Index: head/science/Makefile =================================================================== --- head/science/Makefile (revision 478179) +++ head/science/Makefile (revision 478180) @@ -1,262 +1,263 @@ # $FreeBSD$ # COMMENT = Scientific ports SUBDIR += 2d-rewriter SUBDIR += ALPSCore SUBDIR += InsightToolkit SUBDIR += MOOSE-neural-simulator SUBDIR += PETSc SUBDIR += R-cran-AMORE SUBDIR += R-cran-DCluster SUBDIR += R-cran-Epi 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 += aircraft-datcom SUBDIR += antioch SUBDIR += atompaw SUBDIR += avogadro SUBDIR += bddsolve SUBDIR += bft SUBDIR += bodr SUBDIR += brian SUBDIR += buddy SUBDIR += cdcl SUBDIR += cdf 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 += colt SUBDIR += coot SUBDIR += crf++ SUBDIR += datawarrior SUBDIR += dcl SUBDIR += devisor SUBDIR += dft_tools SUBDIR += dkh SUBDIR += dlib-cpp SUBDIR += dlpoly-classic SUBDIR += eccodes SUBDIR += ecs SUBDIR += epte SUBDIR += erd SUBDIR += fastcap SUBDIR += fasthenry SUBDIR += fisicalab SUBDIR += fsom SUBDIR += fvcom SUBDIR += fvcom-mpi SUBDIR += fvm SUBDIR += gabedit SUBDIR += gchemutils SUBDIR += gdma SUBDIR += getdp SUBDIR += ghemical SUBDIR += ghmm SUBDIR += gnudatalanguage SUBDIR += gramps SUBDIR += grib_api SUBDIR += gromacs SUBDIR += gsmc SUBDIR += gtamsanalyzer SUBDIR += gwyddion SUBDIR += h5utils SUBDIR += harminv SUBDIR += hdf SUBDIR += hdf5 SUBDIR += hdf5-18 SUBDIR += hypre SUBDIR += iboview SUBDIR += isaac-cfd SUBDIR += jstrack SUBDIR += kalzium SUBDIR += kalzium-kde4 SUBDIR += kst2 SUBDIR += lamprop SUBDIR += libaec SUBDIR += libccp4 SUBDIR += libcint SUBDIR += libctl SUBDIR += libefp SUBDIR += libgeodecomp SUBDIR += libghemical SUBDIR += libint SUBDIR += libkml SUBDIR += liblinear SUBDIR += liboglappth SUBDIR += libquantum SUBDIR += libssm SUBDIR += libsvm SUBDIR += libsvm-python SUBDIR += libxc SUBDIR += linsmith + SUBDIR += madness SUBDIR += massxpert SUBDIR += mbdyn SUBDIR += mcstas SUBDIR += mcstas-comps SUBDIR += mcxtrace SUBDIR += mcxtrace-comps SUBDIR += medit SUBDIR += meep SUBDIR += mei SUBDIR += metaf2xml SUBDIR += metaphysicl SUBDIR += minc2 SUBDIR += mmdb2 SUBDIR += mol2ps SUBDIR += mpb SUBDIR += mpqc SUBDIR += mpqc-mpich SUBDIR += multiwfn SUBDIR += ncs SUBDIR += netcdf SUBDIR += netcdf-cxx SUBDIR += netcdf-fortran SUBDIR += nifticlib SUBDIR += nwchem SUBDIR += octopus SUBDIR += openbabel SUBDIR += openkim SUBDIR += openstructure 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 += paje SUBDIR += paraview SUBDIR += pcmsolver SUBDIR += pnetcdf SUBDIR += psychopy SUBDIR += pulseview SUBDIR += py-DendroPy SUBDIR += py-MDAnalysis SUBDIR += py-MDAnalysisTests SUBDIR += py-OpenFermion SUBDIR += py-PyQuante SUBDIR += py-ScientificPython SUBDIR += py-SimpleSpectral SUBDIR += py-abipy SUBDIR += py-cdo SUBDIR += py-coards SUBDIR += py-dlib SUBDIR += py-gsd SUBDIR += py-h5py SUBDIR += py-hcluster SUBDIR += py-kinematics SUBDIR += py-mdp SUBDIR += py-mlpy SUBDIR += py-mmtf-python SUBDIR += py-netCDF4 SUBDIR += py-obspy SUBDIR += py-openpiv SUBDIR += py-paida SUBDIR += py-pupynere SUBDIR += py-pyaixi SUBDIR += py-pydicom SUBDIR += py-pymatgen SUBDIR += py-pymol SUBDIR += py-pyosf SUBDIR += py-pysal SUBDIR += py-pyteomics SUBDIR += py-pyteomics.biolccc SUBDIR += py-qspin SUBDIR += py-quantities SUBDIR += py-rmf SUBDIR += py-scikit-fuzzy SUBDIR += py-scikit-learn SUBDIR += py-scikit-sparse SUBDIR += py-scimath SUBDIR += py-scipy SUBDIR += py-scoria SUBDIR += py-spglib SUBDIR += py-veusz SUBDIR += py-ws2300 SUBDIR += pybrain SUBDIR += pycdf SUBDIR += pynn SUBDIR += qcl SUBDIR += qmcpack SUBDIR += qtresistors SUBDIR += quantum-espresso 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 += sigrok-cli SUBDIR += sigrok-firmware SUBDIR += sigrok-firmware-fx2lafw SUBDIR += sigrok-firmware-utils SUBDIR += silo SUBDIR += simlib SUBDIR += simsmith SUBDIR += spglib SUBDIR += step SUBDIR += step-kde4 SUBDIR += svmlight SUBDIR += szip SUBDIR += tfel SUBDIR += triqs SUBDIR += udunits SUBDIR += v_sim SUBDIR += vmd SUBDIR += voro++ SUBDIR += xcrysden SUBDIR += xdrawchem SUBDIR += xfce4-equake-plugin SUBDIR += xmakemol .include Index: head/science/madness/Makefile =================================================================== --- head/science/madness/Makefile (nonexistent) +++ head/science/madness/Makefile (revision 478180) @@ -0,0 +1,29 @@ +# $FreeBSD$ + +PORTNAME= madness +DISTVERSION= 0.10.1.20180823 +CATEGORIES= science + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Multiresolution adaptive numeric environment for scientific simulation + +LICENSE= GPLv2 +LICENSE_FILE= ${WRKSRC}/LICENSE + +BUILD_DEPENDS= libsysinfo>0:devel/libsysinfo +LIB_DEPENDS= libblas.so:math/blas \ + liblapack.so:math/lapack \ + libmpich.so:net/mpich2 \ + libtbb.so:devel/tbb \ + libtcmalloc.so:devel/google-perftools \ + libxc.so:science/libxc + +USES= cmake:outsource compiler:c++14-lang fortran localbase:ldflags +USE_GITHUB= yes +GH_ACCOUNT= m-a-d-n-e-s-s +GH_TAGNAME= ebb3fd7 +USE_LDCONFIG= yes + +CMAKE_ARGS= -DLAPACK_LIBRARIES:STRING="-L${LOCALBASE}/lib -llapack -lblas -L${LOCALBASE}/lib/gcc${GCC_DEFAULT} -lgcc_s" + +.include Property changes on: head/science/madness/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/madness/distinfo =================================================================== --- head/science/madness/distinfo (nonexistent) +++ head/science/madness/distinfo (revision 478180) @@ -0,0 +1,3 @@ +TIMESTAMP = 1535353560 +SHA256 (m-a-d-n-e-s-s-madness-0.10.1.20180823-ebb3fd7_GH0.tar.gz) = fe1901c335dfcff9323f6a6fde528a5a10998c21d3c21d727040ece2ffb55118 +SIZE (m-a-d-n-e-s-s-madness-0.10.1.20180823-ebb3fd7_GH0.tar.gz) = 6829265 Property changes on: head/science/madness/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/madness/files/patch-src_CMakeLists.txt =================================================================== --- head/science/madness/files/patch-src_CMakeLists.txt (nonexistent) +++ head/science/madness/files/patch-src_CMakeLists.txt (revision 478180) @@ -0,0 +1,11 @@ +--- src/CMakeLists.txt.orig 2018-08-27 06:57:22 UTC ++++ src/CMakeLists.txt +@@ -2,7 +2,7 @@ + + add_subdirectory(madness) + add_subdirectory(apps) +-add_subdirectory(examples) ++#add_subdirectory(examples) + + install(FILES madness.h + DESTINATION "${MADNESS_INSTALL_INCLUDEDIR}" Property changes on: head/science/madness/files/patch-src_CMakeLists.txt ___________________________________________________________________ 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/madness/files/patch-src_madness_world_thread.cc =================================================================== --- head/science/madness/files/patch-src_madness_world_thread.cc (nonexistent) +++ head/science/madness/files/patch-src_madness_world_thread.cc (revision 478180) @@ -0,0 +1,22 @@ +--- src/madness/world/thread.cc.orig 2018-08-24 00:32:22 UTC ++++ src/madness/world/thread.cc +@@ -44,6 +44,8 @@ + #include + #include + #include ++#include ++#include + + #if defined(HAVE_IBMBGQ) and defined(HPM) + extern "C" unsigned int HPM_Prof_init_thread(void); +@@ -248,8 +250,8 @@ namespace madness { + } + } + +-#ifndef ON_A_MAC +- cpu_set_t mask; ++#if !defined(ON_A_MAC) && !defined(__FreeBSD__) // need to port to FreeBSD ++ cpuset_t mask; + CPU_ZERO(&mask); + for (int i=lo; i<=hi; ++i) CPU_SET(i,&mask); + if (sched_setaffinity(0, sizeof(mask), &mask) == -1) { Property changes on: head/science/madness/files/patch-src_madness_world_thread.cc ___________________________________________________________________ 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/madness/files/patch-src_madness_world_worldmem.h =================================================================== --- head/science/madness/files/patch-src_madness_world_worldmem.h (nonexistent) +++ head/science/madness/files/patch-src_madness_world_worldmem.h (revision 478180) @@ -0,0 +1,11 @@ +--- src/madness/world/worldmem.h.orig 2018-08-27 07:36:33 UTC ++++ src/madness/world/worldmem.h +@@ -49,7 +49,7 @@ + #elif defined(ON_A_MAC) + #include + #elif defined(X86_32) +-#include ++#include + #elif defined(X86_64) + #include + #include Property changes on: head/science/madness/files/patch-src_madness_world_worldmem.h ___________________________________________________________________ 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/madness/pkg-descr =================================================================== --- head/science/madness/pkg-descr (nonexistent) +++ head/science/madness/pkg-descr (revision 478180) @@ -0,0 +1,14 @@ +MADNESS provides a high-level environment for the solution of integral and +differential equations in many dimensions using adaptive, fast methods with +guaranteed precision based on multi-resolution analysis and novel separated +representations. There are three main components to MADNESS. At the lowest +level is a new petascale parallel programming environment that increases +programmer productivity and code performance/scalability while maintaining +backward compatibility with current programming tools such as MPI and Global +Arrays. The numerical capabilities built upon the parallel tools provide a +high-level environment for composing and solving numerical problems in many +(1-6+) dimensions. Finally, built upon the numerical tools are new applications +with initial focus upon chemistry, atomic and molecular physics, material +science, and nuclear structure. + +WWW: https://github.com/m-a-d-n-e-s-s/madness Property changes on: head/science/madness/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/madness/pkg-plist =================================================================== --- head/science/madness/pkg-plist (nonexistent) +++ head/science/madness/pkg-plist (revision 478180) @@ -0,0 +1,190 @@ +bin/mcpfit +bin/moldft +bin/mraplot +bin/tdse +bin/tdse4 +include/chem/AC.h +include/chem/CC2.h +include/chem/CCPotentials.h +include/chem/CCStructures.h +include/chem/CalculationParameters.h +include/chem/SCF.h +include/chem/SCFOperators.h +include/chem/SCFProtocol.h +include/chem/TDHF.h +include/chem/atomutil.h +include/chem/cheminfo.h +include/chem/corepotential.h +include/chem/correlationfactor.h +include/chem/electronic_correlation_factor.h +include/chem/gth_pseudopotential.h +include/chem/molecular_optimizer.h +include/chem/molecularbasis.h +include/chem/molecule.h +include/chem/molopt.h +include/chem/mp2.h +include/chem/nemo.h +include/chem/pcm.h +include/chem/potentialmanager.h +include/chem/projector.h +include/chem/vibanal.h +include/chem/xcfunctional.h +include/madness.h +include/madness/config.h +include/madness/constants.h +include/madness/external/muParser/muParser.h +include/madness/external/muParser/muParserBase.h +include/madness/external/muParser/muParserBytecode.h +include/madness/external/muParser/muParserCallback.h +include/madness/external/muParser/muParserDLL.h +include/madness/external/muParser/muParserDef.h +include/madness/external/muParser/muParserError.h +include/madness/external/muParser/muParserFixes.h +include/madness/external/muParser/muParserInt.h +include/madness/external/muParser/muParserStack.h +include/madness/external/muParser/muParserTest.h +include/madness/external/muParser/muParserToken.h +include/madness/external/muParser/muParserTokenReader.h +include/madness/external/tinyxml/tinystr.h +include/madness/external/tinyxml/tinyxml.h +include/madness/fortran_ctypes.h +include/madness/madness_config.h +include/madness/misc/cfft.h +include/madness/misc/interpolation_1d.h +include/madness/misc/misc.h +include/madness/misc/phandler.h +include/madness/misc/ran.h +include/madness/mra/adquad.h +include/madness/mra/convolution1d.h +include/madness/mra/derivative.h +include/madness/mra/displacements.h +include/madness/mra/funcdefaults.h +include/madness/mra/funcimpl.h +include/madness/mra/funcplot.h +include/madness/mra/function_common_data.h +include/madness/mra/function_factory.h +include/madness/mra/function_interface.h +include/madness/mra/functypedefs.h +include/madness/mra/gfit.h +include/madness/mra/indexit.h +include/madness/mra/key.h +include/madness/mra/lbdeux.h +include/madness/mra/leafop.h +include/madness/mra/legendre.h +include/madness/mra/mra.h +include/madness/mra/mraimpl.h +include/madness/mra/nonlinsol.h +include/madness/mra/operator.h +include/madness/mra/power.h +include/madness/mra/qmprop.h +include/madness/mra/sdf_domainmask.h +include/madness/mra/sdf_shape_3D.h +include/madness/mra/simplecache.h +include/madness/mra/twoscale.h +include/madness/mra/vmra.h +include/madness/mra/vmra1.h +include/madness/tensor/aligned.h +include/madness/tensor/basetensor.h +include/madness/tensor/cblas.h +include/madness/tensor/clapack.h +include/madness/tensor/clapack_fortran.h +include/madness/tensor/distributed_matrix.h +include/madness/tensor/elem.h +include/madness/tensor/gentensor.h +include/madness/tensor/mxm.h +include/madness/tensor/slice.h +include/madness/tensor/solvers.h +include/madness/tensor/srconf.h +include/madness/tensor/systolic.h +include/madness/tensor/tensor.h +include/madness/tensor/tensor_lapack.h +include/madness/tensor/tensor_macros.h +include/madness/tensor/tensor_spec.h +include/madness/tensor/tensorexcept.h +include/madness/tensor/tensoriter.h +include/madness/tensor/tensoriter_spec.h +include/madness/tensor/tensortrain.h +include/madness/tensor/type_data.h +include/madness/tensor/vector_factory.h +include/madness/tensor/vmath.h +include/madness/world/MADworld.h +include/madness/world/archive.h +include/madness/world/array_addons.h +include/madness/world/atomicint.h +include/madness/world/bgq_atomics.h +include/madness/world/binary_fstream_archive.h +include/madness/world/binsorter.h +include/madness/world/buffer_archive.h +include/madness/world/deferred_cleanup.h +include/madness/world/dependency_interface.h +include/madness/world/dist_cache.h +include/madness/world/distributed_id.h +include/madness/world/dqueue.h +include/madness/world/function_traits.h +include/madness/world/future.h +include/madness/world/group.h +include/madness/world/info.h +include/madness/world/madness_exception.h +include/madness/world/mem_func_wrapper.h +include/madness/world/meta.h +include/madness/world/mpi_archive.h +include/madness/world/nodefaults.h +include/madness/world/parallel_archive.h +include/madness/world/parsec.h +include/madness/world/posixmem.h +include/madness/world/print.h +include/madness/world/print_seq.h +include/madness/world/range.h +include/madness/world/safempi.h +include/madness/world/stack.h +include/madness/world/stubmpi.h +include/madness/world/taskfn.h +include/madness/world/text_fstream_archive.h +include/madness/world/thread.h +include/madness/world/timers.h +include/madness/world/type_traits.h +include/madness/world/uniqueid.h +include/madness/world/vector.h +include/madness/world/vector_archive.h +include/madness/world/world.h +include/madness/world/world_object.h +include/madness/world/world_task_queue.h +include/madness/world/worldam.h +include/madness/world/worlddc.h +include/madness/world/worldgop.h +include/madness/world/worldhash.h +include/madness/world/worldhashmap.h +include/madness/world/worldmem.h +include/madness/world/worldmpi.h +include/madness/world/worldmutex.h +include/madness/world/worldpapi.h +include/madness/world/worldprofile.h +include/madness/world/worldptr.h +include/madness/world/worldref.h +include/madness/world/worldrmi.h +include/madness/world/worldtypes.h +lib/cmake/madness/madness-config-version.cmake +lib/cmake/madness/madness-config.cmake +lib/cmake/madness/madness-targets-%%CMAKE_BUILD_TYPE%%.cmake +lib/cmake/madness/madness-targets.cmake +lib/cmake/madness/madworld-targets-%%CMAKE_BUILD_TYPE%%.cmake +lib/cmake/madness/madworld-targets.cmake +lib/libMADchem.so +lib/libMADlinalg.so +lib/libMADmisc.so +lib/libMADmra.so +lib/libMADmuparser.so +lib/libMADtensor.so +lib/libMADtinyxml.so +lib/libMADworld.so +lib/libmadness.so +libdata/pkgconfig/MADNESS.pc +%%DATADIR%%/0.10.1/data/6-31g +%%DATADIR%%/0.10.1/data/autocorr +%%DATADIR%%/0.10.1/data/coeffs +%%DATADIR%%/0.10.1/data/gaussleg +%%DATADIR%%/0.10.1/data/mcp +%%DATADIR%%/0.10.1/data/mcp2 +%%DATADIR%%/0.10.1/data/mcp_guess +%%DATADIR%%/0.10.1/data/sto-3g +%%DATADIR%%/0.10.1/data/sto-6g Property changes on: head/science/madness/pkg-plist ___________________________________________________________________ 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