[pkgsrc/trunk]: pkgsrc/math math/plumed: added package for the MD algorithm l...

[thor <thor%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/9e660f0f1267
branches:  trunk
changeset: 381538:9e660f0f1267
user:      thor <thor%pkgsrc.org@localhost>
date:      Fri Jul 08 19:47:59 2022 +0000

description:
math/plumed: added package for the MD algorithm library

diffstat:

 math/Makefile                              |     3 +-
 math/plumed/DESCR                          |     9 +
 math/plumed/Makefile                       |    42 +
 math/plumed/PLIST                          |   530 ++++++++++++++
 math/plumed/distinfo                       |     8 +
 math/plumed/options.mk                     |    17 +
 math/plumed/patches/patch-Makefile.conf.in |    17 +
 math/plumed/patches/patch-configure        |  1016 ++++++++++++++++++++++++++++
 math/plumed/patches/patch-configure.ac     |   588 ++++++++++++++++
 9 files changed, 2229 insertions(+), 1 deletions(-)

diffs (truncated from 2276 to 300 lines):

diff -r 4db42a05d239 -r 9e660f0f1267 math/Makefile
--- a/math/Makefile     Fri Jul 08 18:10:54 2022 +0000
+++ b/math/Makefile     Fri Jul 08 19:47:59 2022 +0000
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.546 2022/06/12 14:35:53 bacon Exp $
+# $NetBSD: Makefile,v 1.547 2022/07/08 19:47:59 thor Exp $
 
 COMMENT=       Mathematics
 
@@ -362,6 +362,7 @@
 SUBDIR+=       pear-Numbers_Words
 SUBDIR+=       php-bcmath
 SUBDIR+=       php-stats
+SUBDIR+=       plumed
 SUBDIR+=       ppl
 SUBDIR+=       prng
 SUBDIR+=       pspp
diff -r 4db42a05d239 -r 9e660f0f1267 math/plumed/DESCR
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/math/plumed/DESCR Fri Jul 08 19:47:59 2022 +0000
@@ -0,0 +1,9 @@
+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.
+
+These techniques can be used in combination with a large toolbox
+of collective variables that describe complex processes in physics,
+chemistry, material science, and biology.
diff -r 4db42a05d239 -r 9e660f0f1267 math/plumed/Makefile
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/math/plumed/Makefile      Fri Jul 08 19:47:59 2022 +0000
@@ -0,0 +1,42 @@
+# $NetBSD: Makefile,v 1.1 2022/07/08 19:47:59 thor Exp $
+
+DISTNAME=      plumed-2.8.0
+CATEGORIES=    math
+MASTER_SITES=  ${MASTER_SITE_GITHUB:=plumed/plumed2/releases/download/v2.8.0/}
+EXTRACT_SUFX=  .tgz
+
+MAINTAINER=    thor%NetBSD.org@localhost
+HOMEPAGE=      https://www.plumed.org/
+COMMENT=       Molecular dynamics support library
+LICENSE=       gnu-lgpl-v3
+
+GNU_CONFIGURE= yes
+USE_LANGUAGES= c c++ fortran
+USE_TOOLS+=    gmake bash
+
+TEST_TARGET=   check
+
+CONFIGURE_ARGS+=       --enable-gsl
+CONFIGURE_ARGS+=       --enable-external-blas --enable-external-lapack
+CONFIGURE_ARGS+=       LIBS='${LAPACK_LIBS}'
+CONFIGURE_ARGS+=       LIBRARY_PATH='${LIBRARY_PATH}:${PREFIX}/lib'
+CONFIGURE_ARGS+=       --enable-rpath
+# Python module should be a separate package, I suppose.
+# it is a versioned .so file, so differing pythons might coexist.
+CONFIGURE_ARGS+=       --disable-python
+
+SUBST_CLASSES+=                envbash
+SUBST_STAGE.envbash=   pre-configure
+SUBST_FILES.envbash=   src/lib/Makefile
+SUBST_SED.envbash=     -e 's,/usr/bin/env bash,${BASH},'
+
+REPLACE_BASH+= scripts/*.sh patches/*.sh
+
+.include "options.mk"
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/blas.buildlink3.mk"
+.include "../../math/fftw/buildlink3.mk"
+.include "../../math/gsl/buildlink3.mk"
+
+.include "../../mk/bsd.pkg.mk"
diff -r 4db42a05d239 -r 9e660f0f1267 math/plumed/PLIST
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/math/plumed/PLIST Fri Jul 08 19:47:59 2022 +0000
@@ -0,0 +1,530 @@
+@comment $NetBSD: PLIST,v 1.1 2022/07/08 19:47:59 thor Exp $
+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/GenericMolInfo.h
+include/plumed/core/MDAtoms.h
+include/plumed/core/PlumedMain.h
+include/plumed/core/PlumedMainInitializer.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/Tree.h
+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