Merge remote-tracking branch 'upstream/master' into 2020
This commit is contained in:
tomswinburne
3
.gitattributes
vendored
Normal file
3
.gitattributes
vendored
Normal file
@ -0,0 +1,3 @@
|
|||||||
|
.gitattributes export-ignore
|
||||||
|
.gitignore export-ignore
|
||||||
|
.github export-ignore
|
||||||
11
.github/CODEOWNERS
vendored
11
.github/CODEOWNERS
vendored
@ -10,6 +10,7 @@ lib/molfile/* @akohlmey
|
|||||||
lib/qmmm/* @akohlmey
|
lib/qmmm/* @akohlmey
|
||||||
lib/vtk/* @rbberger
|
lib/vtk/* @rbberger
|
||||||
lib/kim/* @ellio167
|
lib/kim/* @ellio167
|
||||||
|
lib/mesont/* @iafoss
|
||||||
|
|
||||||
# whole packages
|
# whole packages
|
||||||
src/COMPRESS/* @akohlmey
|
src/COMPRESS/* @akohlmey
|
||||||
@ -25,6 +26,7 @@ src/USER-COLVARS/* @giacomofiorin
|
|||||||
src/USER-INTEL/* @wmbrownintel
|
src/USER-INTEL/* @wmbrownintel
|
||||||
src/USER-MANIFOLD/* @Pakketeretet2
|
src/USER-MANIFOLD/* @Pakketeretet2
|
||||||
src/USER-MEAMC/* @martok
|
src/USER-MEAMC/* @martok
|
||||||
|
src/USER-MESONT/* @iafoss
|
||||||
src/USER-MOFFF/* @hheenen
|
src/USER-MOFFF/* @hheenen
|
||||||
src/USER-MOLFILE/* @akohlmey
|
src/USER-MOLFILE/* @akohlmey
|
||||||
src/USER-NETCDF/* @pastewka
|
src/USER-NETCDF/* @pastewka
|
||||||
@ -111,14 +113,23 @@ src/fix_nh.* @athomps
|
|||||||
src/info.* @akohlmey @rbberger
|
src/info.* @akohlmey @rbberger
|
||||||
src/timer.* @akohlmey
|
src/timer.* @akohlmey
|
||||||
src/min* @sjplimp @stanmoore1
|
src/min* @sjplimp @stanmoore1
|
||||||
|
src/utils.* @akohlmey @rbberger
|
||||||
|
|
||||||
# tools
|
# tools
|
||||||
tools/msi2lmp/* @akohlmey
|
tools/msi2lmp/* @akohlmey
|
||||||
tools/emacs/* @HaoZeke
|
tools/emacs/* @HaoZeke
|
||||||
|
tools/singularity/* @akohlmey @rbberger
|
||||||
|
tools/code_standard/* @rbberger
|
||||||
|
tools/valgrind/* @akohlmey
|
||||||
|
|
||||||
|
# tests
|
||||||
|
unittest/* @akohlmey @rbberger
|
||||||
|
|
||||||
# cmake
|
# cmake
|
||||||
cmake/* @junghans @rbberger
|
cmake/* @junghans @rbberger
|
||||||
cmake/Modules/Packages/USER-COLVARS.cmake @junghans @rbberger @giacomofiorin
|
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
|
||||||
python/* @rbberger
|
python/* @rbberger
|
||||||
|
|||||||
4
.github/CONTRIBUTING.md
vendored
4
.github/CONTRIBUTING.md
vendored
@ -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.
|
* 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`.
|
* 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
|
* 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.
|
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.
|
||||||
|
|
||||||
|
|||||||
1
.github/PULL_REQUEST_TEMPLATE.md
vendored
1
.github/PULL_REQUEST_TEMPLATE.md
vendored
@ -34,6 +34,7 @@ By submitting this pull request, I agree, that my contribution will be included
|
|||||||
- [ ] The added/updated documentation is integrated and tested with the documentation build system
|
- [ ] The 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 conventional build system
|
||||||
- [ ] The feature has been verified to work with the CMake based 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
|
- [ ] A package specific README file has been included or updated
|
||||||
- [ ] One or more example input decks are included
|
- [ ] One or more example input decks are included
|
||||||
|
|
||||||
|
|||||||
29
.github/codecov.yml
vendored
Normal file
29
.github/codecov.yml
vendored
Normal file
@ -0,0 +1,29 @@
|
|||||||
|
comment: false
|
||||||
|
coverage:
|
||||||
|
notify:
|
||||||
|
slack:
|
||||||
|
default:
|
||||||
|
url: "secret:HWZbvgtc6OD7F3v3PfrK3/rzCJvScbh69Fi1CkLwuHK0+wIBIHVR+Q5i7q6F9Ln4OChbiRGtYAEUUsT8/jmBu4qDpIi8mx746codc0z/Z3aafLd24pBrCEPLvdCfIZxqPnw3TuUgGhwmMDZf0+thg8YNUr/MbOZ7Li2L6+ZbYuA="
|
||||||
|
threshold: 10%
|
||||||
|
only_pulls: false
|
||||||
|
branches:
|
||||||
|
- "master"
|
||||||
|
flags:
|
||||||
|
- "unit"
|
||||||
|
paths:
|
||||||
|
- "src"
|
||||||
|
status:
|
||||||
|
project:
|
||||||
|
default:
|
||||||
|
branches:
|
||||||
|
- "master"
|
||||||
|
paths:
|
||||||
|
- "src"
|
||||||
|
informational: true
|
||||||
|
patch:
|
||||||
|
default:
|
||||||
|
branches:
|
||||||
|
- "master"
|
||||||
|
paths:
|
||||||
|
- "src"
|
||||||
|
informational: true
|
||||||
@ -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.
|
|
||||||
@ -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 $t
|
|
||||||
@ -1,37 +0,0 @@
|
|||||||
# bulk Cu lattice
|
|
||||||
|
|
||||||
newton off
|
|
||||||
package gpu force/neigh 0 0 1
|
|
||||||
processors * * * grid numa
|
|
||||||
|
|
||||||
variable x index 1
|
|
||||||
variable y index 1
|
|
||||||
variable z index 1
|
|
||||||
|
|
||||||
variable xx equal 20*$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
|
|
||||||
@ -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 $t
|
|
||||||
@ -1,35 +0,0 @@
|
|||||||
# 3d Lennard-Jones melt
|
|
||||||
|
|
||||||
newton off
|
|
||||||
package gpu force/neigh 0 0 1
|
|
||||||
processors * * * grid numa
|
|
||||||
|
|
||||||
variable x index 1
|
|
||||||
variable y index 1
|
|
||||||
variable z index 1
|
|
||||||
|
|
||||||
variable xx equal 20*$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
|
|
||||||
@ -1,30 +0,0 @@
|
|||||||
# Rhodopsin model
|
|
||||||
|
|
||||||
units real
|
|
||||||
neigh_modify delay 5 every 1
|
|
||||||
|
|
||||||
atom_style full
|
|
||||||
atom_modify map hash
|
|
||||||
bond_style harmonic
|
|
||||||
angle_style charmm
|
|
||||||
dihedral_style charmm
|
|
||||||
improper_style harmonic
|
|
||||||
pair_style lj/charmm/coul/long 8.0 10.0
|
|
||||||
pair_modify mix arithmetic
|
|
||||||
kspace_style pppm 1e-4
|
|
||||||
|
|
||||||
read_data data.rhodo
|
|
||||||
|
|
||||||
replicate $x $y $z
|
|
||||||
|
|
||||||
fix 1 all shake 0.0001 5 0 m 1.0 a 232
|
|
||||||
fix 2 all npt temp 300.0 300.0 100.0 &
|
|
||||||
z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
|
|
||||||
|
|
||||||
special_bonds charmm
|
|
||||||
|
|
||||||
thermo 50
|
|
||||||
thermo_style multi
|
|
||||||
timestep 2.0
|
|
||||||
|
|
||||||
run $t
|
|
||||||
@ -1,39 +0,0 @@
|
|||||||
# Rhodopsin model
|
|
||||||
|
|
||||||
newton off
|
|
||||||
package gpu force/neigh 0 0 1
|
|
||||||
processors * * * grid numa
|
|
||||||
|
|
||||||
variable x index 1
|
|
||||||
variable y index 1
|
|
||||||
variable z index 1
|
|
||||||
|
|
||||||
units real
|
|
||||||
neigh_modify delay 5 every 1
|
|
||||||
|
|
||||||
atom_style full
|
|
||||||
atom_modify map hash
|
|
||||||
bond_style harmonic
|
|
||||||
angle_style charmm
|
|
||||||
dihedral_style charmm
|
|
||||||
improper_style harmonic
|
|
||||||
pair_style lj/charmm/coul/long/gpu 8.0 ${cutoff}
|
|
||||||
pair_modify mix arithmetic
|
|
||||||
kspace_style pppm/gpu 1e-4
|
|
||||||
|
|
||||||
read_data data.rhodo
|
|
||||||
|
|
||||||
replicate $x $y $z
|
|
||||||
|
|
||||||
fix 1 all shake 0.0001 5 0 m 1.0 a 232
|
|
||||||
fix 2 all npt temp 300.0 300.0 100.0 &
|
|
||||||
z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
|
|
||||||
|
|
||||||
special_bonds charmm
|
|
||||||
|
|
||||||
thermo 50
|
|
||||||
# thermo_style multi
|
|
||||||
timestep 2.0
|
|
||||||
|
|
||||||
run 15
|
|
||||||
run 100
|
|
||||||
@ -1,42 +0,0 @@
|
|||||||
# Rhodopsin model
|
|
||||||
|
|
||||||
newton off
|
|
||||||
package gpu force/neigh 0 0 1
|
|
||||||
partition yes 1 processors * * * grid twolevel ${grid} * * * &
|
|
||||||
part 1 2 multiple
|
|
||||||
partition yes 2 processors * * * part 1 2 multiple
|
|
||||||
|
|
||||||
variable x index 1
|
|
||||||
variable y index 1
|
|
||||||
variable z index 1
|
|
||||||
|
|
||||||
units real
|
|
||||||
neigh_modify delay 5 every 1
|
|
||||||
|
|
||||||
atom_style full
|
|
||||||
atom_modify map hash
|
|
||||||
bond_style harmonic
|
|
||||||
angle_style charmm
|
|
||||||
dihedral_style charmm
|
|
||||||
improper_style harmonic
|
|
||||||
pair_style lj/charmm/coul/long/gpu 8.0 ${cutoff}
|
|
||||||
pair_modify mix arithmetic
|
|
||||||
kspace_style pppm/gpu 1e-4
|
|
||||||
|
|
||||||
read_data data.rhodo
|
|
||||||
|
|
||||||
replicate $x $y $z
|
|
||||||
|
|
||||||
fix 1 all shake 0.0001 5 0 m 1.0 a 232
|
|
||||||
fix 2 all npt temp 300.0 300.0 100.0 &
|
|
||||||
z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
|
|
||||||
|
|
||||||
special_bonds charmm
|
|
||||||
|
|
||||||
thermo 50
|
|
||||||
# thermo_style multi
|
|
||||||
timestep 2.0
|
|
||||||
|
|
||||||
run_style verlet/split
|
|
||||||
run 15
|
|
||||||
run 100
|
|
||||||
@ -1,2 +0,0 @@
|
|||||||
rc = 4.0
|
|
||||||
delr = 0.1
|
|
||||||
1
bench/POTENTIALS/Ni.meam
Symbolic link
1
bench/POTENTIALS/Ni.meam
Symbolic link
@ -0,0 +1 @@
|
|||||||
|
../../potentials/Ni.meam
|
||||||
@ -1,17 +0,0 @@
|
|||||||
# Stillinger-Weber parameters for various elements and mixtures
|
|
||||||
# multiple entries can be added to this file, LAMMPS reads the ones it needs
|
|
||||||
# these entries are in LAMMPS "metal" units:
|
|
||||||
# epsilon = eV; sigma = Angstroms
|
|
||||||
# other quantities are unitless
|
|
||||||
|
|
||||||
# format of a single entry (one or more lines):
|
|
||||||
# element 1, element 2, element 3,
|
|
||||||
# epsilon, sigma, a, lambda, gamma, costheta0, A, B, p, q, tol
|
|
||||||
|
|
||||||
# Here are the original parameters in metal units, for Silicon from:
|
|
||||||
#
|
|
||||||
# Stillinger and Weber, Phys. Rev. B, v. 31, p. 5262, (1985)
|
|
||||||
#
|
|
||||||
|
|
||||||
Si Si Si 2.1683 2.0951 1.80 21.0 1.20 -0.333333333333
|
|
||||||
7.049556277 0.6022245584 4.0 0.0 0.0
|
|
||||||
1
bench/POTENTIALS/Si.sw
Symbolic link
1
bench/POTENTIALS/Si.sw
Symbolic link
@ -0,0 +1 @@
|
|||||||
|
../../potentials/Si.sw
|
||||||
@ -1,16 +0,0 @@
|
|||||||
# Tersoff parameters for various elements and mixtures
|
|
||||||
# multiple entries can be added to this file, LAMMPS reads the ones it needs
|
|
||||||
# these entries are in LAMMPS "metal" units:
|
|
||||||
# A,B = eV; lambda1,lambda2,lambda3 = 1/Angstroms; R,D = Angstroms
|
|
||||||
# other quantities are unitless
|
|
||||||
|
|
||||||
# This is the Si parameterization from a particular Tersoff paper:
|
|
||||||
# J. Tersoff, PRB, 37, 6991 (1988)
|
|
||||||
# See the SiCGe.tersoff file for different Si variants.
|
|
||||||
|
|
||||||
# format of a single entry (one or more lines):
|
|
||||||
# element 1, element 2, element 3,
|
|
||||||
# m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A
|
|
||||||
|
|
||||||
Si Si Si 3.0 1.0 1.3258 4.8381 2.0417 0.0000 22.956
|
|
||||||
0.33675 1.3258 95.373 3.0 0.2 3.2394 3264.7
|
|
||||||
1
bench/POTENTIALS/Si.tersoff
Symbolic link
1
bench/POTENTIALS/Si.tersoff
Symbolic link
@ -0,0 +1 @@
|
|||||||
|
../../potentials/Si.tersoff
|
||||||
@ -1,24 +0,0 @@
|
|||||||
# bulk Ni in MEAM
|
|
||||||
|
|
||||||
units metal
|
|
||||||
atom_style atomic
|
|
||||||
|
|
||||||
lattice fcc 3.52
|
|
||||||
region box block 0 20 0 20 0 20
|
|
||||||
create_box 1 box
|
|
||||||
create_atoms 1 box
|
|
||||||
|
|
||||||
pair_style meam
|
|
||||||
pair_coeff * * library.meam Ni4 Ni.meam Ni4
|
|
||||||
|
|
||||||
velocity all create 1600.0 376847 loop geom
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 5 every 1
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
thermo 50
|
|
||||||
|
|
||||||
run 100
|
|
||||||
@ -1,22 +0,0 @@
|
|||||||
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
|
|
||||||
|
|
||||||
units real
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.reax
|
|
||||||
|
|
||||||
#replicate 7 8 10
|
|
||||||
replicate 7 8 5
|
|
||||||
|
|
||||||
velocity all create 300.0 9999
|
|
||||||
|
|
||||||
pair_style reax
|
|
||||||
pair_coeff * * ffield.reax 1 2 3 4
|
|
||||||
|
|
||||||
timestep 0.1
|
|
||||||
fix 2 all nve
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
thermo_style custom step temp ke pe pxx pyy pzz etotal
|
|
||||||
|
|
||||||
run 100
|
|
||||||
@ -1,162 +0,0 @@
|
|||||||
# meam data from vax files fcc,bcc,dia 11/4/92
|
|
||||||
# elt lat z ielement atwt
|
|
||||||
# alpha b0 b1 b2 b3 alat esub asub
|
|
||||||
# t0 t1 t2 t3 rozero ibar
|
|
||||||
|
|
||||||
'Sn5' 'dia' 4. 50 118.
|
|
||||||
5.09 5.00 16.0 04.0 5.0 6.483 3.14 1.00
|
|
||||||
1.0 2.00 5.756 -0.30 1. 0
|
|
||||||
'Sn' 'dia' 4. 50 118.
|
|
||||||
5.09 5.42 8.0 5.0 6.0 6.483 3.14 1.12
|
|
||||||
1.0 3.0 5.707 +0.30 1. 0
|
|
||||||
'Cu' 'fcc' 12. 29 63.54
|
|
||||||
5.10570729 3.634 2.20 6 2.20 3.62 3.54 1.07
|
|
||||||
1.0 3.13803254 2.49438711 2.95269237 1. 0
|
|
||||||
'Ag' 'fcc' 12. 47 107.870
|
|
||||||
5.89222008 4.456 2.20 6 2.20 4.08 2.85 1.06
|
|
||||||
1.0 5.54097609 2.45015783 1.28843988 1. 0
|
|
||||||
'Au' 'fcc' 12. 79 196.967
|
|
||||||
6.34090112 5.449 2.20 6 2.20 4.07 3.93 1.04
|
|
||||||
1.0 1.58956328 1.50776392 2.60609758 1. 0
|
|
||||||
'Ni1' 'fcc' 12. 28 58.71
|
|
||||||
4.99 2.45 2.20 6 2.20 3.52 4.45 1.10
|
|
||||||
1.0 3.57 1.60 3.70 1.0 0
|
|
||||||
'Ni2' 'fcc' 12. 28 58.71
|
|
||||||
4.99 2.45 2.20 6 2.20 3.52 4.45 1.10
|
|
||||||
1.0 3.57 1.60 3.70 1.0 3
|
|
||||||
'Ni3' 'fcc' 12. 28 58.71
|
|
||||||
4.99 2.45 1.50 6 1.50 3.52 4.45 1.10
|
|
||||||
1.0 3.57 1.60 3.70 1.0 3
|
|
||||||
'Ni4' 'fcc' 12. 28 58.71
|
|
||||||
4.99 2.45 1.50 6 1.50 3.52 4.45 1.10
|
|
||||||
1.0 3.57 1.60 3.70 1.0 0
|
|
||||||
'Ni' 'fcc' 12. 28 58.71
|
|
||||||
4.99 2.64 1.50 4.50 1.50 3.52 4.45 1.10
|
|
||||||
1.0 1.692 4.987 3.683 1.0 1
|
|
||||||
'Nix' 'fcc' 12. 28 58.71
|
|
||||||
4.99 2.64 1.50 4.50 1.50 3.52 4.45 1.10
|
|
||||||
1.0 0.00 0.000 3.683 1.0 1
|
|
||||||
'Ni' 'fcc' 12. 28 58.71
|
|
||||||
4.99 3.25 0.80 4 1.50 3.52 4.45 1.07
|
|
||||||
1.0 -4.052 13.14 3.786 1.0 1
|
|
||||||
'Pd' 'fcc' 12. 46 106.4
|
|
||||||
6.43230473 4.975 2.20 6 2.20 3.89 3.91 1.01
|
|
||||||
1.0 2.33573516 1.38343023 4.47989049 1. 0
|
|
||||||
'Pt' 'fcc' 12. 78 195.09
|
|
||||||
6.44221724 4.673 2.20 6 2.20 3.92 5.77 1.04
|
|
||||||
1.0 2.73335406 -1.3759593 3.29322278 1. 0
|
|
||||||
'Al' 'fcc' 12. 13 26.9815
|
|
||||||
4.61 2.21 2.20 6.0 2.20 4.05 3.58 1.07
|
|
||||||
1.0 -1.78 -2.21 8.01 0.6 0
|
|
||||||
'Al' 'fcc' 12. 13 26.9815
|
|
||||||
4.69 1.56 4.00 5.5 0.60 4.05 3.36 1.09
|
|
||||||
1.0 -0.251 -3.450 8.298 0.6 1
|
|
||||||
'Al' 'fcc' 12. 13 26.9815
|
|
||||||
4.69 1.58 1.00 6.0 0.60 4.05 3.36 1.09
|
|
||||||
1.0 -0.808 -2.614 8.298 0.6 1
|
|
||||||
'Pb' 'fcc' 12. 82 207.19
|
|
||||||
6.0564428 5.306 2.20 6 2.20 4.95 2.04 1.01
|
|
||||||
1.0 2.74022352 3.06323991 1.2 1. 0
|
|
||||||
'Rh' 'fcc' 12. 45 102.905
|
|
||||||
6.0045385 1.131 1.00 2 1.00 3.8 5.75 1.05
|
|
||||||
1.0 2.9900 4.60231784 4.8 1. 0
|
|
||||||
'Ir' 'fcc' 12. 77 192.2
|
|
||||||
6.52315787 1.13 1.00 2 1.00 3.84 6.93 1.05
|
|
||||||
1.0 1.50000 8.09942666 4.8 1. 0
|
|
||||||
'Li' 'bcc' 8. 3 6.939
|
|
||||||
2.97244804 1.425 1.00 1.00169907 1.00 3.509 1.65 0.87
|
|
||||||
1.0 0.26395017 0.44431129 -0.2 1. 0
|
|
||||||
'Na' 'bcc' 8. 11 22.9898
|
|
||||||
3.64280541 2.313 1.00 1.00173951 1.00 4.291 1.13 0.9
|
|
||||||
1.0 3.55398839 0.68807569 -0.2 1. 0
|
|
||||||
'K' 'bcc' 8. 19 39.102
|
|
||||||
3.90128376 2.687 1.00 1.00186667 1.00 5.344 0.94 0.92
|
|
||||||
1.0 5.09756981 0.69413264 -0.2 1. 0
|
|
||||||
'V' 'bcc' 8. 23 50.942
|
|
||||||
4.83265262 4.113 1.00 1.00095022 1.00 3.04 5.3 1
|
|
||||||
1.0 4.20161301 4.09946561 -1 1. 0
|
|
||||||
'Nb' 'bcc' 8. 41 92.906
|
|
||||||
4.79306197 4.374 1.00 1.00101441 1.00 3.301 7.47 1
|
|
||||||
1.0 3.75762849 3.82514598 -1 1. 0
|
|
||||||
'Ta' 'bcc' 8. 73 180.948
|
|
||||||
4.89528669 3.709 1.00 1.00099783 1.00 3.303 8.09 0.99
|
|
||||||
1.0 6.08617812 3.35255804 -2.9 1. 0
|
|
||||||
'Cr' 'bcc' 8. 24 51.996
|
|
||||||
5.12169218 3.224 1.00 1.00048646 1.00 2.885 4.1 0.94
|
|
||||||
1.0 -0.207535 12.2600006 -1.9 1. 0
|
|
||||||
'Mo' 'bcc' 8. 42 95.94
|
|
||||||
5.84872871 4.481 1.00 1.00065204 1.00 3.15 6.81 0.99
|
|
||||||
1.0 3.47727181 9.48582009 -2.9 1. 0
|
|
||||||
'W' 'bcc' 8. 74 183.85
|
|
||||||
5.62777409 3.978 1.00 1.00065894 1.00 3.165 8.66 0.98
|
|
||||||
1.0 3.16353338 8.24586928 -2.7 1. 0
|
|
||||||
'WL' 'bcc' 8 74 183.85
|
|
||||||
5.6831 6.54 1 1 1 3.1639 8.66 0.4
|
|
||||||
1 -0.6 0.3 -8.7 1 3
|
|
||||||
'Fe' 'bcc' 8. 26 55.847
|
|
||||||
5.07292627 2.935 1.00 1.00080073 1.00 2.866 4.29 0.89
|
|
||||||
1.0 5.13579244 4.12042448 -2.7 1. 0
|
|
||||||
'Si' 'dia' 4. 14 28.086
|
|
||||||
4.87 4.8 4.8 4.8 4.8 5.431 4.63 1.
|
|
||||||
1.0 3.30 5.105 -0.80 1. 1
|
|
||||||
'Si97' 'dia' 4. 14 28.086
|
|
||||||
4.87 4.4 5.5 5.5 5.5 5.431 4.63 1.
|
|
||||||
1.0 3.13 4.47 -1.80 2.05 0
|
|
||||||
'Si92' 'dia' 4. 14 28.086
|
|
||||||
4.87 4.4 5.5 5.5 5.5 5.431 4.63 1.
|
|
||||||
1.0 3.13 4.47 -1.80 2.35 0
|
|
||||||
'Six' 'dia' 4 14 28.086
|
|
||||||
4.87 4.4 5.5 5.5 5.5 5.431 4.63 1.0
|
|
||||||
1.0 2.05 4.47 -1.8 2.05 0
|
|
||||||
'Sixb' 'dia' 4 14 28.086
|
|
||||||
4.87 4.4 5.5 5.5 5.5 5.431 4.63 1.0
|
|
||||||
1.0 2.05 4.47 -1.8 2.5 0
|
|
||||||
'Mg' 'hcp' 12. 12 24.305
|
|
||||||
5.45 2.70 0.0 0.35 3.0 3.20 1.55 1.11
|
|
||||||
1.0 8.00 04.1 -02.0 1.0 0
|
|
||||||
'C' 'dia' 4. 6 12.0111
|
|
||||||
4.38 4.10 4.200 5.00 3.00 3.567 7.37 1.000
|
|
||||||
1.0 5.0 9.34 -1.00 2.25 1
|
|
||||||
'C' 'dia' 4. 6 12.0111
|
|
||||||
4.38 5.20 3.87 4.00 4.50 3.567 7.37 1.278
|
|
||||||
1.0 15. 2.09 -6.00 2.5 1
|
|
||||||
'C' 'dia' 4. 6 12.0111
|
|
||||||
4.38 4.50 4.00 3.50 4.80 3.567 7.37 1.00
|
|
||||||
1.0 10.5 1.54 -8.75 3.2 1
|
|
||||||
'C' 'dia' 4. 6 12.0111
|
|
||||||
4.38 3.30 2.80 1.50 3.20 3.567 7.37 1.00
|
|
||||||
1.0 10.3 1.54 -8.80 2.5 1
|
|
||||||
'C' 'dia' 4. 6 12.0111
|
|
||||||
4.38 4.60 3.45 4.00 4.20 3.567 7.37 1.061
|
|
||||||
1.0 15.0 1.74 -8.00 2.5 1
|
|
||||||
'C' 'dia' 4. 6 12.0111
|
|
||||||
4.38 4.50 4.00 3.50 4.80 3.567 7.37 1.00
|
|
||||||
1.0 10.5 1.54 -8.75 3.2 1
|
|
||||||
'h' 'dim' 1. 1 1.0079
|
|
||||||
2.96 2.70 3.5 3.4 3.4 0.74 2.235 2.27
|
|
||||||
1.0 0.19 0.00 0.00 20.00 0
|
|
||||||
'h' 'dim' 1. 1 1.0079
|
|
||||||
2.96 2.00 4.0 4.0 0.0 0.74 2.235 1.00
|
|
||||||
1.0 -0.60 -0.80 -0.0 01.0 1
|
|
||||||
'H' 'dim' 1. 1 1.0079
|
|
||||||
2.96 2.96 3.0 3.0 3.0 0.74 2.235 2.50
|
|
||||||
1.0 0.20 -0.10 0.0 0.5 0
|
|
||||||
'H' 'dim' 1. 1 1.0079
|
|
||||||
2.96 2.0 3.0 4.0 0.0 0.74 2.225 1.00
|
|
||||||
1.0 -0.5 -1.00 0.0 0.15 1
|
|
||||||
'H' 'dim' 1. 1 1.0079
|
|
||||||
2.96 2.00 2.0 2.0 2.0 0.74 2.235 1.00
|
|
||||||
1.0 -0.60 -0.80 -0.0 01.0 2
|
|
||||||
'Hni' 'dim' 1. 1 1.0079
|
|
||||||
2.96 2.96 3.0 3.0 3.0 0.74 2.235 2.50
|
|
||||||
1.0 0.2 -0.1 0.0 0.5 0
|
|
||||||
'Hni' 'dim' 1. 1 1.0079
|
|
||||||
2.96 2.96 3.0 2.0 3.0 0.74 2.235 36.4
|
|
||||||
1.0 0.2 6.0 0.0 22.8 0
|
|
||||||
'Vac' 'fcc' 12. 1 1.
|
|
||||||
0 0 0.0 0 0.0 1E+08 0 1
|
|
||||||
0 0 0 0 1. 0
|
|
||||||
'zz' 'zzz' 99. 1 1.
|
|
||||||
0 0 0.0 0 0.0 0. 0. 0.
|
|
||||||
0 0 0 0 1. 0
|
|
||||||
|
|
||||||
1
bench/POTENTIALS/library.meam
Symbolic link
1
bench/POTENTIALS/library.meam
Symbolic link
@ -0,0 +1 @@
|
|||||||
|
../../potentials/library.meam
|
||||||
@ -1,84 +0,0 @@
|
|||||||
LAMMPS (16 Mar 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# bulk Ni in MEAM
|
|
||||||
|
|
||||||
units metal
|
|
||||||
atom_style atomic
|
|
||||||
|
|
||||||
lattice fcc 3.52
|
|
||||||
Lattice spacing in x,y,z = 3.52 3.52 3.52
|
|
||||||
region box block 0 20 0 20 0 20
|
|
||||||
create_box 1 box
|
|
||||||
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
create_atoms 1 box
|
|
||||||
Created 32000 atoms
|
|
||||||
Time spent = 0.00186539 secs
|
|
||||||
|
|
||||||
pair_style meam
|
|
||||||
WARNING: The pair_style meam command is unsupported. Please use pair_style meam/c instead (../pair_meam.cpp:51)
|
|
||||||
pair_coeff * * library.meam Ni4 Ni.meam Ni4
|
|
||||||
|
|
||||||
velocity all create 1600.0 376847 loop geom
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 5 every 1
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
thermo 50
|
|
||||||
|
|
||||||
run 100
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 5 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 5
|
|
||||||
ghost atom cutoff = 5
|
|
||||||
binsize = 2.5, bins = 29 29 29
|
|
||||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
|
||||||
(1) pair meam, perpetual
|
|
||||||
attributes: full, newton on
|
|
||||||
pair build: full/bin/atomonly
|
|
||||||
stencil: full/bin/3d
|
|
||||||
bin: standard
|
|
||||||
(2) pair meam, perpetual, half/full from (1)
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: halffull/newton
|
|
||||||
stencil: none
|
|
||||||
bin: none
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 55.91 | 55.91 | 55.91 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 1600 -142400 0 -135782.09 20259.18
|
|
||||||
50 885.10702 -139411.51 0 -135750.54 32425.433
|
|
||||||
100 895.5097 -139454.3 0 -135750.3 31804.187
|
|
||||||
Loop time of 30.6278 on 1 procs for 100 steps with 32000 atoms
|
|
||||||
|
|
||||||
Performance: 1.410 ns/day, 17.015 hours/ns, 3.265 timesteps/s
|
|
||||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 30.088 | 30.088 | 30.088 | 0.0 | 98.24
|
|
||||||
Neigh | 0.48914 | 0.48914 | 0.48914 | 0.0 | 1.60
|
|
||||||
Comm | 0.015916 | 0.015916 | 0.015916 | 0.0 | 0.05
|
|
||||||
Output | 0.00022554 | 0.00022554 | 0.00022554 | 0.0 | 0.00
|
|
||||||
Modify | 0.025481 | 0.025481 | 0.025481 | 0.0 | 0.08
|
|
||||||
Other | | 0.009055 | | | 0.03
|
|
||||||
|
|
||||||
Nlocal: 32000 ave 32000 max 32000 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 13576 ave 13576 max 13576 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 780360 ave 780360 max 780360 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 1.56072e+06 ave 1.56072e+06 max 1.56072e+06 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 1560720
|
|
||||||
Ave neighs/atom = 48.7725
|
|
||||||
Neighbor list builds = 8
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:30
|
|
||||||
@ -1,84 +0,0 @@
|
|||||||
LAMMPS (16 Mar 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# bulk Ni in MEAM
|
|
||||||
|
|
||||||
units metal
|
|
||||||
atom_style atomic
|
|
||||||
|
|
||||||
lattice fcc 3.52
|
|
||||||
Lattice spacing in x,y,z = 3.52 3.52 3.52
|
|
||||||
region box block 0 20 0 20 0 20
|
|
||||||
create_box 1 box
|
|
||||||
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
create_atoms 1 box
|
|
||||||
Created 32000 atoms
|
|
||||||
Time spent = 0.000587463 secs
|
|
||||||
|
|
||||||
pair_style meam
|
|
||||||
WARNING: The pair_style meam command is unsupported. Please use pair_style meam/c instead (../pair_meam.cpp:51)
|
|
||||||
pair_coeff * * library.meam Ni4 Ni.meam Ni4
|
|
||||||
|
|
||||||
velocity all create 1600.0 376847 loop geom
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify delay 5 every 1
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
timestep 0.005
|
|
||||||
thermo 50
|
|
||||||
|
|
||||||
run 100
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 5 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 5
|
|
||||||
ghost atom cutoff = 5
|
|
||||||
binsize = 2.5, bins = 29 29 29
|
|
||||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
|
||||||
(1) pair meam, perpetual
|
|
||||||
attributes: full, newton on
|
|
||||||
pair build: full/bin/atomonly
|
|
||||||
stencil: full/bin/3d
|
|
||||||
bin: standard
|
|
||||||
(2) pair meam, perpetual, half/full from (1)
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: halffull/newton
|
|
||||||
stencil: none
|
|
||||||
bin: none
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 17.41 | 17.41 | 17.41 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 1600 -142400 0 -135782.09 20259.18
|
|
||||||
50 885.10702 -139411.51 0 -135750.54 32425.433
|
|
||||||
100 895.5097 -139454.3 0 -135750.3 31804.187
|
|
||||||
Loop time of 8.21941 on 4 procs for 100 steps with 32000 atoms
|
|
||||||
|
|
||||||
Performance: 5.256 ns/day, 4.566 hours/ns, 12.166 timesteps/s
|
|
||||||
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 8.0277 | 8.0384 | 8.0504 | 0.3 | 97.80
|
|
||||||
Neigh | 0.12555 | 0.12645 | 0.12713 | 0.2 | 1.54
|
|
||||||
Comm | 0.024279 | 0.036776 | 0.048389 | 4.5 | 0.45
|
|
||||||
Output | 9.4414e-05 | 0.00011903 | 0.00018597 | 0.0 | 0.00
|
|
||||||
Modify | 0.01252 | 0.012608 | 0.012795 | 0.1 | 0.15
|
|
||||||
Other | | 0.005028 | | | 0.06
|
|
||||||
|
|
||||||
Nlocal: 8000 ave 8045 max 7947 min
|
|
||||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
|
||||||
Nghost: 6066.75 ave 6120 max 6021 min
|
|
||||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
|
||||||
Neighs: 195090 ave 196403 max 193697 min
|
|
||||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
|
||||||
FullNghs: 390180 ave 392616 max 387490 min
|
|
||||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 1560720
|
|
||||||
Ave neighs/atom = 48.7725
|
|
||||||
Neighbor list builds = 8
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:08
|
|
||||||
@ -1,86 +0,0 @@
|
|||||||
LAMMPS (16 Mar 2018)
|
|
||||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
|
|
||||||
|
|
||||||
units real
|
|
||||||
atom_style charge
|
|
||||||
|
|
||||||
read_data data.reax
|
|
||||||
orthogonal box = (0 0 0) to (9.49107 9.49107 6.99123)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
58 atoms
|
|
||||||
|
|
||||||
#replicate 7 8 10
|
|
||||||
replicate 7 8 5
|
|
||||||
orthogonal box = (0 0 0) to (66.4375 75.9285 34.9562)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
16240 atoms
|
|
||||||
Time spent = 0.000834942 secs
|
|
||||||
|
|
||||||
velocity all create 300.0 9999
|
|
||||||
|
|
||||||
pair_style reax
|
|
||||||
WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
|
|
||||||
pair_coeff * * ffield.reax 1 2 3 4
|
|
||||||
|
|
||||||
timestep 0.1
|
|
||||||
fix 2 all nve
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
thermo_style custom step temp ke pe pxx pyy pzz etotal
|
|
||||||
|
|
||||||
run 100
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 12
|
|
||||||
ghost atom cutoff = 12
|
|
||||||
binsize = 6, bins = 12 13 6
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair reax, perpetual
|
|
||||||
attributes: half, newton off
|
|
||||||
pair build: half/bin/newtoff
|
|
||||||
stencil: half/bin/3d/newtoff
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 115.8 | 115.8 | 115.8 Mbytes
|
|
||||||
Step Temp KinEng PotEng Pxx Pyy Pzz TotEng
|
|
||||||
0 300 14521.612 -1616144.2 22296.712 -29858.677 5721.0921 -1601622.5
|
|
||||||
10 298.98728 14472.591 -1616093.9 21955.847 -24067.096 7389.148 -1601621.3
|
|
||||||
20 294.76158 14268.045 -1615890.1 19179.258 -10513.494 10789.925 -1601622
|
|
||||||
30 288.56967 13968.323 -1615591.2 13854.377 5833.02 13949.731 -1601622.9
|
|
||||||
40 282.06725 13653.571 -1615278.2 6259.9845 19406.33 14947.939 -1601624.6
|
|
||||||
50 274.84112 13303.787 -1614931.9 -2009.6832 26964.336 13346.855 -1601628.2
|
|
||||||
60 266.20153 12885.585 -1614519.7 -8441.1641 28485.532 10195.429 -1601634.1
|
|
||||||
70 259.17085 12545.262 -1614184.2 -11426.993 24941.516 6572.2953 -1601638.9
|
|
||||||
80 259.73004 12572.33 -1614216.7 -10867.598 16928.461 3033.9021 -1601644.3
|
|
||||||
90 269.2352 13032.431 -1614679 -7962.3129 4931.5317 -280.22164 -1601646.6
|
|
||||||
100 280.67181 13586.024 -1615234.3 -3606.1519 -8769.8482 -2527.5887 -1601648.3
|
|
||||||
Loop time of 358.104 on 1 procs for 100 steps with 16240 atoms
|
|
||||||
|
|
||||||
Performance: 0.002 ns/day, 9947.338 hours/ns, 0.279 timesteps/s
|
|
||||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 358.07 | 358.07 | 358.07 | 0.0 | 99.99
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.01623 | 0.01623 | 0.01623 | 0.0 | 0.00
|
|
||||||
Output | 0.0013328 | 0.0013328 | 0.0013328 | 0.0 | 0.00
|
|
||||||
Modify | 0.012679 | 0.012679 | 0.012679 | 0.0 | 0.00
|
|
||||||
Other | | 0.006895 | | | 0.00
|
|
||||||
|
|
||||||
Nlocal: 16240 ave 16240 max 16240 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 32428 ave 32428 max 32428 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 6.69975e+06 ave 6.69975e+06 max 6.69975e+06 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 6699752
|
|
||||||
Ave neighs/atom = 412.546
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:06:02
|
|
||||||
@ -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
|
|
||||||
@ -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
|
|
||||||
@ -3,16 +3,24 @@
|
|||||||
# This file is part of LAMMPS
|
# This file is part of LAMMPS
|
||||||
# Created by Christoph Junghans and Richard Berger
|
# Created by Christoph Junghans and Richard Berger
|
||||||
cmake_minimum_required(VERSION 3.10)
|
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)
|
project(lammps CXX)
|
||||||
set(SOVERSION 0)
|
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_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)
|
set(LAMMPS_SOURCE_DIR ${LAMMPS_DIR}/src)
|
||||||
get_filename_component(LAMMPS_PYTHON_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../python ABSOLUTE)
|
set(LAMMPS_LIB_SOURCE_DIR ${LAMMPS_DIR}/lib)
|
||||||
get_filename_component(LAMMPS_POTENTIALS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../potentials ABSOLUTE)
|
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)
|
find_package(Git)
|
||||||
|
|
||||||
@ -24,6 +32,12 @@ endif()
|
|||||||
# Cmake modules/macros are in a subdirectory to keep this file cleaner
|
# Cmake modules/macros are in a subdirectory to keep this file cleaner
|
||||||
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules)
|
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: ${CMAKE_LIBRARY_PATH}")
|
||||||
|
endif()
|
||||||
|
|
||||||
include(LAMMPSUtils)
|
include(LAMMPSUtils)
|
||||||
|
|
||||||
get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h PROJECT_VERSION)
|
get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h PROJECT_VERSION)
|
||||||
@ -43,7 +57,6 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
|
|||||||
# compiler tests
|
# compiler tests
|
||||||
# these need ot be done early (before further tests).
|
# these need ot be done early (before further tests).
|
||||||
#####################################################################
|
#####################################################################
|
||||||
include(CheckCCompilerFlag)
|
|
||||||
include(CheckIncludeFileCXX)
|
include(CheckIncludeFileCXX)
|
||||||
|
|
||||||
# set required compiler flags and compiler/CPU arch specific optimizations
|
# set required compiler flags and compiler/CPU arch specific optimizations
|
||||||
@ -56,27 +69,10 @@ if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
|
|||||||
endif()
|
endif()
|
||||||
endif()
|
endif()
|
||||||
|
|
||||||
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
|
|
||||||
set(CMAKE_TUNE_DEFAULT "-ffast-math -march=native")
|
|
||||||
endif()
|
|
||||||
|
|
||||||
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")
|
|
||||||
set(CMAKE_TUNE_DEFAULT "-ffast-math -march=native")
|
|
||||||
endif()
|
|
||||||
|
|
||||||
# we require C++11 without extensions
|
# we require C++11 without extensions
|
||||||
set(CMAKE_CXX_STANDARD 11)
|
set(CMAKE_CXX_STANDARD 11)
|
||||||
set(CMAKE_CXX_STANDARD_REQUIRED ON)
|
set(CMAKE_CXX_STANDARD_REQUIRED ON)
|
||||||
set(CMAKE_CXX_EXTENSIONS OFF)
|
set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
|
||||||
|
|
||||||
# GNU compiler specific features for testing
|
|
||||||
if (${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 #
|
# User input options #
|
||||||
@ -108,11 +104,11 @@ install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
|
|||||||
option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
|
option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
|
||||||
|
|
||||||
set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
|
set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
|
||||||
GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MOLECULE PERI POEMS QEQ
|
GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS
|
||||||
REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
|
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-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-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-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-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)
|
USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
|
||||||
@ -160,9 +156,6 @@ else()
|
|||||||
enable_language(C)
|
enable_language(C)
|
||||||
file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
|
file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
|
||||||
add_library(mpi_stubs STATIC ${MPI_SOURCES})
|
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})
|
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>)
|
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)
|
install(FILES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps/mpi)
|
||||||
@ -192,13 +185,14 @@ if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0")
|
|||||||
target_compile_definitions(lammps PRIVATE -DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
|
target_compile_definitions(lammps PRIVATE -DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
|
||||||
endif()
|
endif()
|
||||||
|
|
||||||
option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)
|
option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" ${ENABLE_TESTING})
|
||||||
if(LAMMPS_EXCEPTIONS)
|
if(LAMMPS_EXCEPTIONS)
|
||||||
target_compile_definitions(lammps PUBLIC -DLAMMPS_EXCEPTIONS)
|
target_compile_definitions(lammps PUBLIC -DLAMMPS_EXCEPTIONS)
|
||||||
endif()
|
endif()
|
||||||
|
|
||||||
# "hard" dependencies between packages resulting
|
# "hard" dependencies between packages resulting
|
||||||
# in an error instead of skipping over files
|
# in an error instead of skipping over files
|
||||||
|
pkg_depends(MLIAP SNAP)
|
||||||
pkg_depends(MPIIO MPI)
|
pkg_depends(MPIIO MPI)
|
||||||
pkg_depends(USER-ATC MANYBODY)
|
pkg_depends(USER-ATC MANYBODY)
|
||||||
pkg_depends(USER-LB MPI)
|
pkg_depends(USER-LB MPI)
|
||||||
@ -237,6 +231,48 @@ if(BUILD_OMP)
|
|||||||
target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
|
target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
|
||||||
endif()
|
endif()
|
||||||
|
|
||||||
|
# Compiler specific features for testing
|
||||||
|
if(${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)
|
if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
|
||||||
enable_language(C)
|
enable_language(C)
|
||||||
find_package(LAPACK)
|
find_package(LAPACK)
|
||||||
@ -249,9 +285,6 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
|
|||||||
enable_language(Fortran)
|
enable_language(Fortran)
|
||||||
file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
|
file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
|
||||||
add_library(linalg STATIC ${LAPACK_SOURCES})
|
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_target_properties(linalg PROPERTIES OUTPUT_NAME lammps_linalg${LAMMPS_MACHINE})
|
||||||
set(BLAS_LIBRARIES "$<TARGET_FILE:linalg>")
|
set(BLAS_LIBRARIES "$<TARGET_FILE:linalg>")
|
||||||
set(LAPACK_LIBRARIES "$<TARGET_FILE:linalg>")
|
set(LAPACK_LIBRARIES "$<TARGET_FILE:linalg>")
|
||||||
@ -325,17 +358,10 @@ foreach(PKG_WITH_INCL KSPACE PYTHON VORONOI USER-COLVARS USER-MOLFILE USER-NETCD
|
|||||||
endif()
|
endif()
|
||||||
endforeach()
|
endforeach()
|
||||||
|
|
||||||
set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler specific optimization or instrumentation")
|
set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler and machine specific optimization flags (compilation only)")
|
||||||
separate_arguments(CMAKE_TUNE_FLAGS)
|
separate_arguments(CMAKE_TUNE_FLAGS)
|
||||||
include(CheckCXXCompilerFlag)
|
|
||||||
foreach(_FLAG ${CMAKE_TUNE_FLAGS})
|
foreach(_FLAG ${CMAKE_TUNE_FLAGS})
|
||||||
string(REGEX REPLACE "[=\"]" "" _FLAGX ${_FLAG})
|
target_compile_options(lammps PRIVATE ${_FLAG})
|
||||||
check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAGX})
|
|
||||||
if(COMPILER_SUPPORTS${_FLAGX})
|
|
||||||
target_compile_options(lammps PRIVATE ${_FLAG})
|
|
||||||
else()
|
|
||||||
message(WARNING "${_FLAG} found in CMAKE_TUNE_FLAGS, but not supported by the compiler, skipping")
|
|
||||||
endif()
|
|
||||||
endforeach()
|
endforeach()
|
||||||
########################################################################
|
########################################################################
|
||||||
# Basic system tests (standard libraries, headers, functions, types) #
|
# Basic system tests (standard libraries, headers, functions, types) #
|
||||||
@ -357,6 +383,15 @@ target_link_libraries(lammps PRIVATE ${MATH_LIBRARIES})
|
|||||||
include(StyleHeaderUtils)
|
include(StyleHeaderUtils)
|
||||||
RegisterStyles(${LAMMPS_SOURCE_DIR})
|
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} ${LAMMPS_POTENTIALS_DIR})
|
||||||
|
endif()
|
||||||
|
endforeach()
|
||||||
|
|
||||||
##############################################
|
##############################################
|
||||||
# add sources of enabled packages
|
# add sources of enabled packages
|
||||||
############################################
|
############################################
|
||||||
@ -403,17 +438,20 @@ endforeach()
|
|||||||
##############################################
|
##############################################
|
||||||
# add lib sources of (simple) enabled packages
|
# add lib sources of (simple) enabled packages
|
||||||
############################################
|
############################################
|
||||||
foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD)
|
foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT)
|
||||||
if(PKG_${SIMPLE_LIB})
|
if(PKG_${SIMPLE_LIB})
|
||||||
string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
|
string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
|
||||||
string(TOLOWER "${PKG_LIB}" PKG_LIB)
|
string(TOLOWER "${PKG_LIB}" PKG_LIB)
|
||||||
file(GLOB_RECURSE ${PKG_LIB}_SOURCES
|
if(PKG_LIB STREQUAL mesont)
|
||||||
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c
|
enable_language(Fortran)
|
||||||
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
|
file(GLOB_RECURSE ${PKG_LIB}_SOURCES
|
||||||
add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
|
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.f90)
|
||||||
if(NOT BUILD_SHARED_LIBS)
|
else()
|
||||||
install(TARGETS ${PKG_LIB} EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
|
file(GLOB_RECURSE ${PKG_LIB}_SOURCES
|
||||||
|
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c
|
||||||
|
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
|
||||||
endif()
|
endif()
|
||||||
|
add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
|
||||||
set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE})
|
set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE})
|
||||||
target_link_libraries(lammps PRIVATE ${PKG_LIB})
|
target_link_libraries(lammps PRIVATE ${PKG_LIB})
|
||||||
if(PKG_LIB STREQUAL awpmd)
|
if(PKG_LIB STREQUAL awpmd)
|
||||||
@ -434,7 +472,12 @@ if(PKG_USER-ATC)
|
|||||||
if(LAMMPS_SIZES STREQUAL BIGBIG)
|
if(LAMMPS_SIZES STREQUAL BIGBIG)
|
||||||
message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG")
|
message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG")
|
||||||
endif()
|
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_include_directories(atc PRIVATE ${LAMMPS_SOURCE_DIR})
|
||||||
target_compile_definitions(atc PRIVATE -DLAMMPS_${LAMMPS_SIZES})
|
target_compile_definitions(atc PRIVATE -DLAMMPS_${LAMMPS_SIZES})
|
||||||
endif()
|
endif()
|
||||||
@ -495,7 +538,7 @@ execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HE
|
|||||||
# Generate lmpgitversion.h
|
# Generate lmpgitversion.h
|
||||||
######################################
|
######################################
|
||||||
add_custom_target(gitversion COMMAND ${CMAKE_COMMAND}
|
add_custom_target(gitversion COMMAND ${CMAKE_COMMAND}
|
||||||
-DCMAKE_CURRENT_SOURCE_DIR="${CMAKE_CURRENT_SOURCE_DIR}"
|
-DLAMMPS_DIR="${LAMMPS_DIR}"
|
||||||
-DGIT_EXECUTABLE="${GIT_EXECUTABLE}"
|
-DGIT_EXECUTABLE="${GIT_EXECUTABLE}"
|
||||||
-DGIT_FOUND="${GIT_FOUND}"
|
-DGIT_FOUND="${GIT_FOUND}"
|
||||||
-DLAMMPS_STYLE_HEADERS_DIR="${LAMMPS_STYLE_HEADERS_DIR}"
|
-DLAMMPS_STYLE_HEADERS_DIR="${LAMMPS_STYLE_HEADERS_DIR}"
|
||||||
@ -520,14 +563,15 @@ endif()
|
|||||||
|
|
||||||
set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
|
set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
|
||||||
set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
|
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}>)
|
target_include_directories(lammps PUBLIC $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>)
|
||||||
file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps)
|
file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps)
|
||||||
foreach(_HEADER ${LAMMPS_CXX_HEADERS})
|
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_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_custom_target(${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER})
|
||||||
add_dependencies(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()
|
endforeach()
|
||||||
target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/includes>)
|
target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/includes>)
|
||||||
add_library(LAMMPS::lammps ALIAS lammps)
|
add_library(LAMMPS::lammps ALIAS lammps)
|
||||||
@ -536,15 +580,16 @@ set(LAMMPS_API_DEFINES)
|
|||||||
foreach(_DEF ${LAMMPS_DEFINES})
|
foreach(_DEF ${LAMMPS_DEFINES})
|
||||||
set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${_DEF}")
|
set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${_DEF}")
|
||||||
endforeach()
|
endforeach()
|
||||||
configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
|
if(BUILD_SHARED_LIBS)
|
||||||
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
|
install(TARGETS lammps EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
|
||||||
install(EXPORT LAMMPS_Targets FILE LAMMPS_Targets.cmake NAMESPACE LAMMPS:: DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
|
configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
|
||||||
file(GLOB MODULE_FILES ${CMAKE_CURRENT_SOURCE_DIR}/Modules/Find*.cmake)
|
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
|
||||||
install(FILES ${MODULE_FILES} DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
|
install(EXPORT LAMMPS_Targets FILE LAMMPS_Targets.cmake NAMESPACE LAMMPS:: DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
|
||||||
include(CMakePackageConfigHelpers)
|
include(CMakePackageConfigHelpers)
|
||||||
configure_file(LAMMPSConfig.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake @ONLY)
|
configure_file(LAMMPSConfig.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake @ONLY)
|
||||||
write_basic_package_version_file("LAMMPSConfigVersion.cmake" VERSION ${PROJECT_VERSION} COMPATIBILITY ExactVersion)
|
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 ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
|
install(FILES "${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)
|
install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1)
|
||||||
|
|
||||||
if(BUILD_TOOLS)
|
if(BUILD_TOOLS)
|
||||||
@ -554,10 +599,16 @@ if(BUILD_TOOLS)
|
|||||||
|
|
||||||
include(CheckGeneratorSupport)
|
include(CheckGeneratorSupport)
|
||||||
if(CMAKE_GENERATOR_SUPPORT_FORTRAN)
|
if(CMAKE_GENERATOR_SUPPORT_FORTRAN)
|
||||||
enable_language(Fortran)
|
include(CheckLanguage)
|
||||||
add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
|
check_language(Fortran)
|
||||||
target_link_libraries(chain.x PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
|
if(CMAKE_Fortran_COMPILER)
|
||||||
install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR})
|
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()
|
else()
|
||||||
message(WARNING "CMake build doesn't support fortran, skipping building 'chain.x'")
|
message(WARNING "CMake build doesn't support fortran, skipping building 'chain.x'")
|
||||||
endif()
|
endif()
|
||||||
@ -598,6 +649,8 @@ install(
|
|||||||
###############################################################################
|
###############################################################################
|
||||||
if(BUILD_SHARED_LIBS)
|
if(BUILD_SHARED_LIBS)
|
||||||
if(CMAKE_VERSION VERSION_LESS 3.12)
|
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
|
find_package(PythonInterp) # Deprecated since version 3.12
|
||||||
if(PYTHONINTERP_FOUND)
|
if(PYTHONINTERP_FOUND)
|
||||||
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
|
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
|
||||||
@ -649,6 +702,7 @@ endif()
|
|||||||
|
|
||||||
include(Testing)
|
include(Testing)
|
||||||
include(CodeCoverage)
|
include(CodeCoverage)
|
||||||
|
include(CodingStandard)
|
||||||
|
|
||||||
###############################################################################
|
###############################################################################
|
||||||
# Print package summary
|
# Print package summary
|
||||||
@ -693,6 +747,12 @@ if (${_index} GREATER -1)
|
|||||||
endif()
|
endif()
|
||||||
message(STATUS "<<< Linker flags: >>>")
|
message(STATUS "<<< Linker flags: >>>")
|
||||||
message(STATUS "Executable name: ${LAMMPS_BINARY}")
|
message(STATUS "Executable name: ${LAMMPS_BINARY}")
|
||||||
|
if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
|
||||||
|
get_target_property(OPTIONS lammps LINK_OPTIONS)
|
||||||
|
if(OPTIONS)
|
||||||
|
message(STATUS "Linker options: ${OPTIONS}")
|
||||||
|
endif()
|
||||||
|
endif()
|
||||||
if(CMAKE_EXE_LINKER_FLAGS)
|
if(CMAKE_EXE_LINKER_FLAGS)
|
||||||
message(STATUS "Executable linker flags: ${CMAKE_EXE_LINKER_FLAGS}")
|
message(STATUS "Executable linker flags: ${CMAKE_EXE_LINKER_FLAGS}")
|
||||||
endif()
|
endif()
|
||||||
@ -753,3 +813,6 @@ if(PKG_KSPACE)
|
|||||||
endif()
|
endif()
|
||||||
endif()
|
endif()
|
||||||
endif()
|
endif()
|
||||||
|
if(BUILD_DOC)
|
||||||
|
message(STATUS "<<< Building HTML Manual >>>")
|
||||||
|
endif()
|
||||||
|
|||||||
@ -1,87 +1,5 @@
|
|||||||
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR})
|
|
||||||
include(CMakeFindDependencyMacro)
|
include(CMakeFindDependencyMacro)
|
||||||
if(@BUILD_MPI@)
|
if(@BUILD_MPI@)
|
||||||
find_dependency(MPI REQUIRED CXX)
|
find_dependency(MPI REQUIRED CXX)
|
||||||
endif()
|
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")
|
include("${CMAKE_CURRENT_LIST_DIR}/LAMMPS_Targets.cmake")
|
||||||
|
|||||||
@ -15,14 +15,35 @@ if(ENABLE_COVERAGE)
|
|||||||
gen_coverage_xml
|
gen_coverage_xml
|
||||||
COMMAND ${GCOVR_BINARY} -s -x -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o 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}
|
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(
|
add_custom_target(
|
||||||
gen_coverage_html
|
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}
|
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()
|
||||||
endif()
|
endif()
|
||||||
|
|||||||
34
cmake/Modules/CodingStandard.cmake
Normal file
34
cmake/Modules/CodingStandard.cmake
Normal 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()
|
||||||
@ -2,10 +2,19 @@
|
|||||||
# Build documentation
|
# Build documentation
|
||||||
###############################################################################
|
###############################################################################
|
||||||
option(BUILD_DOC "Build LAMMPS HTML documentation" OFF)
|
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)
|
file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
|
||||||
|
|
||||||
@ -20,16 +29,15 @@ if(BUILD_DOC)
|
|||||||
OUTPUT requirements.txt
|
OUTPUT requirements.txt
|
||||||
DEPENDS docenv
|
DEPENDS docenv
|
||||||
COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/utils/requirements.txt requirements.txt
|
COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/utils/requirements.txt requirements.txt
|
||||||
COMMAND ${DOCENV_BINARY_DIR}/pip install -r requirements.txt --upgrade
|
|
||||||
COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
|
COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
|
||||||
|
COMMAND ${DOCENV_BINARY_DIR}/pip install --use-feature=2020-resolver -r requirements.txt --upgrade
|
||||||
)
|
)
|
||||||
|
|
||||||
# download mathjax distribution and unpack to folder "mathjax"
|
# download mathjax distribution and unpack to folder "mathjax"
|
||||||
file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
|
if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax/es5)
|
||||||
"${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
|
file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
|
||||||
EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7)
|
"${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
|
||||||
|
EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7)
|
||||||
if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax)
|
|
||||||
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
|
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-*)
|
file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
|
||||||
execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${CMAKE_CURRENT_BINARY_DIR}/mathjax)
|
execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${CMAKE_CURRENT_BINARY_DIR}/mathjax)
|
||||||
@ -37,11 +45,18 @@ if(BUILD_DOC)
|
|||||||
file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax)
|
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/)
|
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
|
# note, this may run in parallel with other tasks, so we must not use multiple processes here
|
||||||
add_custom_command(
|
add_custom_command(
|
||||||
OUTPUT html
|
OUTPUT html
|
||||||
DEPENDS ${DOC_SOURCES} docenv requirements.txt
|
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 ${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
|
# copy selected image files to html output tree
|
||||||
@ -56,17 +71,17 @@ if(BUILD_DOC)
|
|||||||
set(HTML_IMAGE_TARGETS "")
|
set(HTML_IMAGE_TARGETS "")
|
||||||
foreach(_IMG ${HTML_EXTRA_IMAGES})
|
foreach(_IMG ${HTML_EXTRA_IMAGES})
|
||||||
string(PREPEND _IMG JPG/)
|
string(PREPEND _IMG JPG/)
|
||||||
list(APPEND HTML_IMAGE_TARGETS "html/${_IMG}")
|
list(APPEND HTML_IMAGE_TARGETS "${CMAKE_CURRENT_BINARY_DIR}/html/${_IMG}")
|
||||||
add_custom_command(
|
add_custom_command(
|
||||||
OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/html/${_IMG}
|
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}
|
COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/src/${_IMG} ${CMAKE_BINARY_DIR}/html/${_IMG}
|
||||||
)
|
)
|
||||||
endforeach()
|
endforeach()
|
||||||
|
|
||||||
add_custom_target(
|
add_custom_target(
|
||||||
doc ALL
|
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}
|
SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES}
|
||||||
)
|
)
|
||||||
|
|
||||||
|
|||||||
46
cmake/Modules/FindClangFormat.cmake
Normal file
46
cmake/Modules/FindClangFormat.cmake
Normal 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)
|
||||||
@ -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)
|
|
||||||
@ -6,12 +6,12 @@
|
|||||||
# TBB_MALLOC_FOUND - True if tbb found.
|
# TBB_MALLOC_FOUND - True if tbb found.
|
||||||
#
|
#
|
||||||
|
|
||||||
|
|
||||||
########################################################
|
########################################################
|
||||||
# TBB Malloc
|
# TBB Malloc
|
||||||
|
|
||||||
find_path(TBB_MALLOC_INCLUDE_DIR NAMES tbb/tbb.h PATHS $ENV{TBBROOT}/include)
|
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/gcc4.4
|
||||||
$ENV{TBBROOT}/lib/intel64/gcc4.1)
|
$ENV{TBBROOT}/lib/intel64/gcc4.1)
|
||||||
|
|
||||||
|
|||||||
30
cmake/Modules/FindYAML.cmake
Normal file
30
cmake/Modules/FindYAML.cmake
Normal 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)
|
||||||
79
cmake/Modules/GTest.cmake
Normal file
79
cmake/Modules/GTest.cmake
Normal file
@ -0,0 +1,79 @@
|
|||||||
|
message(STATUS "Downloading and building Google Test library")
|
||||||
|
|
||||||
|
if(CMAKE_BUILD_TYPE STREQUAL Debug)
|
||||||
|
set(GTEST_LIB_POSTFIX d)
|
||||||
|
else()
|
||||||
|
set(GTEST_LIB_POSTFIX)
|
||||||
|
endif()
|
||||||
|
|
||||||
|
include(ExternalProject)
|
||||||
|
set(GTEST_URL "https://github.com/google/googletest/archive/release-1.10.0.tar.gz" CACHE STRING "URL for GTest tarball")
|
||||||
|
mark_as_advanced(GTEST_URL)
|
||||||
|
ExternalProject_Add(googletest
|
||||||
|
URL ${GTEST_URL}
|
||||||
|
URL_MD5 ecd1fa65e7de707cd5c00bdac56022cd
|
||||||
|
SOURCE_DIR "${CMAKE_BINARY_DIR}/gtest-src"
|
||||||
|
BINARY_DIR "${CMAKE_BINARY_DIR}/gtest-build"
|
||||||
|
CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_GTEST_OPTS}
|
||||||
|
-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
|
||||||
|
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
|
||||||
|
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
|
||||||
|
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
|
||||||
|
-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
|
||||||
|
BUILD_BYPRODUCTS <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest${GTEST_LIB_POSTFIX}.a
|
||||||
|
<BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock${GTEST_LIB_POSTFIX}.a
|
||||||
|
<BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest_main${GTEST_LIB_POSTFIX}.a
|
||||||
|
<BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock_main${GTEST_LIB_POSTFIX}.a
|
||||||
|
LOG_DOWNLOAD ON
|
||||||
|
LOG_CONFIGURE ON
|
||||||
|
LOG_BUILD ON
|
||||||
|
INSTALL_COMMAND ""
|
||||||
|
TEST_COMMAND "")
|
||||||
|
|
||||||
|
ExternalProject_Get_Property(googletest SOURCE_DIR)
|
||||||
|
set(GTEST_INCLUDE_DIR ${SOURCE_DIR}/googletest/include)
|
||||||
|
set(GMOCK_INCLUDE_DIR ${SOURCE_DIR}/googlemock/include)
|
||||||
|
|
||||||
|
# workaround for CMake 3.10 on ubuntu 18.04
|
||||||
|
file(MAKE_DIRECTORY ${GTEST_INCLUDE_DIR})
|
||||||
|
file(MAKE_DIRECTORY ${GMOCK_INCLUDE_DIR})
|
||||||
|
|
||||||
|
ExternalProject_Get_Property(googletest BINARY_DIR)
|
||||||
|
set(GTEST_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest${GTEST_LIB_POSTFIX}.a)
|
||||||
|
set(GMOCK_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock${GTEST_LIB_POSTFIX}.a)
|
||||||
|
set(GTEST_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest_main${GTEST_LIB_POSTFIX}.a)
|
||||||
|
set(GMOCK_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock_main${GTEST_LIB_POSTFIX}.a)
|
||||||
|
|
||||||
|
# Prevent GoogleTest from overriding our compiler/linker options
|
||||||
|
# when building with Visual Studio
|
||||||
|
set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
|
||||||
|
|
||||||
|
find_package(Threads QUIET)
|
||||||
|
|
||||||
|
add_library(GTest::GTest UNKNOWN IMPORTED)
|
||||||
|
set_target_properties(GTest::GTest PROPERTIES
|
||||||
|
IMPORTED_LOCATION ${GTEST_LIBRARY_PATH}
|
||||||
|
INTERFACE_INCLUDE_DIRECTORIES ${GTEST_INCLUDE_DIR}
|
||||||
|
INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
|
||||||
|
add_dependencies(GTest::GTest googletest)
|
||||||
|
|
||||||
|
add_library(GTest::GMock UNKNOWN IMPORTED)
|
||||||
|
set_target_properties(GTest::GMock PROPERTIES
|
||||||
|
IMPORTED_LOCATION ${GMOCK_LIBRARY_PATH}
|
||||||
|
INTERFACE_INCLUDE_DIRECTORIES ${GMOCK_INCLUDE_DIR}
|
||||||
|
INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
|
||||||
|
add_dependencies(GTest::GMock googletest)
|
||||||
|
|
||||||
|
add_library(GTest::GTestMain UNKNOWN IMPORTED)
|
||||||
|
set_target_properties(GTest::GTestMain PROPERTIES
|
||||||
|
IMPORTED_LOCATION ${GTEST_MAIN_LIBRARY_PATH}
|
||||||
|
INTERFACE_INCLUDE_DIRECTORIES ${GTEST_INCLUDE_DIR}
|
||||||
|
INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
|
||||||
|
add_dependencies(GTest::GTestMain googletest)
|
||||||
|
|
||||||
|
add_library(GTest::GMockMain UNKNOWN IMPORTED)
|
||||||
|
set_target_properties(GTest::GMockMain PROPERTIES
|
||||||
|
IMPORTED_LOCATION ${GMOCK_MAIN_LIBRARY_PATH}
|
||||||
|
INTERFACE_INCLUDE_DIRECTORIES ${GMOCK_INCLUDE_DIR}
|
||||||
|
INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
|
||||||
|
add_dependencies(GTest::GMockMain googletest)
|
||||||
@ -85,3 +85,26 @@ function(GenerateBinaryHeader varname outfile files)
|
|||||||
file(APPEND ${outfile} "const unsigned int ${varname}_size = sizeof(${varname});\n")
|
file(APPEND ${outfile} "const unsigned int ${varname}_size = sizeof(${varname});\n")
|
||||||
endforeach()
|
endforeach()
|
||||||
endfunction(GenerateBinaryHeader)
|
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)
|
||||||
|
|||||||
@ -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)")
|
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)
|
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)
|
list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
|
||||||
|
|
||||||
@ -53,33 +64,44 @@ if(GPU_API STREQUAL "CUDA")
|
|||||||
|
|
||||||
# build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
|
# build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
|
||||||
# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
|
# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
|
||||||
set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH} ")
|
set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH}")
|
||||||
# Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
|
# Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
|
||||||
if((CUDA_VERSION VERSION_GREATER "3.1") AND (CUDA_VERSION VERSION_LESS "9.0"))
|
if((CUDA_VERSION VERSION_GREATER_EQUAL "3.2") AND (CUDA_VERSION VERSION_LESS "9.0"))
|
||||||
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_20,code=[sm_20,compute_20] ")
|
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_20,code=[sm_20,compute_20] ")
|
||||||
endif()
|
endif()
|
||||||
# Kepler (GPU Arch 3.x) is supported by CUDA 5 and later
|
# Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
|
||||||
if(CUDA_VERSION VERSION_GREATER "4.9")
|
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
|
||||||
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35] ")
|
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] ")
|
||||||
|
endif()
|
||||||
|
# Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11
|
||||||
|
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
|
||||||
|
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35]")
|
||||||
endif()
|
endif()
|
||||||
# Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
|
# Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
|
||||||
if(CUDA_VERSION VERSION_GREATER "5.9")
|
if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
|
||||||
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] ")
|
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")
|
||||||
endif()
|
endif()
|
||||||
# Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
|
# Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
|
||||||
if(CUDA_VERSION VERSION_GREATER "7.9")
|
if(CUDA_VERSION VERSION_GREATER_EQUAL "8.0")
|
||||||
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] ")
|
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")
|
||||||
endif()
|
endif()
|
||||||
# Volta (GPU Arch 7.0) is supported by CUDA 9 and later
|
# Volta (GPU Arch 7.0) is supported by CUDA 9 and later
|
||||||
if(CUDA_VERSION VERSION_GREATER "8.9")
|
if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
|
||||||
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_70,code=[sm_70,compute_70] ")
|
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")
|
||||||
endif()
|
endif()
|
||||||
# Turing (GPU Arch 7.5) is supported by CUDA 10 and later
|
# Turing (GPU Arch 7.5) is supported by CUDA 10 and later
|
||||||
if(CUDA_VERSION VERSION_GREATER "9.9")
|
if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
|
||||||
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ")
|
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
|
||||||
|
endif()
|
||||||
|
# Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
|
||||||
|
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
|
||||||
|
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
|
||||||
|
endif()
|
||||||
|
if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
|
||||||
|
message(WARNING "Unsupported CUDA version. Use at your own risk.")
|
||||||
endif()
|
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})
|
-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}
|
cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
|
||||||
@ -115,7 +137,7 @@ if(GPU_API STREQUAL "CUDA")
|
|||||||
elseif(GPU_API STREQUAL "OPENCL")
|
elseif(GPU_API STREQUAL "OPENCL")
|
||||||
if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
|
if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
|
||||||
# download and unpack support binaries for compilation of windows binaries.
|
# download and unpack support binaries for compilation of windows binaries.
|
||||||
set(LAMMPS_THIRDPARTY_URL "http://download.lammps.org/thirdparty")
|
set(LAMMPS_THIRDPARTY_URL "https://download.lammps.org/thirdparty")
|
||||||
file(DOWNLOAD "${LAMMPS_THIRDPARTY_URL}/opencl-win-devel.tar.gz" "${CMAKE_CURRENT_BINARY_DIR}/opencl-win-devel.tar.gz"
|
file(DOWNLOAD "${LAMMPS_THIRDPARTY_URL}/opencl-win-devel.tar.gz" "${CMAKE_CURRENT_BINARY_DIR}/opencl-win-devel.tar.gz"
|
||||||
EXPECTED_MD5 2c00364888d5671195598b44c2e0d44d)
|
EXPECTED_MD5 2c00364888d5671195598b44c2e0d44d)
|
||||||
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf opencl-win-devel.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
|
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf opencl-win-devel.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
|
||||||
@ -215,30 +237,41 @@ elseif(GPU_API STREQUAL "HIP")
|
|||||||
|
|
||||||
# build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
|
# build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
|
||||||
# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
|
# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
|
||||||
set(HIP_CUDA_GENCODE "-arch=${HIP_ARCH} ")
|
set(HIP_CUDA_GENCODE "-arch=${HIP_ARCH}")
|
||||||
# Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
|
# Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
|
||||||
if((CUDA_VERSION VERSION_GREATER "3.1") AND (CUDA_VERSION VERSION_LESS "9.0"))
|
if((CUDA_VERSION VERSION_GREATER_EQUAL "3.2") AND (CUDA_VERSION VERSION_LESS "9.0"))
|
||||||
string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_20,code=[sm_20,compute_20] ")
|
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_20,code=[sm_20,compute_20]")
|
||||||
endif()
|
endif()
|
||||||
# Kepler (GPU Arch 3.x) is supported by CUDA 5 and later
|
# Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
|
||||||
if(CUDA_VERSION VERSION_GREATER "4.9")
|
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
|
||||||
string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35] ")
|
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30]")
|
||||||
|
endif()
|
||||||
|
# Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11.0
|
||||||
|
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
|
||||||
|
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_35,code=[sm_35,compute_35]")
|
||||||
endif()
|
endif()
|
||||||
# Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
|
# Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
|
||||||
if(CUDA_VERSION VERSION_GREATER "5.9")
|
if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
|
||||||
string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] ")
|
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")
|
||||||
endif()
|
endif()
|
||||||
# Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
|
# Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
|
||||||
if(CUDA_VERSION VERSION_GREATER "7.9")
|
if(CUDA_VERSION VERSION_GREATER_EQUAL "8.0")
|
||||||
string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] ")
|
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")
|
||||||
endif()
|
endif()
|
||||||
# Volta (GPU Arch 7.0) is supported by CUDA 9 and later
|
# Volta (GPU Arch 7.0) is supported by CUDA 9 and later
|
||||||
if(CUDA_VERSION VERSION_GREATER "8.9")
|
if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
|
||||||
string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_70,code=[sm_70,compute_70] ")
|
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")
|
||||||
endif()
|
endif()
|
||||||
# Turing (GPU Arch 7.5) is supported by CUDA 10 and later
|
# Turing (GPU Arch 7.5) is supported by CUDA 10 and later
|
||||||
if(CUDA_VERSION VERSION_GREATER "9.9")
|
if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
|
||||||
string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ")
|
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
|
||||||
|
endif()
|
||||||
|
# Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
|
||||||
|
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
|
||||||
|
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
|
||||||
|
endif()
|
||||||
|
if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
|
||||||
|
message(WARNING "Unsupported CUDA version. Use at your own risk.")
|
||||||
endif()
|
endif()
|
||||||
endif()
|
endif()
|
||||||
|
|
||||||
@ -257,10 +290,17 @@ elseif(GPU_API STREQUAL "HIP")
|
|||||||
if(HIP_PLATFORM STREQUAL "hcc")
|
if(HIP_PLATFORM STREQUAL "hcc")
|
||||||
configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY)
|
configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY)
|
||||||
|
|
||||||
add_custom_command(OUTPUT ${CUBIN_FILE}
|
if(HIP_COMPILER STREQUAL "clang")
|
||||||
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}
|
add_custom_command(OUTPUT ${CUBIN_FILE}
|
||||||
DEPENDS ${CU_CPP_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}
|
||||||
COMMENT "Generating ${CU_NAME}.cubin")
|
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")
|
elseif(HIP_PLATFORM STREQUAL "nvcc")
|
||||||
add_custom_command(OUTPUT ${CUBIN_FILE}
|
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}
|
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}
|
||||||
@ -365,9 +405,6 @@ if(NOT BUILD_MPI)
|
|||||||
else()
|
else()
|
||||||
target_link_libraries(gpu PRIVATE MPI::MPI_CXX)
|
target_link_libraries(gpu PRIVATE MPI::MPI_CXX)
|
||||||
endif()
|
endif()
|
||||||
if(NOT BUILD_SHARED_LIBS)
|
|
||||||
install(TARGETS gpu EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
|
|
||||||
endif()
|
|
||||||
target_compile_definitions(gpu PRIVATE -DLAMMPS_${LAMMPS_SIZES})
|
target_compile_definitions(gpu PRIVATE -DLAMMPS_${LAMMPS_SIZES})
|
||||||
set_target_properties(gpu PROPERTIES OUTPUT_NAME lammps_gpu${LAMMPS_MACHINE})
|
set_target_properties(gpu PROPERTIES OUTPUT_NAME lammps_gpu${LAMMPS_MACHINE})
|
||||||
target_sources(lammps PRIVATE ${GPU_SOURCES})
|
target_sources(lammps PRIVATE ${GPU_SOURCES})
|
||||||
|
|||||||
@ -56,9 +56,6 @@ if(DOWNLOAD_KIM)
|
|||||||
INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include/kim-api")
|
INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include/kim-api")
|
||||||
target_link_libraries(lammps PRIVATE LAMMPS::KIM)
|
target_link_libraries(lammps PRIVATE LAMMPS::KIM)
|
||||||
add_dependencies(LAMMPS::KIM kim_build)
|
add_dependencies(LAMMPS::KIM kim_build)
|
||||||
if(NOT BUILD_SHARED_LIBS)
|
|
||||||
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
|
|
||||||
endif()
|
|
||||||
else()
|
else()
|
||||||
find_package(PkgConfig REQUIRED)
|
find_package(PkgConfig REQUIRED)
|
||||||
pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=${KIM-API_MIN_VERSION})
|
pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=${KIM-API_MIN_VERSION})
|
||||||
|
|||||||
@ -35,8 +35,8 @@ if(DOWNLOAD_KOKKOS)
|
|||||||
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
|
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
|
||||||
include(ExternalProject)
|
include(ExternalProject)
|
||||||
ExternalProject_Add(kokkos_build
|
ExternalProject_Add(kokkos_build
|
||||||
URL https://github.com/kokkos/kokkos/archive/3.1.00.tar.gz
|
URL https://github.com/kokkos/kokkos/archive/3.1.01.tar.gz
|
||||||
URL_MD5 f638a6c786f748a602b26faa0e96ebab
|
URL_MD5 3ccb2100f7fc316891e7dad3bc33fa37
|
||||||
CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
|
CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
|
||||||
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
|
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
|
||||||
)
|
)
|
||||||
@ -49,14 +49,8 @@ if(DOWNLOAD_KOKKOS)
|
|||||||
INTERFACE_LINK_LIBRARIES ${CMAKE_DL_LIBS})
|
INTERFACE_LINK_LIBRARIES ${CMAKE_DL_LIBS})
|
||||||
target_link_libraries(lammps PRIVATE LAMMPS::KOKKOS)
|
target_link_libraries(lammps PRIVATE LAMMPS::KOKKOS)
|
||||||
add_dependencies(LAMMPS::KOKKOS kokkos_build)
|
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)
|
elseif(EXTERNAL_KOKKOS)
|
||||||
find_package(Kokkos 3.1)
|
find_package(Kokkos 3.1.01 REQUIRED CONFIG)
|
||||||
if(NOT Kokkos_FOUND)
|
|
||||||
message(FATAL_ERROR "KOKKOS library version 3.1 or later not found, help CMake to find it by setting KOKKOS_LIBRARY, or set DOWNLOAD_KOKKOS=ON to download it")
|
|
||||||
endif()
|
|
||||||
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
|
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
|
||||||
else()
|
else()
|
||||||
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
|
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
|
||||||
|
|||||||
@ -2,7 +2,7 @@ option(FFT_SINGLE "Use single precision FFTs instead of double precision FFTs" O
|
|||||||
set(FFTW "FFTW3")
|
set(FFTW "FFTW3")
|
||||||
if(FFT_SINGLE)
|
if(FFT_SINGLE)
|
||||||
set(FFTW "FFTW3F")
|
set(FFTW "FFTW3F")
|
||||||
target_compile_definitions(lammps PUBLIC -DFFT_SINGLE)
|
target_compile_definitions(lammps PRIVATE -DFFT_SINGLE)
|
||||||
endif()
|
endif()
|
||||||
find_package(${FFTW} QUIET)
|
find_package(${FFTW} QUIET)
|
||||||
if(${FFTW}_FOUND)
|
if(${FFTW}_FOUND)
|
||||||
@ -17,8 +17,8 @@ string(TOUPPER ${FFT} FFT)
|
|||||||
|
|
||||||
if(FFT STREQUAL "FFTW3")
|
if(FFT STREQUAL "FFTW3")
|
||||||
find_package(${FFTW} REQUIRED)
|
find_package(${FFTW} REQUIRED)
|
||||||
target_compile_definitions(lammps PUBLIC -DFFT_FFTW3)
|
target_compile_definitions(lammps PRIVATE -DFFT_FFTW3)
|
||||||
target_link_libraries(lammps PUBLIC ${FFTW}::${FFTW})
|
target_link_libraries(lammps PRIVATE ${FFTW}::${FFTW})
|
||||||
if(FFTW3_OMP_LIBRARY OR FFTW3F_OMP_LIBRARY)
|
if(FFTW3_OMP_LIBRARY OR FFTW3F_OMP_LIBRARY)
|
||||||
option(FFT_FFTW_THREADS "Use threaded FFTW library" ON)
|
option(FFT_FFTW_THREADS "Use threaded FFTW library" ON)
|
||||||
else()
|
else()
|
||||||
|
|||||||
@ -6,7 +6,7 @@ if(TARGET LATTE::latte)
|
|||||||
return()
|
return()
|
||||||
endif()
|
endif()
|
||||||
|
|
||||||
find_package(LATTE)
|
find_package(LATTE 1.2.2 CONFIG)
|
||||||
if(LATTE_FOUND)
|
if(LATTE_FOUND)
|
||||||
set(DOWNLOAD_LATTE_DEFAULT OFF)
|
set(DOWNLOAD_LATTE_DEFAULT OFF)
|
||||||
else()
|
else()
|
||||||
@ -17,8 +17,8 @@ if(DOWNLOAD_LATTE)
|
|||||||
message(STATUS "LATTE download requested - we will build our own")
|
message(STATUS "LATTE download requested - we will build our own")
|
||||||
include(ExternalProject)
|
include(ExternalProject)
|
||||||
ExternalProject_Add(latte_build
|
ExternalProject_Add(latte_build
|
||||||
URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz
|
URL https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz
|
||||||
URL_MD5 85ac414fdada2d04619c8f936344df14
|
URL_MD5 820e73a457ced178c08c71389a385de7
|
||||||
SOURCE_SUBDIR cmake
|
SOURCE_SUBDIR cmake
|
||||||
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} -DCMAKE_INSTALL_LIBDIR=lib
|
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} -DCMAKE_INSTALL_LIBDIR=lib
|
||||||
-DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
|
-DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
|
||||||
@ -34,14 +34,7 @@ if(DOWNLOAD_LATTE)
|
|||||||
INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
|
INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
|
||||||
target_link_libraries(lammps PRIVATE LAMMPS::LATTE)
|
target_link_libraries(lammps PRIVATE LAMMPS::LATTE)
|
||||||
add_dependencies(LAMMPS::LATTE latte_build)
|
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()
|
else()
|
||||||
find_package(LATTE)
|
find_package(LATTE 1.2.2 REQUIRED CONFIG)
|
||||||
if(NOT LATTE_FOUND)
|
target_link_libraries(lammps PRIVATE LATTE::latte)
|
||||||
message(FATAL_ERROR "LATTE library not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
|
|
||||||
endif()
|
|
||||||
# latte needs lapack
|
|
||||||
target_link_libraries(lammps PRIVATE LATTE::latte ${LAPACK_LIBRARIES})
|
|
||||||
endif()
|
endif()
|
||||||
|
|||||||
@ -7,9 +7,6 @@ file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F
|
|||||||
${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
|
${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
|
||||||
|
|
||||||
add_library(cslib STATIC ${cslib_SOURCES})
|
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})
|
target_compile_definitions(cslib PRIVATE -DLAMMPS_${LAMMPS_SIZES})
|
||||||
set_target_properties(cslib PROPERTIES OUTPUT_NAME lammps_cslib${LAMMPS_MACHINE})
|
set_target_properties(cslib PROPERTIES OUTPUT_NAME lammps_cslib${LAMMPS_MACHINE})
|
||||||
if(BUILD_MPI)
|
if(BUILD_MPI)
|
||||||
|
|||||||
@ -35,9 +35,6 @@ if(DOWNLOAD_MSCG)
|
|||||||
INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
|
INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
|
||||||
target_link_libraries(lammps PRIVATE LAMMPS::MSCG)
|
target_link_libraries(lammps PRIVATE LAMMPS::MSCG)
|
||||||
add_dependencies(LAMMPS::MSCG mscg_build)
|
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()
|
else()
|
||||||
find_package(MSCG)
|
find_package(MSCG)
|
||||||
if(NOT MSCG_FOUND)
|
if(NOT MSCG_FOUND)
|
||||||
|
|||||||
@ -9,9 +9,6 @@ if(COLVARS_LEPTON)
|
|||||||
set(LEPTON_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton)
|
set(LEPTON_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton)
|
||||||
file(GLOB LEPTON_SOURCES ${LEPTON_DIR}/src/[^.]*.cpp)
|
file(GLOB LEPTON_SOURCES ${LEPTON_DIR}/src/[^.]*.cpp)
|
||||||
add_library(lepton STATIC ${LEPTON_SOURCES})
|
add_library(lepton STATIC ${LEPTON_SOURCES})
|
||||||
if(NOT BUILD_SHARED_LIBS)
|
|
||||||
install(TARGETS lepton EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
|
|
||||||
endif()
|
|
||||||
# Change the define below to LEPTON_BUILDING_SHARED_LIBRARY when linking Lepton as a DLL with MSVC
|
# Change the define below to LEPTON_BUILDING_SHARED_LIBRARY when linking Lepton as a DLL with MSVC
|
||||||
target_compile_definitions(lepton PRIVATE -DLEPTON_BUILDING_STATIC_LIBRARY)
|
target_compile_definitions(lepton PRIVATE -DLEPTON_BUILDING_STATIC_LIBRARY)
|
||||||
set_target_properties(lepton PROPERTIES OUTPUT_NAME lammps_lepton${LAMMPS_MACHINE})
|
set_target_properties(lepton PROPERTIES OUTPUT_NAME lammps_lepton${LAMMPS_MACHINE})
|
||||||
@ -19,9 +16,6 @@ if(COLVARS_LEPTON)
|
|||||||
endif()
|
endif()
|
||||||
|
|
||||||
add_library(colvars STATIC ${COLVARS_SOURCES})
|
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})
|
target_compile_definitions(colvars PRIVATE -DLAMMPS_${LAMMPS_SIZES})
|
||||||
set_target_properties(colvars PROPERTIES OUTPUT_NAME lammps_colvars${LAMMPS_MACHINE})
|
set_target_properties(colvars PROPERTIES OUTPUT_NAME lammps_colvars${LAMMPS_MACHINE})
|
||||||
target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
|
target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
|
||||||
|
|||||||
@ -77,7 +77,7 @@ else()
|
|||||||
foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
|
foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
|
||||||
check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAG})
|
check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAG})
|
||||||
if(COMPILER_SUPPORTS${_FLAG})
|
if(COMPILER_SUPPORTS${_FLAG})
|
||||||
target_compile_options(lammps PRIVATE ${_FLAG})
|
target_compile_options(lammps PRIVATE ${_FLAG})
|
||||||
endif()
|
endif()
|
||||||
endforeach()
|
endforeach()
|
||||||
endif()
|
endif()
|
||||||
|
|||||||
@ -1,8 +1,5 @@
|
|||||||
set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
|
set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
|
||||||
add_library(molfile INTERFACE)
|
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})
|
target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
|
||||||
# no need to link with -ldl on windows
|
# no need to link with -ldl on windows
|
||||||
if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
|
if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
|
||||||
|
|||||||
@ -1,11 +1,17 @@
|
|||||||
# USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
|
# 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"
|
# NetCDF library enables dump style "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
|
||||||
find_package(NetCDF)
|
|
||||||
if(NETCDF_FOUND)
|
# may use NetCDF or PNetCDF with MPI, but must have NetCDF without
|
||||||
find_package(PNetCDF)
|
if(NOT BUILD_MPI)
|
||||||
else(NETCDF_FOUND)
|
find_package(NetCDF REQUIRED)
|
||||||
find_package(PNetCDF REQUIRED)
|
else()
|
||||||
endif(NETCDF_FOUND)
|
find_package(NetCDF)
|
||||||
|
if(NETCDF_FOUND)
|
||||||
|
find_package(PNetCDF)
|
||||||
|
else()
|
||||||
|
find_package(PNetCDF REQUIRED)
|
||||||
|
endif()
|
||||||
|
endif()
|
||||||
|
|
||||||
if(NETCDF_FOUND)
|
if(NETCDF_FOUND)
|
||||||
target_link_libraries(lammps PRIVATE NetCDF::NetCDF)
|
target_link_libraries(lammps PRIVATE NetCDF::NetCDF)
|
||||||
|
|||||||
@ -70,9 +70,6 @@ if(DOWNLOAD_PLUMED)
|
|||||||
ExternalProject_get_property(plumed_build INSTALL_DIR)
|
ExternalProject_get_property(plumed_build INSTALL_DIR)
|
||||||
add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
|
add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
|
||||||
add_dependencies(LAMMPS::PLUMED plumed_build)
|
add_dependencies(LAMMPS::PLUMED plumed_build)
|
||||||
if(NOT BUILD_SHARED_LIBS)
|
|
||||||
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
|
|
||||||
endif()
|
|
||||||
if(PLUMED_MODE STREQUAL "STATIC")
|
if(PLUMED_MODE STREQUAL "STATIC")
|
||||||
set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumed.a INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
|
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")
|
elseif(PLUMED_MODE STREQUAL "SHARED")
|
||||||
|
|||||||
@ -1,12 +1,6 @@
|
|||||||
enable_language(C)
|
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)
|
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})
|
set_target_properties(qmmm PROPERTIES OUTPUT_NAME lammps_qmmm${LAMMPS_MACHINE})
|
||||||
target_link_libraries(lammps PRIVATE qmmm)
|
target_link_libraries(lammps PRIVATE qmmm)
|
||||||
target_include_directories(qmmm PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/qmmm)
|
target_include_directories(qmmm PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/qmmm)
|
||||||
|
|||||||
@ -14,10 +14,16 @@ endif()
|
|||||||
option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
|
option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
|
||||||
if(DOWNLOAD_SCAFACOS)
|
if(DOWNLOAD_SCAFACOS)
|
||||||
message(STATUS "ScaFaCoS download requested - we will build our own")
|
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)
|
include(ExternalProject)
|
||||||
ExternalProject_Add(scafacos_build
|
ExternalProject_Add(scafacos_build
|
||||||
URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
|
URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
|
||||||
URL_MD5 bd46d74e3296bd8a444d731bb10c1738
|
URL_MD5 bd46d74e3296bd8a444d731bb10c1738
|
||||||
|
PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
|
||||||
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc
|
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc
|
||||||
--enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
|
--enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
|
||||||
--with-internal-fftw --with-internal-pfft
|
--with-internal-fftw --with-internal-pfft
|
||||||
@ -52,9 +58,6 @@ if(DOWNLOAD_SCAFACOS)
|
|||||||
INTERFACE_LINK_LIBRARIES "${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")
|
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;${INSTALL_DIR}/lib/libfcs_fftw3.a;MPI::MPI_Fortran;MPI::MPI_C")
|
||||||
target_link_libraries(lammps PRIVATE LAMMPS::SCAFACOS)
|
target_link_libraries(lammps PRIVATE LAMMPS::SCAFACOS)
|
||||||
add_dependencies(LAMMPS::SCAFACOS scafacos_build)
|
add_dependencies(LAMMPS::SCAFACOS scafacos_build)
|
||||||
if(NOT BUILD_SHARED_LIBS)
|
|
||||||
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
|
|
||||||
endif()
|
|
||||||
else()
|
else()
|
||||||
find_package(PkgConfig REQUIRED)
|
find_package(PkgConfig REQUIRED)
|
||||||
pkg_check_modules(SCAFACOS REQUIRED IMPORTED_TARGET scafacos)
|
pkg_check_modules(SCAFACOS REQUIRED IMPORTED_TARGET scafacos)
|
||||||
|
|||||||
@ -9,8 +9,8 @@ if(DOWNLOAD_EIGEN3)
|
|||||||
message(STATUS "Eigen3 download requested - we will build our own")
|
message(STATUS "Eigen3 download requested - we will build our own")
|
||||||
include(ExternalProject)
|
include(ExternalProject)
|
||||||
ExternalProject_Add(Eigen3_build
|
ExternalProject_Add(Eigen3_build
|
||||||
URL http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz
|
URL https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz
|
||||||
URL_MD5 f2a417d083fe8ca4b8ed2bc613d20f07
|
URL_MD5 9e30f67e8531477de4117506fe44669b
|
||||||
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
|
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
|
||||||
)
|
)
|
||||||
ExternalProject_get_property(Eigen3_build SOURCE_DIR)
|
ExternalProject_get_property(Eigen3_build SOURCE_DIR)
|
||||||
@ -18,9 +18,6 @@ if(DOWNLOAD_EIGEN3)
|
|||||||
set_target_properties(LAMMPS::EIGEN3 PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}")
|
set_target_properties(LAMMPS::EIGEN3 PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}")
|
||||||
target_link_libraries(lammps PRIVATE LAMMPS::EIGEN3)
|
target_link_libraries(lammps PRIVATE LAMMPS::EIGEN3)
|
||||||
add_dependencies(LAMMPS::EIGEN3 Eigen3_build)
|
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()
|
else()
|
||||||
find_package(Eigen3 NO_MODULE)
|
find_package(Eigen3 NO_MODULE)
|
||||||
mark_as_advanced(Eigen3_DIR)
|
mark_as_advanced(Eigen3_DIR)
|
||||||
|
|||||||
@ -24,7 +24,11 @@ if(DOWNLOAD_VORO)
|
|||||||
ExternalProject_Add(voro_build
|
ExternalProject_Add(voro_build
|
||||||
URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
|
URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
|
||||||
URL_MD5 2338b824c3b7b25590e18e8df5d68af9
|
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 ${VORO_BUILD_OPTIONS}
|
||||||
|
BUILD_IN_SOURCE 1
|
||||||
|
INSTALL_COMMAND ""
|
||||||
BUILD_BYPRODUCTS <SOURCE_DIR>/src/libvoro++.a
|
BUILD_BYPRODUCTS <SOURCE_DIR>/src/libvoro++.a
|
||||||
)
|
)
|
||||||
ExternalProject_get_property(voro_build SOURCE_DIR)
|
ExternalProject_get_property(voro_build SOURCE_DIR)
|
||||||
@ -35,9 +39,6 @@ if(DOWNLOAD_VORO)
|
|||||||
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/src")
|
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/src")
|
||||||
target_link_libraries(lammps PRIVATE LAMMPS::VORO)
|
target_link_libraries(lammps PRIVATE LAMMPS::VORO)
|
||||||
add_dependencies(LAMMPS::VORO voro_build)
|
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()
|
else()
|
||||||
find_package(VORO)
|
find_package(VORO)
|
||||||
if(NOT VORO_FOUND)
|
if(NOT VORO_FOUND)
|
||||||
|
|||||||
@ -3,49 +3,53 @@
|
|||||||
###############################################################################
|
###############################################################################
|
||||||
option(ENABLE_TESTING "Enable testing" OFF)
|
option(ENABLE_TESTING "Enable testing" OFF)
|
||||||
if(ENABLE_TESTING)
|
if(ENABLE_TESTING)
|
||||||
enable_testing()
|
find_program(VALGRIND_BINARY NAMES valgrind)
|
||||||
option(LAMMPS_TESTING_SOURCE_DIR "Location of lammps-testing source directory" "")
|
# generate custom suppression file
|
||||||
option(LAMMPS_TESTING_GIT_TAG "Git tag of lammps-testing" "master")
|
file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "\n")
|
||||||
mark_as_advanced(LAMMPS_TESTING_SOURCE_DIR LAMMPS_TESTING_GIT_TAG)
|
file(GLOB VALGRIND_SUPPRESSION_FILES ${LAMMPS_TOOLS_DIR}/valgrind/[^.]*.supp)
|
||||||
|
foreach(SUPP ${VALGRIND_SUPPRESSION_FILES})
|
||||||
|
file(READ ${SUPP} SUPPRESSIONS)
|
||||||
|
file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "${SUPPRESSIONS}")
|
||||||
|
endforeach()
|
||||||
|
set(VALGRIND_DEFAULT_OPTIONS "--leak-check=full --show-leak-kinds=all --track-origins=yes --suppressions=${CMAKE_BINARY_DIR}/lammps.supp")
|
||||||
|
|
||||||
if (CMAKE_VERSION VERSION_GREATER "3.10.3" AND NOT LAMMPS_TESTING_SOURCE_DIR)
|
set(MEMORYCHECK_COMMAND "${VALGRIND_BINARY}" CACHE FILEPATH "Memory Check Command")
|
||||||
include(FetchContent)
|
set(MEMORYCHECK_COMMAND_OPTIONS "${VALGRIND_DEFAULT_OPTIONS}" CACHE STRING "Memory Check Command Options")
|
||||||
|
|
||||||
FetchContent_Declare(lammps-testing
|
# check if a faster linker is available.
|
||||||
GIT_REPOSITORY https://github.com/lammps/lammps-testing.git
|
# only verified with GNU and Clang compilers and new CMake
|
||||||
GIT_TAG ${LAMMPS_TESTING_GIT_TAG}
|
if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
|
||||||
)
|
if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
|
||||||
|
OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
|
||||||
FetchContent_GetProperties(lammps-testing)
|
include(CheckCXXCompilerFlag)
|
||||||
if(NOT lammps-testing_POPULATED)
|
set(CMAKE_CUSTOM_LINKER_DEFAULT default)
|
||||||
message(STATUS "Downloading tests...")
|
check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG)
|
||||||
FetchContent_Populate(lammps-testing)
|
check_cxx_compiler_flag(-fuse-ld=gold HAVE_GOLD_LINKER_FLAG)
|
||||||
|
check_cxx_compiler_flag(-fuse-ld=bfd HAVE_BFD_LINKER_FLAG)
|
||||||
|
find_program(HAVE_LLD_LINKER_BIN lld ld.lld)
|
||||||
|
find_program(HAVE_GOLD_LINKER_BIN ld.gold)
|
||||||
|
find_program(HAVE_BFD_LINKER_BIN ld.bfd)
|
||||||
|
if(HAVE_LLD_LINKER_FLAG AND HAVE_LLD_LINKER_BIN)
|
||||||
|
set(CMAKE_CUSTOM_LINKER_DEFAULT lld)
|
||||||
|
elseif(HAVE_GOLD_LINKER_FLAG AND HAVE_GOLD_LINKER_BIN)
|
||||||
|
set(CMAKE_CUSTOM_LINKER_DEFAULT gold)
|
||||||
|
elseif(HAVE_BFD_LINKER_FLAG AND HAVE_BFD_LINKER_BIN)
|
||||||
|
set(CMAKE_CUSTOM_LINKER_DEFAULT bfd)
|
||||||
|
endif()
|
||||||
|
set(CMAKE_CUSTOM_LINKER_VALUES lld gold bfd default)
|
||||||
|
set(CMAKE_CUSTOM_LINKER ${CMAKE_CUSTOM_LINKER_DEFAULT} CACHE STRING "Choose a custom linker for faster linking (lld, gold, bfd, default)")
|
||||||
|
validate_option(CMAKE_CUSTOM_LINKER CMAKE_CUSTOM_LINKER_VALUES)
|
||||||
|
mark_as_advanced(CMAKE_CUSTOM_LINKER)
|
||||||
|
if(NOT "${CMAKE_CUSTOM_LINKER}" STREQUAL "default")
|
||||||
|
target_link_options(lammps PUBLIC -fuse-ld=${CMAKE_CUSTOM_LINKER})
|
||||||
|
endif()
|
||||||
endif()
|
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()
|
endif()
|
||||||
|
|
||||||
add_test(NAME ShowHelp COMMAND $<TARGET_FILE:lmp> -help)
|
include(CTest)
|
||||||
|
|
||||||
if(EXISTS ${LAMMPS_TESTING_SOURCE_DIR})
|
enable_testing()
|
||||||
message(STATUS "Running test discovery...")
|
get_filename_component(LAMMPS_UNITTEST_DIR ${LAMMPS_SOURCE_DIR}/../unittest ABSOLUTE)
|
||||||
|
get_filename_component(LAMMPS_UNITTEST_BIN ${CMAKE_BINARY_DIR}/unittest ABSOLUTE)
|
||||||
file(GLOB_RECURSE TEST_SCRIPTS ${LAMMPS_TESTING_SOURCE_DIR}/tests/core/*/in.*)
|
add_subdirectory(${LAMMPS_UNITTEST_DIR} ${LAMMPS_UNITTEST_BIN})
|
||||||
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()
|
|
||||||
endif()
|
endif()
|
||||||
|
|||||||
@ -3,17 +3,19 @@ set(temp_git_commit "(unknown)")
|
|||||||
set(temp_git_branch "(unknown)")
|
set(temp_git_branch "(unknown)")
|
||||||
set(temp_git_describe "(unknown)")
|
set(temp_git_describe "(unknown)")
|
||||||
set(temp_git_info "false")
|
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")
|
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
|
OUTPUT_VARIABLE temp_git_commit
|
||||||
ERROR_QUIET
|
ERROR_QUIET
|
||||||
OUTPUT_STRIP_TRAILING_WHITESPACE)
|
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
|
OUTPUT_VARIABLE temp_git_branch
|
||||||
ERROR_QUIET
|
ERROR_QUIET
|
||||||
OUTPUT_STRIP_TRAILING_WHITESPACE)
|
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
|
OUTPUT_VARIABLE temp_git_describe
|
||||||
ERROR_QUIET
|
ERROR_QUIET
|
||||||
OUTPUT_STRIP_TRAILING_WHITESPACE)
|
OUTPUT_STRIP_TRAILING_WHITESPACE)
|
||||||
|
|||||||
@ -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-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
|
||||||
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
|
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-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-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
|
||||||
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
|
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
|
||||||
USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)
|
USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)
|
||||||
|
|||||||
@ -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-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
|
||||||
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
|
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-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-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
|
||||||
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
|
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
|
||||||
USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)
|
USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)
|
||||||
|
|||||||
17
cmake/presets/download.cmake
Normal file
17
cmake/presets/download.cmake
Normal 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)
|
||||||
|
|
||||||
@ -1,10 +1,10 @@
|
|||||||
set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
|
set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
|
||||||
GRANULAR KSPACE LATTE MANYBODY MC MISC MOLECULE OPT PERI
|
GRANULAR KSPACE LATTE MANYBODY MC MISC MLIAP MOLECULE OPT
|
||||||
POEMS QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
|
PERI POEMS QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
|
||||||
USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
|
USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
|
||||||
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
|
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
|
||||||
USER-FEP USER-INTEL USER-MANIFOLD USER-MEAMC USER-MESODPD
|
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-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC
|
||||||
USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
|
USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
|
||||||
USER-YAFF)
|
USER-YAFF)
|
||||||
|
|||||||
@ -2,13 +2,13 @@
|
|||||||
# external libraries. Compared to all_on.cmake some more unusual packages
|
# external libraries. Compared to all_on.cmake some more unusual packages
|
||||||
# are removed. The resulting binary should be able to run most inputs.
|
# are removed. The resulting binary should be able to run most inputs.
|
||||||
|
|
||||||
set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL
|
set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
|
||||||
DIPOLE GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI
|
GRANULAR KSPACE MANYBODY MC MISC MLIAP MOLECULE OPT PERI
|
||||||
POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
|
POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
|
||||||
USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
|
USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
|
||||||
USER-DPD USER-DRUDE USER-FEP USER-MEAMC USER-MESODPD
|
USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC USER-MESODPD
|
||||||
USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION
|
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})
|
foreach(PKG ${ALL_PACKAGES})
|
||||||
set(PKG_${PKG} ON CACHE BOOL "" FORCE)
|
set(PKG_${PKG} ON CACHE BOOL "" FORCE)
|
||||||
|
|||||||
@ -3,7 +3,7 @@
|
|||||||
|
|
||||||
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MPIIO MSCG PYTHON
|
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MPIIO MSCG PYTHON
|
||||||
VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB
|
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)
|
USER-SCAFACOS USER-SMD USER-VTK)
|
||||||
|
|
||||||
foreach(PKG ${PACKAGES_WITH_LIB})
|
foreach(PKG ${PACKAGES_WITH_LIB})
|
||||||
|
|||||||
0
doc/src/99/crib.html
Executable file → Normal file
0
doc/src/99/crib.html
Executable file → Normal file
@ -136,6 +136,10 @@ src directory.
|
|||||||
.. _cmake_presets:
|
.. _cmake_presets:
|
||||||
|
|
||||||
CMake presets for installing many packages
|
CMake presets for installing many packages
|
||||||
|
<<<<<<< HEAD
|
||||||
|
=======
|
||||||
|
""""""""""""""""""""""""""""""""""""""""""
|
||||||
|
>>>>>>> upstream/master
|
||||||
|
|
||||||
Instead of specifying all the CMake options via the command-line,
|
Instead of specifying all the CMake options via the command-line,
|
||||||
CMake allows initializing its settings cache using script files.
|
CMake allows initializing its settings cache using script files.
|
||||||
@ -168,7 +172,8 @@ one of them as a starting point and customize it to your needs.
|
|||||||
in a single cmake run, or change settings incrementally by running
|
in a single cmake run, or change settings incrementally by running
|
||||||
cmake with new flags.
|
cmake with new flags.
|
||||||
|
|
||||||
**Example:**
|
Example
|
||||||
|
"""""""
|
||||||
|
|
||||||
.. code-block:: bash
|
.. code-block:: bash
|
||||||
|
|
||||||
|
|||||||
@ -150,7 +150,10 @@ OPT.
|
|||||||
* :doc:`orient/bcc <fix_orient>`
|
* :doc:`orient/bcc <fix_orient>`
|
||||||
* :doc:`orient/fcc <fix_orient>`
|
* :doc:`orient/fcc <fix_orient>`
|
||||||
* :doc:`orient/eco <fix_orient_eco>`
|
* :doc:`orient/eco <fix_orient_eco>`
|
||||||
|
<<<<<<< HEAD
|
||||||
* :doc:`pafi <fix_pafi>`
|
* :doc:`pafi <fix_pafi>`
|
||||||
|
=======
|
||||||
|
>>>>>>> upstream/master
|
||||||
* :doc:`phonon <fix_phonon>`
|
* :doc:`phonon <fix_phonon>`
|
||||||
* :doc:`pimd <fix_pimd>`
|
* :doc:`pimd <fix_pimd>`
|
||||||
* :doc:`planeforce <fix_planeforce>`
|
* :doc:`planeforce <fix_planeforce>`
|
||||||
|
|||||||
@ -1,264 +0,0 @@
|
|||||||
Using LAMMPS with Bash on Windows
|
|
||||||
=================================
|
|
||||||
|
|
||||||
**written by Richard Berger**
|
|
||||||
|
|
||||||
----------
|
|
||||||
|
|
||||||
Starting with Windows 10 you can install Linux tools directly in Windows. This
|
|
||||||
allows you to compile LAMMPS following the same procedure as on a real Ubuntu
|
|
||||||
Linux installation. Software can be easily installed using the package manager
|
|
||||||
via apt-get and all files are accessible in both the Windows Explorer and your
|
|
||||||
Linux shell (bash). This avoids switching to a different operating system or
|
|
||||||
installing a virtual machine. Everything runs on Windows.
|
|
||||||
|
|
||||||
.. seealso::
|
|
||||||
|
|
||||||
You can find more detailed information at the `Windows Subsystem for Linux Installation Guide for Windows 10 <https://docs.microsoft.com/en-us/windows/wsl/install-win10>`_.
|
|
||||||
|
|
||||||
Installing Bash on Windows
|
|
||||||
--------------------------
|
|
||||||
|
|
||||||
Prerequisites
|
|
||||||
^^^^^^^^^^^^^
|
|
||||||
|
|
||||||
* Windows 10 (64bit only)
|
|
||||||
* Latest updates installed
|
|
||||||
|
|
||||||
Enable developer mode
|
|
||||||
^^^^^^^^^^^^^^^^^^^^^
|
|
||||||
|
|
||||||
You enable this feature by first opening Windows Settings and enabling
|
|
||||||
Developer mode. Go to the Windows settings and search for "developer". This
|
|
||||||
will allow you to install software which comes from outside of the Windows
|
|
||||||
Store. You might be prompted to reboot your compute. Please do so.
|
|
||||||
|
|
||||||
.. image:: JPG/bow_tutorial_01_small.png
|
|
||||||
:target: JPG/bow_tutorial_01.png
|
|
||||||
|
|
||||||
.. image:: JPG/bow_tutorial_02_small.png
|
|
||||||
:target: JPG/bow_tutorial_02.png
|
|
||||||
|
|
||||||
.. image:: JPG/bow_tutorial_03_small.png
|
|
||||||
:target: JPG/bow_tutorial_03.png
|
|
||||||
|
|
||||||
Install Windows Subsystem for Linux
|
|
||||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
|
||||||
|
|
||||||
Next you must ensure that the Window Subsystem for Linux is installed. Again,
|
|
||||||
search for "enable windows features" in the Settings dialog. This opens a
|
|
||||||
dialog with a list of features you can install. Add a checkmark to Windows
|
|
||||||
Subsystem for Linux (Beta) and press OK.
|
|
||||||
|
|
||||||
.. image:: JPG/bow_tutorial_04_small.png
|
|
||||||
:target: JPG/bow_tutorial_04.png
|
|
||||||
|
|
||||||
.. image:: JPG/bow_tutorial_05.png
|
|
||||||
:target: JPG/bow_tutorial_05.png
|
|
||||||
|
|
||||||
Install Bash for Windows
|
|
||||||
^^^^^^^^^^^^^^^^^^^^^^^^
|
|
||||||
|
|
||||||
After installation completes, type "bash" in the Windows Start menu search.
|
|
||||||
Select the first found option. This will launch a command-line window which
|
|
||||||
will prompt you about installing Ubuntu on Windows. Confirm with "y" and press
|
|
||||||
enter. This will then download Ubuntu for Windows.
|
|
||||||
|
|
||||||
.. image:: JPG/bow_tutorial_06.png
|
|
||||||
|
|
||||||
.. image:: JPG/bow_tutorial_07.png
|
|
||||||
|
|
||||||
During installation, you will be asked for a new password. This will be used
|
|
||||||
for installing new software and running commands with sudo.
|
|
||||||
|
|
||||||
.. image:: JPG/bow_tutorial_08.png
|
|
||||||
|
|
||||||
Type exit to close the command-line window.
|
|
||||||
|
|
||||||
Go to the Start menu and type "bash" again. This time you will see a "Bash on
|
|
||||||
Ubuntu on Windows" Icon. Start this program.
|
|
||||||
|
|
||||||
.. image:: JPG/bow_tutorial_09.png
|
|
||||||
|
|
||||||
Congratulations, you have installed **Bash on Ubuntu on Windows**\ .
|
|
||||||
|
|
||||||
.. image:: JPG/bow_tutorial_10.png
|
|
||||||
|
|
||||||
----------
|
|
||||||
|
|
||||||
Compiling LAMMPS in Bash on Windows
|
|
||||||
-----------------------------------
|
|
||||||
|
|
||||||
The installation of LAMMPS in this environment is identical to working inside
|
|
||||||
of a real Ubuntu Linux installation. At the time writing, it uses Ubuntu 16.04.
|
|
||||||
|
|
||||||
Installing prerequisite packages
|
|
||||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
|
||||||
|
|
||||||
First upgrade all existing packages using
|
|
||||||
|
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
sudo apt update
|
|
||||||
sudo apt upgrade -y
|
|
||||||
|
|
||||||
Next install the following packages, which include compilers and libraries
|
|
||||||
needed for various LAMMPS features:
|
|
||||||
|
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
sudo apt install -y build-essential ccache gfortran openmpi-bin libopenmpi-dev libfftw3-dev libjpeg-dev libpng-dev python-dev python-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev hdf5-tools
|
|
||||||
|
|
||||||
Files in Ubuntu on Windows
|
|
||||||
^^^^^^^^^^^^^^^^^^^^^^^^^^
|
|
||||||
|
|
||||||
When you launch "Bash on Ubuntu on Windows" you will start out in your Linux
|
|
||||||
user home directory /home/[username]\ . You can access your Windows user directory
|
|
||||||
using the /mnt/c/Users/[username] folder.
|
|
||||||
|
|
||||||
Download LAMMPS
|
|
||||||
^^^^^^^^^^^^^^^
|
|
||||||
|
|
||||||
Obtain a copy of the LAMMPS code and go into it using "cd"
|
|
||||||
|
|
||||||
Option 1: Downloading LAMMPS tarball using wget
|
|
||||||
"""""""""""""""""""""""""""""""""""""""""""""""
|
|
||||||
|
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
wget https://lammps.sandia.gov/tars/lammps-stable.tar.gz
|
|
||||||
tar xvzf lammps-stable.tar.gz
|
|
||||||
cd lammps-31Mar17
|
|
||||||
|
|
||||||
Option 2: Obtaining LAMMPS code from GitHub
|
|
||||||
"""""""""""""""""""""""""""""""""""""""""""
|
|
||||||
|
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
git clone https://github.com/lammps/lammps.git
|
|
||||||
cd lammps
|
|
||||||
|
|
||||||
Compiling LAMMPS
|
|
||||||
^^^^^^^^^^^^^^^^
|
|
||||||
|
|
||||||
At this point you can compile LAMMPS like on Ubuntu Linux.
|
|
||||||
|
|
||||||
Compiling serial version
|
|
||||||
""""""""""""""""""""""""
|
|
||||||
|
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
cd src/
|
|
||||||
make -j 4 serial
|
|
||||||
|
|
||||||
This will create an executable called lmp_serial in the src/ directory
|
|
||||||
|
|
||||||
Compiling MPI version
|
|
||||||
"""""""""""""""""""""
|
|
||||||
|
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
cd src/
|
|
||||||
make -j 4 mpi
|
|
||||||
|
|
||||||
This will create an executable called lmp_mpi in the src/ directory
|
|
||||||
|
|
||||||
----------
|
|
||||||
|
|
||||||
Finally, please note the absolute path of your src folder. You can get this using
|
|
||||||
|
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
pwd
|
|
||||||
|
|
||||||
or
|
|
||||||
|
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
echo $PWD
|
|
||||||
|
|
||||||
To run any examples you need the location of the executable. For now, let us
|
|
||||||
save this location in a temporary variable
|
|
||||||
|
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
LAMMPS_DIR=$PWD
|
|
||||||
|
|
||||||
----------
|
|
||||||
|
|
||||||
Running an example script
|
|
||||||
^^^^^^^^^^^^^^^^^^^^^^^^^
|
|
||||||
|
|
||||||
Once compiled you can execute some of the LAMMPS examples. Switch into the
|
|
||||||
examples/melt folder
|
|
||||||
|
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
cd ../examples/melt
|
|
||||||
|
|
||||||
The full path of the serial executable is $LAMMPS_DIR/lmp_serial, while the mpi
|
|
||||||
version is $LAMMPS_DIR/lmp_mpi. You can run the melt example with either
|
|
||||||
version as follows:
|
|
||||||
|
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
$LAMMPS_DIR/lmp_serial -in in.melt
|
|
||||||
|
|
||||||
or
|
|
||||||
|
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
mpirun -np 4 $LAMMPS_DIR/lmp_mpi -in in.melt
|
|
||||||
|
|
||||||
Note the use of our variable $LAMMPS_DIR, which expands into the full path of
|
|
||||||
the LAMMPS src folder we saved earlier.
|
|
||||||
|
|
||||||
Adding your executable directory to your PATH
|
|
||||||
"""""""""""""""""""""""""""""""""""""""""""""
|
|
||||||
|
|
||||||
You can avoid having to type the full path of your LAMMPS binary by adding its
|
|
||||||
parent folder to the PATH environment variable as follows:
|
|
||||||
|
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
export PATH=$LAMMPS_DIR:$PATH
|
|
||||||
|
|
||||||
Input scripts can then be run like this:
|
|
||||||
|
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
lmp_serial -in in.melt
|
|
||||||
|
|
||||||
or
|
|
||||||
|
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
mpirun -np 4 lmp_mpi -in in.melt
|
|
||||||
|
|
||||||
However, this PATH variable will not persist if you close your bash window.
|
|
||||||
To persist this setting edit the $HOME/.bashrc file using your favorite editor
|
|
||||||
and add this line
|
|
||||||
|
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
export PATH=/full/path/to/your/lammps/src:$PATH
|
|
||||||
|
|
||||||
**Example:**
|
|
||||||
|
|
||||||
For an executable lmp_serial with a full path
|
|
||||||
|
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
/home/richard/lammps/src/lmp_serial
|
|
||||||
|
|
||||||
the PATH variable should be
|
|
||||||
|
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
export PATH=/home/richard/lammps/src:$PATH
|
|
||||||
|
|
||||||
.. note::
|
|
||||||
|
|
||||||
This should give you a jump start when trying to run LAMMPS on Windows.
|
|
||||||
To become effective in this environment I encourage you to look into Linux
|
|
||||||
tutorials explaining Bash and Basic Unix commands (e.g., `Linux Journey <https://linuxjourney.com>`_)
|
|
||||||
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Reference in New Issue
Block a user