science/plumed: update 2.8.0 → 2.9.3

3 files changed, 168 insertions, 72 deletions

diff --git a/science/plumed/Makefile b/science/plumed/Makefile
index cf0ec9948065..0e8a83c8fcfe 100644
--- a/science/plumed/Makefile
+++ b/science/plumed/Makefile
@@ -1,6 +1,5 @@
 PORTNAME=	plumed
-DISTVERSION=	2.8.0
-PORTREVISION=	2
+DISTVERSION=	2.9.3
 CATEGORIES=	science graphics
 MASTER_SITES=	https://github.com/${PORTNAME}/${PORTNAME}2/releases/download/v${DISTVERSION}/
 
@@ -46,4 +45,6 @@ post-install:
 	@${RMDIR} ${STAGEDIR}${PREFIX}/lib/plumed/obj
 	@cd ${STAGEDIR}${PREFIX} && ${STRIP_CMD} bin/plumed lib/plumed/plumed-runtime lib/libplumed.so lib/libplumedKernel.so
 
+# tests as of 2.9.3: 277 tests performed, 352 tests not applicable
+
 .include <bsd.port.mk>
diff --git a/science/plumed/distinfo b/science/plumed/distinfo
index 7f199b706e8b..578262619f8a 100644
--- a/science/plumed/distinfo
+++ b/science/plumed/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1652729274
-SHA256 (plumed-2.8.0.tgz) = 24b243c531fa83752be5e54f5f0b677164855da539bc2b2c5b00dcc9f192aa82
-SIZE (plumed-2.8.0.tgz) = 107630231
+TIMESTAMP = 1737474140
+SHA256 (plumed-2.9.3.tgz) = 2ba5095bc7c7cfde1ca95780c1240d852b7dc1b00c9de5b31e607120449ff827
+SIZE (plumed-2.9.3.tgz) = 118993592
diff --git a/science/plumed/pkg-plist b/science/plumed/pkg-plist
index ce031e5ccc6b..5e12bcbf2910 100644
--- a/science/plumed/pkg-plist
+++ b/science/plumed/pkg-plist
@@ -84,6 +84,7 @@ include/plumed/core/FlexibleBin.h
 include/plumed/core/GREX.h
 include/plumed/core/GenericMolInfo.h
 include/plumed/core/MDAtoms.h
+include/plumed/core/ModuleMap.h
 include/plumed/core/PlumedMain.h
 include/plumed/core/PlumedMainInitializer.h
 include/plumed/core/TargetDist.h
@@ -226,74 +227,145 @@ lib/libplumedKernel.so
 lib/libplumedWrapper.a
 lib/plumed/fortran/plumed.f90
 lib/plumed/fortran/plumed_f08.f90
+lib/plumed/json/syntax.json
 lib/plumed/modulefile
-lib/plumed/patches/gromacs-2019.6.config
-lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/CMakeLists.txt
-lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/CMakeLists.txt.preplumed
-lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdlib/force.cpp
-lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdlib/force.cpp.preplumed
-lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/legacymdrunoptions.cpp
-lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed
-lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/legacymdrunoptions.h
-lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/legacymdrunoptions.h.preplumed
-lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/md.cpp
-lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/md.cpp.preplumed
-lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/minimize.cpp
-lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/minimize.cpp.preplumed
-lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/replicaexchange.cpp
-lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/replicaexchange.cpp.preplumed
-lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/replicaexchange.h
-lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/replicaexchange.h.preplumed
-lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/runner.cpp
-lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/runner.cpp.preplumed
-lib/plumed/patches/gromacs-2020.6.config
-lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/CMakeLists.txt
-lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/CMakeLists.txt.preplumed
-lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdlib/expanded.cpp
-lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdlib/expanded.cpp.preplumed
-lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdlib/expanded.h
-lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdlib/expanded.h.preplumed
-lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdlib/force.cpp
-lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdlib/force.cpp.preplumed
-lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/legacymdrunoptions.cpp
-lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed
-lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/legacymdrunoptions.h
-lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/legacymdrunoptions.h.preplumed
-lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/md.cpp
-lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/md.cpp.preplumed
-lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/minimize.cpp
-lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/minimize.cpp.preplumed
-lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/replicaexchange.cpp
-lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/replicaexchange.cpp.preplumed
-lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/replicaexchange.h
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-lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdlib/expanded.cpp
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-lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdlib/sim_util.cpp
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+lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/replicaexchange.h.preplumed
+lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/rerun.cpp
+lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/rerun.cpp.preplumed
+lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/runner.cpp
+lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/runner.cpp.preplumed
+lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/modularsimulator/expandedensembleelement.cpp
+lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/modularsimulator/expandedensembleelement.cpp.preplumed
+lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/taskassignment/decidegpuusage.cpp
+lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/taskassignment/decidegpuusage.cpp.preplumed
+lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/taskassignment/include/gromacs/taskassignment/decidegpuusage.h
+lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/taskassignment/include/gromacs/taskassignment/decidegpuusage.h.preplumed
 lib/plumed/patches/namd-2.12.config
 lib/plumed/patches/namd-2.12.diff
 lib/plumed/patches/namd-2.13.config
@@ -319,6 +391,28 @@ lib/plumed/patches/qespresso-6.2.diff/PW/src/plugin_initialization.f90
 lib/plumed/patches/qespresso-6.2.diff/PW/src/plugin_initialization.f90.preplumed
 lib/plumed/patches/qespresso-6.2.diff/PW/src/run_pwscf.f90
 lib/plumed/patches/qespresso-6.2.diff/PW/src/run_pwscf.f90.preplumed
+lib/plumed/patches/qespresso-7.0.config
+lib/plumed/patches/qespresso-7.0.diff/Modules/Makefile
+lib/plumed/patches/qespresso-7.0.diff/Modules/Makefile.preplumed
+lib/plumed/patches/qespresso-7.0.diff/PW/src/forces.f90
+lib/plumed/patches/qespresso-7.0.diff/PW/src/forces.f90.preplumed
+lib/plumed/patches/qespresso-7.0.diff/PW/src/plugin_ext_forces.f90
+lib/plumed/patches/qespresso-7.0.diff/PW/src/plugin_ext_forces.f90.preplumed
+lib/plumed/patches/qespresso-7.0.diff/PW/src/plugin_initialization.f90
+lib/plumed/patches/qespresso-7.0.diff/PW/src/plugin_initialization.f90.preplumed
+lib/plumed/patches/qespresso-7.0.diff/PW/src/run_pwscf.f90
+lib/plumed/patches/qespresso-7.0.diff/PW/src/run_pwscf.f90.preplumed
+lib/plumed/patches/qespresso-7.2.config
+lib/plumed/patches/qespresso-7.2.diff/Modules/Makefile
+lib/plumed/patches/qespresso-7.2.diff/Modules/Makefile.preplumed
+lib/plumed/patches/qespresso-7.2.diff/PW/src/forces.f90
+lib/plumed/patches/qespresso-7.2.diff/PW/src/forces.f90.preplumed
+lib/plumed/patches/qespresso-7.2.diff/PW/src/plugin_ext_forces.f90
+lib/plumed/patches/qespresso-7.2.diff/PW/src/plugin_ext_forces.f90.preplumed
+lib/plumed/patches/qespresso-7.2.diff/PW/src/plugin_initialization.f90
+lib/plumed/patches/qespresso-7.2.diff/PW/src/plugin_initialization.f90.preplumed
+lib/plumed/patches/qespresso-7.2.diff/PW/src/run_pwscf.f90
+lib/plumed/patches/qespresso-7.2.diff/PW/src/run_pwscf.f90.preplumed
 lib/plumed/plumed-config
 lib/plumed/plumed-mklib
 lib/plumed/plumed-newcv
@@ -486,6 +580,7 @@ lib/plumed/vim/help/REWEIGHT_METAD.txt
 lib/plumed/vim/help/REWEIGHT_TEMP_PRESS.txt
 lib/plumed/vim/help/REWEIGHT_WHAM.txt
 lib/plumed/vim/help/RMSD.txt
+lib/plumed/vim/help/SANS.txt
 lib/plumed/vim/help/SAXS.txt
 lib/plumed/vim/help/SELECT.txt
 lib/plumed/vim/help/SELECTOR.txt