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fixing merge conflicts

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jtclemm
2024-01-12 11:12:02 -07:00
parent 3f677f798a 35214120ad
commit 073a72d933
4127 changed files with 269518 additions and 218989 deletions
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9
.github/CODEOWNERS vendored
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@ -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/KIM.cmake @rbberger @ellio167
cmake/Modules/Packages/COLVARS.cmake @giacomofiorin
cmake/Modules/Packages/KIM.cmake @ellio167
cmake/presets/*.cmake @akohlmey
# python

24
.github/CONTRIBUTING.md vendored
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@ -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 on programming style and requirement in the LAMMPS manual](https://www.lammps.org/doc/Modify_style.html)
* [The GitHub tutorial in the LAMMPS manual](http://lammps.sandia.gov/doc/Howto_github.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://docs.lammps.org/Modify_requirements.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 on programming style and requirement in the LAMMPS manual](https://lammps.sandia.gov/doc/Modify_contribute.html)
* [The GitHub tutorial in the LAMMPS manual](http://lammps.sandia.gov/doc/Howto_github.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://docs.lammps.org/Modify_requirements.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.

4
.github/workflows/codeql-analysis.yml vendored
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@ -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'

4
.github/workflows/compile-msvc.yml vendored
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@ -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'

8
.github/workflows/coverity.yml vendored
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@ -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

2
.github/workflows/unittest-macos.yml vendored
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@ -21,7 +21,7 @@ jobs:
steps:
- name: Checkout repository
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
fetch-depth: 2

3
.gitignore vendored
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@ -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

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

36
bench/in.chain.scaled
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@ -1,32 +1,32 @@
# FENE beadspring benchmark
variable x index 1
variable y index 1
variable z index 1
variable x index 1
variable y index 1
variable z index 1
units lj
atom_style bond
atom_modify map hash
units lj
atom_style bond
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
neigh_modify every 1 delay 1
neighbor 0.4 bin
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_modify shift yes
pair_coeff 1 1 1.0 1.0 1.12
pair_style lj/cut 1.12
pair_modify shift yes
pair_coeff 1 1 1.0 1.0 1.12
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
thermo 100
timestep 0.012
timestep 0.012
run 100
run 100

44
bench/in.chute
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@ -1,33 +1,33 @@
# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
units lj
atom_style sphere
boundary p p fs
newton off
comm_modify vel yes
units lj
atom_style sphere
boundary p p fs
newton off
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_coeff * *
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
neighbor 0.1 bin
neigh_modify every 1 delay 0
neighbor 0.1 bin
neigh_modify every 1 delay 0
timestep 0.0001
timestep 0.0001
group bottom type 2
group active subtract all bottom
neigh_modify exclude group bottom bottom
group bottom type 2
group active subtract all bottom
neigh_modify exclude group bottom bottom
fix 1 all gravity 1.0 chute 26.0
fix 2 bottom freeze
fix 3 active nve/sphere
fix 1 all gravity 1.0 chute 26.0
fix 2 bottom freeze
fix 3 active nve/sphere
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify norm no
thermo 100
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify norm no
thermo 100
run 100
run 100

50
bench/in.chute.scaled
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@ -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 y index 1
variable x index 1
variable y index 1
units lj
atom_style sphere
boundary p p fs
newton off
comm_modify vel yes
units lj
atom_style sphere
boundary p p fs
newton off
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_coeff * *
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
neighbor 0.1 bin
neigh_modify every 1 delay 0
neighbor 0.1 bin
neigh_modify every 1 delay 0
timestep 0.0001
timestep 0.0001
group bottom type 2
group active subtract all bottom
neigh_modify exclude group bottom bottom
group bottom type 2
group active subtract all bottom
neigh_modify exclude group bottom bottom
fix 1 all gravity 1.0 chute 26.0
fix 2 bottom freeze
fix 3 active nve/sphere
fix 1 all gravity 1.0 chute 26.0
fix 2 bottom freeze
fix 3 active nve/sphere
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify norm no
thermo 100
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify norm no
thermo 100
run 100
run 100

40
bench/in.eam
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@ -1,32 +1,32 @@
# bulk Cu lattice
variable x index 1
variable y index 1
variable z index 1
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
units metal
atom_style atomic
units metal
atom_style atomic
lattice fcc 3.615
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
lattice fcc 3.615
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
pair_style eam
pair_coeff 1 1 Cu_u3.eam
pair_style 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
thermo 50
timestep 0.005
thermo 50
run 100
run 100

40
bench/in.lj
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@ -1,30 +1,30 @@
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
units lj
atom_style atomic
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
mass 1 1.0
lattice fcc 0.8442
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 1.44 87287 loop geom
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
fix 1 all nve
run 100
run 100

28
bench/in.rhodo
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@ -1,27 +1,27 @@
# Rhodopsin model
units real
neigh_modify delay 5 every 1
units real
neigh_modify delay 5 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data data.rhodo
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
thermo 50
thermo_style multi
thermo_style multi
timestep 2.0
run 100
run 100

38
bench/in.rhodo.scaled
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@ -1,34 +1,34 @@
# Rhodopsin model
variable x index 1
variable y index 1
variable z index 1
variable x index 1
variable y index 1
variable z index 1
units real
neigh_modify delay 5 every 1
units real
neigh_modify delay 5 every 1
atom_style full
atom_modify map hash
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
atom_style full
atom_modify map hash
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data data.rhodo
replicate $x $y $z
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
thermo 50
thermo_style multi
thermo_style multi
timestep 2.0
run 100
run 100

615
cmake/CMakeLists.jpeg
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@ -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()

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# 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

228
cmake/CMakeLists.txt
View File

@ -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 3.10)
cmake_minimum_required(VERSION 3.16)
########################################
# 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 "${CMAKE_TUNE_DEFAULT} -Xcudafe --diag_suppress=unrecognized_pragma")
endif()
# we require C++11 without extensions. Kokkos requires at least C++14 (currently)
# we require C++11 without extensions. Kokkos requires at least C++17 (currently)
if(NOT CMAKE_CXX_STANDARD)
set(CMAKE_CXX_STANDARD 11)
endif()
if(CMAKE_CXX_STANDARD LESS 11)
message(FATAL_ERROR "C++ standard must be set to at least 11")
endif()
if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 14))
set(CMAKE_CXX_STANDARD 14)
if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 17))
set(CMAKE_CXX_STANDARD 17)
endif()
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
@ -155,6 +144,7 @@ if(MSVC)
add_compile_options(/Zc:__cplusplus)
add_compile_options(/wd4244)
add_compile_options(/wd4267)
add_compile_options(/wd4250)
add_compile_options(/EHsc)
endif()
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
@ -168,17 +158,20 @@ endif()
########################################################################
# User input options #
########################################################################
# set path to python interpreter and thus enforcing python version when
# in a virtual environment and PYTHON_EXECUTABLE is not set on command line
if(DEFINED ENV{VIRTUAL_ENV} AND NOT PYTHON_EXECUTABLE)
if(CMAKE_HOST_SYSTEM_NAME STREQUAL "Windows")
set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/Scripts/python.exe")
else()
set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/bin/python")
endif()
# backward compatibility with CMake before 3.12 and older LAMMPS documentation
if (PYTHON_EXECUTABLE)
set(Python_EXECUTABLE "${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 MAIN_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/main.cpp)
file(GLOB ALL_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/[^.]*.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_include_directories(lammps PRIVATE ${JPEG_INCLUDE_DIRS})
target_link_libraries(lammps PRIVATE ${JPEG_LIBRARIES})
else()
target_link_libraries(lammps PRIVATE JPEG::JPEG)
endif()
target_link_libraries(lammps PRIVATE JPEG::JPEG)
endif()
find_package(PNG QUIET)
@ -522,7 +515,7 @@ else()
endif()
foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM LATTE MSCG COMPRESS ML-PACE LEPTON)
PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON)
if(PKG_${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}_HEADERS ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.h)
file(GLOB ${PKG}_SOURCES CONFIGURE_DEPENDS ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
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}_HEADERS ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.h)
file(GLOB ${PKG}_SOURCES CONFIGURE_DEPENDS ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
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)
# adjust so we find Python 3 versions before Python 2 on old systems with old CMake
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()
# backward compatibility
find_package(Python COMPONENTS Interpreter)
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)
if(OPTIONS)
message(STATUS "Linker options: ${OPTIONS}")
endif()
get_target_property(OPTIONS lammps LINK_OPTIONS)
if(OPTIONS)
message(STATUS "Linker options: ${OPTIONS}")
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 >>>
-- Primary FFT lib: ${FFT}")
if(FFT_SINGLE)
message(STATUS "Using single precision FFTs")
else()
message(STATUS "Using double precision FFTs")
endif()
if(FFT_FFTW_THREADS OR FFT_MKL_THREADS)
message(STATUS "Using threaded FFTs")
else()
message(STATUS "Using non-threaded FFTs")
endif()
if(PKG_KOKKOS)
if(Kokkos_ENABLE_CUDA)
if(FFT STREQUAL "KISS")
message(STATUS "Kokkos FFT: KISS")
else()
message(STATUS "Kokkos FFT: cuFFT")
endif()
elseif(Kokkos_ENABLE_HIP)
if(FFT STREQUAL "KISS")
message(STATUS "Kokkos FFT: KISS")
else()
message(STATUS "Kokkos FFT: hipFFT")
endif()
if (LMP_HEFFTE)
message(STATUS "<<< FFT settings >>>
-- Primary FFT lib: heFFTe")
if (HEFFTE_BACKEND)
message(STATUS "heFFTe backend: ${HEFFTE_BACKEND}")
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)

195
cmake/CMakeLists.zlib
View File

@ -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()

53
cmake/CMakeSettings.json
View File

@ -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"
}
]
}
]
}

14
cmake/Modules/CodingStandard.cmake
View File

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

16
cmake/Modules/DetectHIPInstallation.cmake Normal file
View File

@ -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})

26
cmake/Modules/Documentation.cmake
View File

@ -4,21 +4,19 @@
option(BUILD_DOC "Build LAMMPS HTML documentation" OFF)
if(BUILD_DOC)
# Sphinx 3.x requires at least Python 3.5
if(CMAKE_VERSION VERSION_LESS 3.12)
find_package(PythonInterp 3.5 REQUIRED)
set(VIRTUALENV ${PYTHON_EXECUTABLE} -m venv)
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)
# Current Sphinx versions require at least Python 3.8
# use default (or custom) Python executable, if version is sufficient
if(Python_VERSION VERSION_GREATER_EQUAL 3.8)
set(Python3_EXECUTABLE ${Python_EXECUTABLE})
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()

12
cmake/Modules/FindClangFormat.cmake
View File

@ -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}")

10
cmake/Modules/FindCythonize.cmake
View File

@ -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)
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()
find_package(Python 3.6 COMPONENTS Interpreter QUIET)
# Use the Cython executable that lives next to the Python executable
# if it is a local installation.

7
cmake/Modules/LAMMPSInterfacePlugin.cmake
View File

@ -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(/EHsc)
endif()
add_compile_options(/wd4250)
add_compile_options(/EHsc)
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})

22
cmake/Modules/LAMMPSUtils.cmake
View File

@ -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_PACKAGES ${CONFIGURE_DEPENDS} ${source_dir}/packages_*.h)
file(GLOB SRC_AUTOGEN_FILES CONFIGURE_DEPENDS ${source_dir}/style_*.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"
"\n"
"Please run\n"
"make -C ${source_dir} purge\n"
"to remove\n"
"########################################################################")
"Found header file ${source_dir}/${FILENAME} generated by the make-based build system\n"
"\n"
"Please run\n"
"make -C ${source_dir} purge\n"
"to remove\n"
"########################################################################")
endif()
endforeach()
endfunction()
@ -152,7 +152,7 @@ endfunction(FetchPotentials)
# set CMAKE_LINUX_DISTRO and CMAKE_DISTRO_VERSION on Linux
if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (EXISTS /etc/os-release))
file(STRINGS /etc/os-release distro REGEX "^NAME=")
string(REGEX REPLACE "NAME=\"?([^\"]*)\"?" "\\1" distro "${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})

2
cmake/Modules/Packages/COLVARS.cmake
View File

@ -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)

139
cmake/Modules/Packages/GPU.cmake
View File

@ -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_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
file(GLOB GPU_LIB_CUDPP_SOURCES CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
file(GLOB GPU_LIB_CUDPP_CU CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
endif()
# build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH}")
# apply the following to build "fat" CUDA binaries only for known CUDA toolkits since version 8.0
# only the Kepler achitecture and beyond is supported
# comparison chart according to: https://en.wikipedia.org/wiki/CUDA#GPUs_supported
if(CUDA_VERSION VERSION_LESS 8.0)
message(FATAL_ERROR "CUDA Toolkit version 8.0 or later is required")
elseif(CUDA_VERSION VERSION_GREATER_EQUAL "13.0")
message(WARNING "Untested CUDA Toolkit version ${CUDA_VERSION}. Use at your own risk")
set(GPU_CUDA_GENCODE "-arch=all")
elseif(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
set(GPU_CUDA_GENCODE "-arch=all")
else()
# Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] ")
endif()
# Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_35,code=[sm_35,compute_35]")
endif()
# Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")
endif()
# Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "8.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")
endif()
# Volta (GPU Arch 7.0) is supported by CUDA 9 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")
endif()
# Turing (GPU Arch 7.5) is supported by CUDA 10 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
endif()
# Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
endif()
# Ampere (GPU Arch 8.6) is supported by CUDA 11.1 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
endif()
# Lovelace (GPU Arch 8.9) is supported by CUDA 11.8 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.8")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
endif()
# Hopper (GPU Arch 9.0) is supported by CUDA 12.0 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
if(CUDA_BUILD_MULTIARCH)
# apply the following to build "fat" CUDA binaries only for known CUDA toolkits since version 8.0
# only the Kepler achitecture and beyond is supported
# comparison chart according to: https://en.wikipedia.org/wiki/CUDA#GPUs_supported
if(CUDA_VERSION VERSION_LESS 8.0)
message(FATAL_ERROR "CUDA Toolkit version 8.0 or later is required")
elseif(CUDA_VERSION VERSION_GREATER_EQUAL "13.0")
message(WARNING "Untested CUDA Toolkit version ${CUDA_VERSION}. Use at your own risk")
set(GPU_CUDA_GENCODE "-arch=all")
elseif(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
set(GPU_CUDA_GENCODE "-arch=all")
else()
# Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] ")
endif()
# Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_35,code=[sm_35,compute_35]")
endif()
# Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")
endif()
# Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "8.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")
endif()
# Volta (GPU Arch 7.0) is supported by CUDA 9 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")
endif()
# Turing (GPU Arch 7.5) is supported by CUDA 10 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
endif()
# Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
endif()
# Ampere (GPU Arch 8.6) is supported by CUDA 11.1 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
endif()
# Lovelace (GPU Arch 8.9) is supported by CUDA 11.8 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.8")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
endif()
# Hopper (GPU Arch 9.0) is supported by CUDA 12.0 and later
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)
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})
include(DetectHIPInstallation)
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 "")

9
cmake/Modules/Packages/KIM.cmake
View File

@ -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_include_directories(lammps PRIVATE ${CURL_INCLUDE_DIRS})
target_link_libraries(lammps PRIVATE ${CURL_LIBRARIES})
else()
target_link_libraries(lammps PRIVATE CURL::libcurl)
endif()
target_link_libraries(lammps PRIVATE CURL::libcurl)
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)

30
cmake/Modules/Packages/KOKKOS.cmake
View File

@ -1,7 +1,8 @@
########################################################################
# As of version 3.3.0 Kokkos requires C++14
if(CMAKE_CXX_STANDARD LESS 14)
message(FATAL_ERROR "The KOKKOS package requires the C++ standard to be set to at least C++14")
# As of version 4.0.0 Kokkos requires C++17
if(CMAKE_CXX_STANDARD LESS 17)
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
if((OpenMP_CXX_VERSION VERSION_LESS 3.1) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC"))
# 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") 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_MD5 "f140e02b826223b1045207d9bc10d404" CACHE STRING "MD5 checksum of 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 "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

36
cmake/Modules/Packages/KSPACE.cmake
View File

@ -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})

54
cmake/Modules/Packages/LATTE.cmake
View File

@ -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()

4
cmake/Modules/Packages/LEPTON.cmake
View File

@ -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})

38
cmake/Modules/Packages/MDI.cmake
View File

@ -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_MD5 "7a222353ae8e03961d5365e6cd48baee" CACHE STRING "MD5 checksum 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 "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)
if(NOT PYTHON_VERSION_STRING)
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
# 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()
find_package(Python QUIET COMPONENTS Development)
if(Python_Development_FOUND)
set(MDI_USE_PYTHON_PLUGINS ON)
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 ${PYTHON_LIBRARIES})
else()
list(APPEND MDI_DEP_LIBS Python::Python)
endif()
list(APPEND MDI_DEP_LIBS Python::Python)
endif()
# need to add support for dlopen/dlsym, except when compiling for Windows.
if(NOT (CMAKE_SYSTEM_NAME STREQUAL "Windows"))
list(APPEND MDI_DEP_LIBS "${CMAKE_DL_LIBS}")

23
cmake/Modules/Packages/ML-IAP.cmake
View File

@ -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)
else()
# assume we have NumPy
set(Python_NumPy_FOUND ON)
endif()
find_package(Python COMPONENTS NumPy QUIET)
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)
endif()
find_package(Python COMPONENTS NumPy REQUIRED)
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(PYTHONLIBS_VERSION_STRING VERSION_LESS 3.6)
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()
if(Python_VERSION VERSION_LESS 3.6)
message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later")
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)

53
cmake/Modules/Packages/ML-PACE.cmake
View File

@ -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
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()
# LOCAL_ML-PACE points to top-level dir with local lammps-user-pace repo,
# to make it easier to check local build without going through the public github releases
if(LOCAL_ML-PACE)
set(lib-pace "${LOCAL_ML-PACE}")
else()
message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
endif()
# download library sources to build folder
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(
COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
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)
# uncompress downloaded sources
execute_process(
COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
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)
endif()
add_subdirectory(${lib-pace} build-pace)
set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})

28
cmake/Modules/Packages/MSCG.cmake
View File

@ -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})

235
cmake/Modules/Packages/PLUMED.cmake
View File

@ -1,106 +1,169 @@
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)
# Plumed2 support for PLUMED package
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()
if(BUILD_MPI)
set(PLUMED_CONFIG_MPI "--enable-mpi")
set(PLUMED_CONFIG_CC ${CMAKE_MPI_C_COMPILER})
set(PLUMED_CONFIG_CXX ${CMAKE_MPI_CXX_COMPILER})
set(PLUMED_CONFIG_CPP "-I ${MPI_CXX_INCLUDE_PATH}")
set(PLUMED_CONFIG_LIB "${MPI_CXX_LIBRARIES}")
set(PLUMED_CONFIG_DEP "mpi4win_build")
else()
set(PLUMED_CONFIG_MPI "--disable-mpi")
set(PLUMED_CONFIG_CC ${CMAKE_C_COMPILER})
set(PLUMED_CONFIG_CXX ${CMAKE_CXX_COMPILER})
set(PLUMED_CONFIG_CPP "")
set(PLUMED_CONFIG_LIB "")
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(DOWNLOAD_PLUMED_DEFAULT ON)
if(PKG_CONFIG_FOUND)
pkg_check_modules(PLUMED QUIET plumed)
if(PLUMED_FOUND)
set(DOWNLOAD_PLUMED_DEFAULT OFF)
endif()
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")
option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT})
if(DOWNLOAD_PLUMED)
if(BUILD_MPI)
set(PLUMED_CONFIG_MPI "--enable-mpi")
set(PLUMED_CONFIG_CC ${CMAKE_MPI_C_COMPILER})
set(PLUMED_CONFIG_CXX ${CMAKE_MPI_CXX_COMPILER})
mark_as_advanced(PLUMED_URL)
mark_as_advanced(PLUMED_MD5)
GetFallbackURL(PLUMED_URL PLUMED_FALLBACK)
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (CMAKE_CROSSCOMPILING))
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")
set(PLUMED_CONFIG_CC ${CMAKE_C_COMPILER})
set(PLUMED_CONFIG_CXX ${CMAKE_CXX_COMPILER})
message(FATAL_ERROR "Unsupported target system: ${CMAKE_SYSTEM_NAME}/${CMAKE_SYSTEM_PROCESSOR}")
endif()
if(BUILD_OMP)
set(PLUMED_CONFIG_OMP "--enable-openmp")
else()
set(PLUMED_CONFIG_OMP "--disable-openmp")
endif()
message(STATUS "PLUMED download requested - we will build our own")
if(PLUMED_MODE STREQUAL "STATIC")
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${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)
message(STATUS "Downloading and cross-compiling Plumed2 for ${CMAKE_SYSTEM_NAME}/${CMAKE_SYSTEM_PROCESSOR} with ${CROSS_CONFIGURE}")
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}
)
ExternalProject_get_property(plumed_build INSTALL_DIR)
add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
add_dependencies(LAMMPS::PLUMED plumed_build)
if(PLUMED_MODE STREQUAL "STATIC")
set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
elseif(PLUMED_MODE STREQUAL "SHARED")
set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}")
elseif(PLUMED_MODE STREQUAL "RUNTIME")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${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}")
BUILD_BYPRODUCTS ${PLUMED_BUILD_BYPRODUCTS}
)
ExternalProject_get_property(plumed_build INSTALL_DIR)
add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
add_dependencies(LAMMPS::PLUMED plumed_build)
if(PLUMED_MODE STREQUAL "STATIC")
set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
elseif(PLUMED_MODE STREQUAL "SHARED")
set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}")
elseif(PLUMED_MODE STREQUAL "RUNTIME")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${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}")
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)

34
cmake/Modules/Packages/PYTHON.cmake
View File

@ -1,29 +1,11 @@
if(CMAKE_VERSION VERSION_LESS 3.12)
if(NOT PYTHON_VERSION_STRING)
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
# 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()
if(NOT Python_INTERPRETER)
# backward compatibility with CMake before 3.12 and older LAMMPS documentation
if(PYTHON_EXECUTABLE)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
# search for the library matching the selected 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)
find_package(Python COMPONENTS Interpreter)
endif()
find_package(Python REQUIRED COMPONENTS Interpreter Development)
target_link_libraries(lammps PRIVATE Python::Python)
target_compile_definitions(lammps PRIVATE -DLMP_PYTHON)

4
cmake/Modules/StyleHeaderUtils.cmake
View File

@ -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})

46
cmake/Modules/Testing.cmake
View File

@ -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)
if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
AND ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
if(((CMAKE_LINUX_DISTRO STREQUAL "Ubuntu") AND (CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04))
# 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_CXX_COMPILER_ID STREQUAL "GNU") OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
if(((CMAKE_LINUX_DISTRO STREQUAL "Ubuntu") AND
((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 ${CMAKE_CUSTOM_LINKER_DEFAULT} CACHE STRING "Choose a custom linker for faster linking (lld, gold, bfd, default)")
set(CMAKE_CUSTOM_LINKER_VALUES mold lld gold bfd default)
set(CMAKE_CUSTOM_LINKER ${CMAKE_CUSTOM_LINKER_DEFAULT} CACHE STRING "Choose a custom linker for faster linking (mold, lld, gold, bfd, default)")
validate_option(CMAKE_CUSTOM_LINKER CMAKE_CUSTOM_LINKER_VALUES)
mark_as_advanced(CMAKE_CUSTOM_LINKER)
if(NOT "${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)
if(CMAKE_CXX_FLAGS)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage")
endif()
else()
target_compile_options(lammps PUBLIC --coverage)
target_link_options(lammps PUBLIC --coverage)
endif()
target_compile_options(lammps PUBLIC --coverage)
target_link_options(lammps PUBLIC --coverage)
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 (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
if(CMAKE_VERSION VERSION_LESS 3.13)
if(CMAKE_CXX_FLAGS)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
endif()
else()
target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
endif()
target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
else()
message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.")
set(ENABLE_SANITIZER "none")

17
cmake/Modules/Tools.cmake
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@ -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()

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34
cmake/packaging/MacOSXBundleInfo.plist.in Normal file
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@ -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>

69
cmake/packaging/README.macos Normal file
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@ -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.

77
cmake/packaging/build_linux_tgz.sh Executable file
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@ -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

111
cmake/packaging/build_macos_dmg.sh Executable file
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@ -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

64
cmake/packaging/build_windows_cross_zip.sh Executable file
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@ -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

35
cmake/packaging/build_windows_vs.cmake Normal file
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@ -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)

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cmake/packaging/linux_wrapper.sh Executable file
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@ -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/${EXENAME}" "$@"

30
cmake/packaging/png2iconset.sh Executable file
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@ -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

3
cmake/presets/all_off.cmake
View File

@ -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

3
cmake/presets/all_on.cmake
View File

@ -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

4
cmake/presets/download.cmake
View File

@ -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)

11
cmake/presets/gpu-cuda.cmake Normal file
View File

@ -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)

2
cmake/presets/kokkos-cuda.cmake
View File

@ -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)

12
cmake/presets/macos-multiarch.cmake Normal file
View File

@ -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)

2
cmake/presets/mingw-cross.cmake
View File

@ -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()

2
cmake/presets/most.cmake
View File

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

3
cmake/presets/nolib.cmake
View File

@ -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

2
cmake/presets/windows.cmake
View File

@ -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

4
doc/Makefile
View File

@ -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
@(\

4
doc/lammps.1
View File

@ -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

5
doc/src/Bibliography.rst
View File

@ -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)

21
doc/src/Build_basics.rst
View File

@ -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``,
``ML-SNAP``, ``DIFFRACTION``, and ``DPD-REACT`` packages. Furthermore,
some packages support OpenMP threading indirectly through the libraries
they interface to: e.g. ``LATTE``, ``KSPACE``, and ``COLVARS``. See the
:doc:`Packages details <Packages_details>` page for more info on these
packages, and the pages for their respective commands for OpenMP
threading info.
support included as well. These are commands in the ``ML-SNAP``,
``DIFFRACTION``, and ``DPD-REACT`` packages. Furthermore, some packages
support OpenMP threading indirectly through the libraries they interface
to: e.g. ``KSPACE``, and ``COLVARS``. See the :doc:`Packages details
<Packages_details>` page for more info on these packages, and the pages
for their respective commands for OpenMP threading info.
For CMake, if you use ``BUILD_OMP=yes``, you can use these packages
and turn on their native OpenMP support and turn on their native OpenMP
@ -489,8 +488,9 @@ using CMake or Make.
.. code-block:: bash
-D BUILD_TOOLS=value # yes or no (default)
-D BUILD_LAMMPS_SHELL=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). 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

30
doc/src/Build_cmake.rst
View File

@ -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;
version 3.12 or later is preferred.
LAMMPS currently requires that CMake version 3.16 or later is available.
.. 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
addition to LAMMPS thanks to the efforts of Christoph Junghans (LANL)
and Richard Berger (Temple U). Using CMake has multiple advantages that
are specifically helpful for people with limited experience in compiling
software or for people that want to modify or extend LAMMPS.
through :doc:`(manually customized) makefiles <Build_make>`. Using
CMake has multiple advantages that are specifically helpful for
people with limited experience in compiling software or for people
that want to modify or extend LAMMPS.
- CMake can detect available hardware, tools, features, and libraries
and adapt the LAMMPS default build configuration accordingly.
- CMake can generate files for different build tools and integrated
development environments (IDE).
- CMake supports customization of settings with a command line, text
mode, or graphical user interface. No knowledge of file formats or
complex command line syntax is required.
mode, or graphical user interface. No manual editing of files,
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
multi-config build system, but not all of it has been ported. This is in
particular applicable to compiling packages that require additional libraries
that would be downloaded and compiled by CMake. The "windows" preset file
tries to keep track of which packages can be compiled natively with the
MSVC compilers out-of-the box. Not all of those external libraries are
portable to Windows, either.
The CMake scripts in LAMMPS have basic support for being compiled using
a multi-config build system, but not all of it has been ported. This is
in particular applicable to compiling packages that require additional
libraries that would be downloaded and compiled by CMake. The
``windows.cmake`` preset file tries to keep track of which packages can
be compiled natively with the MSVC compilers out-of-the box. Not all of
the external libraries are portable to Windows, either.
Installing CMake

45
doc/src/Build_development.rst
View File

@ -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
``test_angle_style`` are implemented. They will compare forces, energies and
(global) stress for all atoms after a ``run 0`` calculation and after a
few steps of MD with :doc:`fix nve <fix_nve>`, each in multiple variants
with different settings and also for multiple accelerated styles. If a
prerequisite style or package is missing, the individual tests are
skipped. All tests will be executed on a single MPI process, so using
the CMake option ``-D BUILD_MPI=off`` can significantly speed up testing,
since this will skip the MPI initialization for each test run.
Below is an example command and output:
suffix. Currently the programs ``test_pair_style``, ``test_bond_style``,
``test_angle_style``, ``test_dihedral_style``, and
``test_improper_style`` are implemented. They will compare forces,
energies and (global) stress for all atoms after a ``run 0`` calculation
and after a few steps of MD with :doc:`fix nve <fix_nve>`, each in
multiple variants with different settings and also for multiple
accelerated styles. If a prerequisite style or package is missing, the
individual tests are skipped. All force style tests will be executed on
a single MPI process, so using the CMake option ``-D BUILD_MPI=off`` can
significantly speed up testing, since this will skip the MPI
initialization for each test run. Below is an example command and
output:
.. 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
or the ``gold`` linker available with GNU binutils can speed up this step
substantially. CMake will by default test if any of the two can be
enabled and use it when ``ENABLE_TESTING`` is active. It can also be
selected manually through the ``CMAKE_CUSTOM_LINKER`` CMake variable.
Allowed values are ``lld``, ``gold``, ``bfd``, or ``default``. The
``default`` option will use the system default linker otherwise, the
linker is chosen explicitly. This option is only available for the
GNU or Clang C++ compiler.
Linux systems). Alternatives like the ``mold`` linker, the ``lld``
linker of the LLVM project, or the ``gold`` linker available with GNU
binutils can speed up this step substantially (in this order). CMake
will by default test if any of the three can be enabled and use it when
``ENABLE_TESTING`` is active. It can also be selected manually through
the ``CMAKE_CUSTOM_LINKER`` CMake variable. Allowed values are
``mold``, ``lld``, ``gold``, ``bfd``, or ``default``. The ``default``
option will use the system default linker otherwise, the linker is
chosen explicitly. This option is only available for the GNU or Clang
C++ 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
--------------------

418
doc/src/Build_extras.rst
View File

@ -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
to include support for **all** major GPU architectures supported by this toolkit.
Thus the GPU_ARCH setting is merely an optimization, to have code for
the preferred GPU architecture directly included rather than having to wait
for the JIT compiler of the CUDA driver to translate it.
CMake can detect which version of the CUDA toolkit is used and thus will
try to include support for **all** major GPU architectures supported by
this toolkit. Thus the GPU_ARCH setting is merely an optimization, to
have code for the preferred GPU architecture directly included rather
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
is required and a GPU architecture of Kepler or later, which must *also* be
supported by the CUDA toolkit in use **and** the CUDA driver in use.
When compiling for OpenCL, OpenCL version 1.2 or later is required and the
GPU must be supported by the GPU driver and OpenCL runtime bundled with the driver.
When compiling for CUDA or HIP with CUDA, version 8.0 or later of the
CUDA toolkit is required and a GPU architecture of Kepler or later,
which must *also* be supported by the CUDA toolkit in use **and** the
CUDA driver in use. When compiling for OpenCL, OpenCL version 1.2 or
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``
using the traditional build procedure. CMake will detect files generated by that
process and will terminate with an error and a suggestion for how to remove them.
When building with CMake, you **must NOT** build the GPU library in
``lib/gpu`` using the traditional build procedure. CMake will detect
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
link with a static OpenCL ICD loader library and standard OpenCL headers. This
way no local OpenCL development headers or library needs to be present and only
OpenCL compatible drivers need to be installed to use OpenCL. If this is not
desired, you can set :code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
If you are compiling for OpenCL, the default setting is to download,
build, and link with a static OpenCL ICD loader library and standard
OpenCL headers. This way no local OpenCL development headers or library
needs to be present and only OpenCL compatible drivers need to be
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
with ``-D BUILD_OMP=on`` this will also be enabled.
The GPU library has some multi-thread support using OpenMP. If LAMMPS
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
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`
and the linker to work correctly.
If you are compiling with HIP, note that before running CMake you will
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` and the linker to work correctly.
Using CHIP-SPV implementation of HIP is now supported. It allows one to run HIP
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
yet support hipCUB. The use of HIP for Intel GPUs is still experimental so you
should only use this option in preparations to run on Aurora system at ANL.
.. versionadded:: 3Aug2022
Using the CHIP-SPV implementation of HIP is supported. It allows one to
run HIP 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 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
* - VEGA906
- AMD GPU MI50/MI60
* - AMD_GFX908
- GPU
- AMD GPU MI50/MI60 GFX906
* - VEGA908
- AMD GPU MI100
* - AMD_GFX90A
- GPU
- AMD GPU MI100 GFX908
* - VEGA90A
- AMD GPU MI200
* - 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
``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
can identify its location.
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
with CUDA device parallelization (for GPUs with CC 5.0 and up)
with some common packages enabled, you can do the following:
the KOKKOS package and enable some hardware choices. For GPU
support those preset files must be customized to match the
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
script. But on some systems this may cause problems when linking
or the dependency is not desired. Try enabling
can identify their locations and pass that info to the ELECTRODE
build script. But on some systems this may cause problems when
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

4
doc/src/Build_make.rst
View File

@ -117,8 +117,8 @@ their settings may become outdated, too:
.. code-block:: bash
make mac # build serial LAMMPS on a Mac
make mac_mpi # build parallel LAMMPS on a Mac
make mac # build serial LAMMPS on macOS
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

8
doc/src/Build_manual.rst
View File

@ -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
download additional files and tools are required. This download is
usually only required once or after the documentation folder is returned
to a pristine state with ``make clean-all``.
Python interpreter version 3.8 or later, the ``doxygen`` tools and
internet access to download additional files and tools are required.
This download is usually only required once or after the documentation
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

3
doc/src/Build_package.rst
View File

@ -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

73
doc/src/Build_settings.rst
View File

@ -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.
With this option enabled, LAMMPS errors do not kill the calling code.
Instead, the call stack is unwound and control returns to the caller,
e.g. to Python. Of course, the calling code has to be set up to
*catch* exceptions 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>
LAMMPS errors do not kill the calling code, but throw an exception. In
the C-library interface, the call stack is unwound and control returns
to the caller, e.g. to Python or a code that is coupled to LAMMPS. The
error status can then be queried. When using C++ directly, the calling
code has to be set up to *catch* exceptions thrown from within LAMMPS.
.. note::

14
doc/src/Commands_compute.rst
View File

@ -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/cylinder <compute_stress_profile>`
* :doc:`stress/cartesian <compute_stress_cartesian>`
* :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>`

4
doc/src/Commands_dump.rst
View File

@ -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>`

16
doc/src/Commands_fix.rst
View File

@ -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>`

28
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@ -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>`

54
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@ -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
-----------------

1
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@ -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

88
doc/src/Developer_atom.rst Normal file
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@ -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.

4
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@ -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
value per grid cell. The two that end in "_multi" allocate an array
two methods that end in "_offset" allocate an array which stores a single
value per grid cell. The two that end in "_last" allocate an array
which stores *Nvalues* per grid cell.
.. code-block:: c++

2
doc/src/Developer_notes.rst
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@ -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
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

155
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@ -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
situations where LAMMPS will stop with an error, i.e. handle so-called
"death tests". Here the LAMMPS code will operate differently depending
on whether it was configured to throw C++ exceptions on errors or call
either ``exit()`` or ``MPI_Abort()``. In the latter case, the test code
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:
The specifics of so-called "death tests", i.e. conditions where LAMMPS
should fail and throw an exception, 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
unit tests is incomplete since the Fortran module it is based on is
incomplete as well.
turn call the functions in the LAMMPS Fortran module.
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
these tests the relative error (epsilon) is lowered by a common factor
due to the additional numerical noise, but the tests are still comparing
to the same reference data.
INTEL, KOKKOS (OpenMP only)) and for the latter three with 4 OpenMP
threads enabled. For these tests the relative error (epsilon) is lowered
by a common factor due to the additional numerical noise, but the tests
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
fashion and share support functions with the pair style tester. The final
group of tests in this section is for fix styles that add/manipulate forces
and velocities, e.g. for time integration, thermostats and more.
The ``test_bond_style``, ``test_angle_style``, ``test_dihedral_style``, and
``test_improper_style`` tester programs are set up in a similar fashion and
share support functions with the pair style tester. The final group of
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
for a style that is similar to one to be tested. The file name should follow
the naming conventions described above and after copying the file, the first
step is to replace the style names where needed. The coefficient values
do not have to be meaningful, just in a reasonable range for the given system.
It does not matter if some forces are large, for as long as they do not diverge.
Adding a new test is easiest done by copying and modifying an existing YAML
file for a style that is similar to one to be tested. The file name should
follow the naming conventions described above and after copying the file,
the first step is to replace the style names where needed. The coefficient
values do not have to be meaningful, just in a reasonable range for the
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.

2
doc/src/Developer_updating.rst
View File

@ -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

249
doc/src/Developer_write.rst
View File

@ -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
implement many things using fixes:
- 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
.. toctree::
:maxdepth: 1
Developer_write_pair
Developer_write_fix

245
doc/src/Developer_write_fix.rst Normal file
View File

@ -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

1354
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File diff suppressed because it is too large Load Diff

6
doc/src/Errors_messages.rst
View File

@ -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.

4
doc/src/Examples.rst
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@ -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 |

237
doc/src/Fortran.rst
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@ -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
USE LIBLAMMPS
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int64_t
USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT
TYPE(lammps) :: lmp
INTEGER(KIND=c_int64_t), POINTER :: natoms
REAL(KIND=c_double), POINTER :: dt
INTEGER(KIND=c_int64_t), POINTER :: ntimestep
REAL(KIND=c_double) :: pe, ke
PROGRAM testprop
USE LIBLAMMPS
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int64_t, c_int
USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT
TYPE(lammps) :: lmp
INTEGER(KIND=c_int64_t), POINTER :: natoms, ntimestep, bval
REAL(KIND=c_double), POINTER :: dt, dval
INTEGER(KIND=c_int), POINTER :: nfield, typ, ival
INTEGER(KIND=c_int) :: i
CHARACTER(LEN=11) :: key
REAL(KIND=c_double) :: pe, ke
lmp = lammps()
CALL lmp%file('in.sysinit')
natoms = lmp%extract_global('natoms')
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'), &
' local and ', lmp%extract_setting('nghost'), ' ghost atoms. ', &
lmp%extract_setting('ntypes'), ' atom types'
lmp = lammps()
CALL lmp%file('in.sysinit')
natoms = lmp%extract_global('natoms')
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'), &
' local and ', lmp%extract_setting('nghost'), ' ghost atoms. ', &
lmp%extract_setting('ntypes'), ' atom types'
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')
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')
PRINT*, 'PE = ', pe
PRINT*, 'KE = ', ke
ntimestep = lmp%last_thermo('step', 0)
nfield = lmp%last_thermo('num', 0)
WRITE(OUTPUT_UNIT,'(A,I0,A,I0)') '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)
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.)
END PROGRAM testprop
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
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
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,
but you can automatically reallocate it to the correct length after the
If :f:func:`extract_global` 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, 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.
The latter has to be :ref:`enabled at compile time <exceptions>`.
This function checks if exceptions were enabled.
When using the library interface with C++ exceptions enabled, the library
interface functions will "catch" them, and the error status can then be
checked by calling :f:func:`has_error`. The most recent error message can be
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.
When using the library interface, the library interface functions
will "catch" exceptions, and then the error status can be checked by
calling :f:func:`has_error`. The most recent error message can be
retrieved via :f:func:`get_last_error_message`. This allows 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`.
: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.

4
doc/src/Howto.rst
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@ -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

4
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@ -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

8
doc/src/Howto_body.rst
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@ -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
squares with rounded circles at the vertices. Special cases for N = 1
(circle) and N = 2 (rod with rounded ends) can also be specified.
:doc:`pair_style body/rounded/polygon <pair_body_rounded_polygon>` page for
a diagram of two squares with rounded circles at the vertices. Special cases
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

18
doc/src/Howto_bpm.rst
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@ -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*
keyword present in all bpm bond styles and by using the following special
bond settings
feel pair interactions. This can be accomplished by setting the *overlay/pair*
keyword present in all bpm bond styles to *yes* and requires using the
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

78
doc/src/Howto_broken_bonds.rst
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@ -1,48 +1,56 @@
Broken Bonds
============
Typically, bond interactions persist for the duration of a simulation in
LAMMPS. However, there are some exceptions that allow for bonds to
break, including the :doc:`quartic bond style <bond_quartic>` and the
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.
Typically, molecular bond interactions persist for the duration of a
simulation in LAMMPS. However, some commands break bonds dynamically,
including the following:
Users are normally able to weight the contribution of pair forces to atoms
that are bonded using the :doc:`special_bonds command <special_bonds>`.
When bonds break, this is not always the case. For the quartic bond style,
pair forces are always turned off between bonded particles. LAMMPS does
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.
* :doc:`bond_style quartic <bond_quartic>`
* :doc:`fix bond/break <fix_bond_break>`
* :doc:`fix bond/react <fix_bond_react>`
* :doc:`BPM package <Howto_bpm>` bond styles
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.
A bond can break if it is stretched beyond a user-defined threshold or
more generally if other criteria are met.
Bonds can also be broken by fixes which change bond topology, including
:doc:`fix bond/break <fix_bond_break>` and
:doc:`fix bond/react <fix_bond_react>`. These fixes will automatically
trigger a rebuild of the neighbor list and update special bond data structures
when bonds are broken.
For the quartic bond style, when a bond is broken its bond type is set
to 0 to effectively break it and pairwise forces between the two atoms
in the broken bond are "turned on". Angles, dihedrals, etc cannot be
defined for a system when :doc:`bond_style quartic <bond_quartic>` is
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
:doc:`delete_bonds <delete_bonds>` command can also be used to query the
status of broken bonds or permanently delete them, e.g.:
Similarly, bond styles in the BPM package are also incompatible with
angles, dihedrals, etc. and when a bond breaks its type is set to zero.
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
to tally the current number of bonds per atom, excluding broken bonds.
The compute :doc:`count/type <compute_count_type>` command tallies the
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.

41
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@ -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
tied to a specific platform or build system and thus generate the files
necessary to build and develop for different build systems and on
Berger (LANL). One of the key strengths of CMake is that it is not
tied to a specific platform or build system. Instead it generates the
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
later is recommended).
interchangeably. As of LAMMPS version 2 August 2023, the minimum
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
- macOS: launch the Terminal application.
- Windows 10: install and run the :doc:`Windows Subsystem for Linux <Howto_wsl>`
- Linux: any Terminal window will work or text console
- macOS: launch the Terminal application
- 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,
as they will trigger a reset of cached internal CMake settings and thus
reset settings to their default values.
are an exception to the mechanism of updating the configuration
incrementally, as they will trigger a reset of cached internal CMake
settings and thus reset settings to their default values.
Compilation and build targets
-----------------------------

18
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@ -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
this scenario, LAMMPS is the driver code. During timestepping, the
fix is invoked, and can make library calls to the other code, which
has been linked to LAMMPS as a library. This is the way the
:ref:`LATTE <PKG-LATTE>` package, which performs density-functional
tight-binding calculations using the `LATTE software
<https://github.com/lanl/LATTE>`_ to compute forces, is interfaced to
LAMMPS. See the :doc:`fix latte <fix_latte>` command for more
1. Define a new :doc:`fix <fix>` or :doc:`compute <compute>` command
that calls the other code. In this scenario, LAMMPS is the driver
code. During timestepping, the fix or compute is invoked, and can
make library calls to the other code, which has been linked to LAMMPS
as a library. This is the way the :ref:`VORONOI <PKG-VORONOI>`
package, which computes Voronoi tesselations using the `Voro++
library <http://math.lbl.gov/voro++>`_, is interfaced to LAMMPS. See
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

700
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@ -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.

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