Date: Tue, 02 Jun 2026 22:51:21 +0000 From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: e9132ac6910d - main - science/plumed: update 2.=?utf-8?Q?9.3 =E2=86=92?= 2.10.0 Message-ID: <6a1f5e69.4578e.33d3dd29@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=e9132ac6910d4de81b62c1dfa2389ea808e7127f commit e9132ac6910d4de81b62c1dfa2389ea808e7127f Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2026-06-02 19:32:17 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2026-06-02 22:51:15 +0000 science/plumed: update 2.9.3 → 2.10.0 --- science/plumed/Makefile | 15 ++- science/plumed/distinfo | 6 +- science/plumed/pkg-plist | 338 ++++++++++++++++++++++++++--------------------- 3 files changed, 198 insertions(+), 161 deletions(-) diff --git a/science/plumed/Makefile b/science/plumed/Makefile index ddd1d5c0b11e..811a6199a98e 100644 --- a/science/plumed/Makefile +++ b/science/plumed/Makefile @@ -1,19 +1,20 @@ PORTNAME= plumed -DISTVERSION= 2.9.3 -PORTREVISION= 2 +DISTVERSION= 2.10.0 CATEGORIES= science graphics MASTER_SITES= https://github.com/${PORTNAME}/${PORTNAME}2/releases/download/v${DISTVERSION}/ MAINTAINER= yuri@FreeBSD.org COMMENT= PLUgin for MolEcular Dynamics -WWW= https://www.plumed.org/ +WWW= https://www.plumed.org/ \ + https://github.com/plumed/plumed2 LICENSE= LGPL3 LICENSE_FILE= ${WRKSRC}/COPYING.LESSER BROKEN_i386= undefined reference to `__atomic_load' -BUILD_DEPENDS= bash:shells/bash +BUILD_DEPENDS= bash:shells/bash \ + bash-completion>0:shells/bash-completion LIB_DEPENDS= libblas.so:math/blas \ libfftw3.so:math/fftw3 \ libgsl.so:math/gsl \ @@ -21,7 +22,7 @@ LIB_DEPENDS= libblas.so:math/blas \ RUN_DEPENDS= bash:shells/bash TEST_DEPENDS= gawk:lang/gawk -USES= autoreconf compiler:c++11-lang gmake localbase pkgconfig shebangfix tar:tgz +USES= autoreconf compiler:c++11-lang fortran gmake localbase pkgconfig shebangfix tar:tgz USE_LDCONFIG= yes SHEBANG_GLOB= *.sh @@ -32,12 +33,13 @@ SHEBANG_FILES= src/maketools/makecmd \ regtest/scripts/what GNU_CONFIGURE= yes -CONFIGURE_ARGS= --enable-shared --disable-python +CONFIGURE_ARGS= --enable-shared --disable-python # see https://github.com/plumed/plumed2/issues/1422 TEST_TARGET= check # the 'installcheck' target checks installed version # 1 test is known to fail: https://github.com/plumed/plumed2/issues/782 BINARY_ALIAS= make=${GMAKE} # only needed for tests +BINARY_ALIAS+= python3=false # Python bindings should be in a separate port, see https://github.com/plumed/plumed2/issues/1422 post-patch: @${REINPLACE_CMD} -e 's|#! /bin/bash|#! ${LOCALBASE}/bin/bash|' ${WRKSRC}/src/lib/Makefile @@ -47,5 +49,6 @@ post-install: @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 +# tests as of 2.10.0: many tests fail due to compilation issues, see https://github.com/plumed/plumed2/issues/1421 .include <bsd.port.mk> diff --git a/science/plumed/distinfo b/science/plumed/distinfo index 578262619f8a..a9c37c627f02 100644 --- a/science/plumed/distinfo +++ b/science/plumed/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1737474140 -SHA256 (plumed-2.9.3.tgz) = 2ba5095bc7c7cfde1ca95780c1240d852b7dc1b00c9de5b31e607120449ff827 -SIZE (plumed-2.9.3.tgz) = 118993592 +TIMESTAMP = 1780424890 +SHA256 (plumed-2.10.0.tgz) = 5aaf718ac530a1c8df6e0644c22acc84ad4202778106a1d584477057775f2995 +SIZE (plumed-2.10.0.tgz) = 125558641 diff --git a/science/plumed/pkg-plist b/science/plumed/pkg-plist index 5e12bcbf2910..a1670641a9f6 100644 --- a/science/plumed/pkg-plist +++ b/science/plumed/pkg-plist @@ -1,11 +1,6 @@ bin/plumed bin/plumed-config bin/plumed-patch -include/plumed/analysis/AnalysisBase.h -include/plumed/analysis/AverageVessel.h -include/plumed/analysis/DataCollectionObject.h -include/plumed/analysis/LandmarkSelectionBase.h -include/plumed/analysis/ReadAnalysisFrames.h include/plumed/asmjit/arch.h include/plumed/asmjit/arm.h include/plumed/asmjit/asmjit.h @@ -47,7 +42,6 @@ include/plumed/asmjit/x86misc.h include/plumed/asmjit/x86operand.h include/plumed/asmjit/x86regalloc_p.h include/plumed/asmjit/zone.h -include/plumed/bias/ActionRegister.h include/plumed/bias/Bias.h include/plumed/bias/ReweightBase.h include/plumed/blas/blas.h @@ -55,52 +49,69 @@ include/plumed/blas/def_external.h include/plumed/blas/def_internal.h include/plumed/blas/real.h include/plumed/cltools/CLTool.h -include/plumed/cltools/CLToolRegister.h -include/plumed/colvar/ActionRegister.h include/plumed/colvar/Colvar.h +include/plumed/colvar/ColvarShortcut.h include/plumed/colvar/CoordinationBase.h +include/plumed/colvar/MultiColvarTemplate.h include/plumed/colvar/PathMSDBase.h +include/plumed/colvar/RMSDVector.h include/plumed/config/Config.h include/plumed/config/version.h include/plumed/core/Action.h include/plumed/core/ActionAnyorder.h include/plumed/core/ActionAtomistic.h +include/plumed/core/ActionForInterface.h include/plumed/core/ActionPilot.h include/plumed/core/ActionRegister.h include/plumed/core/ActionSet.h include/plumed/core/ActionSetup.h include/plumed/core/ActionShortcut.h +include/plumed/core/ActionToGetData.h +include/plumed/core/ActionToPutData.h include/plumed/core/ActionWithArguments.h +include/plumed/core/ActionWithMatrix.h include/plumed/core/ActionWithValue.h +include/plumed/core/ActionWithVector.h include/plumed/core/ActionWithVirtualAtom.h -include/plumed/core/Atoms.h include/plumed/core/CLTool.h include/plumed/core/CLToolMain.h include/plumed/core/CLToolRegister.h include/plumed/core/Colvar.h -include/plumed/core/DataFetchingObject.h +include/plumed/core/DataPassingObject.h +include/plumed/core/DataPassingTools.h +include/plumed/core/DomainDecomposition.h include/plumed/core/ExchangePatterns.h include/plumed/core/FlexibleBin.h include/plumed/core/GREX.h include/plumed/core/GenericMolInfo.h -include/plumed/core/MDAtoms.h +include/plumed/core/Group.h include/plumed/core/ModuleMap.h +include/plumed/core/PbcAction.h include/plumed/core/PlumedMain.h include/plumed/core/PlumedMainInitializer.h +include/plumed/core/RegisterBase.h include/plumed/core/TargetDist.h include/plumed/core/Value.h include/plumed/core/WithCmd.h -include/plumed/function/ActionRegister.h +include/plumed/function/Between.h +include/plumed/function/Combine.h +include/plumed/function/Custom.h include/plumed/function/Function.h +include/plumed/function/FunctionOfMatrix.h +include/plumed/function/FunctionOfScalar.h +include/plumed/function/FunctionOfVector.h +include/plumed/function/FunctionShortcut.h +include/plumed/function/FunctionTemplateBase.h +include/plumed/function/LessThan.h +include/plumed/function/MoreThan.h +include/plumed/function/Sum.h include/plumed/gridtools/ActionWithGrid.h -include/plumed/gridtools/ActionWithInputGrid.h -include/plumed/gridtools/ActionWithIntegral.h -include/plumed/gridtools/AverageOnGrid.h -include/plumed/gridtools/ContourFindingBase.h -include/plumed/gridtools/GridPrintingBase.h +include/plumed/gridtools/EvaluateGridFunction.h +include/plumed/gridtools/FunctionOfGrid.h +include/plumed/gridtools/GridCoordinatesObject.h include/plumed/gridtools/GridSearch.h -include/plumed/gridtools/GridVessel.h -include/plumed/gridtools/HistogramOnGrid.h +include/plumed/gridtools/Interpolator.h +include/plumed/gridtools/RDF.h include/plumed/isdb/MetainferenceBase.h include/plumed/lapack/def_external.h include/plumed/lapack/def_internal.h @@ -118,10 +129,7 @@ include/plumed/lepton/Operation.h include/plumed/lepton/ParsedExpression.h include/plumed/lepton/Parser.h include/plumed/lepton/windowsIncludes.h -include/plumed/mapping/Mapping.h -include/plumed/mapping/PathBase.h -include/plumed/mapping/PathReparameterization.h -include/plumed/mapping/TrigonometricPathVessel.h +include/plumed/matrixtools/MatrixOperationBase.h include/plumed/molfile/Gromacs.h include/plumed/molfile/endianswap.h include/plumed/molfile/fastio.h @@ -131,36 +139,19 @@ include/plumed/molfile/molfile_plugin.h include/plumed/molfile/periodic_table.h include/plumed/molfile/readpdb.h include/plumed/molfile/vmdplugin.h -include/plumed/multicolvar/ActionVolume.h -include/plumed/multicolvar/AtomValuePack.h -include/plumed/multicolvar/BridgedMultiColvarFunction.h -include/plumed/multicolvar/CatomPack.h -include/plumed/multicolvar/MultiColvarBase.h -include/plumed/multicolvar/MultiColvarFilter.h -include/plumed/multicolvar/VolumeGradientBase.h -include/plumed/reference/ArgumentOnlyDistance.h -include/plumed/reference/DRMSD.h -include/plumed/reference/Direction.h -include/plumed/reference/FakeFrame.h -include/plumed/reference/MetricRegister.h -include/plumed/reference/MultiDomainRMSD.h -include/plumed/reference/RMSDBase.h -include/plumed/reference/ReferenceArguments.h -include/plumed/reference/ReferenceAtoms.h -include/plumed/reference/ReferenceConfiguration.h -include/plumed/reference/ReferenceValuePack.h -include/plumed/reference/SingleDomainRMSD.h +include/plumed/multicolvar/MultiColvarShortcuts.h include/plumed/secondarystructure/SecondaryStructureRMSD.h include/plumed/setup/ActionSetup.h +include/plumed/small_vector/small_vector.h include/plumed/tools/Angle.h include/plumed/tools/AtomNumber.h include/plumed/tools/BiasRepresentation.h include/plumed/tools/Brent1DRootSearch.h +include/plumed/tools/CheckInRange.h include/plumed/tools/Citations.h include/plumed/tools/Communicator.h include/plumed/tools/ConjugateGradient.h include/plumed/tools/DLLoader.h -include/plumed/tools/DynamicList.h include/plumed/tools/ERMSD.h include/plumed/tools/Exception.h include/plumed/tools/File.h @@ -172,11 +163,13 @@ include/plumed/tools/IFile.h include/plumed/tools/KernelFunctions.h include/plumed/tools/Keywords.h include/plumed/tools/LatticeReduction.h +include/plumed/tools/LeptonCall.h include/plumed/tools/LinkCells.h include/plumed/tools/Log.h include/plumed/tools/LoopUnroller.h include/plumed/tools/Matrix.h include/plumed/tools/MatrixSquareBracketsAccess.h +include/plumed/tools/MergeVectorTools.h include/plumed/tools/Minimise1DBrent.h include/plumed/tools/MinimiseBase.h include/plumed/tools/MolDataClass.h @@ -201,22 +194,7 @@ include/plumed/tools/TypesafePtr.h include/plumed/tools/Units.h include/plumed/tools/Vector.h include/plumed/tools/h36.h -include/plumed/vatom/ActionRegister.h include/plumed/vatom/ActionWithVirtualAtom.h -include/plumed/vesselbase/ActionWithAveraging.h -include/plumed/vesselbase/ActionWithInputVessel.h -include/plumed/vesselbase/ActionWithVessel.h -include/plumed/vesselbase/AveragingVessel.h -include/plumed/vesselbase/Between.h -include/plumed/vesselbase/BridgeVessel.h -include/plumed/vesselbase/FunctionVessel.h -include/plumed/vesselbase/LessThan.h -include/plumed/vesselbase/OrderingVessel.h -include/plumed/vesselbase/ShortcutVessel.h -include/plumed/vesselbase/StoreDataVessel.h -include/plumed/vesselbase/ValueVessel.h -include/plumed/vesselbase/Vessel.h -include/plumed/vesselbase/VesselRegister.h include/plumed/wrapper/Plumed.h include/plumed/xdrfile/xdrfile.h include/plumed/xdrfile/xdrfile_trr.h @@ -229,54 +207,6 @@ lib/plumed/fortran/plumed.f90 lib/plumed/fortran/plumed_f08.f90 lib/plumed/json/syntax.json lib/plumed/modulefile -lib/plumed/patches/gromacs-2020.7.config -lib/plumed/patches/gromacs-2020.7.diff/src/gromacs/CMakeLists.txt -lib/plumed/patches/gromacs-2020.7.diff/src/gromacs/CMakeLists.txt.preplumed -lib/plumed/patches/gromacs-2020.7.diff/src/gromacs/mdlib/expanded.cpp -lib/plumed/patches/gromacs-2020.7.diff/src/gromacs/mdlib/expanded.cpp.preplumed -lib/plumed/patches/gromacs-2020.7.diff/src/gromacs/mdlib/expanded.h -lib/plumed/patches/gromacs-2020.7.diff/src/gromacs/mdlib/expanded.h.preplumed -lib/plumed/patches/gromacs-2020.7.diff/src/gromacs/mdlib/force.cpp -lib/plumed/patches/gromacs-2020.7.diff/src/gromacs/mdlib/force.cpp.preplumed -lib/plumed/patches/gromacs-2020.7.diff/src/gromacs/mdrun/legacymdrunoptions.cpp -lib/plumed/patches/gromacs-2020.7.diff/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed -lib/plumed/patches/gromacs-2020.7.diff/src/gromacs/mdrun/legacymdrunoptions.h -lib/plumed/patches/gromacs-2020.7.diff/src/gromacs/mdrun/legacymdrunoptions.h.preplumed -lib/plumed/patches/gromacs-2020.7.diff/src/gromacs/mdrun/md.cpp -lib/plumed/patches/gromacs-2020.7.diff/src/gromacs/mdrun/md.cpp.preplumed -lib/plumed/patches/gromacs-2020.7.diff/src/gromacs/mdrun/minimize.cpp -lib/plumed/patches/gromacs-2020.7.diff/src/gromacs/mdrun/minimize.cpp.preplumed -lib/plumed/patches/gromacs-2020.7.diff/src/gromacs/mdrun/replicaexchange.cpp -lib/plumed/patches/gromacs-2020.7.diff/src/gromacs/mdrun/replicaexchange.cpp.preplumed -lib/plumed/patches/gromacs-2020.7.diff/src/gromacs/mdrun/replicaexchange.h -lib/plumed/patches/gromacs-2020.7.diff/src/gromacs/mdrun/replicaexchange.h.preplumed -lib/plumed/patches/gromacs-2020.7.diff/src/gromacs/mdrun/runner.cpp -lib/plumed/patches/gromacs-2020.7.diff/src/gromacs/mdrun/runner.cpp.preplumed -lib/plumed/patches/gromacs-2021.7.config -lib/plumed/patches/gromacs-2021.7.diff/src/gromacs/CMakeLists.txt -lib/plumed/patches/gromacs-2021.7.diff/src/gromacs/CMakeLists.txt.preplumed -lib/plumed/patches/gromacs-2021.7.diff/src/gromacs/mdlib/expanded.cpp -lib/plumed/patches/gromacs-2021.7.diff/src/gromacs/mdlib/expanded.cpp.preplumed -lib/plumed/patches/gromacs-2021.7.diff/src/gromacs/mdlib/expanded.h -lib/plumed/patches/gromacs-2021.7.diff/src/gromacs/mdlib/expanded.h.preplumed -lib/plumed/patches/gromacs-2021.7.diff/src/gromacs/mdlib/sim_util.cpp -lib/plumed/patches/gromacs-2021.7.diff/src/gromacs/mdlib/sim_util.cpp.preplumed -lib/plumed/patches/gromacs-2021.7.diff/src/gromacs/mdrun/legacymdrunoptions.cpp -lib/plumed/patches/gromacs-2021.7.diff/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed -lib/plumed/patches/gromacs-2021.7.diff/src/gromacs/mdrun/legacymdrunoptions.h -lib/plumed/patches/gromacs-2021.7.diff/src/gromacs/mdrun/legacymdrunoptions.h.preplumed -lib/plumed/patches/gromacs-2021.7.diff/src/gromacs/mdrun/md.cpp -lib/plumed/patches/gromacs-2021.7.diff/src/gromacs/mdrun/md.cpp.preplumed -lib/plumed/patches/gromacs-2021.7.diff/src/gromacs/mdrun/minimize.cpp -lib/plumed/patches/gromacs-2021.7.diff/src/gromacs/mdrun/minimize.cpp.preplumed -lib/plumed/patches/gromacs-2021.7.diff/src/gromacs/mdrun/replicaexchange.cpp -lib/plumed/patches/gromacs-2021.7.diff/src/gromacs/mdrun/replicaexchange.cpp.preplumed -lib/plumed/patches/gromacs-2021.7.diff/src/gromacs/mdrun/replicaexchange.h -lib/plumed/patches/gromacs-2021.7.diff/src/gromacs/mdrun/replicaexchange.h.preplumed -lib/plumed/patches/gromacs-2021.7.diff/src/gromacs/mdrun/rerun.cpp -lib/plumed/patches/gromacs-2021.7.diff/src/gromacs/mdrun/rerun.cpp.preplumed -lib/plumed/patches/gromacs-2021.7.diff/src/gromacs/mdrun/runner.cpp -lib/plumed/patches/gromacs-2021.7.diff/src/gromacs/mdrun/runner.cpp.preplumed lib/plumed/patches/gromacs-2022.5.config lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/CMakeLists.txt lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/CMakeLists.txt.preplumed @@ -366,6 +296,23 @@ lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/taskassignment/decidegpuusage 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/gromacs-2025.0.config +lib/plumed/patches/gromacs-2025.0.diff/cmake/gmxManagePlumed.cmake +lib/plumed/patches/gromacs-2025.0.diff/cmake/gmxManagePlumed.cmake.preplumed +lib/plumed/patches/gromacs-2025.0.diff/src/gromacs/applied_forces/plumed/plumedMDModule.cpp +lib/plumed/patches/gromacs-2025.0.diff/src/gromacs/applied_forces/plumed/plumedMDModule.cpp.preplumed +lib/plumed/patches/gromacs-2025.0.diff/src/gromacs/applied_forces/plumed/plumedOptions.cpp +lib/plumed/patches/gromacs-2025.0.diff/src/gromacs/applied_forces/plumed/plumedOptions.cpp.preplumed +lib/plumed/patches/gromacs-2025.0.diff/src/gromacs/applied_forces/plumed/plumedOptions.h +lib/plumed/patches/gromacs-2025.0.diff/src/gromacs/applied_forces/plumed/plumedOptions.h.preplumed +lib/plumed/patches/gromacs-2025.0.diff/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp +lib/plumed/patches/gromacs-2025.0.diff/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp.preplumed +lib/plumed/patches/gromacs-2025.0.diff/src/gromacs/applied_forces/plumed/plumedforceprovider.h +lib/plumed/patches/gromacs-2025.0.diff/src/gromacs/applied_forces/plumed/plumedforceprovider.h.preplumed +lib/plumed/patches/gromacs-2025.0.diff/src/gromacs/mdrun/runner.cpp +lib/plumed/patches/gromacs-2025.0.diff/src/gromacs/mdrun/runner.cpp.preplumed +lib/plumed/patches/gromacs-2025.0.diff/src/gromacs/mdrunutility/mdmodulesnotifiers.h +lib/plumed/patches/gromacs-2025.0.diff/src/gromacs/mdrunutility/mdmodulesnotifiers.h.preplumed lib/plumed/patches/namd-2.12.config lib/plumed/patches/namd-2.12.diff lib/plumed/patches/namd-2.13.config @@ -440,41 +387,74 @@ lib/plumed/src/lib/Plumed.inc.runtime lib/plumed/src/lib/Plumed.inc.shared lib/plumed/src/lib/Plumed.inc.static lib/plumed/vim/help/ABMD.txt -lib/plumed/vim/help/ADAPTIVE_PATH.txt +lib/plumed/vim/help/ACCUMULATE.txt lib/plumed/vim/help/ALPHABETA.txt lib/plumed/vim/help/ALPHARMSD.txt lib/plumed/vim/help/ANGLE.txt lib/plumed/vim/help/ANGLES.txt +lib/plumed/vim/help/ANGLE_SCALAR.txt +lib/plumed/vim/help/ANGLE_VECTOR.txt lib/plumed/vim/help/ANTIBETARMSD.txt -lib/plumed/vim/help/AROUND.txt +lib/plumed/vim/help/ARGS2VATOM.txt lib/plumed/vim/help/AVERAGE.txt +lib/plumed/vim/help/BAIES.txt +lib/plumed/vim/help/BESSEL.txt +lib/plumed/vim/help/BESSEL_SCALAR.txt +lib/plumed/vim/help/BESSEL_VECTOR.txt +lib/plumed/vim/help/BETWEEN.txt +lib/plumed/vim/help/BETWEEN_MATRIX.txt +lib/plumed/vim/help/BETWEEN_VECTOR.txt lib/plumed/vim/help/BIASVALUE.txt -lib/plumed/vim/help/BRIDGE.txt lib/plumed/vim/help/CALIBER.txt -lib/plumed/vim/help/CAVITY.txt lib/plumed/vim/help/CELL.txt lib/plumed/vim/help/CENTER.txt -lib/plumed/vim/help/CENTER_OF_MULTICOLVAR.txt -lib/plumed/vim/help/COLLECT_FRAMES.txt +lib/plumed/vim/help/CENTER_FAST.txt +lib/plumed/vim/help/CHARGE.txt +lib/plumed/vim/help/CHARGE_SCALAR.txt +lib/plumed/vim/help/CHARGE_VECTOR.txt +lib/plumed/vim/help/COLLECT.txt lib/plumed/vim/help/COM.txt lib/plumed/vim/help/COMBINE.txt +lib/plumed/vim/help/COMBINE_MATRIX.txt +lib/plumed/vim/help/COMBINE_SCALAR.txt +lib/plumed/vim/help/COMBINE_VECTOR.txt lib/plumed/vim/help/COMMITTOR.txt +lib/plumed/vim/help/CONCATENATE.txt lib/plumed/vim/help/CONSTANT.txt lib/plumed/vim/help/CONTACTMAP.txt lib/plumed/vim/help/CONVERT_TO_FES.txt lib/plumed/vim/help/COORDINATION.txt -lib/plumed/vim/help/COORDINATIONNUMBER.txt +lib/plumed/vim/help/COORD_ANGLES.txt +lib/plumed/vim/help/COVARIANCE_MATRIX.txt +lib/plumed/vim/help/CREATE_MASK.txt lib/plumed/vim/help/CS2BACKBONE.txt lib/plumed/vim/help/CUSTOM.txt +lib/plumed/vim/help/CUSTOM_GRID.txt +lib/plumed/vim/help/CUSTOM_MATRIX.txt +lib/plumed/vim/help/CUSTOM_SCALAR.txt +lib/plumed/vim/help/CUSTOM_VECTOR.txt lib/plumed/vim/help/DEBUG.txt -lib/plumed/vim/help/DENSITY.txt +lib/plumed/vim/help/DETERMINANT.txt lib/plumed/vim/help/DHENERGY.txt +lib/plumed/vim/help/DIAGONALIZE.txt +lib/plumed/vim/help/DIFFERENCE.txt +lib/plumed/vim/help/DIFFERENCE_SCALAR.txt +lib/plumed/vim/help/DIFFERENCE_VECTOR.txt lib/plumed/vim/help/DIHCOR.txt +lib/plumed/vim/help/DIHEDRAL_CORRELATION.txt +lib/plumed/vim/help/DIHEDRAL_CORRELATION_SCALAR.txt +lib/plumed/vim/help/DIHEDRAL_CORRELATION_VECTOR.txt lib/plumed/vim/help/DIMER.txt lib/plumed/vim/help/DIPOLE.txt +lib/plumed/vim/help/DIPOLE_SCALAR.txt +lib/plumed/vim/help/DIPOLE_VECTOR.txt +lib/plumed/vim/help/DISPLACEMENT.txt +lib/plumed/vim/help/DISSIMILARITIES.txt lib/plumed/vim/help/DISTANCE.txt lib/plumed/vim/help/DISTANCES.txt -lib/plumed/vim/help/DISTANCE_FROM_CONTOUR.txt +lib/plumed/vim/help/DISTANCE_SCALAR.txt +lib/plumed/vim/help/DISTANCE_VECTOR.txt +lib/plumed/vim/help/DOMAIN_DECOMPOSITION.txt lib/plumed/vim/help/DRMSD.txt lib/plumed/vim/help/DUMPATOMS.txt lib/plumed/vim/help/DUMPCUBE.txt @@ -483,7 +463,9 @@ lib/plumed/vim/help/DUMPFORCES.txt lib/plumed/vim/help/DUMPGRID.txt lib/plumed/vim/help/DUMPMASSCHARGE.txt lib/plumed/vim/help/DUMPMULTICOLVAR.txt +lib/plumed/vim/help/DUMPPDB.txt lib/plumed/vim/help/DUMPPROJECTIONS.txt +lib/plumed/vim/help/DUMPVECTOR.txt lib/plumed/vim/help/EEFSOLV.txt lib/plumed/vim/help/EFFECTIVE_ENERGY_DRIFT.txt lib/plumed/vim/help/EMMI.txt @@ -491,125 +473,176 @@ lib/plumed/vim/help/ENDPLUMED.txt lib/plumed/vim/help/ENERGY.txt lib/plumed/vim/help/ENSEMBLE.txt lib/plumed/vim/help/ERMSD.txt -lib/plumed/vim/help/EUCLIDEAN_DISSIMILARITIES.txt +lib/plumed/vim/help/EUCLIDEAN_DISTANCE.txt +lib/plumed/vim/help/EVALUATE_FUNCTION_FROM_GRID.txt +lib/plumed/vim/help/EVALUATE_FUNCTION_FROM_GRID_SCALAR.txt +lib/plumed/vim/help/EVALUATE_FUNCTION_FROM_GRID_VECTOR.txt lib/plumed/vim/help/EXTENDED_LAGRANGIAN.txt lib/plumed/vim/help/EXTERNAL.txt lib/plumed/vim/help/EXTRACV.txt lib/plumed/vim/help/FAKE.txt -lib/plumed/vim/help/FIND_CONTOUR.txt -lib/plumed/vim/help/FIND_CONTOUR_SURFACE.txt -lib/plumed/vim/help/FIND_SPHERICAL_CONTOUR.txt +lib/plumed/vim/help/FIND_GRID_MAXIMUM.txt +lib/plumed/vim/help/FIND_GRID_MINIMUM.txt lib/plumed/vim/help/FIT_TO_TEMPLATE.txt lib/plumed/vim/help/FIXEDATOM.txt +lib/plumed/vim/help/FLATTEN.txt lib/plumed/vim/help/FLUSH.txt -lib/plumed/vim/help/FOURIER_TRANSFORM.txt lib/plumed/vim/help/FRET.txt lib/plumed/vim/help/FUNCPATHGENERAL.txt lib/plumed/vim/help/FUNCPATHMSD.txt lib/plumed/vim/help/FUNCSUMHILLS.txt +lib/plumed/vim/help/GATHER_REPLICAS.txt +lib/plumed/vim/help/GET.txt lib/plumed/vim/help/GHBFIX.txt lib/plumed/vim/help/GHOST.txt -lib/plumed/vim/help/GPROPERTYMAP.txt -lib/plumed/vim/help/GRID_TO_XYZ.txt +lib/plumed/vim/help/GRADIENT.txt lib/plumed/vim/help/GROUP.txt lib/plumed/vim/help/GYRATION.txt +lib/plumed/vim/help/GYRATION_FAST.txt +lib/plumed/vim/help/GYRATION_TENSOR.txt +lib/plumed/vim/help/HIGHEST.txt +lib/plumed/vim/help/HIGHEST_SCALAR.txt +lib/plumed/vim/help/HIGHEST_VECTOR.txt lib/plumed/vim/help/HISTOGRAM.txt lib/plumed/vim/help/INCLUDE.txt -lib/plumed/vim/help/INCYLINDER.txt -lib/plumed/vim/help/INENVELOPE.txt lib/plumed/vim/help/INPLANEDISTANCES.txt -lib/plumed/vim/help/INSPHERE.txt lib/plumed/vim/help/INTEGRATE_GRID.txt lib/plumed/vim/help/INTERPOLATE_GRID.txt +lib/plumed/vim/help/INVERT_MATRIX.txt lib/plumed/vim/help/JCOUPLING.txt -lib/plumed/vim/help/LANDMARK_SELECT_FPS.txt -lib/plumed/vim/help/LANDMARK_SELECT_RANDOM.txt -lib/plumed/vim/help/LANDMARK_SELECT_STAGED.txt -lib/plumed/vim/help/LANDMARK_SELECT_STRIDE.txt +lib/plumed/vim/help/KDE.txt +lib/plumed/vim/help/KERNEL.txt +lib/plumed/vim/help/KL_ENTROPY.txt +lib/plumed/vim/help/LESS_THAN.txt +lib/plumed/vim/help/LESS_THAN_MATRIX.txt +lib/plumed/vim/help/LESS_THAN_VECTOR.txt lib/plumed/vim/help/LOAD.txt lib/plumed/vim/help/LOCALENSEMBLE.txt -lib/plumed/vim/help/LOCAL_AVERAGE.txt lib/plumed/vim/help/LOWER_WALLS.txt +lib/plumed/vim/help/LOWER_WALLS_SCALAR.txt +lib/plumed/vim/help/LOWEST.txt +lib/plumed/vim/help/LOWEST_SCALAR.txt +lib/plumed/vim/help/LOWEST_VECTOR.txt +lib/plumed/vim/help/MAHALANOBIS_DISTANCE.txt +lib/plumed/vim/help/MASS.txt +lib/plumed/vim/help/MASS_SCALAR.txt +lib/plumed/vim/help/MASS_VECTOR.txt lib/plumed/vim/help/MATHEVAL.txt +lib/plumed/vim/help/MATHEVAL_GRID.txt +lib/plumed/vim/help/MATHEVAL_MATRIX.txt +lib/plumed/vim/help/MATHEVAL_SCALAR.txt +lib/plumed/vim/help/MATHEVAL_VECTOR.txt +lib/plumed/vim/help/MATRIX_PRODUCT.txt +lib/plumed/vim/help/MATRIX_PRODUCT_DIAGONAL.txt +lib/plumed/vim/help/MATRIX_VECTOR_PRODUCT.txt lib/plumed/vim/help/MAXENT.txt -lib/plumed/vim/help/MCOLV_COMBINE.txt -lib/plumed/vim/help/MCOLV_PRODUCT.txt +lib/plumed/vim/help/MEAN.txt +lib/plumed/vim/help/MEAN_SCALAR.txt +lib/plumed/vim/help/MEAN_VECTOR.txt lib/plumed/vim/help/METAD.txt lib/plumed/vim/help/METAINFERENCE.txt -lib/plumed/vim/help/MFILTER_BETWEEN.txt lib/plumed/vim/help/MFILTER_LESS.txt lib/plumed/vim/help/MFILTER_MORE.txt lib/plumed/vim/help/MOLINFO.txt +lib/plumed/vim/help/MOMENTS.txt +lib/plumed/vim/help/MOMENTS_SCALAR.txt +lib/plumed/vim/help/MOMENTS_VECTOR.txt +lib/plumed/vim/help/MORE_THAN.txt +lib/plumed/vim/help/MORE_THAN_MATRIX.txt +lib/plumed/vim/help/MORE_THAN_VECTOR.txt lib/plumed/vim/help/MOVINGRESTRAINT.txt -lib/plumed/vim/help/MTRANSFORM_BETWEEN.txt -lib/plumed/vim/help/MTRANSFORM_LESS.txt -lib/plumed/vim/help/MTRANSFORM_MORE.txt lib/plumed/vim/help/MULTICOLVARDENS.txt lib/plumed/vim/help/MULTI_RMSD.txt -lib/plumed/vim/help/NLINKS.txt lib/plumed/vim/help/NOE.txt -lib/plumed/vim/help/OUTPUT_ANALYSIS_DATA_TO_COLVAR.txt -lib/plumed/vim/help/OUTPUT_ANALYSIS_DATA_TO_PDB.txt +lib/plumed/vim/help/NORMALIZED_EUCLIDEAN_DISTANCE.txt +lib/plumed/vim/help/ONES.txt +lib/plumed/vim/help/OUTER_PRODUCT.txt +lib/plumed/vim/help/PAIRENTROPIES.txt +lib/plumed/vim/help/PAIRENTROPY.txt lib/plumed/vim/help/PARABETARMSD.txt -lib/plumed/vim/help/PATH.txt lib/plumed/vim/help/PATHMSD.txt +lib/plumed/vim/help/PBC.txt lib/plumed/vim/help/PBMETAD.txt lib/plumed/vim/help/PCARMSD.txt -lib/plumed/vim/help/PCAVARS.txt lib/plumed/vim/help/PCS.txt +lib/plumed/vim/help/PDB2CONSTANT.txt lib/plumed/vim/help/PIECEWISE.txt +lib/plumed/vim/help/PIECEWISE_SCALAR.txt +lib/plumed/vim/help/PLANE.txt +lib/plumed/vim/help/PLANES.txt +lib/plumed/vim/help/PLANE_SCALAR.txt +lib/plumed/vim/help/PLANE_VECTOR.txt lib/plumed/vim/help/PLUMED.txt lib/plumed/vim/help/POSITION.txt +lib/plumed/vim/help/POSITION_SCALAR.txt +lib/plumed/vim/help/POSITION_VECTOR.txt lib/plumed/vim/help/PRE.txt lib/plumed/vim/help/PRINT.txt -lib/plumed/vim/help/PRINT_DISSIMILARITY_MATRIX.txt +lib/plumed/vim/help/PRINT_NDX.txt +lib/plumed/vim/help/PRODUCT.txt lib/plumed/vim/help/PROJECTION_ON_AXIS.txt lib/plumed/vim/help/PROPERTYMAP.txt lib/plumed/vim/help/PUCKERING.txt +lib/plumed/vim/help/PUT.txt lib/plumed/vim/help/RANDOM_EXCHANGES.txt lib/plumed/vim/help/RDC.txt +lib/plumed/vim/help/RDF.txt lib/plumed/vim/help/READ.txt -lib/plumed/vim/help/READ_DISSIMILARITY_MATRIX.txt +lib/plumed/vim/help/READMASSCHARGE.txt +lib/plumed/vim/help/REFERENCE_GRID.txt lib/plumed/vim/help/RESCALE.txt -lib/plumed/vim/help/RESELECT_LANDMARKS.txt lib/plumed/vim/help/RESET_CELL.txt lib/plumed/vim/help/RESTART.txt lib/plumed/vim/help/RESTRAINT.txt +lib/plumed/vim/help/RESTRAINT_SCALAR.txt lib/plumed/vim/help/REWEIGHT_BIAS.txt 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/RMSD_SCALAR.txt +lib/plumed/vim/help/RMSD_VECTOR.txt lib/plumed/vim/help/SANS.txt lib/plumed/vim/help/SAXS.txt +lib/plumed/vim/help/SECONDARY_STRUCTURE_RMSD.txt lib/plumed/vim/help/SELECT.txt lib/plumed/vim/help/SELECTOR.txt +lib/plumed/vim/help/SELECT_COMPONENTS.txt +lib/plumed/vim/help/SELECT_WITH_MASK.txt +lib/plumed/vim/help/SHADOW.txt lib/plumed/vim/help/SORT.txt +lib/plumed/vim/help/SORT_SCALAR.txt +lib/plumed/vim/help/SORT_VECTOR.txt +lib/plumed/vim/help/SPHERICAL_KDE.txt lib/plumed/vim/help/STATS.txt -lib/plumed/vim/help/TARGET.txt +lib/plumed/vim/help/SUM.txt +lib/plumed/vim/help/SUM_GRID.txt +lib/plumed/vim/help/SUM_MATRIX.txt +lib/plumed/vim/help/SUM_SCALAR.txt +lib/plumed/vim/help/SUM_VECTOR.txt lib/plumed/vim/help/TEMPLATE.txt -lib/plumed/vim/help/TETRAHEDRALPORE.txt lib/plumed/vim/help/TIME.txt lib/plumed/vim/help/TORSION.txt lib/plumed/vim/help/TORSIONS.txt +lib/plumed/vim/help/TORSION_SCALAR.txt +lib/plumed/vim/help/TORSION_VECTOR.txt +lib/plumed/vim/help/TRANSPOSE.txt lib/plumed/vim/help/UNITS.txt lib/plumed/vim/help/UPDATE_IF.txt lib/plumed/vim/help/UPPER_WALLS.txt +lib/plumed/vim/help/UPPER_WALLS_SCALAR.txt +lib/plumed/vim/help/UWALLS.txt lib/plumed/vim/help/VOLUME.txt -lib/plumed/vim/help/WHAM_HISTOGRAM.txt -lib/plumed/vim/help/WHAM_WEIGHTS.txt +lib/plumed/vim/help/VORONOI.txt +lib/plumed/vim/help/VSTACK.txt lib/plumed/vim/help/WHOLEMOLECULES.txt lib/plumed/vim/help/WRAPAROUND.txt lib/plumed/vim/help/XANGLES.txt lib/plumed/vim/help/XDISTANCES.txt -lib/plumed/vim/help/XYDISTANCES.txt lib/plumed/vim/help/XYTORSIONS.txt -lib/plumed/vim/help/XZDISTANCES.txt lib/plumed/vim/help/XZTORSIONS.txt lib/plumed/vim/help/YANGLES.txt lib/plumed/vim/help/YDISTANCES.txt lib/plumed/vim/help/YXTORSIONS.txt -lib/plumed/vim/help/YZDISTANCES.txt lib/plumed/vim/help/YZTORSIONS.txt lib/plumed/vim/help/ZANGLES.txt lib/plumed/vim/help/ZDISTANCES.txt @@ -621,3 +654,4 @@ lib/plumed/vim/syntax/plumedf.vim libdata/pkgconfig/plumed.pc libdata/pkgconfig/plumedInternals.pc libdata/pkgconfig/plumedWrapper.pc +share/bash-completion/completions/plumedhome | help
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