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Merge pull request #86 from lammps/master

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rebase
This commit is contained in:
Jacob Gissinger
2020-06-26 22:26:40 -06:00
committed by GitHub
parent 2fb71cfb62 51174d4ad1
commit fa17ba7a8f
2202 changed files with 932735 additions and 2069196 deletions
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13
.github/CODEOWNERS vendored
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@ -10,6 +10,7 @@ lib/molfile/* @akohlmey
lib/qmmm/* @akohlmey
lib/vtk/* @rbberger
lib/kim/* @ellio167
lib/mesont/* @iafoss
# whole packages
src/COMPRESS/* @akohlmey
@ -25,6 +26,7 @@ src/USER-COLVARS/* @giacomofiorin
src/USER-INTEL/* @wmbrownintel
src/USER-MANIFOLD/* @Pakketeretet2
src/USER-MEAMC/* @martok
src/USER-MESONT/* @iafoss
src/USER-MOFFF/* @hheenen
src/USER-MOLFILE/* @akohlmey
src/USER-NETCDF/* @pastewka
@ -45,7 +47,7 @@ src/GPU/pair_vashishta_gpu.* @andeplane
src/KOKKOS/pair_vashishta_kokkos.* @andeplane
src/MANYBODY/pair_vashishta_table.* @andeplane
src/MANYBODY/pair_atm.* @sergeylishchuk
src/USER-MISC/fix_bond_react.* @jrgissing
src/USER-REACTION/fix_bond_react.* @jrgissing
src/USER-MISC/*_grem.* @dstelter92
src/USER-MISC/compute_stress_mop*.* @RomainVermorel
@ -111,14 +113,23 @@ src/fix_nh.* @athomps
src/info.* @akohlmey @rbberger
src/timer.* @akohlmey
src/min* @sjplimp @stanmoore1
src/utils.* @akohlmey @rbberger
# tools
tools/msi2lmp/* @akohlmey
tools/emacs/* @HaoZeke
tools/singularity/* @akohlmey @rbberger
tools/code_standard/* @rbberger
tools/valgrind/* @akohlmey
# tests
unittest/* @akohlmey @rbberger
# cmake
cmake/* @junghans @rbberger
cmake/Modules/Packages/USER-COLVARS.cmake @junghans @rbberger @giacomofiorin
cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
cmake/presets/*.cmake @junghans @rbberger @akohlmey
# python
python/* @rbberger

4
.github/CONTRIBUTING.md vendored
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@ -75,7 +75,9 @@ Here is a checklist of steps you need to follow to submit a single file or user
* Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code.
* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). The text files can include mathematical expressions and symbol in ".. math::" sections or ":math:" expressions or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html`, `make pdf` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file. For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`.
* For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/USER for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind
* If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the *.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide.
* For new utility functions or class (i.e. anything that does not depend on a LAMMPS object), new unit tests should be added to the unittest tree.
* When adding a new LAMMPS style, a .yaml file with a test configuration and reference data should be added for the styles where a suitable tester program already exists (e.g. pair styles, bond styles, etc.).
* If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the <name>.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide.
Finally, as a general rule-of-thumb, the more clear and self-explanatory you make your documentation and README files, and the easier you make it for people to get started, e.g. by providing example scripts, the more likely it is that users will try out your new feature.

12
.github/ISSUE_TEMPLATE/bug_report.md vendored
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@ -9,24 +9,24 @@ assignees: ''
**Summary**
_Please provide a clear and concise description of what the bug is._
<!--Please provide a clear and concise description of what the bug is.-->
**LAMMPS Version and Platform**
_Please specify precisely which LAMMPS version this issue was detected with (the first line of the output) and what platform (operating system and its version, hardware) you are running on. If possible, test with the most recent LAMMPS patch version_
<!--Please specify precisely which LAMMPS version this issue was detected with (the first line of the output) and what platform (operating system and its version, hardware) you are running on. If possible, test with the most recent LAMMPS patch version-->
**Expected Behavior**
_Describe the expected behavior. Quote from the LAMMPS manual where needed, or explain why the expected behavior is meaningful, especially when it differs from the manual_
<!--Describe the expected behavior. Quote from the LAMMPS manual where needed, or explain why the expected behavior is meaningful, especially when it differs from the manual-->
**Actual Behavior**
_Describe the actual behavior, how it differs from the expected behavior, and how this can be observed. Try to be specific and do **not** use vague terms like "doesn't work" or "wrong result". Do not assume that the person reading this has any experience with or knowledge of your specific area of research._
<!--Describe the actual behavior, how it differs from the expected behavior, and how this can be observed. Try to be specific and do **not** use vague terms like "doesn't work" or "wrong result". Do not assume that the person reading this has any experience with or knowledge of your specific area of research.-->
**Steps to Reproduce**
_Describe the steps required to (quickly) reproduce the issue. You can attach (small) files to the section below or add URLs where to download an archive with all necessary files. Please try to create an input set that is as minimal and small as possible and reproduces the bug as quickly as possible. **NOTE:** the less effort and time it takes to reproduce your reported bug, the more likely it becomes, that somebody will look into it and fix the problem._
<!--Describe the steps required to (quickly) reproduce the issue. You can attach (small) files to the section below or add URLs where to download an archive with all necessary files. Please try to create an input set that is as minimal and small as possible and reproduces the bug as quickly as possible. **NOTE:** the less effort and time it takes to reproduce your reported bug, the more likely it becomes, that somebody will look into it and fix the problem.-->
**Further Information, Files, and Links**
_Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications_
<!--Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications-->

6
.github/ISSUE_TEMPLATE/feature_request.md vendored
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@ -9,12 +9,12 @@ assignees: ''
**Summary**
_Please provide a brief and concise description of the suggested feature or change_
<!--Please provide a brief and concise description of the suggested feature or change-->
**Detailed Description**
_Please explain how you would like to see LAMMPS enhanced, what feature(s) you are looking for, what specific problems this will solve. If possible, provide references to relevant background information like publications or web pages, and whether you are planning to implement the enhancement yourself or would like to participate in the implementation. If applicable add a reference to an existing bug report or issue that this will address._
<!--Please explain how you would like to see LAMMPS enhanced, what feature(s) you are looking for, what specific problems this will solve. If possible, provide references to relevant background information like publications or web pages, and whether you are planning to implement the enhancement yourself or would like to participate in the implementation. If applicable add a reference to an existing bug report or issue that this will address.-->
**Further Information, Files, and Links**
_Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications_
<!--Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications-->

6
.github/ISSUE_TEMPLATE/generic.md vendored
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@ -9,13 +9,13 @@ assignees: ''
**Summary**
_Please provide a clear and concise description of what this issue report is about._
<!--Please provide a clear and concise description of what this issue report is about.-->
**LAMMPS Version and Platform**
_Please specify precisely which LAMMPS version this issue was detected with (the first line of the output) and what platform (operating system and its version, hardware) you are running on. If possible, test with the most recent LAMMPS patch version_
<!--Please specify precisely which LAMMPS version this issue was detected with (the first line of the output) and what platform (operating system and its version, hardware) you are running on. If possible, test with the most recent LAMMPS patch version-->
**Details**
_Please explain the issue in detail here_
<!--Please explain the issue in detail here-->

15
.github/PULL_REQUEST_TEMPLATE.md vendored
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@ -1,14 +1,14 @@
**Summary**
_Briefly describe the new feature(s), enhancement(s), or bugfix(es) included in this pull request._
<!--Briefly describe the new feature(s), enhancement(s), or bugfix(es) included in this pull request.-->
**Related Issues**
_If this addresses an open GitHub issue for this project, please mention the issue number here, and describe the relation. Use the phrases `fixes #221` or `closes #135`, when you want an issue to be automatically closed when the pull request is merged_
<!--If this addresses an open GitHub issue for this project, please mention the issue number here, and describe the relation. Use the phrases `fixes #221` or `closes #135`, when you want an issue to be automatically closed when the pull request is merged-->
**Author(s)**
_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request. If this pull request adds new files to the distribution, please also provide a suitable "long-lived" e-mail address (ideally something that can outlive your institution's e-mail, in case you change jobs) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this contributed code._
<!--Please state name and affiliation of the author or authors that should be credited with the changes in this pull request. If this pull request adds new files to the distribution, please also provide a suitable "long-lived" e-mail address (ideally something that can outlive your institution's e-mail, in case you change jobs) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this contributed code.-->
**Licensing**
@ -16,15 +16,15 @@ By submitting this pull request, I agree, that my contribution will be included
**Backward Compatibility**
_Please state whether any changes in the pull request will break backward compatibility for inputs, and - if yes - explain what has been changed and why_
<!--Please state whether any changes in the pull request will break backward compatibility for inputs, and - if yes - explain what has been changed and why-->
**Implementation Notes**
_Provide any relevant details about how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected_
<!--Provide any relevant details about how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected-->
**Post Submission Checklist**
_Please check the fields below as they are completed **after** the pull request has been submitted. Delete lines that don't apply_
<!--Please check the fields below as they are completed **after** the pull request has been submitted. Delete lines that don't apply-->
- [ ] The feature or features in this pull request is complete
- [ ] Licensing information is complete
@ -34,11 +34,12 @@ _Please check the fields below as they are completed **after** the pull request
- [ ] The added/updated documentation is integrated and tested with the documentation build system
- [ ] The feature has been verified to work with the conventional build system
- [ ] The feature has been verified to work with the CMake based build system
- [ ] Suitable tests have been added to the unittest tree.
- [ ] A package specific README file has been included or updated
- [ ] One or more example input decks are included
**Further Information, Files, and Links**
_Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)_
<!--Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)-->

14
.github/PULL_REQUEST_TEMPLATE/bug_fix.md vendored
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@ -9,15 +9,15 @@ assignees: ''
**Summary**
_Briefly describe the bug or bugs, that are eliminated by this pull request._
<!--Briefly describe the bug or bugs, that are eliminated by this pull request.-->
**Related Issue(s)**
_If this request addresses or is related to an existing (open) GitHub issue, e.g. a bug report, mention the issue number number here following a pound sign (aka hashmark), e.g.`#222`._
<!--If this request addresses or is related to an existing (open) GitHub issue, e.g. a bug report, mention the issue number number here following a pound sign (aka hashmark), e.g.`#222`.-->
**Author(s)**
_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request_
<!--Please state name and affiliation of the author or authors that should be credited with the changes in this pull request-->
**Licensing**
@ -25,18 +25,18 @@ By submitting this pull request I implicitly accept, that my submission is subje
**Backward Compatibility**
_Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why_
<!--Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why-->
**Detailed Description**
_Provide any relevant details about how the fixed bug can be reproduced, how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected_
<!--Provide any relevant details about how the fixed bug can be reproduced, how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected-->
## Post Submission Checklist
_Please check the fields below as they are completed *after* the pull request is submitted_
<!--Please check the fields below as they are completed *after* the pull request is submitted-->
- [ ] The code in this pull request is complete
- [ ] The source code follows the LAMMPS formatting guidelines
## Further Information, Files, and Links
_Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. to download input decks for testing)_
<!--Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. to download input decks for testing)-->

10
.github/PULL_REQUEST_TEMPLATE/maintenance_refactoring.md vendored
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@ -9,15 +9,15 @@ assignees: ''
**Summary**
_Briefly describe the included changes._
<!--Briefly describe the included changes.-->
**Related Issue(s)**
_If this request addresses or is related to an existing (open) GitHub issue, e.g. a bug report, mention the issue number number here following a pound sign (aka hashmark), e.g.`#222`.
<!--If this request addresses or is related to an existing (open) GitHub issue, e.g. a bug report, mention the issue number number here following a pound sign (aka hashmark), e.g.`#222`.
**Author(s)**
_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request_
<!--Please state name and affiliation of the author or authors that should be credited with the changes in this pull request-->
**Licensing**
@ -25,11 +25,11 @@ By submitting this pull request I implicitly accept, that my submission is subje
**Detailed Description**
_Provide any relevant details about the included changes._
<!--Provide any relevant details about the included changes.-->
## Post Submission Checklist
_Please check the fields below as they are completed *after* the pull request is submitted_
<!--Please check the fields below as they are completed *after* the pull request is submitted-->
- [ ] The pull request is complete
- [ ] The source code follows the LAMMPS formatting guidelines

16
.github/PULL_REQUEST_TEMPLATE/new_feature.md vendored
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@ -9,34 +9,34 @@ assignees: ''
**Summary**
_Briefly describe the new feature(s) included in this pull request._
<!--Briefly describe the new feature(s) included in this pull request.-->
**Related Issues**
_If this addresses an existing (open) GitHub issue, e.g. a feature request, mention the issue number here following a pound sign (aka hashmark), e.g. `#331`._
<!--If this addresses an existing (open) GitHub issue, e.g. a feature request, mention the issue number here following a pound sign (aka hashmark), e.g. `#331`.-->
**Author(s)**
_Please state name and affiliation of the author or authors that should be credited with the features added in this pull request. Please provide a suitable "long-lived" e-mail address (e.g. from gmail, yahoo, outlook, etc.) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this code. now and in the future_
<!--Please state name and affiliation of the author or authors that should be credited with the features added in this pull request. Please provide a suitable "long-lived" e-mail address (e.g. from gmail, yahoo, outlook, etc.) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this code. now and in the future-->
**Licensing**
_Please add *yes* or *no* to the following two statements (please contact @lammps/core if you have questions about this)_
<!--Please add *yes* or *no* to the following two statements (please contact @lammps/core if you have questions about this)-->
My contribution may be licensed as GPL v2 (default LAMMPS license):
My contribution may be licensed as LGPL (for use as a library with proprietary software):
**Backward Compatibility**
_Please state if any of the changes in this pull request will affect backward compatibility for inputs, and - if yes - explain what has been changed and why_
<!--Please state if any of the changes in this pull request will affect backward compatibility for inputs, and - if yes - explain what has been changed and why-->
**Implementation Notes**
_Provide any relevant details about how the new features are implemented, how correctness was verified, what platforms (OS, compiler, MPI, hardware, number of processors, accelerator(s)) it was tested on_
<!--Provide any relevant details about how the new features are implemented, how correctness was verified, what platforms (OS, compiler, MPI, hardware, number of processors, accelerator(s)) it was tested on-->
## Post Submission Checklist
_Please check the fields below as they are completed *after* the pull request has been submitted_
<!--Please check the fields below as they are completed *after* the pull request has been submitted-->
- [ ] The feature or features in this pull request is complete
- [ ] Licensing information is complete
@ -51,6 +51,6 @@ _Please check the fields below as they are completed *after* the pull request ha
## Further Information, Files, and Links
_Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)_
<!--Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)-->

12
.github/PULL_REQUEST_TEMPLATE/update_enhancement.md vendored
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@ -9,11 +9,11 @@ assignees: ''
**Summary**
_Briefly describe what kind of updates or enhancements for a package or feature are included. If you are not the original author of the package or feature, please mention, whether your contribution was created independently or in collaboration/cooperation with the original author._
<!--Briefly describe what kind of updates or enhancements for a package or feature are included. If you are not the original author of the package or feature, please mention, whether your contribution was created independently or in collaboration/cooperation with the original author.-->
**Author(s)**
_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request_
<!--Please state name and affiliation of the author or authors that should be credited with the changes in this pull request-->
**Licensing**
@ -21,15 +21,15 @@ By submitting this pull request I implicitly accept, that my submission is subje
**Backward Compatibility**
_Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why_
<!--Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why-->
**Implementation Notes**
_Provide any relevant details about how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected_
<!--Provide any relevant details about how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected-->
**Post Submission Checklist**
_Please check the fields below as they are completed_
<!--Please check the fields below as they are completed-->
- [ ] The feature or features in this pull request is complete
- [ ] Suitable updates to the existing docs are included
- [ ] One or more example input decks are included
@ -37,6 +37,6 @@ _Please check the fields below as they are completed_
**Further Information, Files, and Links**
_Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)_
<!--Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)-->

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

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

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

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

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

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

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

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

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bench/POTENTIALS/Ni.meam
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rc = 4.0
delr = 0.1

1
bench/POTENTIALS/Ni.meam Symbolic link
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../../potentials/Ni.meam

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

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bench/POTENTIALS/Si.sw Symbolic link
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../../potentials/Si.sw

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

1
bench/POTENTIALS/Si.tersoff Symbolic link
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../../potentials/Si.tersoff

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

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

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

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bench/POTENTIALS/library.meam Symbolic link
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../../potentials/library.meam

84
bench/POTENTIALS/log.16Mar18.meam.1
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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# bulk Ni in MEAM
units metal
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.00186539 secs
pair_style meam
WARNING: The pair_style meam command is unsupported. Please use pair_style meam/c instead (../pair_meam.cpp:51)
pair_coeff * * library.meam Ni4 Ni.meam Ni4
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.005
thermo 50
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5
ghost atom cutoff = 5
binsize = 2.5, bins = 29 29 29
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 55.91 | 55.91 | 55.91 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -142400 0 -135782.09 20259.18
50 885.10702 -139411.51 0 -135750.54 32425.433
100 895.5097 -139454.3 0 -135750.3 31804.187
Loop time of 30.6278 on 1 procs for 100 steps with 32000 atoms
Performance: 1.410 ns/day, 17.015 hours/ns, 3.265 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 30.088 | 30.088 | 30.088 | 0.0 | 98.24
Neigh | 0.48914 | 0.48914 | 0.48914 | 0.0 | 1.60
Comm | 0.015916 | 0.015916 | 0.015916 | 0.0 | 0.05
Output | 0.00022554 | 0.00022554 | 0.00022554 | 0.0 | 0.00
Modify | 0.025481 | 0.025481 | 0.025481 | 0.0 | 0.08
Other | | 0.009055 | | | 0.03
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 13576 ave 13576 max 13576 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 780360 ave 780360 max 780360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.56072e+06 ave 1.56072e+06 max 1.56072e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1560720
Ave neighs/atom = 48.7725
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:30

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bench/POTENTIALS/log.16Mar18.meam.4
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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# bulk Ni in MEAM
units metal
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.000587463 secs
pair_style meam
WARNING: The pair_style meam command is unsupported. Please use pair_style meam/c instead (../pair_meam.cpp:51)
pair_coeff * * library.meam Ni4 Ni.meam Ni4
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.005
thermo 50
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5
ghost atom cutoff = 5
binsize = 2.5, bins = 29 29 29
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 17.41 | 17.41 | 17.41 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -142400 0 -135782.09 20259.18
50 885.10702 -139411.51 0 -135750.54 32425.433
100 895.5097 -139454.3 0 -135750.3 31804.187
Loop time of 8.21941 on 4 procs for 100 steps with 32000 atoms
Performance: 5.256 ns/day, 4.566 hours/ns, 12.166 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.0277 | 8.0384 | 8.0504 | 0.3 | 97.80
Neigh | 0.12555 | 0.12645 | 0.12713 | 0.2 | 1.54
Comm | 0.024279 | 0.036776 | 0.048389 | 4.5 | 0.45
Output | 9.4414e-05 | 0.00011903 | 0.00018597 | 0.0 | 0.00
Modify | 0.01252 | 0.012608 | 0.012795 | 0.1 | 0.15
Other | | 0.005028 | | | 0.06
Nlocal: 8000 ave 8045 max 7947 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 6066.75 ave 6120 max 6021 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 195090 ave 196403 max 193697 min
Histogram: 1 0 0 1 0 0 0 1 0 1
FullNghs: 390180 ave 392616 max 387490 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 1560720
Ave neighs/atom = 48.7725
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:08

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bench/POTENTIALS/log.16Mar18.reax.1
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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
units real
atom_style charge
read_data data.reax
orthogonal box = (0 0 0) to (9.49107 9.49107 6.99123)
1 by 1 by 1 MPI processor grid
reading atoms ...
58 atoms
#replicate 7 8 10
replicate 7 8 5
orthogonal box = (0 0 0) to (66.4375 75.9285 34.9562)
1 by 1 by 1 MPI processor grid
16240 atoms
Time spent = 0.000834942 secs
velocity all create 300.0 9999
pair_style reax
WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
pair_coeff * * ffield.reax 1 2 3 4
timestep 0.1
fix 2 all nve
thermo 10
thermo_style custom step temp ke pe pxx pyy pzz etotal
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 12 13 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair reax, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 115.8 | 115.8 | 115.8 Mbytes
Step Temp KinEng PotEng Pxx Pyy Pzz TotEng
0 300 14521.612 -1616144.2 22296.712 -29858.677 5721.0921 -1601622.5
10 298.98728 14472.591 -1616093.9 21955.847 -24067.096 7389.148 -1601621.3
20 294.76158 14268.045 -1615890.1 19179.258 -10513.494 10789.925 -1601622
30 288.56967 13968.323 -1615591.2 13854.377 5833.02 13949.731 -1601622.9
40 282.06725 13653.571 -1615278.2 6259.9845 19406.33 14947.939 -1601624.6
50 274.84112 13303.787 -1614931.9 -2009.6832 26964.336 13346.855 -1601628.2
60 266.20153 12885.585 -1614519.7 -8441.1641 28485.532 10195.429 -1601634.1
70 259.17085 12545.262 -1614184.2 -11426.993 24941.516 6572.2953 -1601638.9
80 259.73004 12572.33 -1614216.7 -10867.598 16928.461 3033.9021 -1601644.3
90 269.2352 13032.431 -1614679 -7962.3129 4931.5317 -280.22164 -1601646.6
100 280.67181 13586.024 -1615234.3 -3606.1519 -8769.8482 -2527.5887 -1601648.3
Loop time of 358.104 on 1 procs for 100 steps with 16240 atoms
Performance: 0.002 ns/day, 9947.338 hours/ns, 0.279 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 358.07 | 358.07 | 358.07 | 0.0 | 99.99
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.01623 | 0.01623 | 0.01623 | 0.0 | 0.00
Output | 0.0013328 | 0.0013328 | 0.0013328 | 0.0 | 0.00
Modify | 0.012679 | 0.012679 | 0.012679 | 0.0 | 0.00
Other | | 0.006895 | | | 0.00
Nlocal: 16240 ave 16240 max 16240 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 32428 ave 32428 max 32428 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6.69975e+06 ave 6.69975e+06 max 6.69975e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6699752
Ave neighs/atom = 412.546
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:06:02

86
bench/POTENTIALS/log.16Mar18.reax.4
View File

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

69
bench/POTENTIALS/reax_defs.h
View File

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

196
cmake/CMakeLists.txt
View File

@ -3,16 +3,24 @@
# This file is part of LAMMPS
# Created by Christoph Junghans and Richard Berger
cmake_minimum_required(VERSION 3.10)
# set policy to silence warnings about ignoring <PackageName>_ROOT but use it
if(POLICY CMP0074)
cmake_policy(SET CMP0074 NEW)
endif()
########################################
project(lammps CXX)
set(SOVERSION 0)
get_filename_component(LAMMPS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../src ABSOLUTE)
get_filename_component(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib ABSOLUTE)
get_filename_component(LAMMPS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/.. ABSOLUTE)
get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUTE)
get_filename_component(LAMMPS_TOOLS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../tools ABSOLUTE)
get_filename_component(LAMMPS_PYTHON_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../python ABSOLUTE)
get_filename_component(LAMMPS_POTENTIALS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../potentials ABSOLUTE)
set(LAMMPS_SOURCE_DIR ${LAMMPS_DIR}/src)
set(LAMMPS_LIB_SOURCE_DIR ${LAMMPS_DIR}/lib)
set(LAMMPS_DOC_DIR ${LAMMPS_DIR}/doc)
set(LAMMPS_TOOLS_DIR ${LAMMPS_DIR}/tools)
set(LAMMPS_PYTHON_DIR ${LAMMPS_DIR}/python)
set(LAMMPS_POTENTIALS_DIR ${LAMMPS_DIR}/potentials)
find_package(Git)
@ -24,6 +32,12 @@ endif()
# Cmake modules/macros are in a subdirectory to keep this file cleaner
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules)
# make sure LIBRARY_PATH is set if environment variable is set
if (DEFINED ENV{LIBRARY_PATH})
list(APPEND CMAKE_LIBRARY_PATH "$ENV{LIBRARY_PATH}")
message(STATUS "Appending $ENV{LIBRARY_PATH} to CMAKE_LIBRARY_PATH: ${CMAKE_LIBRARY_PATH}")
endif()
include(LAMMPSUtils)
get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h PROJECT_VERSION)
@ -43,7 +57,6 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
# compiler tests
# these need ot be done early (before further tests).
#####################################################################
include(CheckCCompilerFlag)
include(CheckIncludeFileCXX)
# set required compiler flags and compiler/CPU arch specific optimizations
@ -57,11 +70,11 @@ if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
endif()
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
set(CMAKE_TUNE_DEFAULT "-ffast-math -march=native")
set(CMAKE_TUNE_DEFAULT "-march=native")
endif()
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")
set(CMAKE_TUNE_DEFAULT "-ffast-math -march=native")
set(CMAKE_TUNE_DEFAULT "-march=native")
endif()
# we require C++11 without extensions
@ -69,15 +82,6 @@ set(CMAKE_CXX_STANDARD 11)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF)
# GNU compiler specific features for testing
if (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
mark_as_advanced(ENABLE_COVERAGE)
if(ENABLE_COVERAGE)
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
endif()
endif()
########################################################################
# User input options #
########################################################################
@ -108,11 +112,11 @@ install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MOLECULE PERI POEMS QEQ
REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS
QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB
USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION
USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
@ -135,23 +139,20 @@ if(PKG_USER-ADIOS)
target_link_libraries(lammps PRIVATE adios2::adios2)
endif()
if (CMAKE_SYSTEM_NAME STREQUAL Windows)
option(BUILD_MPI "Build MPI version" OFF)
else()
# do MPI detection after language activation,
# in case MPI for these languages is required
if(NOT CMAKE_CROSSCOMPILING)
set(MPI_CXX_SKIP_MPICXX TRUE)
find_package(MPI QUIET)
option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
else()
option(BUILD_MPI "Build MPI version" OFF)
endif()
if(BUILD_MPI)
# We use a non-standard procedure to compile with MPI on windows
if (CMAKE_SYSTEM_NAME STREQUAL Windows)
# We use a non-standard procedure to cross-compile with MPI on Windows
if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)
include(MPI4WIN)
target_link_libraries(lammps PUBLIC MPI::MPI_CXX)
else()
set(MPI_CXX_SKIP_MPICXX ON)
find_package(MPI REQUIRED)
target_link_libraries(lammps PUBLIC MPI::MPI_CXX)
option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
@ -163,9 +164,6 @@ else()
enable_language(C)
file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
add_library(mpi_stubs STATIC ${MPI_SOURCES})
if(NOT BUILD_SHARED_LIBS)
install(TARGETS mpi_stubs EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
endif()
set_target_properties(mpi_stubs PROPERTIES OUTPUT_NAME lammps_mpi_stubs${LAMMPS_MACHINE})
target_include_directories(mpi_stubs PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS> $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/lammps/mpi>)
install(FILES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps/mpi)
@ -202,6 +200,7 @@ endif()
# "hard" dependencies between packages resulting
# in an error instead of skipping over files
pkg_depends(MLIAP SNAP)
pkg_depends(MPIIO MPI)
pkg_depends(USER-ATC MANYBODY)
pkg_depends(USER-LB MPI)
@ -240,6 +239,48 @@ if(BUILD_OMP)
target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
endif()
# Compiler specific features for testing
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
mark_as_advanced(ENABLE_COVERAGE)
if(ENABLE_COVERAGE)
if(CMAKE_VERSION VERSION_LESS 3.13)
if(CMAKE_CXX_FLAGS)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage")
endif()
else()
target_compile_options(lammps PUBLIC --coverage)
target_link_options(lammps PUBLIC --coverage)
endif()
endif()
endif()
set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)")
mark_as_advanced(ENABLE_SANITIZER)
set(ENABLE_SANITIZER_VALUES none address leak thread undefined)
set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES})
validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)
if(NOT ENABLE_SANITIZER STREQUAL "none")
if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
if(CMAKE_VERSION VERSION_LESS 3.13)
if(CMAKE_CXX_FLAGS)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
endif()
else()
target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
endif()
else()
message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.")
set(ENABLE_SANITIZER "none")
endif()
endif()
if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
enable_language(C)
find_package(LAPACK)
@ -252,9 +293,6 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
enable_language(Fortran)
file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
add_library(linalg STATIC ${LAPACK_SOURCES})
if(NOT BUILD_SHARED_LIBS)
install(TARGETS linalg EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
endif()
set_target_properties(linalg PROPERTIES OUTPUT_NAME lammps_linalg${LAMMPS_MACHINE})
set(BLAS_LIBRARIES "$<TARGET_FILE:linalg>")
set(LAPACK_LIBRARIES "$<TARGET_FILE:linalg>")
@ -330,14 +368,8 @@ endforeach()
set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler specific optimization or instrumentation")
separate_arguments(CMAKE_TUNE_FLAGS)
include(CheckCXXCompilerFlag)
foreach(_FLAG ${CMAKE_TUNE_FLAGS})
check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAG})
if(COMPILER_SUPPORTS${_FLAG})
target_compile_options(lammps PRIVATE ${_FLAG})
else()
message(WARNING "${_FLAG} found in CMAKE_TUNE_FLAGS, but not supported by the compiler, skipping")
endif()
target_compile_options(lammps PRIVATE ${_FLAG})
endforeach()
########################################################################
# Basic system tests (standard libraries, headers, functions, types) #
@ -359,6 +391,15 @@ target_link_libraries(lammps PRIVATE ${MATH_LIBRARIES})
include(StyleHeaderUtils)
RegisterStyles(${LAMMPS_SOURCE_DIR})
########################################################
# Fetch missing external files and archives for packages
########################################################
foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
if(PKG_${PKG})
FetchPotentials(${LAMMPS_SOURCE_DIR}/${PKG} ${LAMMPS_POTENTIALS_DIR})
endif()
endforeach()
##############################################
# add sources of enabled packages
############################################
@ -405,17 +446,20 @@ endforeach()
##############################################
# add lib sources of (simple) enabled packages
############################################
foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD)
foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT)
if(PKG_${SIMPLE_LIB})
string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
string(TOLOWER "${PKG_LIB}" PKG_LIB)
file(GLOB_RECURSE ${PKG_LIB}_SOURCES
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
if(NOT BUILD_SHARED_LIBS)
install(TARGETS ${PKG_LIB} EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
if(PKG_LIB STREQUAL mesont)
enable_language(Fortran)
file(GLOB_RECURSE ${PKG_LIB}_SOURCES
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.f90)
else()
file(GLOB_RECURSE ${PKG_LIB}_SOURCES
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
endif()
add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE})
target_link_libraries(lammps PRIVATE ${PKG_LIB})
if(PKG_LIB STREQUAL awpmd)
@ -436,7 +480,12 @@ if(PKG_USER-ATC)
if(LAMMPS_SIZES STREQUAL BIGBIG)
message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG")
endif()
target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES} MPI::MPI_CXX)
target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES})
if(BUILD_MPI)
target_link_libraries(atc PRIVATE MPI::MPI_CXX)
else()
target_link_libraries(atc PRIVATE mpi_stubs)
endif()
target_include_directories(atc PRIVATE ${LAMMPS_SOURCE_DIR})
target_compile_definitions(atc PRIVATE -DLAMMPS_${LAMMPS_SIZES})
endif()
@ -497,7 +546,7 @@ execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HE
# Generate lmpgitversion.h
######################################
add_custom_target(gitversion COMMAND ${CMAKE_COMMAND}
-DCMAKE_CURRENT_SOURCE_DIR="${CMAKE_CURRENT_SOURCE_DIR}"
-DLAMMPS_DIR="${LAMMPS_DIR}"
-DGIT_EXECUTABLE="${GIT_EXECUTABLE}"
-DGIT_FOUND="${GIT_FOUND}"
-DLAMMPS_STYLE_HEADERS_DIR="${LAMMPS_STYLE_HEADERS_DIR}"
@ -522,14 +571,15 @@ endif()
set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
install(TARGETS lammps EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
target_include_directories(lammps PUBLIC $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>)
file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps)
foreach(_HEADER ${LAMMPS_CXX_HEADERS})
add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/${_HEADER})
add_custom_target(${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER})
add_dependencies(lammps ${_HEADER})
install(FILES ${LAMMPS_SOURCE_DIR}/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
if(BUILD_SHARED_LIBS)
install(FILES ${LAMMPS_SOURCE_DIR}/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
endif()
endforeach()
target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/includes>)
add_library(LAMMPS::lammps ALIAS lammps)
@ -538,15 +588,16 @@ set(LAMMPS_API_DEFINES)
foreach(_DEF ${LAMMPS_DEFINES})
set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${_DEF}")
endforeach()
configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
install(EXPORT LAMMPS_Targets FILE LAMMPS_Targets.cmake NAMESPACE LAMMPS:: DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
file(GLOB MODULE_FILES ${CMAKE_CURRENT_SOURCE_DIR}/Modules/Find*.cmake)
install(FILES ${MODULE_FILES} DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
include(CMakePackageConfigHelpers)
configure_file(LAMMPSConfig.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake @ONLY)
write_basic_package_version_file("LAMMPSConfigVersion.cmake" VERSION ${PROJECT_VERSION} COMPATIBILITY ExactVersion)
install(FILES "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake" "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfigVersion.cmake" DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
if(BUILD_SHARED_LIBS)
install(TARGETS lammps EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
install(EXPORT LAMMPS_Targets FILE LAMMPS_Targets.cmake NAMESPACE LAMMPS:: DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
include(CMakePackageConfigHelpers)
configure_file(LAMMPSConfig.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake @ONLY)
write_basic_package_version_file("LAMMPSConfigVersion.cmake" VERSION ${PROJECT_VERSION} COMPATIBILITY ExactVersion)
install(FILES "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake" "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfigVersion.cmake" DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
endif()
install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1)
if(BUILD_TOOLS)
@ -556,10 +607,16 @@ if(BUILD_TOOLS)
include(CheckGeneratorSupport)
if(CMAKE_GENERATOR_SUPPORT_FORTRAN)
enable_language(Fortran)
add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
target_link_libraries(chain.x PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR})
include(CheckLanguage)
check_language(Fortran)
if(CMAKE_Fortran_COMPILER)
enable_language(Fortran)
add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
target_link_libraries(chain.x PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR})
else()
message(WARNING "No suitable Fortran compiler found, skipping building 'chain.x'")
endif()
else()
message(WARNING "CMake build doesn't support fortran, skipping building 'chain.x'")
endif()
@ -600,6 +657,8 @@ install(
###############################################################################
if(BUILD_SHARED_LIBS)
if(CMAKE_VERSION VERSION_LESS 3.12)
# adjust so we find Python 3 versions before Python 2 on old systems with old CMake
set(Python_ADDITIONAL_VERSIONS 3.8 3.7 3.6 3.5)
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
@ -651,6 +710,7 @@ endif()
include(Testing)
include(CodeCoverage)
include(CodingStandard)
###############################################################################
# Print package summary
@ -705,6 +765,7 @@ else()
endif()
if(BUILD_MPI)
message(STATUS "<<< MPI flags >>>
-- MPI_defines: ${MPI_CXX_COMPILE_DEFINITIONS}
-- MPI includes: ${MPI_CXX_INCLUDE_PATH}
-- MPI libraries: ${MPI_CXX_LIBRARIES};${MPI_Fortran_LIBRARIES}")
endif()
@ -754,3 +815,6 @@ if(PKG_KSPACE)
endif()
endif()
endif()
if(BUILD_DOC)
message(STATUS "<<< Building HTML Manual >>>")
endif()

82
cmake/LAMMPSConfig.cmake.in
View File

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

27
cmake/Modules/CodeCoverage.cmake
View File

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

34
cmake/Modules/CodingStandard.cmake Normal file
View File

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

37
cmake/Modules/Documentation.cmake
View File

@ -2,10 +2,19 @@
# Build documentation
###############################################################################
option(BUILD_DOC "Build LAMMPS HTML documentation" OFF)
if(BUILD_DOC)
find_package(PythonInterp 3 REQUIRED)
set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)
if(BUILD_DOC)
# Sphinx 3.x requires at least Python 3.5
if(CMAKE_VERSION VERSION_LESS 3.12)
find_package(PythonInterp 3.5 REQUIRED)
set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv -p ${PYTHON_EXECUTABLE})
else()
find_package(Python3 REQUIRED COMPONENTS Interpreter)
if(Python3_VERSION VERSION_LESS 3.5)
message(FATAL_ERROR "Python 3.5 and up is required to build the HTML documentation")
endif()
set(VIRTUALENV ${Python3_EXECUTABLE} -m virtualenv -p ${Python3_EXECUTABLE})
endif()
file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
@ -25,11 +34,10 @@ if(BUILD_DOC)
)
# download mathjax distribution and unpack to folder "mathjax"
file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
"${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7)
if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax)
if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax/es5)
file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
"${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7)
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${CMAKE_CURRENT_BINARY_DIR}/mathjax)
@ -37,11 +45,18 @@ if(BUILD_DOC)
file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax)
file(COPY ${CMAKE_CURRENT_BINARY_DIR}/mathjax/es5 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax/)
# for increased browser compatibility
if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/html/_static/polyfill.js)
file(DOWNLOAD "https://polyfill.io/v3/polyfill.min.js?features=es6"
"${CMAKE_CURRENT_BINARY_DIR}/html/_static/polyfill.js")
endif()
# note, this may run in parallel with other tasks, so we must not use multiple processes here
add_custom_command(
OUTPUT html
DEPENDS ${DOC_SOURCES} docenv requirements.txt
COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${LAMMPS_DOC_DIR}/src html
COMMAND ${CMAKE_COMMAND} -E create_symlink Manual.html ${CMAKE_CURRENT_BINARY_DIR}/html/index.html
)
# copy selected image files to html output tree
@ -56,17 +71,17 @@ if(BUILD_DOC)
set(HTML_IMAGE_TARGETS "")
foreach(_IMG ${HTML_EXTRA_IMAGES})
string(PREPEND _IMG JPG/)
list(APPEND HTML_IMAGE_TARGETS "html/${_IMG}")
list(APPEND HTML_IMAGE_TARGETS "${CMAKE_CURRENT_BINARY_DIR}/html/${_IMG}")
add_custom_command(
OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/html/${_IMG}
DEPENDS ${LAMMPS_DOC_DIR}/src/${_IMG} html/JPG
DEPENDS ${LAMMPS_DOC_DIR}/src/${_IMG} ${CMAKE_CURRENT_BINARY_DIR}/html/JPG
COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/src/${_IMG} ${CMAKE_BINARY_DIR}/html/${_IMG}
)
endforeach()
add_custom_target(
doc ALL
DEPENDS html html/_static/mathjax/es5 ${HTML_IMAGE_TARGETS}
DEPENDS html ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax/es5 ${HTML_IMAGE_TARGETS}
SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES}
)

46
cmake/Modules/FindClangFormat.cmake Normal file
View File

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

27
cmake/Modules/FindLATTE.cmake
View File

@ -1,27 +0,0 @@
# - Find latte
# Find the native LATTE libraries.
#
# LATTE_LIBRARIES - List of libraries when using latte.
# LATTE_FOUND - True if latte found.
#
find_library(LATTE_LIBRARY NAMES latte)
include(FindPackageHandleStandardArgs)
# handle the QUIETLY and REQUIRED arguments and set LATTE_FOUND to TRUE
# if all listed variables are TRUE
find_package_handle_standard_args(LATTE DEFAULT_MSG LATTE_LIBRARY)
# Copy the results to the output variables and target.
if(LATTE_FOUND)
set(LATTE_LIBRARIES ${LATTE_LIBRARY})
if(NOT TARGET LATTE::latte)
add_library(LATTE::latte UNKNOWN IMPORTED)
set_target_properties(LATTE::latte PROPERTIES
IMPORTED_LOCATION "${LATTE_LIBRARY}")
endif()
endif()
mark_as_advanced(LATTE_LIBRARY)

4
cmake/Modules/FindTBB_MALLOC.cmake
View File

@ -6,12 +6,12 @@
# TBB_MALLOC_FOUND - True if tbb found.
#
########################################################
# TBB Malloc
find_path(TBB_MALLOC_INCLUDE_DIR NAMES tbb/tbb.h PATHS $ENV{TBBROOT}/include)
find_library(TBB_MALLOC_LIBRARY NAMES tbbmalloc PATHS $ENV{TBBROOT}/lib/intel64/gcc4.7
find_library(TBB_MALLOC_LIBRARY NAMES tbbmalloc PATHS $ENV{TBBROOT}/lib/intel64/gcc4.8
$ENV{TBBROOT}/lib/intel64/gcc4.7
$ENV{TBBROOT}/lib/intel64/gcc4.4
$ENV{TBBROOT}/lib/intel64/gcc4.1)

30
cmake/Modules/FindYAML.cmake Normal file
View File

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

77
cmake/Modules/GTest.cmake Normal file
View File

@ -0,0 +1,77 @@
message(STATUS "Downloading and building Google Test library")
if(CMAKE_BUILD_TYPE STREQUAL Debug)
set(GTEST_LIB_POSTFIX d)
else()
set(GTEST_LIB_POSTFIX)
endif()
include(ExternalProject)
ExternalProject_Add(googletest
GIT_REPOSITORY https://github.com/google/googletest.git
GIT_TAG release-1.10.0
SOURCE_DIR "${CMAKE_BINARY_DIR}/gtest-src"
BINARY_DIR "${CMAKE_BINARY_DIR}/gtest-build"
CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_GTEST_OPTS}
-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
BUILD_BYPRODUCTS <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest${GTEST_LIB_POSTFIX}.a
<BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock${GTEST_LIB_POSTFIX}.a
<BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest_main${GTEST_LIB_POSTFIX}.a
<BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock_main${GTEST_LIB_POSTFIX}.a
LOG_DOWNLOAD ON
LOG_CONFIGURE ON
LOG_BUILD ON
INSTALL_COMMAND ""
TEST_COMMAND "")
ExternalProject_Get_Property(googletest SOURCE_DIR)
set(GTEST_INCLUDE_DIR ${SOURCE_DIR}/googletest/include)
set(GMOCK_INCLUDE_DIR ${SOURCE_DIR}/googlemock/include)
# workaround for CMake 3.10 on ubuntu 18.04
file(MAKE_DIRECTORY ${GTEST_INCLUDE_DIR})
file(MAKE_DIRECTORY ${GMOCK_INCLUDE_DIR})
ExternalProject_Get_Property(googletest BINARY_DIR)
set(GTEST_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest${GTEST_LIB_POSTFIX}.a)
set(GMOCK_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock${GTEST_LIB_POSTFIX}.a)
set(GTEST_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest_main${GTEST_LIB_POSTFIX}.a)
set(GMOCK_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock_main${GTEST_LIB_POSTFIX}.a)
# Prevent GoogleTest from overriding our compiler/linker options
# when building with Visual Studio
set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
find_package(Threads QUIET)
add_library(GTest::GTest UNKNOWN IMPORTED)
set_target_properties(GTest::GTest PROPERTIES
IMPORTED_LOCATION ${GTEST_LIBRARY_PATH}
INTERFACE_INCLUDE_DIRECTORIES ${GTEST_INCLUDE_DIR}
IMPORTED_LINK_INTERFACE_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
add_dependencies(GTest::GTest googletest)
add_library(GTest::GMock UNKNOWN IMPORTED)
set_target_properties(GTest::GMock PROPERTIES
IMPORTED_LOCATION ${GMOCK_LIBRARY_PATH}
INTERFACE_INCLUDE_DIRECTORIES ${GMOCK_INCLUDE_DIR}
IMPORTED_LINK_INTERFACE_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
add_dependencies(GTest::GMock googletest)
add_library(GTest::GTestMain UNKNOWN IMPORTED)
set_target_properties(GTest::GTestMain PROPERTIES
IMPORTED_LOCATION ${GTEST_MAIN_LIBRARY_PATH}
INTERFACE_INCLUDE_DIRECTORIES ${GTEST_INCLUDE_DIR}
IMPORTED_LINK_INTERFACE_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
add_dependencies(GTest::GTestMain googletest)
add_library(GTest::GMockMain UNKNOWN IMPORTED)
set_target_properties(GTest::GMockMain PROPERTIES
IMPORTED_LOCATION ${GMOCK_MAIN_LIBRARY_PATH}
INTERFACE_INCLUDE_DIRECTORIES ${GMOCK_INCLUDE_DIR}
IMPORTED_LINK_INTERFACE_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
add_dependencies(GTest::GMockMain googletest)

23
cmake/Modules/LAMMPSUtils.cmake
View File

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

5
cmake/Modules/MPI4WIN.cmake
View File

@ -23,3 +23,8 @@ set_target_properties(MPI::MPI_CXX PROPERTIES
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")

46
cmake/Modules/Packages/GPU.cmake
View File

@ -40,6 +40,17 @@ if(GPU_API STREQUAL "CUDA")
set(GPU_ARCH "sm_50" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
# ensure that no *cubin.h files exist from a compile in the lib/gpu folder
file(GLOB GPU_LIB_OLD_CUBIN_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h)
if (GPU_LIB_OLD_CUBIN_HEADERS)
message(FATAL_ERROR "########################################################################\n"
"Found file(s) generated by the make-based build system in lib/gpu\n"
"Please run\n"
" make -C ${LAMMPS_LIB_SOURCE_DIR}/gpu -f Makefile.serial clean\n"
"to remove\n"
"########################################################################")
endif()
file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
@ -79,7 +90,7 @@ if(GPU_API STREQUAL "CUDA")
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ")
endif()
cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
@ -115,7 +126,7 @@ if(GPU_API STREQUAL "CUDA")
elseif(GPU_API STREQUAL "OPENCL")
if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
# download and unpack support binaries for compilation of windows binaries.
set(LAMMPS_THIRDPARTY_URL "http://download.lammps.org/thirdparty")
set(LAMMPS_THIRDPARTY_URL "https://download.lammps.org/thirdparty")
file(DOWNLOAD "${LAMMPS_THIRDPARTY_URL}/opencl-win-devel.tar.gz" "${CMAKE_CURRENT_BINARY_DIR}/opencl-win-devel.tar.gz"
EXPECTED_MD5 2c00364888d5671195598b44c2e0d44d)
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf opencl-win-devel.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
@ -257,10 +268,17 @@ elseif(GPU_API STREQUAL "HIP")
if(HIP_PLATFORM STREQUAL "hcc")
configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY)
add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
DEPENDS ${CU_CPP_FILE}
COMMENT "Generating ${CU_NAME}.cubin")
if(HIP_COMPILER STREQUAL "clang")
add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
DEPENDS ${CU_CPP_FILE}
COMMENT "Generating ${CU_NAME}.cubin")
else()
add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
DEPENDS ${CU_CPP_FILE}
COMMENT "Generating ${CU_NAME}.cubin")
endif()
elseif(HIP_PLATFORM STREQUAL "nvcc")
add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE}
@ -330,7 +348,7 @@ elseif(GPU_API STREQUAL "HIP")
if(HIP_PLATFORM STREQUAL "nvcc")
target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_NVCC__)
target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/include)
target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
target_include_directories(gpu PRIVATE ${CUDA_INCLUDE_DIRS})
target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
@ -338,6 +356,12 @@ elseif(GPU_API STREQUAL "HIP")
target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/include)
target_include_directories(hip_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
target_link_libraries(hip_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
elseif(HIP_PLATFORM STREQUAL "hcc")
target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_HCC__)
target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_HCC__)
target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include)
endif()
target_link_libraries(lammps PRIVATE gpu)
@ -353,9 +377,11 @@ RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)
get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
target_link_libraries(gpu PRIVATE MPI::MPI_CXX)
if(NOT BUILD_SHARED_LIBS)
install(TARGETS gpu EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
if(NOT BUILD_MPI)
# mpistubs is aliased to MPI::MPI_CXX, but older versions of cmake won't work forward the include path
target_link_libraries(gpu PRIVATE mpi_stubs)
else()
target_link_libraries(gpu PRIVATE MPI::MPI_CXX)
endif()
target_compile_definitions(gpu PRIVATE -DLAMMPS_${LAMMPS_SIZES})
set_target_properties(gpu PROPERTIES OUTPUT_NAME lammps_gpu${LAMMPS_MACHINE})

10
cmake/Modules/Packages/KIM.cmake
View File

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

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

@ -14,16 +14,30 @@ endif()
option(EXTERNAL_KOKKOS "Build against external kokkos library" OFF)
option(DOWNLOAD_KOKKOS "Download the KOKKOS library instead of using the bundled one" OFF)
if(DOWNLOAD_KOKKOS)
# extract Kokkos-related variables and values so we can forward them to the Kokkos library build
get_cmake_property(_VARS VARIABLES)
list(FILTER _VARS INCLUDE REGEX ^Kokkos_)
foreach(_VAR IN LISTS _VARS)
list(APPEND KOKKOS_LIB_BUILD_ARGS "-D${_VAR}=${${_VAR}}")
endforeach()
message(STATUS "KOKKOS download requested - we will build our own")
file(DOWNLOAD https://github.com/kokkos/kokkos/compare/3.0.00...stanmoore1:lammps.diff ${CMAKE_CURRENT_BINARY_DIR}/kokkos-lammps.patch)
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>")
if(CMAKE_REQUEST_PIC)
list(APPEND KOKKOS_LIB_BUILD_ARGS ${CMAKE_REQUEST_PIC})
endif()
# append other CMake variables that need to be forwarded to CMAKE_ARGS
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}")
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_INSTALL_LIBDIR=lib")
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}")
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}")
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_STANDARD=${CMAKE_CXX_STANDARD}")
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
include(ExternalProject)
ExternalProject_Add(kokkos_build
URL https://github.com/kokkos/kokkos/archive/3.0.00.tar.gz
URL_MD5 281c7093aa3a603276e93abdf4be23b9
PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/kokkos-lammps.patch
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC}
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DCMAKE_INSTALL_LIBDIR=lib
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM} -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
URL https://github.com/kokkos/kokkos/archive/3.1.01.tar.gz
URL_MD5 3ccb2100f7fc316891e7dad3bc33fa37
CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
)
ExternalProject_get_property(kokkos_build INSTALL_DIR)
@ -35,14 +49,8 @@ if(DOWNLOAD_KOKKOS)
INTERFACE_LINK_LIBRARIES ${CMAKE_DL_LIBS})
target_link_libraries(lammps PRIVATE LAMMPS::KOKKOS)
add_dependencies(LAMMPS::KOKKOS kokkos_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 3)
if(NOT Kokkos_FOUND)
message(FATAL_ERROR "KOKKOS library not found, help CMake to find it by setting KOKKOS_LIBRARY, or set DOWNLOAD_KOKKOS=ON to download it")
endif()
find_package(Kokkos 3.1.01 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
else()
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)

6
cmake/Modules/Packages/KSPACE.cmake
View File

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

21
cmake/Modules/Packages/LATTE.cmake
View File

@ -1,5 +1,12 @@
enable_language(Fortran)
find_package(LATTE)
# using lammps in a super-build setting
if(TARGET LATTE::latte)
target_link_libraries(lammps PRIVATE LATTE::latte)
return()
endif()
find_package(LATTE 1.2.2 CONFIG)
if(LATTE_FOUND)
set(DOWNLOAD_LATTE_DEFAULT OFF)
else()
@ -10,8 +17,8 @@ if(DOWNLOAD_LATTE)
message(STATUS "LATTE download requested - we will build our own")
include(ExternalProject)
ExternalProject_Add(latte_build
URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz
URL_MD5 85ac414fdada2d04619c8f936344df14
URL https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz
URL_MD5 820e73a457ced178c08c71389a385de7
SOURCE_SUBDIR cmake
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} -DCMAKE_INSTALL_LIBDIR=lib
-DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
@ -27,13 +34,7 @@ if(DOWNLOAD_LATTE)
INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
target_link_libraries(lammps PRIVATE LAMMPS::LATTE)
add_dependencies(LAMMPS::LATTE latte_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
else()
find_package(LATTE)
if(NOT LATTE_FOUND)
message(FATAL_ERROR "LATTE library not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
endif()
find_package(LATTE 1.2.2 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE LATTE::latte)
endif()

3
cmake/Modules/Packages/MESSAGE.cmake
View File

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

3
cmake/Modules/Packages/MSCG.cmake
View File

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

6
cmake/Modules/Packages/USER-COLVARS.cmake
View File

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

2
cmake/Modules/Packages/USER-INTEL.cmake
View File

@ -77,7 +77,7 @@ else()
foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAG})
if(COMPILER_SUPPORTS${_FLAG})
target_compile_options(lammps PRIVATE ${_FLAG})
target_compile_options(lammps PRIVATE ${_FLAG})
endif()
endforeach()
endif()

3
cmake/Modules/Packages/USER-MOLFILE.cmake
View File

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

18
cmake/Modules/Packages/USER-NETCDF.cmake
View File

@ -1,11 +1,17 @@
# USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
# NetCDF library enables dump style "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
find_package(NetCDF)
if(NETCDF_FOUND)
find_package(PNetCDF)
else(NETCDF_FOUND)
find_package(PNetCDF REQUIRED)
endif(NETCDF_FOUND)
# may use NetCDF or PNetCDF with MPI, but must have NetCDF without
if(NOT BUILD_MPI)
find_package(NetCDF REQUIRED)
else()
find_package(NetCDF)
if(NETCDF_FOUND)
find_package(PNetCDF)
else()
find_package(PNetCDF REQUIRED)
endif()
endif()
if(NETCDF_FOUND)
target_link_libraries(lammps PRIVATE NetCDF::NetCDF)

9
cmake/Modules/Packages/USER-PLUMED.cmake
View File

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

6
cmake/Modules/Packages/USER-QMMM.cmake
View File

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

9
cmake/Modules/Packages/USER-SCAFACOS.cmake
View File

@ -14,10 +14,16 @@ endif()
option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
if(DOWNLOAD_SCAFACOS)
message(STATUS "ScaFaCoS download requested - we will build our own")
# version 1.0.1 needs a patch to compile and linke cleanly with GCC 10 and later.
file(DOWNLOAD https://download.lammps.org/thirdparty/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
EXPECTED_HASH MD5=4baa1333bb28fcce102d505e1992d032)
include(ExternalProject)
ExternalProject_Add(scafacos_build
URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
URL_MD5 bd46d74e3296bd8a444d731bb10c1738
PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc
--enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
--with-internal-fftw --with-internal-pfft
@ -52,9 +58,6 @@ if(DOWNLOAD_SCAFACOS)
INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/libfcs.a;${INSTALL_DIR}/lib/libfcs_direct.a;${INSTALL_DIR}/lib/libfcs_ewald.a;${INSTALL_DIR}/lib/libfcs_fmm.a;${INSTALL_DIR}/lib/libfcs_p2nfft.a;${INSTALL_DIR}/lib/libfcs_p3m.a;GSL::gsl;${INSTALL_DIR}/lib/libfcs_near.a;${INSTALL_DIR}/lib/libfcs_gridsort.a;${INSTALL_DIR}/lib/libfcs_resort.a;${INSTALL_DIR}/lib/libfcs_redist.a;${INSTALL_DIR}/lib/libfcs_common.a;${INSTALL_DIR}/lib/libfcs_pnfft.a;${INSTALL_DIR}/lib/libfcs_pfft.a;${INSTALL_DIR}/lib/libfcs_fftw3_mpi.a;${INSTALL_DIR}/lib/libfcs_fftw3.a;MPI::MPI_Fortran;MPI::MPI_C")
target_link_libraries(lammps PRIVATE LAMMPS::SCAFACOS)
add_dependencies(LAMMPS::SCAFACOS scafacos_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
else()
find_package(PkgConfig REQUIRED)
pkg_check_modules(SCAFACOS REQUIRED IMPORTED_TARGET scafacos)

5
cmake/Modules/Packages/USER-SMD.cmake
View File

@ -9,7 +9,7 @@ if(DOWNLOAD_EIGEN3)
message(STATUS "Eigen3 download requested - we will build our own")
include(ExternalProject)
ExternalProject_Add(Eigen3_build
URL http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz
URL https://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz
URL_MD5 f2a417d083fe8ca4b8ed2bc613d20f07
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
)
@ -18,9 +18,6 @@ if(DOWNLOAD_EIGEN3)
set_target_properties(LAMMPS::EIGEN3 PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}")
target_link_libraries(lammps PRIVATE LAMMPS::EIGEN3)
add_dependencies(LAMMPS::EIGEN3 Eigen3_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
else()
find_package(Eigen3 NO_MODULE)
mark_as_advanced(Eigen3_DIR)

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

@ -24,7 +24,11 @@ if(DOWNLOAD_VORO)
ExternalProject_Add(voro_build
URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
URL_MD5 2338b824c3b7b25590e18e8df5d68af9
CONFIGURE_COMMAND "" BUILD_COMMAND make ${VORO_BUILD_OPTIONS} BUILD_IN_SOURCE 1 INSTALL_COMMAND ""
PATCH_COMMAND patch -b -p0 < ${LAMMPS_LIB_SOURCE_DIR}/voronoi/voro-make.patch
CONFIGURE_COMMAND ""
BUILD_COMMAND make ${VORO_BUILD_OPTIONS}
BUILD_IN_SOURCE 1
INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/src/libvoro++.a
)
ExternalProject_get_property(voro_build SOURCE_DIR)
@ -35,9 +39,6 @@ if(DOWNLOAD_VORO)
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/src")
target_link_libraries(lammps PRIVATE LAMMPS::VORO)
add_dependencies(LAMMPS::VORO voro_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
else()
find_package(VORO)
if(NOT VORO_FOUND)

62
cmake/Modules/Testing.cmake
View File

@ -3,49 +3,23 @@
###############################################################################
option(ENABLE_TESTING "Enable testing" OFF)
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 ${LAMMPS_TOOLS_DIR}/valgrind/[^.]*.supp)
foreach(SUPP ${VALGRIND_SUPPRESSION_FILES})
file(READ ${SUPP} SUPPRESSIONS)
file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "${SUPPRESSIONS}")
endforeach()
set(VALGRIND_DEFAULT_OPTIONS "--leak-check=full --show-leak-kinds=all --track-origins=yes --suppressions=${CMAKE_BINARY_DIR}/lammps.supp")
set(MEMORYCHECK_COMMAND "${VALGRIND_BINARY}" CACHE FILEPATH "Memory Check Command")
set(MEMORYCHECK_COMMAND_OPTIONS "${VALGRIND_DEFAULT_OPTIONS}" CACHE STRING "Memory Check Command Options")
include(CTest)
enable_testing()
option(LAMMPS_TESTING_SOURCE_DIR "Location of lammps-testing source directory" "")
option(LAMMPS_TESTING_GIT_TAG "Git tag of lammps-testing" "master")
mark_as_advanced(LAMMPS_TESTING_SOURCE_DIR LAMMPS_TESTING_GIT_TAG)
if (CMAKE_VERSION VERSION_GREATER "3.10.3" AND NOT LAMMPS_TESTING_SOURCE_DIR)
include(FetchContent)
FetchContent_Declare(lammps-testing
GIT_REPOSITORY https://github.com/lammps/lammps-testing.git
GIT_TAG ${LAMMPS_TESTING_GIT_TAG}
)
FetchContent_GetProperties(lammps-testing)
if(NOT lammps-testing_POPULATED)
message(STATUS "Downloading tests...")
FetchContent_Populate(lammps-testing)
endif()
set(LAMMPS_TESTING_SOURCE_DIR ${lammps-testing_SOURCE_DIR})
elseif(NOT LAMMPS_TESTING_SOURCE_DIR)
message(WARNING "Full test-suite requires CMake >= 3.11 or copy of\n"
"https://github.com/lammps/lammps-testing in LAMMPS_TESTING_SOURCE_DIR")
endif()
add_test(NAME ShowHelp COMMAND $<TARGET_FILE:lmp> -help)
if(EXISTS ${LAMMPS_TESTING_SOURCE_DIR})
message(STATUS "Running test discovery...")
file(GLOB_RECURSE TEST_SCRIPTS ${LAMMPS_TESTING_SOURCE_DIR}/tests/core/*/in.*)
foreach(script_path ${TEST_SCRIPTS})
get_filename_component(TEST_NAME ${script_path} EXT)
get_filename_component(SCRIPT_NAME ${script_path} NAME)
get_filename_component(PARENT_DIR ${script_path} DIRECTORY)
string(SUBSTRING ${TEST_NAME} 1 -1 TEST_NAME)
string(REPLACE "-" "_" TEST_NAME ${TEST_NAME})
string(REPLACE "+" "_" TEST_NAME ${TEST_NAME})
set(TEST_NAME "test_core_${TEST_NAME}_serial")
add_test(NAME ${TEST_NAME} COMMAND $<TARGET_FILE:lmp> -in ${SCRIPT_NAME} WORKING_DIRECTORY ${PARENT_DIR})
endforeach()
list(LENGTH TEST_SCRIPTS NUM_TESTS)
message(STATUS "Found ${NUM_TESTS} tests.")
endif()
get_filename_component(LAMMPS_UNITTEST_DIR ${LAMMPS_SOURCE_DIR}/../unittest ABSOLUTE)
get_filename_component(LAMMPS_UNITTEST_BIN ${CMAKE_BINARY_DIR}/unittest ABSOLUTE)
add_subdirectory(${LAMMPS_UNITTEST_DIR} ${LAMMPS_UNITTEST_BIN})
endif()

10
cmake/Modules/generate_lmpgitversion.cmake
View File

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

2
cmake/presets/all_off.cmake
View File

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

2
cmake/presets/all_on.cmake
View File

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

2
cmake/presets/clang.cmake
View File

@ -2,7 +2,7 @@
set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS "-Wall -Wextra -g -O2 -DNDEBG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_CXX "clang++" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)

17
cmake/presets/download.cmake Normal file
View File

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

12
cmake/presets/hip.cmake Normal file
View File

@ -0,0 +1,12 @@
# preset that will enable hipcc plus gcc with support for MPI and OpenMP (on Linux boxes)
set(CMAKE_CXX_COMPILER "hipcc" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_CXX "hipcc" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)

6
cmake/presets/mingw-cross.cmake
View File

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

10
cmake/presets/most.cmake
View File

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

2
cmake/presets/nolib.cmake
View File

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

6
doc/github-development-workflow.md
View File

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

21
doc/include-file-conventions.md
View File

@ -49,22 +49,15 @@ include files provided with LAMMPS are included with double quotes
For headers declaring functions of the C-library, the corresponding
C++ versions should be included (examples: `#include <cstdlib>` or
`#include <cctypes>`). However, these includes are limited to those defined
in the C++98 standard. Some files thus must use the older style until
the minimum C++ standard requirement of LAMMPS is lifted to C++11 or
even beyond (examples: `#include <stdint.h>` versus `#include <cstdint>`
or `#include <inttypes.h>` versus `#include <cinttypes>`).
`#include <cctypes>` instead of `#include <stdlib.h>` or
`#include<ctypes.h>` ).
### C++ Standard Compliance
LAMMPS core files currently correspond to the C++98 standard. Files
requiring C++11 or later are only permitted in (optional) packages
and particularly packages that are not part of the list of commonly
used packages such as MOLECULE, KSPACE, MANYBODY, or RIGID.
Also, LAMMPS uses the C-style stdio library for I/O instead of iostreams.
Since using both at the same time can cause problems, iostreams should
be avoided where possible.
LAMMPS core files use standard conforming C++ compatible with the
C++11 standard, unless explicitly noted. Also, LAMMPS uses the C-style
stdio library for I/O instead of iostreams. Since using both at the
same time can cause problems, iostreams should be avoided where possible.
### Lean Header Files
@ -72,7 +65,7 @@ Header files will typically contain the definition of a (single) class.
These header files should have as few include statements as possible.
This is particularly important for classes that implement a "style" and
thus use a macro of the kind `SomeStyle(some/name,SomeName)`. These will
all be included in the auto-generated `"some_style.h"` files which
all be included in the auto-generated `"some_style.h"` files which
results in a high potential for direct or indirect symbol name clashes.
In the ideal case, the header would only include one file defining the

2
doc/lammps.1
View File

@ -1,4 +1,4 @@
.TH LAMMPS "15 April 2020" "2020-04-15"
.TH LAMMPS "15 June 2020" "2020-06-15"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator.

0
doc/src/99/crib.html Executable file → Normal file
View File

23
doc/src/Build_basics.rst
View File

@ -225,7 +225,7 @@ A few example command lines are:
For compiling with the Clang/LLVM compilers a CMake preset is provided that
can be loaded with `-C ../cmake/presets/clang.cmake`. Similarly,
`-C ../cmake/presets/intel.cmake` should switch the
`-C ../cmake/presets/intel.cmake` should switch the
In addition you can set ``CMAKE_TUNE_FLAGS`` to specifically add
compiler flags to tune for optimal performance on given hosts. By
@ -372,7 +372,8 @@ it. The build step will also create generic soft links, named
``liblammps.a`` and ``liblammps.so``\ , which point to the specific
``liblammps_machine.a/so`` files.
**CMake and make info**\ :
CMake and make info
^^^^^^^^^^^^^^^^^^^
Note that for creating a shared library, all the libraries it depends on
must be compiled to be compatible with shared libraries. This should be
@ -462,7 +463,8 @@ tool. The actual translation is then done via make commands.
.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
.. _sphinx: https://sphinx-doc.org
**Documentation make option**\ :
Documentation make option
^^^^^^^^^^^^^^^^^^^^^^^^^
The following make commands can be issued in the doc folder of the
LAMMPS source distribution.
@ -489,7 +491,8 @@ your system.
current LAMMPS version (HTML and PDF files), from the website
`download page <https://lammps.sandia.gov/download.html>`_.
**CMake build option**\ :
CMake build option
^^^^^^^^^^^^^^^^^^
It is also possible to create the HTML version of the manual within
the :doc:`CMake build directory <Build_cmake>`. The reason for this
@ -512,7 +515,8 @@ Build LAMMPS tools
Some tools described in :doc:`Auxiliary tools <Tools>` can be built directly
using CMake or Make.
**CMake build3**\ :
CMake build
^^^^^^^^^^^
.. code-block:: bash
@ -521,7 +525,8 @@ using CMake or Make.
The generated binaries will also become part of the LAMMPS installation
(see below).
**Traditional make**\ :
Traditional make
^^^^^^^^^^^^^^^^
.. code-block:: bash
@ -545,7 +550,8 @@ a globally visible place on your system, for others to access. Note
that you may need super-user privileges (e.g. sudo) if the directory
you want to copy files to is protected.
**CMake build**\ :
CMake build
^^^^^^^^^^^
.. code-block:: bash
@ -553,7 +559,8 @@ you want to copy files to is protected.
make # perform make after CMake command
make install # perform the installation into prefix
**Traditional make**\ :
Traditional make
^^^^^^^^^^^^^^^^
There is no "install" option in the ``src/Makefile`` for LAMMPS. If
you wish to do this you will need to first build LAMMPS, then manually

2
doc/src/Build_cmake.rst
View File

@ -107,7 +107,7 @@ re-compile and relink the LAMMPS executable with ``cmake --build .`` (or
``cmake .`` and then compile again. The included dependency tracking
should make certain that only the necessary subset of files are
re-compiled. You can also delete compiled objects, libraries and
executables with ``cmake --build . clean`` (or ``make clean``).
executables with ``cmake --build . --target clean`` (or ``make clean``).
After compilation, you may optionally install the LAMMPS executable into
your system with:

328
doc/src/Build_development.rst
View File

@ -8,8 +8,8 @@ useful during development, testing or debugging.
.. _compilation:
Verify compilation flags
------------------------
Monitor compilation flags
-------------------------
Sometimes it is necessary to verify the complete sequence of compilation flags
generated by the CMake build. To enable a more verbose output during
@ -19,7 +19,8 @@ compilation you can use the following option.
-D CMAKE_VERBOSE_MAKEFILE=value # value = no (default) or yes
Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1:
Another way of doing this without reconfiguration is calling make with
variable VERBOSE set to 1:
.. code-block:: bash
@ -33,77 +34,320 @@ Address, Undefined Behavior, and Thread Sanitizer Support
---------------------------------------------------------
Compilers such as GCC and Clang support generating instrumented binaries
which use different sanitizer libraries to detect problems in code
which use different sanitizer libraries to detect problems in the code
during run-time. They can detect issues like:
- `memory leaks <https://clang.llvm.org/docs/AddressSanitizer.html>`_
- `undefined behavior <https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html>`_
- `data races <https://clang.llvm.org/docs/ThreadSanitizer.html>`_
Please note that this kind of instrumentation usually comes with a small
performance hit (much less than using tools like `Valgrind
<https://valgrind.org>`_). The to enable these features additional
compiler flags need to be added to the compilation and linking stages.
This is most easily done through setting the ``CMAKE_TUNE_FLAGS``
variable during configuration. Examples:
Please note that this kind of instrumentation usually comes with a
performance hit (but much less than using tools like `Valgrind
<https://valgrind.org>`_ with a more low level approach). The to enable
these features additional compiler flags need to be added to the
compilation and linking stages. This is done through setting the
``ENABLE_SANITIZER`` variable during configuration. Examples:
.. code-block:: bash
-D CMAKE_TUNE_FLAGS=-fsanitize=address # enable address sanitizer / memory leak checker
-D CMAKE_TUNE_FLAGS=-fsanitize=undefined # enable undefined behavior sanitizer
-D CMAKE_TUNE_FLAGS=-fsanitize=thread # enable thread sanitizer
-D ENABLE_SANITIZER=none # no sanitizer active (default)
-D ENABLE_SANITIZER=address # enable address sanitizer / memory leak checker
-D ENABLE_SANITIZER=leak # enable memory leak checker (only)
-D ENABLE_SANITIZER=undefined # enable undefined behavior sanitizer
-D ENABLE_SANITIZER=thread # enable thread sanitizer
----------
.. _testing:
Code Coverage and Testing
---------------------------------------
Code Coverage and Unit Testing
------------------------------
We do extensive regression testing of the LAMMPS code base on a continuous
basis. Some of the logic to do this has been added to the CMake build so
developers can run the tests directly on their workstation.
The LAMMPS code is subject to multiple levels of automated testing
during development: integration testing (i.e. whether the code compiles
on various platforms and with a variety of settings), unit testing
(i.e. whether certain individual parts of the code produce the expected
results for given inputs), run testing (whether selected complete input
decks run without crashing for multiple configurations), and regression
testing (i.e. whether selected input examples reproduce the same
results over a given number of steps and operations within a given
error margin). The status of this automated testing can be viewed on
`https://ci.lammps.org <https://ci.lammps.org>`_.
The unit testing facility is integrated into the CMake build process
of the LAMMPS source code distribution itself. It can be enabled by
setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
It requires the `YAML <http://pyyaml.org/>`_ library and development
headers to compile and will download and compile a recent version of the
`Googletest <https://github.com/google/googletest/>`_ C++ test framework
for implementing the tests.
After compilation is complete, the unit testing is started in the build
folder using the ``ctest`` command, which is part of the CMake software.
The output of this command will be looking something like this::
[...]$ ctest
Test project /home/akohlmey/compile/lammps/build-testing
Start 1: MolPairStyle:hybrid-overlay
1/109 Test #1: MolPairStyle:hybrid-overlay ......... Passed 0.02 sec
Start 2: MolPairStyle:hybrid
2/109 Test #2: MolPairStyle:hybrid ................. Passed 0.01 sec
Start 3: MolPairStyle:lj_class2
[...]
Start 107: PotentialFileReader
107/109 Test #107: PotentialFileReader ................ Passed 0.04 sec
Start 108: EIMPotentialFileReader
108/109 Test #108: EIMPotentialFileReader ............. Passed 0.03 sec
Start 109: TestSimpleCommands
109/109 Test #109: TestSimpleCommands ................. Passed 0.02 sec
100% tests passed, 0 tests failed out of 26
Total Test time (real) = 25.57 sec
The ``ctest`` command has many options, the most important ones are:
.. list-table::
* - Option
- Function
* - -V
- verbose output: display output of individual test runs
* - -j <num>
- parallel run: run <num> tests in parallel
* - -R <regex>
- run subset of tests matching the regular expression <regex>
* - -E <regex>
- exclude subset of tests matching the regular expression <regex>
* - -N
- dry-run: display list of tests without running them
* - -T memcheck
- run tests with valgrind memory checker (if available)
In its full implementation, the unit test framework will consist of multiple
kinds of tests implemented in different programming languages (C++, C, Python,
Fortran) and testing different aspects of the LAMMPS software and its features.
At the moment only tests for "force styles" are implemented. More on those
in the next section.
.. note::
this is incomplete and only represents a small subset of tests that we run
The unit test framework is new and still under development.
The coverage is only minimal and will be expanded over time.
Tests styles of the same kind of style (e.g. pair styles or
bond styles) are performed with the same executable using
different input files in YAML format. So to add a test for
another pair style can be done by copying the YAML file and
editing the style settings and then running the individual test
program with a flag to update the computed reference data.
Detailed documentation about how to add new test program and
the contents of the YAML files for existing test programs
will be provided in time as well.
Unit tests for force styles
^^^^^^^^^^^^^^^^^^^^^^^^^^^
A large part of LAMMPS are different "styles" for computing non-bonded
and bonded interactions selected through the :doc:`pair_style`,
:doc:`bond_style`, :doc:`angle_style`, :doc:`dihedral_style`,
:doc:`improper_style`, and :doc:`kspace_style`. Since these all share
common interfaces, it is possible to write generic test programs that
will call those common interfaces for small test systems with less than
100 atoms and compare the results with pre-recorded reference results.
A test run is then a a collection multiple individual test runs each
with many comparisons to reference results based on template input
files, individual command settings, relative error margins, and
reference data stored in a YAML format file with ``.yaml``
suffix. Currently the programs ``pair_style``, ``bond_style``, and
``angle_style`` are implemented. They will compare forces, energies and
(global) stress for all atoms after a ``run 0`` calculation and after a
few steps of MD with :doc:`fix nve <fix_nve>`, each in multiple variants
with different settings and also for multiple accelerated styles. If a
prerequisite style or package is missing, the individual tests are
skipped. All tests will be executed on a single MPI process, so using
the CMake option ``-D BUILD_MPI=off`` can significantly speed up testing,
since this will skip the MPI initialization for each test run.
Below is an example command and output:
.. parsed-literal::
[tests]$ pair_style mol-pair-lj_cut.yaml
[==========] Running 6 tests from 1 test suite.
[----------] Global test environment set-up.
[----------] 6 tests from PairStyle
[ RUN ] PairStyle.plain
[ OK ] PairStyle.plain (24 ms)
[ RUN ] PairStyle.omp
[ OK ] PairStyle.omp (18 ms)
[ RUN ] PairStyle.intel
[ OK ] PairStyle.intel (6 ms)
[ RUN ] PairStyle.opt
[ SKIPPED ] PairStyle.opt (0 ms)
[ RUN ] PairStyle.single
[ OK ] PairStyle.single (7 ms)
[ RUN ] PairStyle.extract
[ OK ] PairStyle.extract (6 ms)
[----------] 6 tests from PairStyle (62 ms total)
[----------] Global test environment tear-down
[==========] 6 tests from 1 test suite ran. (63 ms total)
[ PASSED ] 5 tests.
[ SKIPPED ] 1 test, listed below:
[ SKIPPED ] PairStyle.opt
In this particular case, 5 out of 6 sets of tests were conducted, the
tests for the ``lj/cut/opt`` pair style was skipped, since the tests
executable did not include it. To learn what individual tests are performed,
you (currently) need to read the source code. You can use code coverage
recording (see next section) to confirm how well the tests cover the code
paths in the individual source files.
The force style test programs have a common set of options:
.. list-table::
* - Option
- Function
* - -g <newfile>
- regenerate reference data in new YAML file
* - -u
- update reference data in the original YAML file
* - -s
- print error statistics for each group of comparisons
* - -v
- verbose output: also print the executed LAMMPS commands
The ``ctest`` tool has no mechanism to directly pass flags to the individual
test programs, but a workaround has been implemented where these flags can be
set in an environment variable ``TEST_ARGS``. Example:
.. code-block:: bash
-D ENABLE_TESTING=value # enable simple run tests of LAMMPS, value = no (default) or yes
-D LAMMPS_TESTING_SOURCE_DIR=path # path to lammps-testing repository (option if in custom location)
-D LAMMPS_TESTING_GIT_TAG=value # version of lammps-testing repository that should be used, value = master (default) or custom git commit or tag
env TEST_ARGS=-s ctest -V -R BondStyle
If you enable testing in the CMake build it will create an additional
target called "test". You can run them with:
To add a test for a style that is not yet covered, it is usually best
to copy a YAML file for a similar style to a new file, edit the details
of the style (how to call it, how to set its coefficients) and then
run test command with either the *-g* and the replace the initial
test file with the regenerated one or the *-u* option. The *-u* option
will destroy the original file, if the generation run does not complete,
so using *-g* is recommended unless the YAML file is fully tested
and working.
.. admonition:: Recommendations and notes for YAML files
:class: note
- The reference results should be recorded without any code
optimization or related compiler flags enabled.
- The ``epsilon`` parameter defines the relative precision with which
the reference results must be met. The test geometries often have
high and low energy parts and thus a significant impact from
floating-point math truncation errors is to be expected. Some
functional forms and potentials are more noisy than others, so this
parameter needs to be adjusted. Typically a value around 1.0e-13
can be used, but it may need to be as large as 1.0e-8 in some
cases.
- The tests for pair styles from OPT, USER-OMP and USER-INTEL are
performed with automatically rescaled epsilon to account for
additional loss of precision from code optimizations and different
summation orders.
- When compiling with (aggressive) compiler optimization, some tests
are likely to fail. It is recommended to inspect the individual
tests in detail to decide, whether the specific error for a specific
property is acceptable (it often is), or this may be an indication
of mis-compiled code (or an undesired large loss of precision due
to significant reordering of operations and thus less error cancellation).
Tests for other components and utility functions
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Additional tests that validate utility functions or specific components
of LAMMPS are implemented as standalone executable which may, or may not
require creating a suitable LAMMPS instance. These tests are more specific
and do not require YAML format input files. To add a test, either an
existing source file needs to be extended or a new file added, which in turn
requires additions to the ``CMakeLists.txt`` file in the source folder.
Collect and visualize code coverage metrics
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
You can also collect code coverage metrics while running LAMMPS or the
tests by enabling code coverage support during the CMake configuration:
.. code-block:: bash
cmake --build . test
-D ENABLE_COVERAGE=on # enable coverage measurements (off by default)
The test cases used come from the lammps-testing repository. They are
derivatives of the examples folder with some modifications to make the
run faster.
This will instrument all object files to write information about which
lines of code were accessed during execution in files next to the
corresponding object files. These can be post-processed to visually
show the degree of coverage and which code paths are accessed and which
are not taken. When working on unit tests (see above), this can be
extremely helpful to determine which parts of the code are not executed
and thus what kind of tests are still missing. The coverage data is
cumulative, i.e. new data is added with each new run.
You can also collect code coverage metrics while running the tests by
enabling coverage support during building.
Enabling code coverage will also add the following build targets to
generate coverage reports after running the LAMMPS executable or the
unit tests:
.. code-block:: bash
-D ENABLE_COVERAGE=value # enable coverage measurements, value = no (default) or yes
make gen_coverage_html # generate coverage report in HTML format
make gen_coverage_xml # generate coverage report in XML format
make clean_coverage_html # delete folder with HTML format coverage report
make reset_coverage # delete all collected coverage data and HTML output
This will also add the following targets to generate coverage reports
after running the LAMMPS executable:
.. code-block:: bash
make test # run tests first!
make gen_coverage_html # generate coverage report in HTML format
make gen_coverage_xml # generate coverage report in XML format
These reports require GCOVR to be installed. The easiest way to do this
to install it via pip:
These reports require `GCOVR <https://gcovr.com/>`_ to be installed. The easiest way
to do this to install it via pip:
.. code-block:: bash
pip install git+https://github.com/gcovr/gcovr.git
After post-processing with ``gen_coverage_html`` the results are in
a folder ``coverage_html`` and can be viewed with a web browser.
The images below illustrate how the data is presented.
.. list-table::
* - .. figure:: JPG/coverage-overview-top.png
:target: JPG/coverage-overview-top.png
Top of the overview page
- .. figure:: JPG/coverage-overview-manybody.png
:target: JPG/coverage-overview-manybody.png
Styles with good coverage
- .. figure:: JPG/coverage-file-top.png
:target: JPG/coverage-file-top.png
Top of individual source page
- .. figure:: JPG/coverage-file-branches.png
:target: JPG/coverage-file-branches.png
Source page with branches
Coding style utilities
----------------------
To aid with enforcing some of the coding style conventions in LAMMPS
some additional build targets have been added. These require Python 3.5
or later and will only work on Unix-like operating and file systems.
The following options are available.
.. code-block:: bash
make check-whitespace # generate coverage report in HTML format
make fix-whitespace # generate coverage report in XML format
make check-permissions # delete folder with HTML format coverage report
make fix-permissions # delete all collected coverage data and HTML output
For the code in the ``unittest`` tree we are using the `clang-format`
tool (Clang version 8.0 or later is required). If available, the source
code files in the ``unittest`` tree can be updated to conform to the
formatting settings using ``make format-tests``.

665
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@ -1,12 +1,12 @@
Link LAMMPS as a library to another code
========================================
LAMMPS is designed as a library of C++ objects and can thus be
LAMMPS is designed as a library of C++ objects that can be
integrated into other applications including Python scripts.
The files ``src/library.cpp`` and ``src/library.h`` define a
C-style API for using LAMMPS as a library. See the :doc:`Howto
library <Howto_library>` doc page for a description of the interface
and how to extend it for your needs.
library <Howto_library>` page for a description of the interface
and how to use it for your needs.
The :doc:`Build basics <Build_basics>` doc page explains how to build
LAMMPS as either a shared or static library. This results in a file
@ -31,18 +31,18 @@ the suffix ``.so.0`` (or some other number).
communicator with a subset of MPI ranks to the function creating the
LAMMPS instance.
----------
**Link with LAMMPS as a static library**\ :
Link with LAMMPS as a static library
------------------------------------
The calling application can link to LAMMPS as a static library with
compilation and link commands as in the examples shown below. These
are examples for a code written in C in the file *caller.c*.
are examples for a code written in C in the file ``caller.c``.
The benefit of linking to a static library is, that the resulting
executable is independent of that library since all required
executable code from the library is copied into the calling executable.
*CMake build*\ :
CMake build
^^^^^^^^^^^
This assumes that LAMMPS has been configured without setting a
``LAMMPS_MACHINE`` name, installed with "make install", and the
@ -55,7 +55,8 @@ The commands to compile and link a coupled executable are then:
mpicc -c -O $(pkgconf liblammps --cflags) caller.c
mpicxx -o caller caller.o -$(pkgconf liblammps --libs)
*Traditional make*\ :
Traditional make
^^^^^^^^^^^^^^^^
This assumes that LAMMPS has been compiled in the folder
``${HOME}/lammps/src`` with "make mpi". The commands to compile and link
@ -83,20 +84,20 @@ LAMMPS library without any optional packages that depend on libraries
need to include all flags, libraries, and paths for the coupled
executable, that are also required to link the LAMMPS executable.
*CMake build*\ :
CMake build
^^^^^^^^^^^
When using CMake, additional libraries with sources in the lib folder
are built, but not included in ``liblammps.a`` and (currently) not
installed with "make install" and not included in the *pkgconfig*
installed with ``make install`` and not included in the ``pkgconfig``
configuration file. They can be found in the top level build folder,
but you have to determine the necessary link flags manually. It is
therefore recommended to either use the traditional make procedure to
build and link with a static library or build and link with a shared
library instead.
.. TODO: this needs to be updated to reflect that latest CMake changes after they are complete.
*Traditional make*\ :
Traditional make
^^^^^^^^^^^^^^^^
After you have compiled a static LAMMPS library using the conventional
build system for example with "make mode=static serial". And you also
@ -110,10 +111,10 @@ change to:
g++ -o caller caller.o -L${HOME}/lammps/lib/poems \
-L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src -llammps_serial -lpoems -lmpi_stubs
Note, that you need to link with "g++" instead of "gcc", since the
LAMMPS library is C++ code. You can display the currently applied
settings for building LAMMPS for the "serial" machine target by using
the command:
Note, that you need to link with ``g++`` instead of ``gcc`` even if you have
written your code in C, since LAMMPS itself is C++ code. You can display the
currently applied settings for building LAMMPS for the "serial" machine target
by using the command:
.. code-block:: bash
@ -123,25 +124,24 @@ Which should output something like:
.. code-block:: bash
# Compiler:
# Compiler:
CXX=g++
# Linker:
# Linker:
LD=g++
# Compilation:
# Compilation:
CXXFLAGS=-g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -I${HOME}/compile/lammps/lib/poems -I${HOME}/compile/lammps/src/STUBS
# Linking:
# Linking:
LDFLAGS=-g -O
# Libraries:
# Libraries:
LDLIBS=-L${HOME}/compile/lammps/src -llammps_serial -L${HOME}/compile/lammps/lib/poems -L${HOME}/compile/lammps/src/STUBS -lpoems -lmpi_stubs
From this you can gather the necessary paths and flags. With
makefiles for other *machine* configurations you need to do the
equivalent and replace "serial" with the corresponding *machine* name
equivalent and replace "serial" with the corresponding "machine" name
of the makefile.
----------
**Link with LAMMPS as a shared library**\ :
Link with LAMMPS as a shared library
------------------------------------
When linking to LAMMPS built as a shared library, the situation becomes
much simpler, as all dependent libraries and objects are either included
@ -151,7 +151,8 @@ linking the calling executable. Only the *-I* flags are needed. So the
example case from above of the serial version static LAMMPS library with
the POEMS package installed becomes:
*CMake build*\ :
CMake build
^^^^^^^^^^^
The commands with a shared LAMMPS library compiled with the CMake
build process are the same as for the static library.
@ -161,10 +162,11 @@ build process are the same as for the static library.
mpicc -c -O $(pkgconf liblammps --cflags) caller.c
mpicxx -o caller caller.o -$(pkgconf --libs)
*Traditional make*\ :
Traditional make
^^^^^^^^^^^^^^^^
The commands with a shared LAMMPS library compiled with the
traditional make build using "make mode=shared serial" becomes:
traditional make build using ``make mode=shared serial`` becomes:
.. code-block:: bash
@ -231,29 +233,3 @@ If a required library is missing, you would get a 'not found' entry:
libc.so.6 => /usr/lib64/libc.so.6 (0x00007fb7c7b5d000)
/lib64/ld-linux-x86-64.so.2 (0x00007fb7c80a2000)
----------
**Calling the LAMMPS library**\ :
Either flavor of library (static or shared) allows one or more LAMMPS
objects to be instantiated from the calling program. When used from a
C++ program, most of the symbols and functions in LAMMPS are wrapped
in a ``LAMMPS_NS`` namespace; you can safely use any of its classes and
methods from within the calling code, as needed, and you will not incur
conflicts with functions and variables in your code that share the name.
This, however, does not extend to all additional libraries bundled with
LAMMPS in the lib folder and some of the low-level code of some packages.
To be compatible with C, Fortran, Python programs, the library has a simple
C-style interface, provided in ``src/library.cpp`` and ``src/library.h``.
See the :doc:`Python library <Python_library>` doc page for a
description of the Python interface to LAMMPS, which wraps the C-style
interface from a shared library through the `ctypes python module <ctypes_>`_.
See the sample codes in ``examples/COUPLE/simple`` for examples of C++ and
C and Fortran codes that invoke LAMMPS through its library interface.
Other examples in the COUPLE directory use coupling ideas discussed on
the :doc:`Howto couple <Howto_couple>` doc page.
.. _ctypes: https://docs.python.org/3/library/ctypes.html

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@ -45,7 +45,8 @@ packages:
The mechanism for including packages is simple but different for CMake
versus make.
**CMake build**\ :
CMake build
^^^^^^^^^^^
.. code-block:: csh
@ -72,7 +73,8 @@ once with CMake.
invoke cmake. CMake will give an error if that is not the case,
indicating how you can un-install all packages in the src dir.
**Traditional make**\ :
Traditional make
^^^^^^^^^^^^^^^^
.. code-block:: bash
@ -108,7 +110,8 @@ once with make.
within the same command. You can include or exclude multiple packages
in a single make command, e.g. make yes-colloid no-manybody.
**CMake and make info**\ :
CMake and make info
^^^^^^^^^^^^^^^^^^^
Any package can be included or excluded in a LAMMPS build, independent
of all other packages. However, some packages include files derived
@ -132,7 +135,7 @@ src directory.
.. _cmake_presets:
**CMake shortcuts for installing many packages**\ :
CMake presets for installing many packages
Instead of specifying all the CMake options via the command-line,
CMake allows initializing its settings cache using script files.
@ -148,13 +151,14 @@ one of them as a starting point and customize it to your needs.
.. code-block:: bash
cmake -C ../cmake/presets/minimal.cmake [OPTIONS] ../cmake # enable just a few core packages
cmake -C ../cmake/presets/most.cmake [OPTIONS] ../cmake # enable most packages
cmake -C ../cmake/presets/nolib.cmake [OPTIONS] ../cmake # disable packages that do require extra libraries or tools
cmake -C ../cmake/presets/clang.cmake [OPTIONS] ../cmake # change settings to use the Clang compilers by default
cmake -C ../cmake/presets/intel.cmake [OPTIONS] ../cmake # change settings to use the Intel compilers by default
cmake -C ../cmake/presets/all_on.cmake [OPTIONS] ../cmake # enable all packages
cmake -C ../cmake/presets/all_off.cmake [OPTIONS] ../cmake # disable all packages
cmake -C ../cmake/presets/minimal.cmake [OPTIONS] ../cmake # enable just a few core packages
cmake -C ../cmake/presets/most.cmake [OPTIONS] ../cmake # enable most packages
cmake -C ../cmake/presets/download.cmake [OPTIONS] ../cmake # enable packages which download sources or potential files
cmake -C ../cmake/presets/nolib.cmake [OPTIONS] ../cmake # disable packages that do require extra libraries or tools
cmake -C ../cmake/presets/clang.cmake [OPTIONS] ../cmake # change settings to use the Clang compilers by default
cmake -C ../cmake/presets/intel.cmake [OPTIONS] ../cmake # change settings to use the Intel compilers by default
cmake -C ../cmake/presets/all_on.cmake [OPTIONS] ../cmake # enable all packages
cmake -C ../cmake/presets/all_off.cmake [OPTIONS] ../cmake # disable all packages
mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake # compile with MinGW cross compilers
.. note::
@ -184,7 +188,8 @@ one of them as a starting point and customize it to your needs.
----------
**Make shortcuts for installing many packages**\ :
Make shortcuts for installing many packages
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The following commands are useful for managing package source files
and their installation when building LAMMPS via traditional make.

82
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@ -44,7 +44,8 @@ require use of an FFT library to compute 1d FFTs. The KISS FFT
library is included with LAMMPS but other libraries can be faster.
LAMMPS can use them if they are available on your system.
**CMake variables**\ :
CMake build
^^^^^^^^^^^
.. code-block:: bash
@ -74,7 +75,12 @@ to assist:
-D FFT_MKL_THREADS=on # enable using threaded FFTs with MKL libraries
-D MKL_LIBRARIES=path
**Makefile.machine settings**\ :
Traditional make
^^^^^^^^^^^^^^^^
To change the FFT library to be used and its options, you have to edit
your machine Makefile. Below are examples how the makefile variables
could be changed.
.. code-block:: make
@ -104,7 +110,8 @@ As with CMake, you do not need to set paths in ``FFT_INC`` or ``FFT_PATH``, if
the compiler can find the FFT header and library files in its default search path.
You must specify ``FFT_LIB`` with the appropriate FFT libraries to include in the link.
**CMake and make info**\ :
CMake build
^^^^^^^^^^^
The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS
distribution. It is portable across all platforms. Depending on the size
@ -127,7 +134,7 @@ download it from `www.fftw.org <http://www.fftw.org>`_. LAMMPS requires
version 3.X; the legacy version 2.1.X is no longer supported.
Building FFTW for your box should be as simple as ``./configure; make;
make install``\ . The install command typically requires root privileges
make install``. The install command typically requires root privileges
(e.g. invoke it via sudo), unless you specify a local directory with
the "--prefix" option of configure. Type ``./configure --help`` to see
various options.
@ -169,20 +176,25 @@ ARRAY mode.
.. _size:
Size of LAMMPS data types
Size of LAMMPS integer types
------------------------------------
LAMMPS has a few integer data types which can be defined as 4-byte or
8-byte integers. The default setting of "smallbig" is almost always
adequate.
LAMMPS has a few integer data types which can be defined as either
4-byte (= 32-bit) or 8-byte (= 64-bit) integers at compile time.
The default setting of "smallbig" is almost always adequate.
**CMake variable**\ :
CMake build
^^^^^^^^^^^
.. code-block:: bash
-D LAMMPS_SIZES=value # smallbig (default) or bigbig or smallsmall
**Makefile.machine setting**\ :
Traditional build
^^^^^^^^^^^^^^^^^
If you want a setting different from the default, you need to edit your
machine Makefile.
.. code-block:: make
@ -190,7 +202,8 @@ adequate.
The default setting is ``-DLAMMPS_SMALLBIG`` if nothing is specified
**CMake and make info**\ :
CMake and make info
^^^^^^^^^^^^^^^^^^^
The default "smallbig" setting allows for simulations with:
@ -251,7 +264,8 @@ PNG image files. Likewise the :doc:`dump movie <dump_image>` command
outputs movie files in MPEG format. Using these options requires the
following settings:
**CMake variables**\ :
CMake build
^^^^^^^^^^^
.. code-block:: bash
@ -276,7 +290,8 @@ variables:
-D ZLIB_LIBRARIES=path # path to libz.a (.so) file
-D FFMPEG_EXECUTABLE=path # path to ffmpeg executable
**Makefile.machine settings**\ :
Traditional make
^^^^^^^^^^^^^^^^
.. code-block:: make
@ -295,7 +310,8 @@ with a list of graphics libraries to include in the link. You must
insure ffmpeg is in a directory where LAMMPS can find it at runtime,
that is a directory in your PATH environment variable.
**CMake and make info**\ :
CMake and make info
^^^^^^^^^^^^^^^^^^^
Using ``ffmpeg`` to output movie files requires that your machine
supports the "popen" function in the standard runtime library.
@ -318,7 +334,8 @@ If this option is enabled, large files can be read or written with
gzip compression by several LAMMPS commands, including
:doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
**CMake variables**\ :
CMake build
^^^^^^^^^^^
.. code-block:: bash
@ -326,13 +343,15 @@ gzip compression by several LAMMPS commands, including
# default is yes if CMake can find gzip, else no
-D GZIP_EXECUTABLE=path # path to gzip executable if CMake cannot find it
**Makefile.machine setting**\ :
Traditional make
^^^^^^^^^^^^^^^^
.. code-block:: make
LMP_INC = -DLAMMPS_GZIP
**CMake and make info**\ :
CMake and make info
^^^^^^^^^^^^^^^^^^^
This option requires that your machine supports the "popen()" function
in the standard runtime library and that a gzip executable can be
@ -363,7 +382,8 @@ pointers that are aligned to 16-byte boundaries. Using SSE vector
instructions efficiently, however, requires memory blocks being
aligned on 64-byte boundaries.
**CMake variable**\ :
CMake build
^^^^^^^^^^^
.. code-block:: bash
@ -374,7 +394,8 @@ and revert to using the malloc() C-library function instead. When
compiling LAMMPS for Windows systems, malloc() will always be used
and this setting ignored.
**Makefile.machine setting**\ :
Traditional make
^^^^^^^^^^^^^^^^
.. code-block:: make
@ -398,13 +419,15 @@ types, the following setting will be needed. It converts "long long"
to a "long" data type, which should be the desired 8-byte integer on
those systems:
**CMake variable**\ :
CMake build
^^^^^^^^^^^
.. code-block:: bash
-D LAMMPS_LONGLONG_TO_LONG=value # yes or no (default)
**Makefile.machine setting**\ :
Traditional make
^^^^^^^^^^^^^^^^
.. code-block:: make
@ -420,17 +443,26 @@ Exception handling when using LAMMPS as a library
This setting is useful when external codes drive LAMMPS as a library.
With this option enabled, LAMMPS errors do not kill the calling code.
Instead, the call stack is unwound and control returns to the caller,
e.g. to Python. Of course the calling code has to be set up to
*catch* exceptions from within LAMMPS.
e.g. to Python. Of course, the calling code has to be set up to
*catch* exceptions thrown from within LAMMPS.
**CMake variable**\ :
CMake build
^^^^^^^^^^^
.. code-block:: bash
-D LAMMPS_EXCEPTIONS=value # yes or no (default)
**Makefile.machine setting**\ :
Traditional make
^^^^^^^^^^^^^^^^
.. code-block:: make
LMP_INC = -DLAMMPS_EXCEPTIONS
.. note::
When LAMMPS is running in parallel, it is not always possible to
cleanly recover from an exception since not all parallel ranks may
throw an exception and thus other MPI ranks may get stuck waiting for
messages from the ones with errors.

1
doc/src/Commands_all.rst
View File

@ -94,6 +94,7 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`package <package>`
* :doc:`pair_coeff <pair_coeff>`
* :doc:`pair_modify <pair_modify>`
* :doc:`pair_style <pair_style>`
* :doc:`pair_write <pair_write>`
* :doc:`partition <partition>`
* :doc:`prd <prd>`

12
doc/src/Commands_compute.rst
View File

@ -42,7 +42,7 @@ KOKKOS, o = USER-OMP, t = OPT.
* :doc:`com <compute_com>`
* :doc:`com/chunk <compute_com_chunk>`
* :doc:`contact/atom <compute_contact_atom>`
* :doc:`coord/atom <compute_coord_atom>`
* :doc:`coord/atom (k) <compute_coord_atom>`
* :doc:`damage/atom <compute_damage_atom>`
* :doc:`dihedral <compute_dihedral>`
* :doc:`dihedral/local <compute_dihedral_local>`
@ -79,15 +79,13 @@ KOKKOS, o = USER-OMP, t = OPT.
* :doc:`ke/atom/eff <compute_ke_atom_eff>`
* :doc:`ke/eff <compute_ke_eff>`
* :doc:`ke/rigid <compute_ke_rigid>`
* :doc:`meso/e/atom <compute_meso_e_atom>`
* :doc:`meso/rho/atom <compute_meso_rho_atom>`
* :doc:`meso/t/atom <compute_meso_t_atom>`
* :doc:`mesont <compute_mesont>`
* :doc:`momentum <compute_momentum>`
* :doc:`msd <compute_msd>`
* :doc:`msd/chunk <compute_msd_chunk>`
* :doc:`msd/nongauss <compute_msd_nongauss>`
* :doc:`omega/chunk <compute_omega_chunk>`
* :doc:`orientorder/atom <compute_orientorder_atom>`
* :doc:`orientorder/atom (k) <compute_orientorder_atom>`
* :doc:`pair <compute_pair>`
* :doc:`pair/local <compute_pair_local>`
* :doc:`pe <compute_pe>`
@ -133,6 +131,9 @@ KOKKOS, o = USER-OMP, t = OPT.
* :doc:`sna/atom <compute_sna_atom>`
* :doc:`snad/atom <compute_sna_atom>`
* :doc:`snav/atom <compute_sna_atom>`
* :doc:`sph/e/atom <compute_sph_e_atom>`
* :doc:`sph/rho/atom <compute_sph_rho_atom>`
* :doc:`sph/t/atom <compute_sph_t_atom>`
* :doc:`spin <compute_spin>`
* :doc:`stress/atom <compute_stress_atom>`
* :doc:`stress/mop <compute_stress_mop>`
@ -161,5 +162,6 @@ KOKKOS, o = USER-OMP, t = OPT.
* :doc:`torque/chunk <compute_torque_chunk>`
* :doc:`vacf <compute_vacf>`
* :doc:`vcm/chunk <compute_vcm_chunk>`
* :doc:`viscosity/cos <compute_viscosity_cos>`
* :doc:`voronoi/atom <compute_voronoi_atom>`
* :doc:`xrd <compute_xrd>`

6
doc/src/Commands_fix.rst
View File

@ -22,6 +22,7 @@ OPT.
.. table_from_list::
:columns: 5
* :doc:`accelerate/cos <fix_accelerate_cos>`
* :doc:`adapt <fix_adapt>`
* :doc:`adapt/fep <fix_adapt_fep>`
* :doc:`addforce <fix_addforce>`
@ -94,9 +95,7 @@ OPT.
* :doc:`lb/viscous <fix_lb_viscous>`
* :doc:`lineforce <fix_lineforce>`
* :doc:`manifoldforce <fix_manifoldforce>`
* :doc:`meso <fix_meso>`
* :doc:`meso/move <fix_meso_move>`
* :doc:`meso/stationary <fix_meso_stationary>`
* :doc:`momentum (k) <fix_momentum>`
* :doc:`move <fix_move>`
* :doc:`mscg <fix_mscg>`
@ -148,6 +147,7 @@ OPT.
* :doc:`oneway <fix_oneway>`
* :doc:`orient/bcc <fix_orient>`
* :doc:`orient/fcc <fix_orient>`
* :doc:`orient/eco <fix_orient_eco>`
* :doc:`phonon <fix_phonon>`
* :doc:`pimd <fix_pimd>`
* :doc:`planeforce <fix_planeforce>`
@ -201,6 +201,8 @@ OPT.
* :doc:`smd/move_tri_surf <fix_smd_move_triangulated_surface>`
* :doc:`smd/setvel <fix_smd_setvel>`
* :doc:`smd/wall_surface <fix_smd_wall_surface>`
* :doc:`sph <fix_sph>`
* :doc:`sph/stationary <fix_sph_stationary>`
* :doc:`spring <fix_spring>`
* :doc:`spring/chunk <fix_spring_chunk>`
* :doc:`spring/rg <fix_spring_rg>`

6
doc/src/Commands_input.rst
View File

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

9
doc/src/Commands_pair.rst
View File

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

2
doc/src/Developer/developer.tex
View File

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

18
doc/src/Errors_debug.rst
View File

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

22
doc/src/Errors_messages.rst
View File

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

8
doc/src/Errors_warnings.rst
View File

@ -43,17 +43,17 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
Self-explanatory.
*Bond atom missing in box size check*
The 2nd atoms needed to compute a particular bond is missing on this
The second atom needed to compute a particular bond is missing on this
processor. Typically this is because the pairwise cutoff is set too
short or the bond has blown apart and an atom is too far away.
*Bond atom missing in image check*
The 2nd atom in a particular bond is missing on this processor.
The second atom in a particular bond is missing on this processor.
Typically this is because the pairwise cutoff is set too short or the
bond has blown apart and an atom is too far away.
*Bond atoms missing at step %ld*
The 2nd atom needed to compute a particular bond is missing on this
The second atom needed to compute a particular bond is missing on this
processor. Typically this is because the pairwise cutoff is set too
short or the bond has blown apart and an atom is too far away.
@ -486,7 +486,7 @@ This will most likely cause errors in kinetic fluctuations.
a new style.
*No Kspace calculation with verlet/split*
The 2nd partition performs a kspace calculation so the kspace_style
The second partition performs a kspace calculation so the kspace_style
command must be used.
*No automatic unit conversion to XTC file format conventions possible for units lj*

2
doc/src/Examples.rst
View File

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

2
doc/src/Howto_chunk.rst
View File

@ -197,7 +197,7 @@ compress individual polymer chains (molecules) in a mixture, is
explained on the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command doc page.
(7) An example for using one set of per-chunk values for molecule
chunks, to create a 2nd set of micelle-scale chunks (clustered
chunks, to create a second set of micelle-scale chunks (clustered
molecules, due to hydrophobicity), is explained on the :doc:`compute chunk/reduce <compute_reduce_chunk>` command doc page.
(8) An example for using one set of per-chunk values (dipole moment

48
doc/src/Howto_cmake.rst
View File

@ -114,19 +114,19 @@ summary screen will look like this:
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Git: /usr/bin/git (found version "2.25.2")
-- Found Git: /usr/bin/git (found version "2.25.2")
-- Running check for auto-generated files from make-based build system
-- Found MPI_CXX: /usr/lib64/mpich/lib/libmpicxx.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- Found MPI_CXX: /usr/lib64/mpich/lib/libmpicxx.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- Looking for C++ include omp.h
-- Looking for C++ include omp.h - found
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Found JPEG: /usr/lib64/libjpeg.so (found version "62")
-- Found PNG: /usr/lib64/libpng.so (found version "1.6.37")
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11")
-- Found GZIP: /usr/bin/gzip
-- Found FFMPEG: /usr/bin/ffmpeg
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Found JPEG: /usr/lib64/libjpeg.so (found version "62")
-- Found PNG: /usr/lib64/libpng.so (found version "1.6.37")
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11")
-- Found GZIP: /usr/bin/gzip
-- Found FFMPEG: /usr/bin/ffmpeg
-- Performing Test COMPILER_SUPPORTS-ffast-math
-- Performing Test COMPILER_SUPPORTS-ffast-math - Success
-- Performing Test COMPILER_SUPPORTS-march=native
@ -143,7 +143,7 @@ summary screen will look like this:
* JPEG
* PNG
* ZLIB
-- <<< Build configuration >>>
Build type: RelWithDebInfo
Install path: /home/akohlmey/.local
@ -157,7 +157,7 @@ summary screen will look like this:
Options: -ffast-math;-march=native
-- <<< Linker flags: >>>
-- Executable name: lmp
-- Static library flags:
-- Static library flags:
-- <<< MPI flags >>>
-- MPI includes: /usr/include/mpich-x86_64
-- MPI libraries: /usr/lib64/mpich/lib/libmpicxx.so;/usr/lib64/mpich/lib/libmpi.so;
@ -291,7 +291,7 @@ Some common CMake variables
.. list-table::
:header-rows: 1
* - Variable
- Description
* - ``CMAKE_INSTALL_PREFIX``
@ -313,13 +313,13 @@ Some common CMake variables
- Fortran compiler to be used for compilation (default: system specific, ``gfortran`` on Linux)
* - ``CXX_COMPILER_LAUNCHER``
- tool to launch the C++ compiler, e.g. ``ccache`` or ``distcc`` for faster compilation (default: empty)
Some common LAMMPS specific variables
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. list-table::
:header-rows: 1
* - Variable
- Description
* - ``BUILD_MPI``
@ -378,9 +378,9 @@ change some variables later with additional *-D* flags. A few examples:
.. code-block:: bash
cmake -C ../cmake/preset/minimal.cmake -D PKG_MISC=on ../cmake
cmake -C ../cmake/preset/clang.cmake -C ../cmake/preset/most.cmake ../cmake
cmake -C ../cmake/preset/minimal.cmake -D BUILD_MPI=off ../cmake
cmake -C ../cmake/presets/minimal.cmake -D PKG_MISC=on ../cmake
cmake -C ../cmake/presets/clang.cmake -C ../cmake/presets/most.cmake ../cmake
cmake -C ../cmake/presets/minimal.cmake -D BUILD_MPI=off ../cmake
The first command will install the packages ``KSPACE``, ``MANYBODY``,
``MOLECULE``, ``RIGID`` and ``MISC``; the first four from the preset
@ -396,7 +396,7 @@ It is also possible to do this incrementally.
.. code-block:: bash
cmake -C ../cmake/preset/minimal.cmake ../cmake
cmake -C ../cmake/presets/minimal.cmake ../cmake
cmake -D PKG_MISC=on .
will achieve the same configuration like in the first example above. In
@ -415,8 +415,10 @@ This is particularly convenient, if you have set a custom build command
via the ``CMAKE_MAKE_PROGRAM`` variable.
When calling the build program, you can also select which "target" is to
be build through appending the name of the target to the build command.
Example: ``cmake --build . all``. The following abstract targets are available:
be build through appending the ``--target`` flag and the name of the target
to the build command. When using ``make`` as build tool, you can just append
the target name to the command. Example: ``cmake --build . --target all`` or
``make all``. The following abstract targets are available:
.. list-table::
:header-rows: 1
@ -432,11 +434,11 @@ Example: ``cmake --build . all``. The following abstract targets are available:
* - ``install``
- install all target files into folders in ``CMAKE_INSTALL_PREFIX``
* - ``test``
- run some simple tests (if configured with ``-D ENABLE_TESTING=on``)
- run some tests (if configured with ``-D ENABLE_TESTING=on``)
* - ``clean``
- remove all generated files
Choosing generators
-------------------

2
doc/src/Howto_coreshell.rst
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@ -119,7 +119,7 @@ non-polarized ions (ions without an attached satellite particle). The
groups, one for the core atoms, another for the shell atoms.
Non-polarized ions which might also be included in the treated system
should not be included into either of these groups, they are taken
into account by the *group-ID* (2nd argument) of the compute. The
into account by the *group-ID* (second argument) of the compute. The
groups can be defined using the :doc:`group *type*\ <group>` command.
Note that to perform thermostatting using this definition of
temperature, the :doc:`fix modify temp <fix_modify>` command should be

2
doc/src/Howto_multiple.rst
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@ -91,4 +91,4 @@ With these modifications, the 8 simulations of each script would run
on the 3 partitions one after the other until all were finished.
Initially, 3 simulations would be started simultaneously, one on each
partition. When one finished, that partition would then start
the 4th simulation, and so forth, until all 8 were completed.
the fourth simulation, and so forth, until all 8 were completed.

2
doc/src/Howto_restart.rst
View File

@ -28,7 +28,7 @@ scripts are based on. If that script had the line
added to it, it would produce 2 binary restart files (tmp.restart.50
and tmp.restart.100) as it ran.
This script could be used to read the 1st restart file and re-run the
This script could be used to read the first restart file and re-run the
last 50 timesteps:
.. code-block:: LAMMPS

6
doc/src/Howto_triclinic.rst
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@ -85,7 +85,7 @@ where *V* is the volume of the box, **X** is the original vector quantity and
**x** is the vector in the LAMMPS basis.
There is no requirement that a triclinic box be periodic in any
dimension, though it typically should be in at least the 2nd dimension
dimension, though it typically should be in at least the second dimension
of the tilt (y in xy) if you want to enforce a shift in periodic
boundary conditions across that boundary. Some commands that work
with triclinic boxes, e.g. the :doc:`fix deform <fix_deform>` and :doc:`fix npt <fix_nh>` commands, require periodicity or non-shrink-wrap
@ -120,7 +120,7 @@ The 9 parameters, as well as lx,ly,lz, can be output via the
To avoid extremely tilted boxes (which would be computationally
inefficient), LAMMPS normally requires that no tilt factor can skew
the box more than half the distance of the parallel box length, which
is the 1st dimension in the tilt factor (x for xz). This is required
is the first dimension in the tilt factor (x for xz). This is required
both when the simulation box is created, e.g. via the
:doc:`create_box <create_box>` or :doc:`read_data <read_data>` commands,
as well as when the box shape changes dynamically during a simulation,
@ -137,7 +137,7 @@ limit during a dynamics run (e.g. via the :doc:`fix deform <fix_deform>`
command), then the box is "flipped" to an equivalent shape with a tilt
factor within the bounds, so the run can continue. See the :doc:`fix deform <fix_deform>` doc page for further details.
One exception to this rule is if the 1st dimension in the tilt
One exception to this rule is if the first dimension in the tilt
factor (x for xy) is non-periodic. In that case, the limits on the
tilt factor are not enforced, since flipping the box in that dimension
does not change the atom positions due to non-periodicity. In this

21
doc/src/Howto_viscosity.rst
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@ -1,10 +1,11 @@
Calculate viscosity
===================
The shear viscosity eta of a fluid can be measured in at least 5 ways
The shear viscosity eta of a fluid can be measured in at least 6 ways
using various options in LAMMPS. See the examples/VISCOSITY directory
for scripts that implement the 5 methods discussed here for a simple
Lennard-Jones fluid model. Also, see the :doc:`Howto kappa <Howto_kappa>` doc page for an analogous discussion for
Lennard-Jones fluid model and 1 method for SPC/E water model.
Also, see the :doc:`Howto kappa <Howto_kappa>` doc page for an analogous discussion for
thermal conductivity.
Eta is a measure of the propensity of a fluid to transmit momentum in
@ -130,9 +131,25 @@ time-integrated momentum fluxes play the role of Cartesian
coordinates, whose mean-square displacement increases linearly
with time at sufficiently long times.
The sixth is periodic perturbation method. It is also a non-equilibrium MD method.
However, instead of measure the momentum flux in response of applied velocity gradient,
it measures the velocity profile in response of applied stress.
A cosine-shaped periodic acceleration is added to the system via the
:doc:`fix accelerate/cos <fix_accelerate_cos>` command,
and the :doc:`compute viscosity/cos<compute_viscosity_cos>` command is used to monitor the
generated velocity profile and remove the velocity bias before thermostatting.
.. note::
An article by :ref:`(Hess) <Hess3>` discussed the accuracy and efficiency of these methods.
----------
.. _Daivis-viscosity:
**(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
.. _Hess3:
**(Hess)** Hess, B. The Journal of Chemical Physics 2002, 116 (1), 209-217.

68
doc/src/Install_linux.rst
View File

@ -24,12 +24,13 @@ allows you to install LAMMPS with a single command, and stay
up-to-date with the current version of LAMMPS by simply updating your
operating system.
To install the appropriate personal-package archive (PPA), do the
To install the appropriate personal-package archives (PPAs), do the
following once:
.. code-block:: bash
$ sudo add-apt-repository ppa:gladky-anton/lammps
$ sudo add-apt-repository ppa:openkim/latest
$ sudo apt-get update
To install LAMMPS do the following once:
@ -38,7 +39,7 @@ To install LAMMPS do the following once:
$ sudo apt-get install lammps-daily
This downloads an executable named "lmp_daily" to your box, which
This downloads an executable named ``lmp_daily`` to your box, which
can then be used in the usual way to run input scripts:
.. code-block:: bash
@ -60,11 +61,29 @@ To get a copy of the current documentation and examples:
$ sudo apt-get install lammps-daily-doc
which will download the doc files in
/usr/share/doc/lammps-daily-doc/doc and example problems in
/usr/share/doc/lammps-doc/examples.
``/usr/share/doc/lammps-daily-doc/doc`` and example problems in
``/usr/share/doc/lammps-doc/examples``.
Note that you may still wish to download the tarball to get potential
files and auxiliary tools.
To get a copy of the current potentials files:
.. code-block:: bash
$ sudo apt-get install lammps-daily-data
which will download the potentials files to
``/usr/share/lammps-daily/potentials``. The ``lmp_daily`` binary is
hard-coded to look for potential files in this directory (it does not
use the `LAMMPS_POTENTIALS` environment variable, as described
in :doc:`pair_coeff <pair_coeff>` command).
The ``lmp_daily`` binary is built with the :ref:`KIM package <kim>` which
results in the above command also installing the `kim-api` binaries when LAMMPS
is installed. In order to use potentials from `openkim.org <openkim_>`_, you
can install the `openkim-models` package
.. code-block:: bash
$ sudo apt-get install openkim-models
To un-install LAMMPS, do the following:
@ -72,17 +91,8 @@ To un-install LAMMPS, do the following:
$ sudo apt-get remove lammps-daily
Note that the lammps-daily executable is built with the following
sequence of make commands, as if you had done the same with the
unpacked tarball files in the src directory:
.. code-block:: bash
$ make yes-all
$ make no-lib
$ make mpi
Thus it builds with FFTW3 and OpenMPI.
Please use ``lmp_daily -help`` to see which compilation options, packages,
and styles are included in the binary.
Thanks to Anton Gladky (gladky.anton at gmail.com) for setting up this
Ubuntu package capability.
@ -103,14 +113,14 @@ linking to the C library interface (lammps-devel, lammps-mpich-devel,
lammps-openmpi-devel), the header for compiling programs using
the C library interface (lammps-headers), and the LAMMPS python
module for Python 3. All packages can be installed at the same
time and the name of the LAMMPS executable is *lmp* and *lmp_openmpi*
or *lmp_mpich* respectively. By default, *lmp* will refer to the
time and the name of the LAMMPS executable is ``lmp`` and ``lmp_openmpi``
or ``lmp_mpich`` respectively. By default, ``lmp`` will refer to the
serial executable, unless one of the MPI environment modules is loaded
("module load mpi/mpich-x86_64" or "module load mpi/openmpi-x86_64").
(``module load mpi/mpich-x86_64`` or ``module load mpi/openmpi-x86_64``).
Then the corresponding parallel LAMMPS executable can be used.
The same mechanism applies when loading the LAMMPS python module.
To install LAMMPS with OpenMPI and run an input in.lj with 2 CPUs do:
To install LAMMPS with OpenMPI and run an input ``in.lj`` with 2 CPUs do:
.. code-block:: bash
@ -118,10 +128,10 @@ To install LAMMPS with OpenMPI and run an input in.lj with 2 CPUs do:
$ module load mpi/openmpi-x86_64
$ mpirun -np 2 lmp -in in.lj
The "dnf install" command is needed only once. In case of a new LAMMPS
stable release, "dnf update" will automatically update to the newer
The ``dnf install`` command is needed only once. In case of a new LAMMPS
stable release, ``dnf update`` will automatically update to the newer
version as soon at the RPM files are built and uploaded to the download
mirrors. The "module load" command is needed once per (shell) session
mirrors. The ``module load`` command is needed once per (shell) session
or shell terminal instance, unless it is automatically loaded from the
shell profile.
@ -134,7 +144,7 @@ can install the `openkim-models` package
$ dnf install openkim-models
Please use "lmp -help" to see which compilation options, packages,
Please use ``lmp -help`` to see which compilation options, packages,
and styles are included in the binary.
Thanks to Christoph Junghans (LANL) for making LAMMPS available in Fedora.
@ -153,10 +163,10 @@ in the `Extra Packages for Enterprise Linux (EPEL) repository <https://fedorapro
for use with Red Hat Enterprise Linux (RHEL) or CentOS version 7.x
and compatible Linux distributions. Names of packages, executable,
and content are the same as described above for Fedora Linux.
But RHEL/CentOS 7.x uses the "yum" package manager instead of "dnf"
But RHEL/CentOS 7.x uses the ``yum`` package manager instead of ``dnf``
in Fedora 28.
Please use "lmp -help" to see which compilation options, packages,
Please use ``lmp -help`` to see which compilation options, packages,
and styles are included in the binary.
Thanks to Christoph Junghans (LANL) for making LAMMPS available in EPEL.
@ -176,13 +186,13 @@ in OpenSuse as of Leap 15.0. You can install the package with:
$ zypper install lammps
This includes support for OpenMPI. The name of the LAMMPS executable
is *lmp*\ . Thus to run an input in parallel on 2 CPUs you would do:
is ``lmp``. Thus to run an input in parallel on 2 CPUs you would do:
.. code-block:: bash
$ mpirun -np 2 lmp -in in.lj
Please use "lmp -help" to see which compilation options, packages,
Please use ``lmp -help`` to see which compilation options, packages,
and styles are included in the binary.
The LAMMPS binary is built with the :ref:`KIM package <kim>` which

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