tx258/lammps-gran-kokkos
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge remote-tracking branch 'upstream/master' into 2020

Browse Source
This commit is contained in:
tomswinburne
2020-08-24 17:02:53 +02:00
parent e8fb7c7ece 7e1a3bd4d5
commit 2ee6e9077a
1456 changed files with 786486 additions and 2043386 deletions
Download Patch File Download Diff File Expand all files Collapse all files

3
.gitattributes vendored Normal file
View File

@ -0,0 +1,3 @@
.gitattributes export-ignore
.gitignore export-ignore
.github export-ignore

11
.github/CODEOWNERS vendored
View File

@ -10,6 +10,7 @@ lib/molfile/* @akohlmey
lib/qmmm/* @akohlmey
lib/vtk/* @rbberger
lib/kim/* @ellio167
lib/mesont/* @iafoss
# whole packages
src/COMPRESS/* @akohlmey
@ -25,6 +26,7 @@ src/USER-COLVARS/* @giacomofiorin
src/USER-INTEL/* @wmbrownintel
src/USER-MANIFOLD/* @Pakketeretet2
src/USER-MEAMC/* @martok
src/USER-MESONT/* @iafoss
src/USER-MOFFF/* @hheenen
src/USER-MOLFILE/* @akohlmey
src/USER-NETCDF/* @pastewka
@ -111,14 +113,23 @@ src/fix_nh.* @athomps
src/info.* @akohlmey @rbberger
src/timer.* @akohlmey
src/min* @sjplimp @stanmoore1
src/utils.* @akohlmey @rbberger
# tools
tools/msi2lmp/* @akohlmey
tools/emacs/* @HaoZeke
tools/singularity/* @akohlmey @rbberger
tools/code_standard/* @rbberger
tools/valgrind/* @akohlmey
# tests
unittest/* @akohlmey @rbberger
# cmake
cmake/* @junghans @rbberger
cmake/Modules/Packages/USER-COLVARS.cmake @junghans @rbberger @giacomofiorin
cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
cmake/presets/*.cmake @junghans @rbberger @akohlmey
# python
python/* @rbberger

4
.github/CONTRIBUTING.md vendored
View File

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

1
.github/PULL_REQUEST_TEMPLATE.md vendored
View File

@ -34,6 +34,7 @@ By submitting this pull request, I agree, that my contribution will be included
- [ ] The added/updated documentation is integrated and tested with the documentation build system
- [ ] The feature has been verified to work with the conventional build system
- [ ] The feature has been verified to work with the CMake based build system
- [ ] Suitable tests have been added to the unittest tree.
- [ ] A package specific README file has been included or updated
- [ ] One or more example input decks are included

29
.github/codecov.yml vendored Normal file
View 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

51
bench/FERMI/README
View File

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

24
bench/FERMI/in.eam
View File

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

37
bench/FERMI/in.eam.titan
View File

@ -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

22
bench/FERMI/in.lj
View File

@ -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

35
bench/FERMI/in.lj.titan
View File

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

30
bench/FERMI/in.rhodo
View File

@ -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

39
bench/FERMI/in.rhodo.scaled.titan
View File

@ -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

42
bench/FERMI/in.rhodo.split.titan
View File

@ -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

2
bench/POTENTIALS/Ni.meam
View File

@ -1,2 +0,0 @@
rc = 4.0
delr = 0.1

1
bench/POTENTIALS/Ni.meam Symbolic link
View File

@ -0,0 +1 @@
../../potentials/Ni.meam

17
bench/POTENTIALS/Si.sw
View File

@ -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
View File

@ -0,0 +1 @@
../../potentials/Si.sw

16
bench/POTENTIALS/Si.tersoff
View File

@ -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
View File

@ -0,0 +1 @@
../../potentials/Si.tersoff

24
bench/POTENTIALS/in.meam
View File

@ -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

22
bench/POTENTIALS/in.reax
View File

@ -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

162
bench/POTENTIALS/library.meam
View File

@ -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
View File

@ -0,0 +1 @@
../../potentials/library.meam

84
bench/POTENTIALS/log.16Mar18.meam.1
View File

@ -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

84
bench/POTENTIALS/log.16Mar18.meam.4
View File

@ -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

86
bench/POTENTIALS/log.16Mar18.reax.1
View File

@ -1,86 +0,0 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
units real
atom_style charge
read_data data.reax
orthogonal box = (0 0 0) to (9.49107 9.49107 6.99123)
1 by 1 by 1 MPI processor grid
reading atoms ...
58 atoms
#replicate 7 8 10
replicate 7 8 5
orthogonal box = (0 0 0) to (66.4375 75.9285 34.9562)
1 by 1 by 1 MPI processor grid
16240 atoms
Time spent = 0.000834942 secs
velocity all create 300.0 9999
pair_style reax
WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
pair_coeff * * ffield.reax 1 2 3 4
timestep 0.1
fix 2 all nve
thermo 10
thermo_style custom step temp ke pe pxx pyy pzz etotal
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 12 13 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair reax, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 115.8 | 115.8 | 115.8 Mbytes
Step Temp KinEng PotEng Pxx Pyy Pzz TotEng
0 300 14521.612 -1616144.2 22296.712 -29858.677 5721.0921 -1601622.5
10 298.98728 14472.591 -1616093.9 21955.847 -24067.096 7389.148 -1601621.3
20 294.76158 14268.045 -1615890.1 19179.258 -10513.494 10789.925 -1601622
30 288.56967 13968.323 -1615591.2 13854.377 5833.02 13949.731 -1601622.9
40 282.06725 13653.571 -1615278.2 6259.9845 19406.33 14947.939 -1601624.6
50 274.84112 13303.787 -1614931.9 -2009.6832 26964.336 13346.855 -1601628.2
60 266.20153 12885.585 -1614519.7 -8441.1641 28485.532 10195.429 -1601634.1
70 259.17085 12545.262 -1614184.2 -11426.993 24941.516 6572.2953 -1601638.9
80 259.73004 12572.33 -1614216.7 -10867.598 16928.461 3033.9021 -1601644.3
90 269.2352 13032.431 -1614679 -7962.3129 4931.5317 -280.22164 -1601646.6
100 280.67181 13586.024 -1615234.3 -3606.1519 -8769.8482 -2527.5887 -1601648.3
Loop time of 358.104 on 1 procs for 100 steps with 16240 atoms
Performance: 0.002 ns/day, 9947.338 hours/ns, 0.279 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 358.07 | 358.07 | 358.07 | 0.0 | 99.99
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.01623 | 0.01623 | 0.01623 | 0.0 | 0.00
Output | 0.0013328 | 0.0013328 | 0.0013328 | 0.0 | 0.00
Modify | 0.012679 | 0.012679 | 0.012679 | 0.0 | 0.00
Other | | 0.006895 | | | 0.00
Nlocal: 16240 ave 16240 max 16240 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 32428 ave 32428 max 32428 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6.69975e+06 ave 6.69975e+06 max 6.69975e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6699752
Ave neighs/atom = 412.546
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:06:02

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

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

69
bench/POTENTIALS/reax_defs.h
View File

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

199
cmake/CMakeLists.txt
View File

@ -3,16 +3,24 @@
# This file is part of LAMMPS
# Created by Christoph Junghans and Richard Berger
cmake_minimum_required(VERSION 3.10)
# set policy to silence warnings about ignoring <PackageName>_ROOT but use it
if(POLICY CMP0074)
cmake_policy(SET CMP0074 NEW)
endif()
########################################
project(lammps CXX)
set(SOVERSION 0)
get_filename_component(LAMMPS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../src ABSOLUTE)
get_filename_component(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib ABSOLUTE)
get_filename_component(LAMMPS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/.. ABSOLUTE)
get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUTE)
get_filename_component(LAMMPS_TOOLS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../tools ABSOLUTE)
get_filename_component(LAMMPS_PYTHON_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../python ABSOLUTE)
get_filename_component(LAMMPS_POTENTIALS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../potentials ABSOLUTE)
set(LAMMPS_SOURCE_DIR ${LAMMPS_DIR}/src)
set(LAMMPS_LIB_SOURCE_DIR ${LAMMPS_DIR}/lib)
set(LAMMPS_DOC_DIR ${LAMMPS_DIR}/doc)
set(LAMMPS_TOOLS_DIR ${LAMMPS_DIR}/tools)
set(LAMMPS_PYTHON_DIR ${LAMMPS_DIR}/python)
set(LAMMPS_POTENTIALS_DIR ${LAMMPS_DIR}/potentials)
find_package(Git)
@ -24,6 +32,12 @@ endif()
# Cmake modules/macros are in a subdirectory to keep this file cleaner
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules)
# make sure LIBRARY_PATH is set if environment variable is set
if (DEFINED ENV{LIBRARY_PATH})
list(APPEND CMAKE_LIBRARY_PATH "$ENV{LIBRARY_PATH}")
message(STATUS "Appending $ENV{LIBRARY_PATH} to CMAKE_LIBRARY_PATH: ${CMAKE_LIBRARY_PATH}")
endif()
include(LAMMPSUtils)
get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h PROJECT_VERSION)
@ -43,7 +57,6 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
# compiler tests
# these need ot be done early (before further tests).
#####################################################################
include(CheckCCompilerFlag)
include(CheckIncludeFileCXX)
# set required compiler flags and compiler/CPU arch specific optimizations
@ -56,27 +69,10 @@ if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
endif()
endif()
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
set(CMAKE_TUNE_DEFAULT "-ffast-math -march=native")
endif()
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")
set(CMAKE_TUNE_DEFAULT "-ffast-math -march=native")
endif()
# we require C++11 without extensions
set(CMAKE_CXX_STANDARD 11)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF)
# GNU compiler specific features for testing
if (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
mark_as_advanced(ENABLE_COVERAGE)
if(ENABLE_COVERAGE)
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
endif()
endif()
set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
########################################################################
# User input options #
@ -108,11 +104,11 @@ install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MOLECULE PERI POEMS QEQ
REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS
QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB
USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION
USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
@ -160,9 +156,6 @@ else()
enable_language(C)
file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
add_library(mpi_stubs STATIC ${MPI_SOURCES})
if(NOT BUILD_SHARED_LIBS)
install(TARGETS mpi_stubs EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
endif()
set_target_properties(mpi_stubs PROPERTIES OUTPUT_NAME lammps_mpi_stubs${LAMMPS_MACHINE})
target_include_directories(mpi_stubs PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS> $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/lammps/mpi>)
install(FILES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps/mpi)
@ -192,13 +185,14 @@ if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0")
target_compile_definitions(lammps PRIVATE -DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
endif()
option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)
option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" ${ENABLE_TESTING})
if(LAMMPS_EXCEPTIONS)
target_compile_definitions(lammps PUBLIC -DLAMMPS_EXCEPTIONS)
endif()
# "hard" dependencies between packages resulting
# in an error instead of skipping over files
pkg_depends(MLIAP SNAP)
pkg_depends(MPIIO MPI)
pkg_depends(USER-ATC MANYBODY)
pkg_depends(USER-LB MPI)
@ -237,6 +231,48 @@ if(BUILD_OMP)
target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
endif()
# Compiler specific features for testing
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
mark_as_advanced(ENABLE_COVERAGE)
if(ENABLE_COVERAGE)
if(CMAKE_VERSION VERSION_LESS 3.13)
if(CMAKE_CXX_FLAGS)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage")
endif()
else()
target_compile_options(lammps PUBLIC --coverage)
target_link_options(lammps PUBLIC --coverage)
endif()
endif()
endif()
set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)")
mark_as_advanced(ENABLE_SANITIZER)
set(ENABLE_SANITIZER_VALUES none address leak thread undefined)
set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES})
validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)
if(NOT ENABLE_SANITIZER STREQUAL "none")
if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
if(CMAKE_VERSION VERSION_LESS 3.13)
if(CMAKE_CXX_FLAGS)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
endif()
else()
target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
endif()
else()
message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.")
set(ENABLE_SANITIZER "none")
endif()
endif()
if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
enable_language(C)
find_package(LAPACK)
@ -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)
file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
add_library(linalg STATIC ${LAPACK_SOURCES})
if(NOT BUILD_SHARED_LIBS)
install(TARGETS linalg EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
endif()
set_target_properties(linalg PROPERTIES OUTPUT_NAME lammps_linalg${LAMMPS_MACHINE})
set(BLAS_LIBRARIES "$<TARGET_FILE:linalg>")
set(LAPACK_LIBRARIES "$<TARGET_FILE:linalg>")
@ -325,17 +358,10 @@ foreach(PKG_WITH_INCL KSPACE PYTHON VORONOI USER-COLVARS USER-MOLFILE USER-NETCD
endif()
endforeach()
set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler specific optimization or instrumentation")
set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler and machine specific optimization flags (compilation only)")
separate_arguments(CMAKE_TUNE_FLAGS)
include(CheckCXXCompilerFlag)
foreach(_FLAG ${CMAKE_TUNE_FLAGS})
string(REGEX REPLACE "[=\"]" "" _FLAGX ${_FLAG})
check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAGX})
if(COMPILER_SUPPORTS${_FLAGX})
target_compile_options(lammps PRIVATE ${_FLAG})
else()
message(WARNING "${_FLAG} found in CMAKE_TUNE_FLAGS, but not supported by the compiler, skipping")
endif()
target_compile_options(lammps PRIVATE ${_FLAG})
endforeach()
########################################################################
# Basic system tests (standard libraries, headers, functions, types) #
@ -357,6 +383,15 @@ target_link_libraries(lammps PRIVATE ${MATH_LIBRARIES})
include(StyleHeaderUtils)
RegisterStyles(${LAMMPS_SOURCE_DIR})
########################################################
# Fetch missing external files and archives for packages
########################################################
foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
if(PKG_${PKG})
FetchPotentials(${LAMMPS_SOURCE_DIR}/${PKG} ${LAMMPS_POTENTIALS_DIR})
endif()
endforeach()
##############################################
# add sources of enabled packages
############################################
@ -403,17 +438,20 @@ endforeach()
##############################################
# add lib sources of (simple) enabled packages
############################################
foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD)
foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT)
if(PKG_${SIMPLE_LIB})
string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
string(TOLOWER "${PKG_LIB}" PKG_LIB)
file(GLOB_RECURSE ${PKG_LIB}_SOURCES
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
if(NOT BUILD_SHARED_LIBS)
install(TARGETS ${PKG_LIB} EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
if(PKG_LIB STREQUAL mesont)
enable_language(Fortran)
file(GLOB_RECURSE ${PKG_LIB}_SOURCES
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.f90)
else()
file(GLOB_RECURSE ${PKG_LIB}_SOURCES
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
endif()
add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE})
target_link_libraries(lammps PRIVATE ${PKG_LIB})
if(PKG_LIB STREQUAL awpmd)
@ -434,7 +472,12 @@ if(PKG_USER-ATC)
if(LAMMPS_SIZES STREQUAL BIGBIG)
message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG")
endif()
target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES} MPI::MPI_CXX)
target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES})
if(BUILD_MPI)
target_link_libraries(atc PRIVATE MPI::MPI_CXX)
else()
target_link_libraries(atc PRIVATE mpi_stubs)
endif()
target_include_directories(atc PRIVATE ${LAMMPS_SOURCE_DIR})
target_compile_definitions(atc PRIVATE -DLAMMPS_${LAMMPS_SIZES})
endif()
@ -495,7 +538,7 @@ execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HE
# Generate lmpgitversion.h
######################################
add_custom_target(gitversion COMMAND ${CMAKE_COMMAND}
-DCMAKE_CURRENT_SOURCE_DIR="${CMAKE_CURRENT_SOURCE_DIR}"
-DLAMMPS_DIR="${LAMMPS_DIR}"
-DGIT_EXECUTABLE="${GIT_EXECUTABLE}"
-DGIT_FOUND="${GIT_FOUND}"
-DLAMMPS_STYLE_HEADERS_DIR="${LAMMPS_STYLE_HEADERS_DIR}"
@ -520,14 +563,15 @@ endif()
set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
install(TARGETS lammps EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
target_include_directories(lammps PUBLIC $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>)
file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps)
foreach(_HEADER ${LAMMPS_CXX_HEADERS})
add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/${_HEADER})
add_custom_target(${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER})
add_dependencies(lammps ${_HEADER})
install(FILES ${LAMMPS_SOURCE_DIR}/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
if(BUILD_SHARED_LIBS)
install(FILES ${LAMMPS_SOURCE_DIR}/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
endif()
endforeach()
target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/includes>)
add_library(LAMMPS::lammps ALIAS lammps)
@ -536,15 +580,16 @@ set(LAMMPS_API_DEFINES)
foreach(_DEF ${LAMMPS_DEFINES})
set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${_DEF}")
endforeach()
configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
install(EXPORT LAMMPS_Targets FILE LAMMPS_Targets.cmake NAMESPACE LAMMPS:: DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
file(GLOB MODULE_FILES ${CMAKE_CURRENT_SOURCE_DIR}/Modules/Find*.cmake)
install(FILES ${MODULE_FILES} DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
include(CMakePackageConfigHelpers)
configure_file(LAMMPSConfig.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake @ONLY)
write_basic_package_version_file("LAMMPSConfigVersion.cmake" VERSION ${PROJECT_VERSION} COMPATIBILITY ExactVersion)
install(FILES "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake" "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfigVersion.cmake" DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
if(BUILD_SHARED_LIBS)
install(TARGETS lammps EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
install(EXPORT LAMMPS_Targets FILE LAMMPS_Targets.cmake NAMESPACE LAMMPS:: DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
include(CMakePackageConfigHelpers)
configure_file(LAMMPSConfig.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake @ONLY)
write_basic_package_version_file("LAMMPSConfigVersion.cmake" VERSION ${PROJECT_VERSION} COMPATIBILITY ExactVersion)
install(FILES "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake" "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfigVersion.cmake" DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
endif()
install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1)
if(BUILD_TOOLS)
@ -554,10 +599,16 @@ if(BUILD_TOOLS)
include(CheckGeneratorSupport)
if(CMAKE_GENERATOR_SUPPORT_FORTRAN)
enable_language(Fortran)
add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
target_link_libraries(chain.x PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR})
include(CheckLanguage)
check_language(Fortran)
if(CMAKE_Fortran_COMPILER)
enable_language(Fortran)
add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
target_link_libraries(chain.x PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR})
else()
message(WARNING "No suitable Fortran compiler found, skipping building 'chain.x'")
endif()
else()
message(WARNING "CMake build doesn't support fortran, skipping building 'chain.x'")
endif()
@ -598,6 +649,8 @@ install(
###############################################################################
if(BUILD_SHARED_LIBS)
if(CMAKE_VERSION VERSION_LESS 3.12)
# adjust so we find Python 3 versions before Python 2 on old systems with old CMake
set(Python_ADDITIONAL_VERSIONS 3.8 3.7 3.6 3.5)
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
@ -649,6 +702,7 @@ endif()
include(Testing)
include(CodeCoverage)
include(CodingStandard)
###############################################################################
# Print package summary
@ -693,6 +747,12 @@ if (${_index} GREATER -1)
endif()
message(STATUS "<<< Linker flags: >>>")
message(STATUS "Executable name: ${LAMMPS_BINARY}")
if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
get_target_property(OPTIONS lammps LINK_OPTIONS)
if(OPTIONS)
message(STATUS "Linker options: ${OPTIONS}")
endif()
endif()
if(CMAKE_EXE_LINKER_FLAGS)
message(STATUS "Executable linker flags: ${CMAKE_EXE_LINKER_FLAGS}")
endif()
@ -753,3 +813,6 @@ if(PKG_KSPACE)
endif()
endif()
endif()
if(BUILD_DOC)
message(STATUS "<<< Building HTML Manual >>>")
endif()

82
cmake/LAMMPSConfig.cmake.in
View File

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

27
cmake/Modules/CodeCoverage.cmake
View File

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

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

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

39
cmake/Modules/Documentation.cmake
View File

@ -2,10 +2,19 @@
# Build documentation
###############################################################################
option(BUILD_DOC "Build LAMMPS HTML documentation" OFF)
if(BUILD_DOC)
find_package(PythonInterp 3 REQUIRED)
set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)
if(BUILD_DOC)
# Sphinx 3.x requires at least Python 3.5
if(CMAKE_VERSION VERSION_LESS 3.12)
find_package(PythonInterp 3.5 REQUIRED)
set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv -p ${PYTHON_EXECUTABLE})
else()
find_package(Python3 REQUIRED COMPONENTS Interpreter)
if(Python3_VERSION VERSION_LESS 3.5)
message(FATAL_ERROR "Python 3.5 and up is required to build the HTML documentation")
endif()
set(VIRTUALENV ${Python3_EXECUTABLE} -m virtualenv -p ${Python3_EXECUTABLE})
endif()
file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
@ -20,16 +29,15 @@ if(BUILD_DOC)
OUTPUT requirements.txt
DEPENDS docenv
COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/utils/requirements.txt requirements.txt
COMMAND ${DOCENV_BINARY_DIR}/pip install -r requirements.txt --upgrade
COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
COMMAND ${DOCENV_BINARY_DIR}/pip install --use-feature=2020-resolver -r requirements.txt --upgrade
)
# download mathjax distribution and unpack to folder "mathjax"
file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
"${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7)
if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax)
if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax/es5)
file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
"${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7)
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${CMAKE_CURRENT_BINARY_DIR}/mathjax)
@ -37,11 +45,18 @@ if(BUILD_DOC)
file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax)
file(COPY ${CMAKE_CURRENT_BINARY_DIR}/mathjax/es5 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax/)
# for increased browser compatibility
if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/html/_static/polyfill.js)
file(DOWNLOAD "https://polyfill.io/v3/polyfill.min.js?features=es6"
"${CMAKE_CURRENT_BINARY_DIR}/html/_static/polyfill.js")
endif()
# note, this may run in parallel with other tasks, so we must not use multiple processes here
add_custom_command(
OUTPUT html
DEPENDS ${DOC_SOURCES} docenv requirements.txt
COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${LAMMPS_DOC_DIR}/src html
COMMAND ${CMAKE_COMMAND} -E create_symlink Manual.html ${CMAKE_CURRENT_BINARY_DIR}/html/index.html
)
# copy selected image files to html output tree
@ -56,17 +71,17 @@ if(BUILD_DOC)
set(HTML_IMAGE_TARGETS "")
foreach(_IMG ${HTML_EXTRA_IMAGES})
string(PREPEND _IMG JPG/)
list(APPEND HTML_IMAGE_TARGETS "html/${_IMG}")
list(APPEND HTML_IMAGE_TARGETS "${CMAKE_CURRENT_BINARY_DIR}/html/${_IMG}")
add_custom_command(
OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/html/${_IMG}
DEPENDS ${LAMMPS_DOC_DIR}/src/${_IMG} html/JPG
DEPENDS ${LAMMPS_DOC_DIR}/src/${_IMG} ${CMAKE_CURRENT_BINARY_DIR}/html/JPG
COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/src/${_IMG} ${CMAKE_BINARY_DIR}/html/${_IMG}
)
endforeach()
add_custom_target(
doc ALL
DEPENDS html html/_static/mathjax/es5 ${HTML_IMAGE_TARGETS}
DEPENDS html ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax/es5 ${HTML_IMAGE_TARGETS}
SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES}
)

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

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

27
cmake/Modules/FindLATTE.cmake
View File

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

4
cmake/Modules/FindTBB_MALLOC.cmake
View File

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

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

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

79
cmake/Modules/GTest.cmake Normal file
View 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)

23
cmake/Modules/LAMMPSUtils.cmake
View File

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

111
cmake/Modules/Packages/GPU.cmake
View File

@ -40,6 +40,17 @@ if(GPU_API STREQUAL "CUDA")
set(GPU_ARCH "sm_50" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
# ensure that no *cubin.h files exist from a compile in the lib/gpu folder
file(GLOB GPU_LIB_OLD_CUBIN_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h)
if (GPU_LIB_OLD_CUBIN_HEADERS)
message(FATAL_ERROR "########################################################################\n"
"Found file(s) generated by the make-based build system in lib/gpu\n"
"Please run\n"
" make -C ${LAMMPS_LIB_SOURCE_DIR}/gpu -f Makefile.serial clean\n"
"to remove\n"
"########################################################################")
endif()
file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
@ -53,33 +64,44 @@ if(GPU_API STREQUAL "CUDA")
# build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH} ")
set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH}")
# Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
if((CUDA_VERSION VERSION_GREATER "3.1") AND (CUDA_VERSION VERSION_LESS "9.0"))
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_20,code=[sm_20,compute_20] ")
if((CUDA_VERSION VERSION_GREATER_EQUAL "3.2") AND (CUDA_VERSION VERSION_LESS "9.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_20,code=[sm_20,compute_20] ")
endif()
# Kepler (GPU Arch 3.x) is supported by CUDA 5 and later
if(CUDA_VERSION VERSION_GREATER "4.9")
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35] ")
# Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] ")
endif()
# Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35]")
endif()
# Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
if(CUDA_VERSION VERSION_GREATER "5.9")
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] ")
if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")
endif()
# Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
if(CUDA_VERSION VERSION_GREATER "7.9")
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] ")
if(CUDA_VERSION VERSION_GREATER_EQUAL "8.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")
endif()
# Volta (GPU Arch 7.0) is supported by CUDA 9 and later
if(CUDA_VERSION VERSION_GREATER "8.9")
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_70,code=[sm_70,compute_70] ")
if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")
endif()
# Turing (GPU Arch 7.5) is supported by CUDA 10 and later
if(CUDA_VERSION VERSION_GREATER "9.9")
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ")
if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
endif()
# Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
endif()
if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
message(WARNING "Unsupported CUDA version. Use at your own risk.")
endif()
cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
@ -115,7 +137,7 @@ if(GPU_API STREQUAL "CUDA")
elseif(GPU_API STREQUAL "OPENCL")
if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
# download and unpack support binaries for compilation of windows binaries.
set(LAMMPS_THIRDPARTY_URL "http://download.lammps.org/thirdparty")
set(LAMMPS_THIRDPARTY_URL "https://download.lammps.org/thirdparty")
file(DOWNLOAD "${LAMMPS_THIRDPARTY_URL}/opencl-win-devel.tar.gz" "${CMAKE_CURRENT_BINARY_DIR}/opencl-win-devel.tar.gz"
EXPECTED_MD5 2c00364888d5671195598b44c2e0d44d)
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf opencl-win-devel.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
@ -215,30 +237,41 @@ elseif(GPU_API STREQUAL "HIP")
# build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
set(HIP_CUDA_GENCODE "-arch=${HIP_ARCH} ")
set(HIP_CUDA_GENCODE "-arch=${HIP_ARCH}")
# Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
if((CUDA_VERSION VERSION_GREATER "3.1") AND (CUDA_VERSION VERSION_LESS "9.0"))
string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_20,code=[sm_20,compute_20] ")
if((CUDA_VERSION VERSION_GREATER_EQUAL "3.2") AND (CUDA_VERSION VERSION_LESS "9.0"))
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_20,code=[sm_20,compute_20]")
endif()
# Kepler (GPU Arch 3.x) is supported by CUDA 5 and later
if(CUDA_VERSION VERSION_GREATER "4.9")
string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35] ")
# Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30]")
endif()
# Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11.0
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_35,code=[sm_35,compute_35]")
endif()
# Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
if(CUDA_VERSION VERSION_GREATER "5.9")
string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] ")
if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")
endif()
# Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
if(CUDA_VERSION VERSION_GREATER "7.9")
string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] ")
if(CUDA_VERSION VERSION_GREATER_EQUAL "8.0")
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")
endif()
# Volta (GPU Arch 7.0) is supported by CUDA 9 and later
if(CUDA_VERSION VERSION_GREATER "8.9")
string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_70,code=[sm_70,compute_70] ")
if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")
endif()
# Turing (GPU Arch 7.5) is supported by CUDA 10 and later
if(CUDA_VERSION VERSION_GREATER "9.9")
string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ")
if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
endif()
# Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
endif()
if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
message(WARNING "Unsupported CUDA version. Use at your own risk.")
endif()
endif()
@ -257,10 +290,17 @@ elseif(GPU_API STREQUAL "HIP")
if(HIP_PLATFORM STREQUAL "hcc")
configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY)
add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
DEPENDS ${CU_CPP_FILE}
COMMENT "Generating ${CU_NAME}.cubin")
if(HIP_COMPILER STREQUAL "clang")
add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
DEPENDS ${CU_CPP_FILE}
COMMENT "Generating ${CU_NAME}.cubin")
else()
add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
DEPENDS ${CU_CPP_FILE}
COMMENT "Generating ${CU_NAME}.cubin")
endif()
elseif(HIP_PLATFORM STREQUAL "nvcc")
add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE}
@ -365,9 +405,6 @@ if(NOT BUILD_MPI)
else()
target_link_libraries(gpu PRIVATE MPI::MPI_CXX)
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})
set_target_properties(gpu PROPERTIES OUTPUT_NAME lammps_gpu${LAMMPS_MACHINE})
target_sources(lammps PRIVATE ${GPU_SOURCES})

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

@ -56,9 +56,6 @@ if(DOWNLOAD_KIM)
INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include/kim-api")
target_link_libraries(lammps PRIVATE LAMMPS::KIM)
add_dependencies(LAMMPS::KIM kim_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
else()
find_package(PkgConfig REQUIRED)
pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=${KIM-API_MIN_VERSION})

12
cmake/Modules/Packages/KOKKOS.cmake
View File

@ -35,8 +35,8 @@ if(DOWNLOAD_KOKKOS)
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
include(ExternalProject)
ExternalProject_Add(kokkos_build
URL https://github.com/kokkos/kokkos/archive/3.1.00.tar.gz
URL_MD5 f638a6c786f748a602b26faa0e96ebab
URL https://github.com/kokkos/kokkos/archive/3.1.01.tar.gz
URL_MD5 3ccb2100f7fc316891e7dad3bc33fa37
CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
)
@ -49,14 +49,8 @@ if(DOWNLOAD_KOKKOS)
INTERFACE_LINK_LIBRARIES ${CMAKE_DL_LIBS})
target_link_libraries(lammps PRIVATE LAMMPS::KOKKOS)
add_dependencies(LAMMPS::KOKKOS kokkos_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 3.1)
if(NOT Kokkos_FOUND)
message(FATAL_ERROR "KOKKOS library version 3.1 or later not found, help CMake to find it by setting KOKKOS_LIBRARY, or set DOWNLOAD_KOKKOS=ON to download it")
endif()
find_package(Kokkos 3.1.01 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
else()
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)

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

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

17
cmake/Modules/Packages/LATTE.cmake
View File

@ -6,7 +6,7 @@ if(TARGET LATTE::latte)
return()
endif()
find_package(LATTE)
find_package(LATTE 1.2.2 CONFIG)
if(LATTE_FOUND)
set(DOWNLOAD_LATTE_DEFAULT OFF)
else()
@ -17,8 +17,8 @@ if(DOWNLOAD_LATTE)
message(STATUS "LATTE download requested - we will build our own")
include(ExternalProject)
ExternalProject_Add(latte_build
URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz
URL_MD5 85ac414fdada2d04619c8f936344df14
URL https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz
URL_MD5 820e73a457ced178c08c71389a385de7
SOURCE_SUBDIR cmake
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} -DCMAKE_INSTALL_LIBDIR=lib
-DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
@ -34,14 +34,7 @@ if(DOWNLOAD_LATTE)
INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
target_link_libraries(lammps PRIVATE LAMMPS::LATTE)
add_dependencies(LAMMPS::LATTE latte_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
else()
find_package(LATTE)
if(NOT LATTE_FOUND)
message(FATAL_ERROR "LATTE library not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
endif()
# latte needs lapack
target_link_libraries(lammps PRIVATE LATTE::latte ${LAPACK_LIBRARIES})
find_package(LATTE 1.2.2 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE LATTE::latte)
endif()

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

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

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

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

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

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

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

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

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

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

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

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

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

@ -70,9 +70,6 @@ if(DOWNLOAD_PLUMED)
ExternalProject_get_property(plumed_build INSTALL_DIR)
add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
add_dependencies(LAMMPS::PLUMED plumed_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
if(PLUMED_MODE STREQUAL "STATIC")
set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumed.a INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
elseif(PLUMED_MODE STREQUAL "SHARED")

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

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

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

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

7
cmake/Modules/Packages/USER-SMD.cmake
View File

@ -9,8 +9,8 @@ if(DOWNLOAD_EIGEN3)
message(STATUS "Eigen3 download requested - we will build our own")
include(ExternalProject)
ExternalProject_Add(Eigen3_build
URL http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz
URL_MD5 f2a417d083fe8ca4b8ed2bc613d20f07
URL https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz
URL_MD5 9e30f67e8531477de4117506fe44669b
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
)
ExternalProject_get_property(Eigen3_build SOURCE_DIR)
@ -18,9 +18,6 @@ if(DOWNLOAD_EIGEN3)
set_target_properties(LAMMPS::EIGEN3 PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}")
target_link_libraries(lammps PRIVATE LAMMPS::EIGEN3)
add_dependencies(LAMMPS::EIGEN3 Eigen3_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
else()
find_package(Eigen3 NO_MODULE)
mark_as_advanced(Eigen3_DIR)

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

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

82
cmake/Modules/Testing.cmake
View File

@ -3,49 +3,53 @@
###############################################################################
option(ENABLE_TESTING "Enable testing" OFF)
if(ENABLE_TESTING)
enable_testing()
option(LAMMPS_TESTING_SOURCE_DIR "Location of lammps-testing source directory" "")
option(LAMMPS_TESTING_GIT_TAG "Git tag of lammps-testing" "master")
mark_as_advanced(LAMMPS_TESTING_SOURCE_DIR LAMMPS_TESTING_GIT_TAG)
find_program(VALGRIND_BINARY NAMES valgrind)
# generate custom suppression file
file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "\n")
file(GLOB VALGRIND_SUPPRESSION_FILES ${LAMMPS_TOOLS_DIR}/valgrind/[^.]*.supp)
foreach(SUPP ${VALGRIND_SUPPRESSION_FILES})
file(READ ${SUPP} SUPPRESSIONS)
file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "${SUPPRESSIONS}")
endforeach()
set(VALGRIND_DEFAULT_OPTIONS "--leak-check=full --show-leak-kinds=all --track-origins=yes --suppressions=${CMAKE_BINARY_DIR}/lammps.supp")
if (CMAKE_VERSION VERSION_GREATER "3.10.3" AND NOT LAMMPS_TESTING_SOURCE_DIR)
include(FetchContent)
set(MEMORYCHECK_COMMAND "${VALGRIND_BINARY}" CACHE FILEPATH "Memory Check Command")
set(MEMORYCHECK_COMMAND_OPTIONS "${VALGRIND_DEFAULT_OPTIONS}" CACHE STRING "Memory Check Command Options")
FetchContent_Declare(lammps-testing
GIT_REPOSITORY https://github.com/lammps/lammps-testing.git
GIT_TAG ${LAMMPS_TESTING_GIT_TAG}
)
FetchContent_GetProperties(lammps-testing)
if(NOT lammps-testing_POPULATED)
message(STATUS "Downloading tests...")
FetchContent_Populate(lammps-testing)
# check if a faster linker is available.
# only verified with GNU and Clang compilers and new CMake
if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
include(CheckCXXCompilerFlag)
set(CMAKE_CUSTOM_LINKER_DEFAULT default)
check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG)
check_cxx_compiler_flag(-fuse-ld=gold HAVE_GOLD_LINKER_FLAG)
check_cxx_compiler_flag(-fuse-ld=bfd HAVE_BFD_LINKER_FLAG)
find_program(HAVE_LLD_LINKER_BIN lld ld.lld)
find_program(HAVE_GOLD_LINKER_BIN ld.gold)
find_program(HAVE_BFD_LINKER_BIN ld.bfd)
if(HAVE_LLD_LINKER_FLAG AND HAVE_LLD_LINKER_BIN)
set(CMAKE_CUSTOM_LINKER_DEFAULT lld)
elseif(HAVE_GOLD_LINKER_FLAG AND HAVE_GOLD_LINKER_BIN)
set(CMAKE_CUSTOM_LINKER_DEFAULT gold)
elseif(HAVE_BFD_LINKER_FLAG AND HAVE_BFD_LINKER_BIN)
set(CMAKE_CUSTOM_LINKER_DEFAULT bfd)
endif()
set(CMAKE_CUSTOM_LINKER_VALUES lld gold bfd default)
set(CMAKE_CUSTOM_LINKER ${CMAKE_CUSTOM_LINKER_DEFAULT} CACHE STRING "Choose a custom linker for faster linking (lld, gold, bfd, default)")
validate_option(CMAKE_CUSTOM_LINKER CMAKE_CUSTOM_LINKER_VALUES)
mark_as_advanced(CMAKE_CUSTOM_LINKER)
if(NOT "${CMAKE_CUSTOM_LINKER}" STREQUAL "default")
target_link_options(lammps PUBLIC -fuse-ld=${CMAKE_CUSTOM_LINKER})
endif()
endif()
set(LAMMPS_TESTING_SOURCE_DIR ${lammps-testing_SOURCE_DIR})
elseif(NOT LAMMPS_TESTING_SOURCE_DIR)
message(WARNING "Full test-suite requires CMake >= 3.11 or copy of\n"
"https://github.com/lammps/lammps-testing in LAMMPS_TESTING_SOURCE_DIR")
endif()
add_test(NAME ShowHelp COMMAND $<TARGET_FILE:lmp> -help)
include(CTest)
if(EXISTS ${LAMMPS_TESTING_SOURCE_DIR})
message(STATUS "Running test discovery...")
file(GLOB_RECURSE TEST_SCRIPTS ${LAMMPS_TESTING_SOURCE_DIR}/tests/core/*/in.*)
foreach(script_path ${TEST_SCRIPTS})
get_filename_component(TEST_NAME ${script_path} EXT)
get_filename_component(SCRIPT_NAME ${script_path} NAME)
get_filename_component(PARENT_DIR ${script_path} DIRECTORY)
string(SUBSTRING ${TEST_NAME} 1 -1 TEST_NAME)
string(REPLACE "-" "_" TEST_NAME ${TEST_NAME})
string(REPLACE "+" "_" TEST_NAME ${TEST_NAME})
set(TEST_NAME "test_core_${TEST_NAME}_serial")
add_test(NAME ${TEST_NAME} COMMAND $<TARGET_FILE:lmp> -in ${SCRIPT_NAME} WORKING_DIRECTORY ${PARENT_DIR})
endforeach()
list(LENGTH TEST_SCRIPTS NUM_TESTS)
message(STATUS "Found ${NUM_TESTS} tests.")
endif()
enable_testing()
get_filename_component(LAMMPS_UNITTEST_DIR ${LAMMPS_SOURCE_DIR}/../unittest ABSOLUTE)
get_filename_component(LAMMPS_UNITTEST_BIN ${CMAKE_BINARY_DIR}/unittest ABSOLUTE)
add_subdirectory(${LAMMPS_UNITTEST_DIR} ${LAMMPS_UNITTEST_BIN})
endif()

10
cmake/Modules/generate_lmpgitversion.cmake
View File

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

2
cmake/presets/all_off.cmake
View File

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

2
cmake/presets/all_on.cmake
View File

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

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

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

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

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

10
cmake/presets/most.cmake
View File

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

2
cmake/presets/nolib.cmake
View File

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

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

7
doc/src/Build_package.rst
View File

@ -136,6 +136,10 @@ src directory.
.. _cmake_presets:
CMake presets for installing many packages
<<<<<<< HEAD
=======
""""""""""""""""""""""""""""""""""""""""""
>>>>>>> upstream/master
Instead of specifying all the CMake options via the command-line,
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
cmake with new flags.
**Example:**
Example
"""""""
.. code-block:: bash

3
doc/src/Commands_fix.rst
View File

@ -150,7 +150,10 @@ OPT.
* :doc:`orient/bcc <fix_orient>`
* :doc:`orient/fcc <fix_orient>`
* :doc:`orient/eco <fix_orient_eco>`
<<<<<<< HEAD
* :doc:`pafi <fix_pafi>`
=======
>>>>>>> upstream/master
* :doc:`phonon <fix_phonon>`
* :doc:`pimd <fix_pimd>`
* :doc:`planeforce <fix_planeforce>`

264
doc/src/Howto_bash.rst
View File

@ -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>`_)

BIN
doc/src/JPG/balance_nonuniform.jpg
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 77 KiB

BIN
doc/src/JPG/balance_nonuniform_small.jpg
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 16 KiB

BIN
doc/src/JPG/balance_rcb.jpg
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 71 KiB

BIN
doc/src/JPG/balance_rcb_small.jpg
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 15 KiB

BIN
doc/src/JPG/balance_uniform.jpg
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 77 KiB

BIN
doc/src/JPG/balance_uniform_small.jpg
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 17 KiB

BIN
doc/src/JPG/bow_tutorial_01.png
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 32 KiB

BIN
doc/src/JPG/bow_tutorial_01_small.png
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 15 KiB

BIN
doc/src/JPG/bow_tutorial_02.png
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 41 KiB

BIN
doc/src/JPG/bow_tutorial_02_small.png
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 16 KiB

BIN
doc/src/JPG/bow_tutorial_03.png
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 42 KiB

BIN
doc/src/JPG/bow_tutorial_03_small.png
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 20 KiB

BIN
doc/src/JPG/bow_tutorial_04.png
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 54 KiB

BIN
doc/src/JPG/bow_tutorial_04_small.png
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 21 KiB

BIN
doc/src/JPG/bow_tutorial_05.png
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 16 KiB

BIN
doc/src/JPG/bow_tutorial_06.png
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 13 KiB

BIN
doc/src/JPG/bow_tutorial_07.png
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 9.7 KiB

BIN
doc/src/JPG/bow_tutorial_08.png
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 24 KiB

BIN
doc/src/JPG/bow_tutorial_09.png
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 18 KiB

BIN
doc/src/JPG/bow_tutorial_10.png
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 7.6 KiB

BIN
doc/src/JPG/dump1.jpg
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 594 KiB

BIN
doc/src/JPG/dump1_small.jpg
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 16 KiB

BIN
doc/src/JPG/dump2.jpg
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 168 KiB

BIN
doc/src/JPG/dump2_small.jpg
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 6.4 KiB

BIN
doc/src/JPG/gran_funnel.png
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 117 KiB

BIN
doc/src/JPG/gran_funnel_small.jpg
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 2.2 KiB

BIN
doc/src/JPG/gran_mixer.png
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 224 KiB

BIN
doc/src/JPG/gran_mixer_small.jpg
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 3.0 KiB

BIN
doc/src/JPG/hop1.jpg
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 52 KiB

BIN
doc/src/JPG/hop1_small.jpg
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 4.2 KiB

BIN
doc/src/JPG/hop2.jpg
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 52 KiB

BIN
doc/src/JPG/hop2_small.jpg
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 4.1 KiB

BIN
doc/src/JPG/saed_ewald_intersect.jpg
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 110 KiB

Some files were not shown because too many files have changed in this diff Show More