Update/lammps package: new variants for refactoring of code modules (#29788)

* lammps package: kokkos variant, add support for cray-fftw

* lammps package: added bugfix version 20210929.3

* lammps package: added packages molfile, plugin, user-brownian

* lammps package: package refactor at versions 20210702 and 20210728

* lammps package: fix for ml-iap variant

* lammps package: fix for conflicts of dielectric variant

* lammps package: edits for flake8 layout compliance

1 files changed, 321 insertions, 16 deletions

diff --git a/var/spack/repos/builtin/packages/lammps/package.py b/var/spack/repos/builtin/packages/lammps/package.py
index 327ea1a379..89108a4b1a 100644
--- a/var/spack/repos/builtin/packages/lammps/package.py
+++ b/var/spack/repos/builtin/packages/lammps/package.py
@@ -24,6 +24,7 @@ class Lammps(CMakePackage, CudaPackage):
     version('20220107', sha256='fbf6c6814968ae0d772d7b6783079ff4f249a8faeceb39992c344969e9f1edbb')
     version('20211214', sha256='9f7b1ee2394678c1a6baa2c158a62345680a952eee251783e3c246b3f12db4c9')
     version('20211027', sha256='c06f682fcf9d5921ca90c857a104e90fba0fe65decaac9732745e4da49281938')
+    version('20210929.3', sha256='d7df30f7ce0bd8b7c21949cf5bdf1877858815379cddb8a264da7a8cbf699639')
     version('20210929.2', sha256='26586c1e82356b60e40359ee474818003c7788214bfe2bfe9128a3dbe5200b4d')
     version('20210929.1', sha256='3b792e20864bf88b855332486996f2c540deabb4e3507e48fa4ee96ad79615ec')
     version('20210929', sha256='5132f332b582be3006510562ef10bac9ef76d760f34fc08a2af556416c57cf4c')
@@ -77,26 +78,39 @@ class Lammps(CMakePackage, CudaPackage):
         return "https://github.com/lammps/lammps/archive/patch_{0}{1}.tar.gz".format(
             vdate.strftime("%d%b%Y").lstrip('0'), update)
 
+    # List of supported optional packages
+    # Note: package `openmp` in this recipe is called `openmp-package`, to avoid clash
+    # with the pre-existing `openmp` variant
     supported_packages = ['asphere', 'body', 'class2', 'colloid', 'compress',
-                          'coreshell', 'dipole', 'granular', 'kspace',
+                          'coreshell', 'dielectric', 'dipole', 'granular', 'kspace',
                           'kokkos', 'latte', 'manybody', 'mc', 'meam', 'misc',
-                          'mliap', 'molecule', 'mpiio', 'opt', 'peri', 'poems',
-                          'python', 'qeq', 'replica', 'rigid', 'shock', 'snap',
-                          'spin', 'srd', 'user-atc', 'user-adios',
-                          'user-awpmd', 'user-bocs', 'user-cgsdk',
+                          'mliap', 'ml-iap', 'ml-snap', 'molecule', 'mpiio',
+                          'opt', 'peri', 'plugin', 'poems', 'python', 'qeq', 'replica',
+                          'rigid', 'shock', 'snap', 'spin', 'srd', 'voronoi',
+                          'user-atc', 'user-adios',
+                          'user-awpmd', 'user-bocs', 'user-brownian', 'user-cgsdk',
                           'user-colvars', 'user-diffraction', 'user-dpd',
                           'user-drude', 'user-eff', 'user-fep', 'user-h5md',
                           'user-lb', 'user-manifold', 'user-meamc',
-                          'user-mesodpd', 'user-mesont', 'user-mgpt',
-                          'user-misc', 'user-mofff', 'user-netcdf', 'user-omp',
+                          'user-mesodpd', 'user-mesont', 'user-mgpt', 'user-misc',
+                          'user-mofff', 'user-molfile', 'user-netcdf', 'user-omp',
                           'user-phonon', 'user-plumed', 'user-ptm', 'user-qtb',
                           'user-reaction', 'user-reaxc', 'user-sdpd',
                           'user-smd', 'user-smtbq', 'user-sph', 'user-tally',
-                          'user-uef', 'user-yaff', 'voronoi']
+                          'user-uef', 'user-yaff',
+                          'atc', 'adios', 'awpmd', 'bocs', 'brownian', 'cg-sdk',
+                          'colvars', 'diffraction', 'dpd-basic', 'dpd-meso',
+                          'dpd-react', 'dpd-smooth', 'drude', 'eff', 'extra-compute',
+                          'extra-dump', 'extra-fix', 'extra-molecule', 'extra-pair',
+                          'fep', 'h5md', 'interlayer', 'latboltz', 'machdyn',
+                          'manifold', 'mesont', 'mgpt', 'mofff', 'molfile', 'netcdf',
+                          'openmp-package', 'orient', 'phonon', 'plumed', 'ptm', 'qtb',
+                          'reaction', 'reaxff', 'smtbq', 'sph', 'tally', 'uef', 'yaff']
 
     for pkg in supported_packages:
         variant(pkg, default=False,
-                description='Activate the {0} package'.format(pkg))
+                description='Activate the {0} package'
+                .format(pkg.replace('-package', '')))
     variant('lib', default=True,
             description='Build the liblammps in addition to the executable')
     variant('mpi', default=True,
@@ -129,8 +143,11 @@ class Lammps(CMakePackage, CudaPackage):
     depends_on('fftw-api@3', when='+kspace')
     depends_on('voropp+pic', when='+voronoi')
     depends_on('netcdf-c+mpi', when='+user-netcdf')
+    depends_on('netcdf-c+mpi', when='+netcdf')
     depends_on('blas', when='+user-atc')
+    depends_on('blas', when='+atc')
     depends_on('lapack', when='+user-atc')
+    depends_on('lapack', when='+atc')
     depends_on('opencl', when='+opencl')
     depends_on('latte@1.0.1', when='@:20180222+latte')
     depends_on('latte@1.1.1:', when='@20180316:20180628+latte')
@@ -140,8 +157,11 @@ class Lammps(CMakePackage, CudaPackage):
     depends_on('lapack', when='+latte')
     depends_on('python', when='+python')
     depends_on('mpi', when='+user-lb')
+    depends_on('mpi', when='+latboltz')
     depends_on('mpi', when='+user-h5md')
+    depends_on('mpi', when='+h5md')
     depends_on('hdf5', when='+user-h5md')
+    depends_on('hdf5', when='+h5md')
     depends_on('jpeg', when='+jpeg')
     depends_on('kim-api', when='+kim')
     depends_on('libpng', when='+png')
@@ -149,8 +169,15 @@ class Lammps(CMakePackage, CudaPackage):
     depends_on('kokkos+deprecated_code+shared@3.0.00', when='@20200303+kokkos')
     depends_on('kokkos+shared@3.1:', when='@20200505:+kokkos')
     depends_on('adios2', when='+user-adios')
+    depends_on('adios2', when='+adios')
     depends_on('plumed', when='+user-plumed')
+    depends_on('plumed', when='+plumed')
     depends_on('eigen@3:', when='+user-smd')
+    depends_on('eigen@3:', when='+machdyn')
+    depends_on('py-cython', when='+mliap+python')
+    depends_on('py-cython', when='+ml-iap+python')
+    depends_on('py-numpy', when='+mliap+python')
+    depends_on('py-numpy', when='+ml-iap+python')
 
     conflicts('+cuda', when='+opencl')
     conflicts('+body', when='+poems@:20180628')
@@ -158,27 +185,303 @@ class Lammps(CMakePackage, CudaPackage):
     conflicts('+python', when='~lib')
     conflicts('+qeq', when='~manybody')
     conflicts('+user-atc', when='~manybody')
+    conflicts('+atc', when='~manybody')
     conflicts('+user-misc', when='~manybody')
     conflicts('+user-phonon', when='~kspace')
-    conflicts('+user-misc', when='~manybody')
+    conflicts('+phonon', when='~kspace')
     conflicts('%gcc@9:', when='@:20200303+openmp')
     conflicts('+kokkos', when='@:20200227')
+    conflicts('+dielectric', when='~kspace')
+    conflicts('+dielectric', when='@:20210702~user-misc')
+    conflicts('+dielectric', when='@20210728:~extra-pair')
     conflicts(
-        '+meam', when='@20181212:',
-        msg='+meam was removed after @20181212, use +user-meamc instead')
+        '+meam', when='@20181212:20210527',
+        msg='+meam is removed between @20181212 and @20210527, use +user-meamc instead')
     conflicts(
         '+user-meamc', when='@:20181212',
         msg='+user-meamc only added @20181212, use +meam instead')
     conflicts(
         '+user-reaction', when='@:20200303',
         msg='+user-reaction only supported for version 20200505 and later')
+    conflicts(
+        '+plugin', when='@:20210310',
+        msg='+plugin only supported for version 20210408 and later')
+    conflicts(
+        '+user-brownian', when='@:20210408',
+        msg='+user-brownian only supported for version 20210514 and later')
+    conflicts(
+        '+dielectric', when='@:20210527',
+        msg='+dielectric only supported for version 20210702 and later')
+    conflicts(
+        '+dpd-basic', when='@:20210527',
+        msg='+dpd-basic only supported for version 20210702 and later')
     conflicts('+mliap', when='~snap')
+    conflicts('+ml-iap', when='~ml-snap')
     conflicts(
         '+user-adios +mpi', when='^adios2~mpi',
         msg='With +user-adios, mpi setting for adios2 and lammps must be the same')
     conflicts(
         '+user-adios ~mpi', when='^adios2+mpi',
         msg='With +user-adios, mpi setting for adios2 and lammps must be the same')
+    conflicts(
+        '+adios +mpi', when='^adios2~mpi',
+        msg='With +adios, mpi setting for adios2 and lammps must be the same')
+    conflicts(
+        '+adios ~mpi', when='^adios2+mpi',
+        msg='With +adios, mpi setting for adios2 and lammps must be the same')
+
+    # In the following, package refactoring at 2 July 2021
+    conflicts(
+        '+mliap', when='@20210702:',
+        msg='+mliap was removed after @20210527, use +ml-iap instead')
+    conflicts(
+        '+ml-iap', when='@:20210527',
+        msg='+ml-iap only added @20210702, use +mliap instead')
+    conflicts(
+        '+snap', when='@20210702:',
+        msg='+snap was removed after @20210527, use +ml-snap instead')
+    conflicts(
+        '+ml-snap', when='@:20210527',
+        msg='+ml-snap only added @20210702, use +snap instead')
+    #
+    conflicts(
+        '+user-atc', when='@20210702:',
+        msg='+user-atc was removed after @20210527, use +atc instead')
+    conflicts(
+        '+atc', when='@:20210527',
+        msg='+atc only added @20210702, use +user-atc instead')
+    conflicts(
+        '+user-adios', when='@20210702:',
+        msg='+user-adios was removed after @20210527, use +adios instead')
+    conflicts(
+        '+adios', when='@:20210527',
+        msg='+adios only added @20210702, use +user-adios instead')
+    conflicts(
+        '+user-awpmd', when='@20210702:',
+        msg='+user-awpmd was removed after @20210527, use +awpmd instead')
+    conflicts(
+        '+awpmd', when='@:20210527',
+        msg='+awpmd only added @20210702, use +user-awpmd instead')
+    conflicts(
+        '+user-bocs', when='@20210702:',
+        msg='+user-bocs was removed after @20210527, use +bocs instead')
+    conflicts(
+        '+bocs', when='@:20210527',
+        msg='+bocs only added @20210702, use +user-bocs instead')
+    conflicts(
+        '+user-brownian', when='@20210702:',
+        msg='+user-brownian was removed after @20210527, use +brownian instead')
+    conflicts(
+        '+brownian', when='@:20210527',
+        msg='+brownian only added @20210702, use +user-brownian instead')
+    conflicts(
+        '+user-cgsdk', when='@20210702:',
+        msg='+user-cgsdk was removed after @20210527, use +cg-sdk instead')
+    conflicts(
+        '+cg-sdk', when='@:20210527',
+        msg='+cg-sdk only added @20210702, use +user-cgsdk instead')
+    conflicts(
+        '+user-colvars', when='@20210702:',
+        msg='+user-colvars was removed after @20210527, use +colvars instead')
+    conflicts(
+        '+colvars', when='@:20210527',
+        msg='+colvars only added @20210702, use +user-colvars instead')
+    conflicts(
+        '+user-diffraction', when='@20210702:',
+        msg='+user-diffraction was removed after @20210527, use +diffraction instead')
+    conflicts(
+        '+diffraction', when='@:20210527',
+        msg='+diffraction only added @20210702, use +user-diffraction instead')
+    conflicts(
+        '+user-dpd', when='@20210702:',
+        msg='+user-dpd was removed after @20210527, use +dpd-react instead')
+    conflicts(
+        '+dpd-react', when='@:20210527',
+        msg='+dpd-react only added @20210702, use +user-dpd instead')
+    conflicts(
+        '+user-drude', when='@20210702:',
+        msg='+user-drude was removed after @20210527, use +drude instead')
+    conflicts(
+        '+drude', when='@:20210527',
+        msg='+drude only added @20210702, use +user-drude instead')
+    conflicts(
+        '+user-eff', when='@20210702:',
+        msg='+user-eff was removed after @20210527, use +eff instead')
+    conflicts(
+        '+eff', when='@:20210527',
+        msg='+eff only added @20210702, use +user-eff instead')
+    conflicts(
+        '+user-fep', when='@20210702:',
+        msg='+user-fep was removed after @20210527, use +fep instead')
+    conflicts(
+        '+fep', when='@:20210527',
+        msg='+fep only added @20210702, use +user-fep instead')
+    conflicts(
+        '+user-h5md', when='@20210702:',
+        msg='+user-h5md was removed after @20210527, use +h5md instead')
+    conflicts(
+        '+h5md', when='@:20210527',
+        msg='+h5md only added @20210702, use +user-h5md instead')
+    conflicts(
+        '+user-lb', when='@20210702:',
+        msg='+user-lb was removed after @20210527, use +latboltz instead')
+    conflicts(
+        '+latboltz', when='@:20210527',
+        msg='+latboltz only added @20210702, use +user-lb instead')
+    conflicts(
+        '+user-manifold', when='@20210702:',
+        msg='+user-manifold was removed after @20210527, use +manifold instead')
+    conflicts(
+        '+manifold', when='@:20210527',
+        msg='+manifold only added @20210702, use +user-manifold instead')
+    conflicts(
+        '+user-meamc', when='@20210702:',
+        msg='+user-meamc was removed after @20210527, use +meam instead')
+    conflicts(
+        '+user-mesodpd', when='@20210702:',
+        msg='+user-mesodpd was removed after @20210527, use +dpd-meso instead')
+    conflicts(
+        '+dpd-meso', when='@:20210527',
+        msg='+dpd-meso only added @20210702, use +user-mesodpd instead')
+    conflicts(
+        '+user-mesont', when='@20210702:',
+        msg='+user-mesont was removed after @20210527, use +mesont instead')
+    conflicts(
+        '+mesont', when='@:20210527',
+        msg='+mesont only added @20210702, use +user-mesont instead')
+    conflicts(
+        '+user-mgpt', when='@20210702:',
+        msg='+user-mgpt was removed after @20210527, use +mgpt instead')
+    conflicts(
+        '+mgpt', when='@:20210527',
+        msg='+mgpt only added @20210702, use +user-mgpt instead')
+    conflicts(
+        '+user-mofff', when='@20210702:',
+        msg='+user-mofff was removed after @20210527, use +mofff instead')
+    conflicts(
+        '+mofff', when='@:20210527',
+        msg='+mofff only added @20210702, use +user-mofff instead')
+    conflicts(
+        '+user-molfile', when='@20210702:',
+        msg='+user-molfile was removed after @20210527, use +molfile instead')
+    conflicts(
+        '+molfile', when='@:20210527',
+        msg='+molfile only added @20210702, use +user-molfile instead')
+    conflicts(
+        '+user-netcdf', when='@20210702:',
+        msg='+user-netcdf was removed after @20210527, use +netcdf instead')
+    conflicts(
+        '+netcdf', when='@:20210527',
+        msg='+netcdf only added @20210702, use +user-netcdf instead')
+    conflicts(
+        '+user-omp', when='@20210702:',
+        msg='+user-omp was removed after @20210527, use +openmp-package instead')
+    conflicts(
+        '+openmp-package', when='@:20210527',
+        msg='+openmp-package only added @20210702, use +user-omp instead')
+    conflicts(
+        '+user-phonon', when='@20210702:',
+        msg='+user-phonon was removed after @20210527, use +phonon instead')
+    conflicts(
+        '+phonon', when='@:20210527',
+        msg='+phonon only added @20210702, use +user-phonon instead')
+    conflicts(
+        '+user-plumed', when='@20210702:',
+        msg='+user-plumed was removed after @20210527, use +plumed instead')
+    conflicts(
+        '+plumed', when='@:20210527',
+        msg='+plumed only added @20210702, use +user-plumed instead')
+    conflicts(
+        '+user-ptm', when='@20210702:',
+        msg='+user-ptm was removed after @20210527, use +ptm instead')
+    conflicts(
+        '+ptm', when='@:20210527',
+        msg='+ptm only added @20210702, use +user-ptm instead')
+    conflicts(
+        '+user-qtb', when='@20210702:',
+        msg='+user-qtb was removed after @20210527, use +qtb instead')
+    conflicts(
+        '+qtb', when='@:20210527',
+        msg='+qtb only added @20210702, use +user-qtb instead')
+    conflicts(
+        '+user-reaction', when='@20210702:',
+        msg='+user-reaction was removed after @20210527, use +reaction instead')
+    conflicts(
+        '+reaction', when='@:20210527',
+        msg='+reaction only added @20210702, use +user-reaction instead')
+    conflicts(
+        '+user-reaxc', when='@20210702:',
+        msg='+user-reaxc was removed after @20210527, use +reaxff instead')
+    conflicts(
+        '+reaxff', when='@:20210527',
+        msg='+reaxff only added @20210702, use +user-reaxc instead')
+    conflicts(
+        '+user-sdpd', when='@20210702:',
+        msg='+user-sdpd was removed after @20210527, use +dpd-smooth instead')
+    conflicts(
+        '+dpd-smooth', when='@:20210527',
+        msg='+dpd-smooth only added @20210702, use +user-sdpd instead')
+    conflicts(
+        '+user-smd', when='@20210702:',
+        msg='+user-smd was removed after @20210527, use +machdyn instead')
+    conflicts(
+        '+machdyn', when='@:20210527',
+        msg='+machdyn only added @20210702, use +user-smd instead')
+    conflicts(
+        '+user-smtbq', when='@20210702:',
+        msg='+user-smtbq was removed after @20210527, use +smtbq instead')
+    conflicts(
+        '+smtbq', when='@:20210527',
+        msg='+smtbq only added @20210702, use +user-smtbq instead')
+    conflicts(
+        '+user-sph', when='@20210702:',
+        msg='+user-sph was removed after @20210527, use +sph instead')
+    conflicts(
+        '+sph', when='@:20210527',
+        msg='+sph only added @20210702, use +user-sph instead')
+    conflicts(
+        '+user-tally', when='@20210702:',
+        msg='+user-tally was removed after @20210527, use +tally instead')
+    conflicts(
+        '+tally', when='@:20210527',
+        msg='+tally only added @20210702, use +user-tally instead')
+    conflicts(
+        '+user-uef', when='@20210702:',
+        msg='+user-uef was removed after @20210527, use +uef instead')
+    conflicts(
+        '+uef', when='@:20210527',
+        msg='+uef only added @20210702, use +user-uef instead')
+    conflicts(
+        '+user-yaff', when='@20210702:',
+        msg='+user-yaff was removed after @20210527, use +yaff instead')
+    conflicts(
+        '+yaff', when='@:20210527',
+        msg='+yaff only added @20210702, use +user-yaff instead')
+    # In the following, package refactoring at 28 July 2021
+    conflicts(
+        '+user-misc', when='@20210728:',
+        msg='+user-misc was removed after @20210702, and split over multiple packages')
+    conflicts(
+        '+extra-compute', when='@:20210702',
+        msg='+extra-compute only added @20210728, use +user-misc instead')
+    conflicts(
+        '+extra-dump', when='@:20210702',
+        msg='+extra-dump only added @20210728, use +user-misc instead')
+    conflicts(
+        '+extra-fix', when='@:20210702',
+        msg='+extra-fix only added @20210728, use +user-misc instead')
+    conflicts(
+        '+extra-molecule', when='@:20210702',
+        msg='+extra-molecule only added @20210728, use +user-misc instead')
+    conflicts(
+        '+extra-pair', when='@:20210702',
+        msg='+extra-pair only added @20210728, use +user-misc instead')
+    conflicts(
+        '+interlayer', when='@:20210702',
+        msg='+interlayer only added @20210728, use +user-misc instead')
+    conflicts(
+        '+orient', when='@:20210702',
+        msg='+orient only added @20210728, use +user-misc instead')
 
     patch("lib.patch", when="@20170901")
     patch("660.patch", when="@20170922")
@@ -235,7 +538,7 @@ class Lammps(CMakePackage, CudaPackage):
         args.append(self.define_from_variant('WITH_FFMPEG', 'ffmpeg'))
 
         for pkg in self.supported_packages:
-            opt = '-D{0}_{1}'.format(pkg_prefix, pkg.upper())
+            opt = '-D{0}_{1}'.format(pkg_prefix, pkg.replace('-package', '').upper())
             if '+{0}'.format(pkg) in spec:
                 args.append('{0}=ON'.format(opt))
             else:
@@ -255,18 +558,20 @@ class Lammps(CMakePackage, CudaPackage):
                 # for reduced memory use and parallel communication costs
                 # for transposing 3d FFT data.
                 args.append(self.define('FFT_SINGLE', True))
+            if '^cray-fftw' in spec:
+                args.append('-DFFT=FFTW3')
 
         if '+kokkos' in spec:
             args.append('-DEXTERNAL_KOKKOS=ON')
-        if '+user-adios' in spec:
+        if '+user-adios' in spec or '+adios' in spec:
             args.append('-DADIOS2_DIR={0}'.format(self.spec['adios2'].prefix))
-        if '+user-plumed' in spec:
+        if '+user-plumed' in spec or '+plumed' in spec:
             args.append('-DDOWNLOAD_PLUMED=no')
             if '+shared' in self.spec['plumed']:
                 args.append('-DPLUMED_MODE=shared')
             else:
                 args.append('-DPLUMED_MODE=static')
-        if '+user-smd' in spec:
+        if '+user-smd' in spec or '+machdyn' in spec:
             args.append('-DDOWNLOAD_EIGEN3=no')
             args.append('-DEIGEN3_INCLUDE_DIR={0}'.format(
                 self.spec['eigen'].prefix.include))