git: 49c9dc6389ba - main - science/lammps: update patch_21Nov2023 → patch_19Nov2024

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From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Fri, 24 Jan 2025 03:05:43 UTC
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=49c9dc6389ba50d5b0e9732449a59dfb53863045

commit 49c9dc6389ba50d5b0e9732449a59dfb53863045
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2025-01-24 02:00:24 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2025-01-24 03:05:35 +0000

    science/lammps: update patch_21Nov2023 → patch_19Nov2024
---
 science/lammps/Makefile          | 24 ++++--------
 science/lammps/Makefile.packages | 84 ++++++++++++++++++++++++++++++++++++++++
 science/lammps/distinfo          |  6 +--
 science/lammps/pkg-plist         | 16 +++++++-
 4 files changed, 110 insertions(+), 20 deletions(-)

diff --git a/science/lammps/Makefile b/science/lammps/Makefile
index 1e9d4bf98d47..3b4e0f88837b 100644
--- a/science/lammps/Makefile
+++ b/science/lammps/Makefile
@@ -1,11 +1,11 @@
 PORTNAME=	lammps
-PORTVERSION=	${GH_TAGNAME:C/(stable|patch)_([0-9]{1,2})([A-Z][a-z][a-z])([0-9]{4})/\4.\3.\2/S/Jan/01/S/Feb/02/S/Mar/03/S/Apr/04/S/May/05/S/Jun/06/S/Jul/07/S/Aug/08/S/Sep/09/S/Oct/10/S/Nov/11/S/Dec/12/S/_update/./:C/\.([1-9])$/.0\1/}
-PORTREVISION=	6
+PORTVERSION=	${GH_TAGNAME:C/(stable|patch)_([0-9]{1,2})([A-Z][a-z][a-z])([0-9]{4})/\4.\3.\2/S/Jan/01/S/Feb/02/S/Mar/03/S/Apr/04/S/May/05/S/Jun/06/S/Jul/07/S/Aug/08/S/Sep/09/S/Oct/10/S/Nov/11/S/Dec/12/S/_update/./:C/\.([1-9])$/.0\1/:S/.//g}
 CATEGORIES=	science
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Classical molecular dynamics code with a focus on materials modeling
-WWW=		https://lammps.sandia.gov/
+WWW=		https://lammps.sandia.gov/ \
+		https://github.com/lammps/lammps
 
 LICENSE=	GPLv2
 LICENSE_FILE=	${WRKSRC}/LICENSE
@@ -20,13 +20,13 @@ LIB_DEPENDS=	libevent.so:devel/libevent \
 		libssh2.so:security/libssh2 \
 		libzstd.so:archivers/zstd
 
-USES=		blaslapack:openblas cmake:noninja,testing compiler:c++14-lang eigen:3 fortran gnome localbase:ldflags python shebangfix
+USES=		blaslapack:openblas cmake:noninja,testing compiler:c++17-lang eigen:3 fortran gnome localbase:ldflags python shebangfix
 USE_GNOME=	libxml2
 USE_LDCONFIG=	yes
 USE_PYTHON=	cython
 
 USE_GITHUB=	yes
-GH_TAGNAME=	patch_21Nov2023
+GH_TAGNAME=	patch_19Nov2024
 
 SHEBANG_GLOB=	*.sh *.bash
 SHEBANG_FILES=	lib/kokkos/bin/nvcc_wrapper
@@ -39,15 +39,7 @@ CMAKE_ARGS_gcc=	-DBUILD_OMP:BOOL=false
 CMAKE_TESTING_ON=	ENABLE_TESTING # 3 tests fail, see https://github.com/lammps/lammps/issues/3875
 
 # enable packages (for a complete list see STANDARD_PACKAGES in cmake/CMakeLists.txt)
-CMAKE_ON+=	PKG_ASPHERE PKG_ATC PKG_AWPMD PKG_BOCS PKG_BODY PKG_BROWNIAN PKG_CG-DNA PKG_CG-SDK PKG_CLASS2
-CMAKE_ON+=	PKG_COLLOID PKG_COLVARS PKG_COMPRESS PKG_DIELECTRIC PKG_DIFFRACTION PKG_DIPOLE PKG_DPD-BASIC PKG_DPD-MESO PKG_DPD-REACT PKG_DPD-SMOOTH
-CMAKE_ON+=	PKG_DRUDE PKG_EFF PKG_EXTRA-COMPUTE PKG_EXTRA-DUMP PKG_EXTRA-FIX PKG_EXTRA-MOLECULE PKG_EXTRA-PAIR PKG_FEP PKG_GRANULAR PKG_H5MD
-CMAKE_ON+=	PKG_INTERLAYER PKG_KIM PKG_KSPACE PKG_LATBOLTZ PKG_LATTE PKG_MACHDYN PKG_MANIFOLD PKG_MANYBODY PKG_MC
-CMAKE_ON+=	PKG_MEAM PKG_MESSAGE PKG_MGPT PKG_MISC PKG_ML-IAP PKG_ML-RANN
-CMAKE_ON+=	PKG_ML-SNAP PKG_MOFFF PKG_MOLECULE PKG_MOLFILE PKG_MPIIO PKG_ORIENT PKG_PERI PKG_PHONON
-CMAKE_ON+=	PKG_PLUGIN PKG_PLUMED PKG_POEMS PKG_PTM PKG_PYTHON PKG_QEQ PKG_QMMM PKG_QTB PKG_REACTION PKG_REAXFF
-CMAKE_ON+=	PKG_REPLICA PKG_RIGID PKG_SHOCK PKG_SMTBQ PKG_SPH PKG_SPIN PKG_SRD PKG_TALLY PKG_UEF
-CMAKE_ON+=	PKG_VORONOI PKG_YAFF
+CMAKE_ON+=	${LAMMPS_STANDARD_PACKAGES:S/^/PKG_/} # LAMMPS_STANDARD_PACKAGES is defined in Makefile.packages
 # Packages requiring extra downloades or dependencies: PKG_MSCG PKG_ADIOS PKG_MDI PKG_MESONT PKG_ML-PACE PKG_NETCDF PKG_ML-QUIP PKG_SCAFACOS PKG_VTK
 # PKG_ML-HDNNP downloads https://github.com/CompPhysVienna/n2p2/archive/v2.1.4.tar.gz
 
@@ -82,8 +74,7 @@ GZIP_CMAKE_BOOL=	WITH_GZIP
 
 H5MD_DESC=		H5MD package based on the libhdf5 library
 H5MD_CMAKE_BOOL=	PKG_H5MD
-H5MD_LIB_DEPENDS=	libhdf5.so:science/hdf5 \
-			libsz.so:science/libaec
+H5MD_LIB_DEPENDS=	libhdf5.so:science/hdf5
 
 KIM_DESC=		KIM package based on the OpenKim library/repository
 KIM_USES=		pkgconfig
@@ -154,5 +145,6 @@ post-patch-FFMPEG-off:
 post-install:
 	@${RM} -r ${STAGEDIR}${PREFIX}/lib/python*
 
+.include "Makefile.packages"
 .include <../../math/vtk9/Makefile.version>
 .include <bsd.port.mk>
diff --git a/science/lammps/Makefile.packages b/science/lammps/Makefile.packages
new file mode 100644
index 000000000000..b7a1cd173293
--- /dev/null
+++ b/science/lammps/Makefile.packages
@@ -0,0 +1,84 @@
+
+# STANDARD_PACKAGES from cmake/CMakeLists.txt
+
+# Some items were removed from the list either because they are handled seperately through the port options,
+# or because they are ignored (not ported) for now for various reasons.
+
+LAMMPS_STANDARD_PACKAGES= \
+  AMOEBA \
+  ASPHERE \
+  ATC \
+  AWPMD \
+  BOCS \
+  BODY \
+  BPM \
+  BROWNIAN \
+  CG-DNA \
+  CG-SPICA \
+  CLASS2 \
+  COLLOID \
+  COLVARS \
+  COMPRESS \
+  DIELECTRIC \
+  DIFFRACTION \
+  DIPOLE \
+  DPD-BASIC \
+  DPD-MESO \
+  DPD-REACT \
+  DPD-SMOOTH \
+  DRUDE \
+  EFF \
+  ELECTRODE \
+  EXTRA-COMMAND \
+  EXTRA-COMPUTE \
+  EXTRA-DUMP \
+  EXTRA-FIX \
+  EXTRA-MOLECULE \
+  EXTRA-PAIR \
+  FEP \
+  GRANULAR \
+  H5MD \
+  INTERLAYER \
+  KIM \
+  KSPACE \
+  LATBOLTZ \
+  LEPTON \
+  MACHDYN \
+  MANIFOLD \
+  MANYBODY \
+  MC \
+  MEAM \
+  MGPT \
+  MISC \
+  ML-IAP \
+  ML-POD \
+  ML-RANN \
+  ML-SNAP \
+  ML-UF3 \
+  MOFFF \
+  MOLECULE \
+  MOLFILE \
+  ORIENT \
+  PERI \
+  PHONON \
+  PLUGIN \
+  PLUMED \
+  POEMS \
+  PTM \
+  PYTHON \
+  QEQ \
+  QMMM \
+  QTB \
+  REACTION \
+  REAXFF \
+  REPLICA \
+  RIGID \
+  SHOCK \
+  SMTBQ \
+  SPH \
+  SPIN \
+  SRD \
+  TALLY \
+  UEF \
+  VORONOI \
+  YAFF
diff --git a/science/lammps/distinfo b/science/lammps/distinfo
index 776fe8e3a887..b5247fafa1d9 100644
--- a/science/lammps/distinfo
+++ b/science/lammps/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1702577081
-SHA256 (lammps-lammps-2023.11.21-patch_21Nov2023_GH0.tar.gz) = 704d8a990874a425bcdfe0245faf13d712231ba23f014a3ebc27bc14398856f1
-SIZE (lammps-lammps-2023.11.21-patch_21Nov2023_GH0.tar.gz) = 132544299
+TIMESTAMP = 1737671247
+SHA256 (lammps-lammps-20241119-patch_19Nov2024_GH0.tar.gz) = 7d1a825f13eef06d82ed8ae950f4a5ca6da9f6a5979745a85a7a58781e4c6ffa
+SIZE (lammps-lammps-20241119-patch_19Nov2024_GH0.tar.gz) = 142636470
diff --git a/science/lammps/pkg-plist b/science/lammps/pkg-plist
index 315572484b7d..9bd8e9ec2368 100644
--- a/science/lammps/pkg-plist
+++ b/science/lammps/pkg-plist
@@ -185,6 +185,7 @@ libdata/pkgconfig/liblammps.pc
 %%DATADIR%%/potentials/Bi.meam
 %%DATADIR%%/potentials/C.drip
 %%DATADIR%%/potentials/C.lcbop
+%%DATADIR%%/potentials/CBNOH.aip.water.2dm
 %%DATADIR%%/potentials/CC.KC
 %%DATADIR%%/potentials/CC.KC-full
 %%DATADIR%%/potentials/CC.Lebedeva
@@ -196,7 +197,6 @@ libdata/pkgconfig/liblammps.pc
 %%DATADIR%%/potentials/CHAu.ILP
 %%DATADIR%%/potentials/CH_taper.KC
 %%DATADIR%%/potentials/COH.DMC.aip.water.2dm
-%%DATADIR%%/potentials/COH.aip.water.2dm
 %%DATADIR%%/potentials/C_SNAP_2021.10.15.quadratic.snapcoeff
 %%DATADIR%%/potentials/C_SNAP_2021.10.15.quadratic.snapparam
 %%DATADIR%%/potentials/CdTe.bop.table
@@ -267,6 +267,8 @@ libdata/pkgconfig/liblammps.pc
 %%DATADIR%%/potentials/Mo5.2.mgpt.README
 %%DATADIR%%/potentials/Mo5.2.mgpt.parmin
 %%DATADIR%%/potentials/Mo5.2.mgpt.potin
+%%DATADIR%%/potentials/MoCoNiVFeAlCr_2nn.meam
+%%DATADIR%%/potentials/MoS.rebomos
 %%DATADIR%%/potentials/MoS2.ILP
 %%DATADIR%%/potentials/Mo_Chen_PRM2017.snap
 %%DATADIR%%/potentials/Mo_Chen_PRM2017.snapcoeff
@@ -277,10 +279,13 @@ libdata/pkgconfig/liblammps.pc
 %%DATADIR%%/potentials/Mo_Zuo_JPCA2020.snap
 %%DATADIR%%/potentials/Mo_Zuo_JPCA2020.snapcoeff
 %%DATADIR%%/potentials/Mo_Zuo_JPCA2020.snapparam
+%%DATADIR%%/potentials/Nb.uf3
 %%DATADIR%%/potentials/Ni.adp
 %%DATADIR%%/potentials/Ni.meam
 %%DATADIR%%/potentials/NiAlH_jea.eam.alloy
 %%DATADIR%%/potentials/NiAlH_jea.eam.fs
+%%DATADIR%%/potentials/NiO.ctip
+%%DATADIR%%/potentials/NiO.eam.fs
 %%DATADIR%%/potentials/Ni_Mo.mliap.descriptor
 %%DATADIR%%/potentials/Ni_Mo.mliap.model
 %%DATADIR%%/potentials/Ni_Zuo_JPCA2020.quadratic.snap
@@ -291,6 +296,7 @@ libdata/pkgconfig/liblammps.pc
 %%DATADIR%%/potentials/Ni_Zuo_JPCA2020.snapparam
 %%DATADIR%%/potentials/Ni_smf7.eam
 %%DATADIR%%/potentials/Ni_u3.eam
+%%DATADIR%%/potentials/PSiO.nb3b.screened
 %%DATADIR%%/potentials/PdHHe.eam.he
 %%DATADIR%%/potentials/Pd_u3.eam
 %%DATADIR%%/potentials/Pt_Chapman_2020.agni
@@ -330,6 +336,7 @@ libdata/pkgconfig/liblammps.pc
 %%DATADIR%%/potentials/Si_Zuo_JPCA2020.snap
 %%DATADIR%%/potentials/Si_Zuo_JPCA2020.snapcoeff
 %%DATADIR%%/potentials/Si_Zuo_JPCA2020.snapparam
+%%DATADIR%%/potentials/TMD.ILP
 %%DATADIR%%/potentials/Ta06A.mliap
 %%DATADIR%%/potentials/Ta06A.mliap.descriptor
 %%DATADIR%%/potentials/Ta06A.mliap.model
@@ -401,5 +408,12 @@ libdata/pkgconfig/liblammps.pc
 %%DATADIR%%/potentials/lib.comb3
 %%DATADIR%%/potentials/library.meam
 %%DATADIR%%/potentials/library.msmeam
+%%DATADIR%%/potentials/library_2nn.meam
+%%DATADIR%%/potentials/oxdna2_lj.cgdna
+%%DATADIR%%/potentials/oxdna2_real.cgdna
+%%DATADIR%%/potentials/oxdna_lj.cgdna
+%%DATADIR%%/potentials/oxdna_real.cgdna
+%%DATADIR%%/potentials/oxrna2_lj.cgdna
+%%DATADIR%%/potentials/oxrna2_real.cgdna
 %%DATADIR%%/potentials/tmd.sw.mod
 share/man/man1/lmp.1.gz