Index: head/science/Makefile =================================================================== --- head/science/Makefile (revision 533980) +++ head/science/Makefile (revision 533981) @@ -1,345 +1,346 @@ # $FreeBSD$ # COMMENT = Scientific ports SUBDIR += 2d-rewriter SUBDIR += ALPSCore SUBDIR += InsightToolkit SUBDIR += PETSc SUBDIR += R-cran-AMORE SUBDIR += R-cran-DCluster SUBDIR += R-cran-Epi SUBDIR += R-cran-FAdist SUBDIR += R-cran-bayesm SUBDIR += R-cran-cmprsk SUBDIR += R-cran-e1071 SUBDIR += R-cran-eco SUBDIR += R-cran-epicalc SUBDIR += R-cran-etm SUBDIR += R-cran-fastICA SUBDIR += R-cran-kernlab SUBDIR += R-cran-snow SUBDIR += R-cran-som SUBDIR += R-cran-udunits2 SUBDIR += abinit SUBDIR += afni SUBDIR += agrum SUBDIR += aircraft-datcom SUBDIR += antioch SUBDIR += apbs SUBDIR += atom SUBDIR += atompaw SUBDIR += avogadro2 SUBDIR += avogadrolibs SUBDIR += bagel SUBDIR += bddsolve SUBDIR += berkeleygw SUBDIR += bodr SUBDIR += brian SUBDIR += buddy SUBDIR += cdcl SUBDIR += cdf SUBDIR += cdk SUBDIR += cdo SUBDIR += cgnslib SUBDIR += cgribex SUBDIR += checkmol SUBDIR += chemical-mime-data SUBDIR += chemps2 SUBDIR += chemtool SUBDIR += chemtool-devel SUBDIR += chrono SUBDIR += clhep SUBDIR += clipper SUBDIR += code_saturne SUBDIR += colt SUBDIR += coordgenlibs SUBDIR += cp2k SUBDIR += cp2k-data SUBDIR += crf++ SUBDIR += dalton SUBDIR += datawarrior SUBDIR += dcl SUBDIR += devisor SUBDIR += dftbplus SUBDIR += dkh SUBDIR += dlib-cpp SUBDIR += dlpoly-classic SUBDIR += drawxtl SUBDIR += dvc SUBDIR += eccodes SUBDIR += elk SUBDIR += elmerfem SUBDIR += epte SUBDIR += erd SUBDIR += erkale SUBDIR += erkale-pseudopotentials SUBDIR += esys-particle SUBDIR += fastcap SUBDIR += fasthenry SUBDIR += fisicalab SUBDIR += fleur SUBDIR += fsom SUBDIR += fvcom SUBDIR += fvcom-mpi SUBDIR += gabedit SUBDIR += gamess-us SUBDIR += gchemutils SUBDIR += gdma SUBDIR += getdp SUBDIR += ghemical SUBDIR += ghmm SUBDIR += gnudatalanguage SUBDIR += gpaw-setups SUBDIR += gramps SUBDIR += grib_api SUBDIR += gromacs SUBDIR += gsmc SUBDIR += gtamsanalyzer SUBDIR += h5utils SUBDIR += h5z-zfp SUBDIR += harminv SUBDIR += hdf SUBDIR += hdf5 SUBDIR += hdf5-18 SUBDIR += healpix SUBDIR += highfive SUBDIR += hypre SUBDIR += iboview SUBDIR += isaac-cfd SUBDIR += jdftx SUBDIR += jmol SUBDIR += jstrack SUBDIR += kalzium SUBDIR += kim-api SUBDIR += kst2 SUBDIR += lammps SUBDIR += lamprop SUBDIR += latte SUBDIR += libaec SUBDIR += libccp4 SUBDIR += libcint SUBDIR += libctl SUBDIR += libefp SUBDIR += libgeodecomp SUBDIR += libghemical SUBDIR += libgridxc SUBDIR += libint SUBDIR += libint2 SUBDIR += libkml SUBDIR += liblinear SUBDIR += libmsym SUBDIR += liboglappth SUBDIR += libquantum SUBDIR += libssm SUBDIR += libsvm SUBDIR += libsvm-python SUBDIR += libvdwxc SUBDIR += libxc SUBDIR += liggghts SUBDIR += lm SUBDIR += luscus SUBDIR += madness SUBDIR += maeparser SUBDIR += massxpert SUBDIR += mbdyn SUBDIR += mcstas SUBDIR += mcstas-comps SUBDIR += mcxtrace SUBDIR += mcxtrace-comps SUBDIR += mdynamix SUBDIR += medit SUBDIR += metaphysicl SUBDIR += minc2 SUBDIR += mmdb2 SUBDIR += mmtf-cpp SUBDIR += mol2ps SUBDIR += molgif SUBDIR += molscript SUBDIR += molsketch SUBDIR += mpb SUBDIR += mpqc SUBDIR += msms SUBDIR += multiwfn SUBDIR += namd SUBDIR += nest SUBDIR += netcdf SUBDIR += netcdf-cxx SUBDIR += netcdf-fortran SUBDIR += nifticlib SUBDIR += nwchem SUBDIR += nwchem-data SUBDIR += octopus SUBDIR += openbabel SUBDIR += openkim SUBDIR += openkim-models SUBDIR += openmx SUBDIR += opensim-core SUBDIR += opensph SUBDIR += opsin SUBDIR += p5-Algorithm-SVMLight SUBDIR += p5-Chemistry-3DBuilder SUBDIR += p5-Chemistry-Bond-Find SUBDIR += p5-Chemistry-Canonicalize SUBDIR += p5-Chemistry-Elements SUBDIR += p5-Chemistry-File-MDLMol SUBDIR += p5-Chemistry-File-Mopac SUBDIR += p5-Chemistry-File-PDB SUBDIR += p5-Chemistry-File-SLN SUBDIR += p5-Chemistry-File-SMARTS SUBDIR += p5-Chemistry-File-SMILES SUBDIR += p5-Chemistry-File-VRML SUBDIR += p5-Chemistry-File-XYZ SUBDIR += p5-Chemistry-FormulaPattern SUBDIR += p5-Chemistry-InternalCoords SUBDIR += p5-Chemistry-Isotope SUBDIR += p5-Chemistry-MacroMol SUBDIR += p5-Chemistry-MidasPattern SUBDIR += p5-Chemistry-Mok SUBDIR += p5-Chemistry-Mol SUBDIR += p5-Chemistry-Pattern SUBDIR += p5-Chemistry-Reaction SUBDIR += p5-Chemistry-Ring SUBDIR += p5-Geo-BUFR SUBDIR += p5-Geo-Coordinates-Converter SUBDIR += p5-Geo-Coordinates-Converter-iArea SUBDIR += p5-Geo-ReadGRIB SUBDIR += p5-Geo-WebService-Elevation-USGS SUBDIR += p5-Mcstas-Tools SUBDIR += p5-PerlMol SUBDIR += p5-Physics-Unit SUBDIR += packmol SUBDIR += pagmo2 SUBDIR += paje SUBDIR += paraview SUBDIR += pcmsolver + SUBDIR += plumed SUBDIR += pnetcdf SUBDIR += pulseview SUBDIR += py-DendroPy SUBDIR += py-GPy SUBDIR += py-GPyOpt SUBDIR += py-MDAnalysis SUBDIR += py-MDAnalysisTests SUBDIR += py-OpenFermion SUBDIR += py-PyFR SUBDIR += py-PyQuante SUBDIR += py-SimpleSpectral SUBDIR += py-abipy SUBDIR += py-asdf SUBDIR += py-ase SUBDIR += py-avogadrolibs SUBDIR += py-cdo SUBDIR += py-chainer SUBDIR += py-chainer-chemistry SUBDIR += py-chempy SUBDIR += py-coards SUBDIR += py-dlib SUBDIR += py-eccodes-python SUBDIR += py-geolinks SUBDIR += py-geomet SUBDIR += py-geometer SUBDIR += py-gpaw SUBDIR += py-gsd SUBDIR += py-h5json SUBDIR += py-h5py SUBDIR += py-kim-query SUBDIR += py-kinematics SUBDIR += py-kliff SUBDIR += py-lifelines SUBDIR += py-mdp SUBDIR += py-mlpy SUBDIR += py-mmtf-python SUBDIR += py-molmod SUBDIR += py-netCDF4 SUBDIR += py-obspy SUBDIR += py-oddt SUBDIR += py-openpiv SUBDIR += py-paida SUBDIR += py-paramz SUBDIR += py-phono3py SUBDIR += py-phonopy SUBDIR += py-pupynere SUBDIR += py-pyaixi SUBDIR += py-pycsw SUBDIR += py-pydicom SUBDIR += py-pygeodesy SUBDIR += py-pygeometa SUBDIR += py-pymatgen SUBDIR += py-pymol SUBDIR += py-pyosf SUBDIR += py-pysal SUBDIR += py-pyteomics SUBDIR += py-qcelemental SUBDIR += py-qcengine SUBDIR += py-qspin SUBDIR += py-quantities SUBDIR += py-rmf SUBDIR += py-rmsd SUBDIR += py-ruffus SUBDIR += py-scikit-fuzzy SUBDIR += py-scikit-learn SUBDIR += py-scikit-optimize SUBDIR += py-scikit-sparse SUBDIR += py-scimath SUBDIR += py-scipy SUBDIR += py-scoria SUBDIR += py-spglib SUBDIR += py-tensorflow SUBDIR += py-tensorflow-estimator SUBDIR += py-veusz SUBDIR += py-ws2300 SUBDIR += pybrain SUBDIR += pynn SUBDIR += qbox SUBDIR += qcl SUBDIR += qiskit-aer SUBDIR += qmcpack SUBDIR += quantum-espresso SUBDIR += quantum-espresso-pseudopotentials SUBDIR += qwalk SUBDIR += rdkit SUBDIR += rmf SUBDIR += rubygem-ai4r SUBDIR += rubygem-cdo SUBDIR += rubygem-rgeo SUBDIR += rubygem-rgeo-geojson SUBDIR += rubygem-rgeo-proj4 SUBDIR += rubygem-rgeo-shapefile SUBDIR += rubygem-ruby-dcl SUBDIR += rubygem-ruby-netcdf SUBDIR += scidavis SUBDIR += siesta SUBDIR += sigrok-cli SUBDIR += sigrok-firmware SUBDIR += sigrok-firmware-fx2lafw SUBDIR += sigrok-firmware-utils SUBDIR += silo SUBDIR += simbody SUBDIR += simgrid SUBDIR += simint SUBDIR += simlib SUBDIR += simsmith SUBDIR += smoldyn SUBDIR += sparta SUBDIR += spglib SUBDIR += step SUBDIR += svmlight SUBDIR += szip SUBDIR += teem SUBDIR += tfel SUBDIR += tinker SUBDIR += udunits SUBDIR += v_sim SUBDIR += vipster SUBDIR += vmd SUBDIR += voro++ SUBDIR += wannier90 SUBDIR += wwplot SUBDIR += wxmacmolplt SUBDIR += xcrysden SUBDIR += xdrawchem SUBDIR += xfce4-equake-plugin SUBDIR += yoda .include Index: head/science/plumed/Makefile =================================================================== --- head/science/plumed/Makefile (nonexistent) +++ head/science/plumed/Makefile (revision 533981) @@ -0,0 +1,35 @@ +# $FreeBSD$ + +PORTNAME= plumed +DISTVERSIONPREFIX= v +DISTVERSION= 2.6.0 +CATEGORIES= science graphics + +MAINTAINER= yuri@FreeBSD.org +COMMENT= PLUgin for MolEcular Dynamics + +LICENSE= LGPL3 +LICENSE_FILE= ${WRKSRC}/COPYING.LESSER + +BUILD_DEPENDS= bash:shells/bash \ + xxd:editors/vim-console +RUN_DEPENDS= bash:shells/bash + +USES= autoreconf gmake pkgconfig shebangfix +SHEBANG_GLOB= *.sh +SHEBANG_FILES= src/maketools/makecmd +GNU_CONFIGURE= yes +USE_GITHUB= yes +GH_PROJECT= plumed2 +USE_LDCONFIG= yes + +CONFIGURE_ARGS= --enable-shared --disable-python + +post-patch: + @${REINPLACE_CMD} -e 's|#! /bin/bash|#! ${LOCALBASE}/bin/bash|' ${WRKSRC}/src/lib/Makefile + +post-install: + @${RMDIR} ${STAGEDIR}${PREFIX}/lib/plumed/obj + @cd ${STAGEDIR}${PREFIX} && ${STRIP_CMD} bin/plumed lib/plumed/plumed-runtime lib/libplumed.so lib/libplumedKernel.so + +.include Property changes on: head/science/plumed/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/plumed/distinfo =================================================================== --- head/science/plumed/distinfo (nonexistent) +++ head/science/plumed/distinfo (revision 533981) @@ -0,0 +1,3 @@ +TIMESTAMP = 1588612750 +SHA256 (plumed-plumed2-v2.6.0_GH0.tar.gz) = 3d57ae460607a49547ef38a52c4ac93493a3966857c352280a9c05f5dcdb1820 +SIZE (plumed-plumed2-v2.6.0_GH0.tar.gz) = 74664958 Property changes on: head/science/plumed/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/plumed/files/patch-configure.ac =================================================================== --- head/science/plumed/files/patch-configure.ac (nonexistent) +++ head/science/plumed/files/patch-configure.ac (revision 533981) @@ -0,0 +1,20 @@ +--- configure.ac.orig 2020-05-04 17:58:19 UTC ++++ configure.ac +@@ -889,6 +889,17 @@ if test "$shared" == true ; then + PLUMED_CHECK_LDFLAGS([-Wl,-Bsymbolic]) + fi + ;; ++ (FreeBSD) ++ AC_MSG_NOTICE([*** Special settings for dynamic libraries on Linux ***]) ++ AC_MSG_NOTICE([Dynamic library extension is 'so']) ++ AC_MSG_NOTICE([LDSHARED and LDFLAGS need special flags]) ++ SOEXT=so ++ LDSHARED="$LDSHARED -shared" ++ PLUMED_CHECK_LDFLAGS([-rdynamic]) ++ if test "$bsymbolic" == true ; then ++ PLUMED_CHECK_LDFLAGS([-Wl,-Bsymbolic]) ++ fi ++ ;; + (*) + AC_MSG_NOTICE([*** Dynamic library only enabled on OSX and Linux ***]) + esac Property changes on: head/science/plumed/files/patch-configure.ac ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/plumed/pkg-descr =================================================================== --- head/science/plumed/pkg-descr (nonexistent) +++ head/science/plumed/pkg-descr (revision 533981) @@ -0,0 +1,8 @@ +PLUMED is an open-source, community-developed library that provides a wide +range of different methods, which include: +* enhanced-sampling algorithms +* free-energy methods +* tools to analyze the vast amounts of data produced by molecular dynamics (MD) + simulations. + +WWW: https://www.plumed.org/ Property changes on: head/science/plumed/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/plumed/pkg-plist =================================================================== --- head/science/plumed/pkg-plist (nonexistent) +++ head/science/plumed/pkg-plist (revision 533981) @@ -0,0 +1,491 @@ +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 +include/plumed/asmjit/asmjit_apibegin.h +include/plumed/asmjit/asmjit_apiend.h +include/plumed/asmjit/asmjit_build.h +include/plumed/asmjit/assembler.h +include/plumed/asmjit/base.h +include/plumed/asmjit/codebuilder.h +include/plumed/asmjit/codecompiler.h +include/plumed/asmjit/codeemitter.h +include/plumed/asmjit/codeholder.h +include/plumed/asmjit/constpool.h +include/plumed/asmjit/cpuinfo.h +include/plumed/asmjit/func.h +include/plumed/asmjit/globals.h +include/plumed/asmjit/inst.h +include/plumed/asmjit/logging.h +include/plumed/asmjit/misc_p.h +include/plumed/asmjit/moved_string.h +include/plumed/asmjit/operand.h +include/plumed/asmjit/osutils.h +include/plumed/asmjit/regalloc_p.h +include/plumed/asmjit/runtime.h +include/plumed/asmjit/simdtypes.h +include/plumed/asmjit/utils.h +include/plumed/asmjit/vmem.h +include/plumed/asmjit/x86.h +include/plumed/asmjit/x86assembler.h +include/plumed/asmjit/x86builder.h +include/plumed/asmjit/x86compiler.h +include/plumed/asmjit/x86emitter.h +include/plumed/asmjit/x86globals.h +include/plumed/asmjit/x86inst.h +include/plumed/asmjit/x86instimpl_p.h +include/plumed/asmjit/x86internal_p.h +include/plumed/asmjit/x86logging_p.h +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 +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/CoordinationBase.h +include/plumed/colvar/PathMSDBase.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/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/ActionWithArguments.h +include/plumed/core/ActionWithValue.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/ExchangePatterns.h +include/plumed/core/FlexibleBin.h +include/plumed/core/GREX.h +include/plumed/core/MDAtoms.h +include/plumed/core/PlumedMain.h +include/plumed/core/PlumedMainInitializer.h +include/plumed/core/SetupMolInfo.h +include/plumed/core/TargetDist.h +include/plumed/core/Value.h +include/plumed/core/WithCmd.h +include/plumed/function/ActionRegister.h +include/plumed/function/Function.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/GridSearch.h +include/plumed/gridtools/GridVessel.h +include/plumed/gridtools/HistogramOnGrid.h +include/plumed/isdb/MetainferenceBase.h +include/plumed/lapack/def_external.h +include/plumed/lapack/def_internal.h +include/plumed/lapack/lapack.h +include/plumed/lapack/lapack_limits.h +include/plumed/lapack/real.h +include/plumed/lepton/CompiledExpression.h +include/plumed/lepton/CustomFunction.h +include/plumed/lepton/Exception.h +include/plumed/lepton/ExpressionProgram.h +include/plumed/lepton/ExpressionTreeNode.h +include/plumed/lepton/Lepton.h +include/plumed/lepton/MSVC_erfc.h +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/molfile/Gromacs.h +include/plumed/molfile/endianswap.h +include/plumed/molfile/fastio.h +include/plumed/molfile/largefiles.h +include/plumed/molfile/libmolfile_plugin.h +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/secondarystructure/SecondaryStructureRMSD.h +include/plumed/setup/ActionSetup.h +include/plumed/tools/Angle.h +include/plumed/tools/AtomNumber.h +include/plumed/tools/BiasRepresentation.h +include/plumed/tools/Brent1DRootSearch.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 +include/plumed/tools/FileBase.h +include/plumed/tools/ForwardDecl.h +include/plumed/tools/Grid.h +include/plumed/tools/HistogramBead.h +include/plumed/tools/IFile.h +include/plumed/tools/KernelFunctions.h +include/plumed/tools/Keywords.h +include/plumed/tools/LatticeReduction.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/Minimise1DBrent.h +include/plumed/tools/MinimiseBase.h +include/plumed/tools/MolDataClass.h +include/plumed/tools/MultiValue.h +include/plumed/tools/NeighborList.h +include/plumed/tools/OFile.h +include/plumed/tools/OpenMP.h +include/plumed/tools/PDB.h +include/plumed/tools/Pbc.h +include/plumed/tools/PlumedHandle.h +include/plumed/tools/RMSD.h +include/plumed/tools/Random.h +include/plumed/tools/RootFindingBase.h +include/plumed/tools/Stopwatch.h +include/plumed/tools/Subprocess.h +include/plumed/tools/SwitchingFunction.h +include/plumed/tools/Tensor.h +include/plumed/tools/Tools.h +include/plumed/tools/Torsion.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 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