colorize them in the image
+accordingly.  Otherwise the default predefined sequence of colors is
+assigned to the different atom types.
+
+.. image:: JPG/lammps-gui-image.png
+   :align: center
+   :scale: 50%
+
+The default image size, some default image quality settings, the view
+style and some colors can be changed in the ``Preferences`` dialog
+window.  From the image viewer window further adjustments can be made:
+actual image size, high-quality (SSAO) rendering, anti-aliasing, view
+style, display of box or axes, zoom factor.  The view of the system
+can be rotated horizontally and vertically.  It is also possible to
+only display the atoms within a group defined in the input script
+(default is "all").  After each change, the image is rendered again
+and the display updated.  The small palette icon on the top left will
+be colored while LAMMPS is running to render the new image; it will be
+grayed out when it is finished.  When there are many atoms to render
+and high quality images with anti-aliasing are requested, re-rendering
+may take several seconds.  From the ``File`` menu of the image window,
+the current image can be saved to a file or copied into the
+cut-n-paste buffer for pasting into another application.
+
+Editor Functions
+----------------
+
+The editor has most of the usual functionality that similar programs
+have: text selection via mouse or with cursor moves while holding the
+Shift key, Cut (`Ctrl-X`), Copy (`Ctrl-C`), Paste (`Ctrl-V`), Undo
+(`Ctrl-Z`), Redo (`Ctrl-Shift-Z`), Select All (`Ctrl-A`).  When trying
+to exit the editor with a modified buffer, a dialog will pop up asking
+whether to cancel the exit operation, or to save or not save the buffer
+contents to a file.
+
+Context Specific Word Completion
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+By default, LAMMPS GUI will display a small pop-up frame with possible
+choices for LAMMPS input script commands or styles after 2 characters of
+a word have been typed.
+
+.. image:: JPG/lammps-gui-complete.png
+   :align: center
+   :scale: 75%
+
+The word can then be completed through selecting an entry by scrolling
+up and down with the cursor keys and selecting with the 'Enter' key or
+by clicking on the entry with the mouse.  The automatic completion
+pop-up can be disabled in the ``Preferences`` dialog, but the completion
+can still be requested manually by either hitting the 'Shift-TAB' key or
+by right-clicking with the mouse and selecting the option from the
+context menu.  Most of the completion information is taken from the
+LAMMPS instance and thus it will be adjusted to only show available
+options that have been enabled while compiling LAMMPS. That, however,
+excludes accelerated styles and commands; for improved clarity, only the
+non-suffix version of styles are shown.
+
+Line Reformatting
+^^^^^^^^^^^^^^^^^
+
+The editor supports reformatting lines according to the syntax in order
+to have consistently aligned lines.  This primarily means adding
+whitespace padding to commands, type specifiers, IDs and names.  This
+reformatting is performed by default when hitting the 'Enter' key to
+start a new line.  This feature can be turned on or off in the
+``Preferences`` dialog, but it can still be manually performed by
+hitting the 'TAB' key.  The amount of padding can also be changed in the
+``Preferences`` dialog.
+
+Internally this functionality is achieved by splitting the line into
+"words" and then putting it back together with padding added where the
+context can be detected; otherwise a single space is used between words.
+
+Context Specific Help
+^^^^^^^^^^^^^^^^^^^^^
+
+.. image:: JPG/lammps-gui-popup-help.png
+   :align: center
+   :scale: 50%
+
+A unique feature of the LAMMPS GUI is the option to look up the
+documentation for the command in the current line.  This can be done by
+either clicking the right mouse button or by using the `Ctrl-?` keyboard
+shortcut.  When clicking the mouse there are additional entries in the
+context menu that will open the corresponding documentation page in the
+online LAMMPS documentation.  When using the keyboard, the first of
+those entries will be chosen directly.
+
+Menu
+----
+
+The menu bar has entries ``File``, ``Edit``, ``Run``, ``View``, and
+``About``.  Instead of using the mouse to click on them, the individual
+menus can also be activated by hitting the `Alt` key together with the
+corresponding underlined letter, that is `Alt-F` will activate the
+``File`` menu.  For the corresponding activated sub-menus, the key
+corresponding the underlined letters can again be used to select entries
+instead of using the mouse.
+
+File
+^^^^
+
+The ``File`` menu offers the usual options:
+
+- ``New`` will clear the current buffer and reset the file name to ``*unknown*``
+- ``Open`` will open a dialog to select a new file
+- ``Save`` will save the current file; if the file name is ``*unknown*``
+  a dialog will open to select a new file name
+- ``Save As`` will open a dialog to select and new file name and save
+  the buffer to it
+- ``Quit`` will exit LAMMPS GUI. If there are unsaved changes, a dialog
+  will appear to either cancel the operation, or to save or not save the
+  edited file.
+
+In addition, up to 5 recent file names will be listed after the
+``Open`` entry that allows re-opening recent files.  This list is
+stored when quitting and recovered when starting again.
+
+Edit
+^^^^
+
+The ``Edit`` menu offers the usual editor functions like ``Undo``,
+``Redo``, ``Cut``, ``Copy``, ``Paste``.  It can also open a
+``Preferences`` dialog (keyboard shortcut `Ctrl-P`) and allows deletion
+of all stored preferences so they will be reset to default values.
+
+Run
+^^^
+
+The ``Run`` menu has options to start and stop a LAMMPS process.
+Rather than calling the LAMMPS executable as a separate executable,
+the LAMMPS GUI is linked to the LAMMPS library and thus can run LAMMPS
+internally through the :ref:`LAMMPS C-library interface
+<lammps_c_api>`.
+
+Specifically, a LAMMPS instance will be created by calling
+:cpp:func:`lammps_open_no_mpi`.  The buffer contents then executed by
+calling :cpp:func:`lammps_commands_string`.  Certain commands and
+features are only available after a LAMMPS instance is created.  Its
+presence is indicated by a small LAMMPS ``L`` logo in the status bar
+at the bottom left of the main window.  As an alternative, it is also
+possible to run LAMMPS using the contents of the edited file by
+reading the file.  This is mainly provided as a fallback option in
+case the input uses some feature that is not available when running
+from a string buffer.
+
+The LAMMPS calculation will be run in a concurrent thread so that the
+GUI can stay responsive and be updated during the run.  This can be
+used to tell the running LAMMPS instance to stop at the next timestep.
+The ``Stop LAMMPS`` entry will do this by calling
+:cpp:func:`lammps_force_timeout`, which is equivalent to a :doc:`timer
+timeout 0 <timer>` command.
+
+The ``Set Variables...`` entry will open a dialog box where
+:doc:`index style variables <variable>` can be set. Those variables
+will be passed to the LAMMPS instance when it is created and are thus
+set *before* a run is started.
+
+.. image:: JPG/lammps-gui-variables.png
+   :align: center
+   :scale: 75%
+
+The ``Set Variables`` dialog will be pre-populated with entries that
+are set as index variables in the input and any variables that are
+used but not defined, if the built-in parser can detect them.  New
+rows for additional variables can be added through the ``Add Row``
+button and existing rows can be deleted by clicking on the ``X`` icons
+on the right.
+
+The ``Create Image`` entry will send a :doc:`dump image <dump_image>`
+command to the LAMMPS instance, read the resulting file, and show it
+in an ``Image Viewer`` window.
+
+The ``View in OVITO`` entry will launch `OVITO <https://ovito.org>`_
+with a :doc:`data file <write_data>` containing the current state of
+the system.  This option is only available if the LAMMPS GUI can find
+the OVITO executable in the system path.
+
+The ``View in VMD`` entry will launch VMD with a :doc:`data file
+<write_data>` containing the current state of the system.  This option
+is only available if the LAMMPS GUI can find the VMD executable in the
+system path.
+
+View
+^^^^
+
+The ``View`` menu offers to show or hide additional windows with log
+output, charts, slide show, variables, or snapshot images.  The
+default settings for their visibility can be changed in the
+``Preferences dialog``.
+
+About
+^^^^^
+
+The ``About`` menu finally offers a couple of dialog windows and an
+option to launch the LAMMPS online documentation in a web browser.
+The ``About LAMMPS`` entry displays a dialog with a summary of the
+configuration settings of the LAMMPS library in use and the version
+number of LAMMPS GUI itself.  The ``Quick Help`` displays a dialog
+with a minimal description of LAMMPS GUI.  The ``LAMMPS GUI Howto``
+entry will open this documentation page from the online documentation
+in a web browser window.  The ``LAMMPS Manual`` entry will open the
+main page of the LAMMPS documentation in the web browser.
+
+-----
+
+Preferences
+-----------
+
+The ``Preferences`` dialog allows customization of the behavior and
+look of the LAMMPS GUI application.  The settings are grouped and each
+group is displayed within a tab.
+
+.. |guiprefs1| image:: JPG/lammps-gui-prefs-general.png
+   :width: 24%
+
+.. |guiprefs2| image:: JPG/lammps-gui-prefs-accel.png
+   :width: 24%
+
+.. |guiprefs3| image:: JPG/lammps-gui-prefs-image.png
+   :width: 24%
+
+.. |guiprefs4| image:: JPG/lammps-gui-prefs-editor.png
+   :width: 24%
+
+|guiprefs1|  |guiprefs2|  |guiprefs3|  |guiprefs4|
+
+General Settings:
+^^^^^^^^^^^^^^^^^
+
+- *Echo input to log:* when checked, all input commands, including
+  variable expansions, will be echoed to the log window. This is
+  equivalent to using `-echo screen` at the command line.  There is no
+  log *file* produced by default, since LAMMPS GUI uses `-log none`.
+- *Include citation details:* when checked full citation info will be
+  included to the log window.  This is equivalent to using `-cite
+  screen` on the command line.
+- *Show log window by default:* when checked, the screen output of a
+  LAMMPS run will be collected in a log window during the run
+- *Show chart window by default:* when checked, the thermodynamic
+  output of a LAMMPS run will be collected and displayed in a chart
+  window as line graphs.
+- *Show slide show window by default:* when checked, a slide show
+  window will be shown with images from a dump image command, if
+  present, in the LAMMPS input.
+- *Replace log window on new run:* when checked, an existing log
+  window will be replaced on a new LAMMPS run, otherwise each run will
+  create a new log window.
+- *Replace chart window on new run:* when checked, an existing chart
+  window will be replaced on a new LAMMPS run, otherwise each run will
+  create a new chart window.
+- *Replace image window on new render:* when checked, an existing
+  chart window will be replaced when a new snapshot image is requested,
+  otherwise each command will create a new image window.
+- *Path to LAMMPS Shared Library File:* this option is only visible
+  when LAMMPS GUI was compiled to load the LAMMPS library at run time
+  instead of being linked to it directly.  With the ``Browse..`` button
+  or by changing the text, a different shared library file with a
+  different compilation of LAMMPS with different settings or from a
+  different version can be loaded.  After this setting was changed,
+  LAMMPS GUI needs to be re-launched.
+- *Select Default Font:* Opens a font selection dialog where the type
+  and size for the default font (used for everything but the editor and
+  log) of the application can be set.
+- *Select Text Font:* Opens a font selection dialog where the type and
+  size for the text editor and log font of the application can be set.
+- *GUI update interval:* Allows to set the time interval between GUI
+  and data updates during a LAMMPS run in milliseconds. The default is
+  to update the GUI every 100 milliseconds. This is good for most cases.
+  For LAMMPS runs that run very fast, however, data may be missed and
+  through lowering this interval, this can be corrected. However, this
+  will make the GUI use more resources, which may be a problem on some
+  computers with slower CPUs. The default value is 100 milliseconds.
+
+Accelerators:
+^^^^^^^^^^^^^
+
+This tab enables selection of an accelerator package for LAMMPS to use
+and is equivalent to using the `-suffix` and `-package` flags on the
+command line.  Only settings supported by the LAMMPS library and local
+hardware are available.  The `Number of threads` field allows setting
+the maximum number of threads for the accelerator packages that use
+threads.
+
+Snapshot Image:
+^^^^^^^^^^^^^^^
+
+This tab allows setting defaults for the snapshot images displayed in
+the ``Image Viewer`` window, such as its dimensions and the zoom
+factor applied.  The *Antialias* switch will render images with twice
+the number of pixels for width and height and then smoothly scale the
+image back to the requested size.  This produces higher quality images
+with smoother edges at the expense of requiring more CPU time to
+render the image.  The *HQ Image mode* option turns on screen space
+ambient occlusion (SSAO) mode when rendering images.  This is also
+more time consuming, but produces a more 'spatial' representation of
+the system shading of atoms by their depth.  The *VDW Style* checkbox
+selects whether atoms are represented by space filling spheres when
+checked or by smaller spheres and sticks.  Finally there are a couple
+of drop down lists to select the background and box colors.
+
+Editor Settings:
+^^^^^^^^^^^^^^^^
+
+This tab allows tweaking settings of the editor window.  Specifically
+the amount of padding to be added to LAMMPS commands, types or type
+ranges, IDs (e.g. for fixes), and names (e.g. for groups).  The value
+set is the minimum width for the text element and it can be chosen in
+the range between 1 and 32.
+
+The two settings which follow enable or disable the automatic
+reformatting when hitting the 'Enter' key and the automatic display of
+the completion pop-up window.
+
+-----------
+
+Keyboard Shortcuts
+------------------
+
+Almost all functionality is accessible from the menu of the editor
+window or through keyboard shortcuts.  The following shortcuts are
+available (On macOS use the Command key instead of Ctrl/Control).
+
+.. list-table::
+   :header-rows: 1
+   :widths: auto
+
+   * - Shortcut
+     - Function
+     - Shortcut
+     - Function
+     - Shortcut
+     - Function
+   * - Ctrl+N
+     - New File
+     - Ctrl+Z
+     - Undo edit
+     - Ctrl+Enter
+     - Run Input
+   * - Ctrl+O
+     - Open File
+     - Ctrl+Shift+Z
+     - Redo edit
+     - Ctrl+/
+     - Stop Active Run
+   * - Ctrl+S
+     - Save File
+     - Ctrl+C
+     - Copy text
+     - Ctrl+Shift+V
+     - Set Variables
+   * - Ctrl+Shift+S
+     - Save File As
+     - Ctrl+X
+     - Cut text
+     - Ctrl+I
+     - Snapshot Image
+   * - Ctrl+Q
+     - Quit Application
+     - Ctrl+V
+     - Paste text
+     - Ctrl+L
+     - Slide Show
+   * - Ctrl+W
+     - Close Window
+     - Ctrl+A
+     - Select All
+     - Ctrl+P
+     - Preferences
+   * - Ctrl+Shift+A
+     - About LAMMPS
+     - Ctrl+Shift+H
+     - Quick Help
+     - Ctrl+Shift+G
+     - LAMMPS GUI Howto
+   * - Ctrl+Shift+M
+     - LAMMPS Manual
+     - Ctrl+?
+     - Context Help
+     - Ctrl+Shift+W
+     - Show Variables
+   * - Ctrl+Shift+Enter
+     - Run File
+     - TAB
+     - Reformat line
+     - Shift+TAB
+     - Show Completions
+
+Further editing keybindings `are documented with the Qt documentation
+<https://doc.qt.io/qt-5/qplaintextedit.html#editing-key-bindings>`_.  In
+case of conflicts the list above takes precedence.
+
+All other windows only support a subset of keyboard shortcuts listed
+above.  Typically, the shortcuts `Ctrl-/` (Stop Run), `Ctrl-W` (Close
+Window), and `Ctrl-Q` (Quit Application) are supported.