Index: head/science/Makefile =================================================================== --- head/science/Makefile (revision 480686) +++ head/science/Makefile (revision 480687) @@ -1,289 +1,290 @@ # $FreeBSD$ # 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 += atom SUBDIR += atompaw SUBDIR += avogadro + SUBDIR += bagel 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 += cp2k SUBDIR += crf++ SUBDIR += dalton SUBDIR += datawarrior SUBDIR += dcl SUBDIR += devisor SUBDIR += dft_tools SUBDIR += dftbplus SUBDIR += dkh SUBDIR += dlib-cpp SUBDIR += dlpoly-classic SUBDIR += eccodes SUBDIR += ecs SUBDIR += elk SUBDIR += epte SUBDIR += erd SUBDIR += fastcap SUBDIR += fasthenry SUBDIR += fisicalab SUBDIR += fleur 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 += jdftx SUBDIR += jstrack SUBDIR += kalzium SUBDIR += kalzium-kde4 SUBDIR += kst2 SUBDIR += lammps SUBDIR += lamprop 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 += liboglappth SUBDIR += libquantum SUBDIR += libssm SUBDIR += libsvm SUBDIR += libsvm-python SUBDIR += libxc SUBDIR += linsmith SUBDIR += lm SUBDIR += luscus SUBDIR += madness SUBDIR += massxpert SUBDIR += mbdyn SUBDIR += mcstas SUBDIR += mcstas-comps SUBDIR += mcxtrace SUBDIR += mcxtrace-comps SUBDIR += mdynamix SUBDIR += medit SUBDIR += meep SUBDIR += mei SUBDIR += metaf2xml SUBDIR += metaphysicl SUBDIR += minc2 SUBDIR += mmdb2 SUBDIR += mol2ps SUBDIR += mpb SUBDIR += mpqc SUBDIR += msms SUBDIR += multiwfn SUBDIR += namd SUBDIR += ncs SUBDIR += netcdf SUBDIR += netcdf-cxx SUBDIR += netcdf-fortran SUBDIR += nifticlib SUBDIR += nwchem SUBDIR += octopus SUBDIR += openbabel SUBDIR += openkim SUBDIR += openmx 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-PyFR SUBDIR += py-MDAnalysis SUBDIR += py-MDAnalysisTests SUBDIR += py-OpenFermion SUBDIR += py-PyQuante SUBDIR += py-ScientificPython SUBDIR += py-SimpleSpectral SUBDIR += py-abipy SUBDIR += py-ase SUBDIR += py-cdo SUBDIR += py-chempy SUBDIR += py-coards SUBDIR += py-dlib SUBDIR += py-gpaw SUBDIR += py-gsd SUBDIR += py-h5py SUBDIR += py-hcluster SUBDIR += py-kinematics SUBDIR += py-mdp SUBDIR += py-mlpy SUBDIR += py-mmtf-python SUBDIR += py-molmod SUBDIR += py-netCDF4 SUBDIR += py-obspy SUBDIR += py-openpiv SUBDIR += py-paida SUBDIR += py-phono3py SUBDIR += py-phonopy 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 += qbox 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 += siesta 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 += teem SUBDIR += tfel SUBDIR += triqs SUBDIR += udunits SUBDIR += v_sim SUBDIR += vmd SUBDIR += voro++ SUBDIR += wannier90 SUBDIR += xcrysden SUBDIR += xdrawchem SUBDIR += xfce4-equake-plugin SUBDIR += xmakemol .include Index: head/science/bagel/Makefile =================================================================== --- head/science/bagel/Makefile (nonexistent) +++ head/science/bagel/Makefile (revision 480687) @@ -0,0 +1,52 @@ +# $FreeBSD$ + +PORTNAME= bagel +DISTVERSIONPREFIX= v +DISTVERSION= 1.1.2-21 +DISTVERSIONSUFFIX= -g2a9472a50 +CATEGORIES= science +DIST_SUBDIR= ${PORTNAME}${PKGNAMESUFFIX} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Brilliantly Advanced General Electronic-structure Library + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/COPYING + +BROKEN_i386= error: static_assert failed "size_t is assumed to be the same size as unsigned long long" + +LIB_DEPENDS= libboost_serialization.so:devel/boost-libs \ + libcblas.so:math/cblas + +USES= autoreconf fortran gmake libtool localbase python:build +GNU_CONFIGURE= yes +CONFIGURE_ARGS= --datarootdir=${DATADIR} +USE_GITHUB= yes +GH_ACCOUNT= nubakery +USE_LDCONFIG= yes + +OPTIONS_DEFINE= MPI LIBXC SCALAPACK SMITH # SLATER (needs a separate lib) +OPTIONS_DEFAULT= MPI LIBXC SCALAPACK SMITH + +MPI_CONFIGURE_ON= --with-mpi=openmpi +MPI_CONFIGURE_OFF= --with-mpi=no +MPI_LIB_DEPENDS= libmpicxx.so:net/mpich # openmpi option erroneously links to mpich (due to a name clash) + +LIBXC_DESC= Build DFT with libxc +LIBXC_CONFIGURE_WITH= libxc +LIBXC_LIB_DEPENDS= libxc.so:science/libxc + +SCALAPACK_DESC= Use ScaLapack library for parallelized linear algebra +SCALAPACK_CONFIGURE_ENABLE= libxc +SCALAPACK_MAKE_ARGS= EXTRA_LIBS="-lcblas" +SCALAPACK_MAKE_ARGS_OFF= EXTRA_LIBS="-lcblas -llapack -lblas" # -llapack -lblas are a replacement of libscalapack +SCALAPACK_LIB_DEPENDS= libscalapack.so:math/scalapack +SCALAPACK_LIB_DEPENDS_OFF= liblapack.so:math/lapack \ + libblas.so:math/blas +SCALAPACK_IMPLIES= MPI + +SMITH_DESC= Compile SMITH generated code +SMITH_CONFIGURE_ENABLE= smith +SMITH_IMPLIES= MPI + +.include Property changes on: head/science/bagel/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/bagel/distinfo =================================================================== --- head/science/bagel/distinfo (nonexistent) +++ head/science/bagel/distinfo (revision 480687) @@ -0,0 +1,3 @@ +TIMESTAMP = 1537894347 +SHA256 (bagel/nubakery-bagel-v1.1.2-21-g2a9472a50_GH0.tar.gz) = 63829bd536de5d3e780eea84bc4e7d4b57bf21706509de3325db6697971dd084 +SIZE (bagel/nubakery-bagel-v1.1.2-21-g2a9472a50_GH0.tar.gz) = 41466284 Property changes on: head/science/bagel/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/bagel/files/patch-src_Makefile.am =================================================================== --- head/science/bagel/files/patch-src_Makefile.am (nonexistent) +++ head/science/bagel/files/patch-src_Makefile.am (revision 480687) @@ -0,0 +1,11 @@ +--- src/Makefile.am.orig 2018-09-25 05:30:51 UTC ++++ src/Makefile.am +@@ -1,7 +1,7 @@ + SUBDIRS = util molecule integral df opt grad pt2 wfn scf multi smith prop ci response asd mat1e basis + AM_CXXFLAGS=-I$(top_srcdir) + +-INTLIBS = opt/libbagel_opt.la multi/zcasscf/libbagel_zcasscf.la ci/zfci/libbagel_zfci.la ci/fci/libbagel_fci.la ci/ras/libbagel_ras.la response/libbagel_response.la scf/libbagel_scf.la multi/casscf/libbagel_casscf.la pt2/libbagel_pt2.la grad/libbagel_grad.la wfn/libbagel_wfn.la df/libbagel_df.la smith/libbagel_smith.la prop/libbagel_prop.la asd/libbagel_asd.la asd/dmrg/libbagel_asd_dmrg.la asd/orbital/libbagel_asd_orbital.la asd/dimer/libbagel_dimer.la asd/multisite/libbagel_multisite.la ci/ciutil/libbagel_ciutil.la mat1e/libbagel_mat1e.la integral/libbagel_integral.la molecule/libbagel_molecule.la util/io/libbagel_io.la util/libbagel_util.la util/parallel/libbagel_parallel.la util/math/libbagel_math.la util/input/libbagel_input.la ++INTLIBS = opt/libbagel_opt.la multi/zcasscf/libbagel_zcasscf.la ci/zfci/libbagel_zfci.la ci/fci/libbagel_fci.la ci/ras/libbagel_ras.la response/libbagel_response.la scf/libbagel_scf.la multi/casscf/libbagel_casscf.la pt2/libbagel_pt2.la grad/libbagel_grad.la wfn/libbagel_wfn.la df/libbagel_df.la smith/libbagel_smith.la prop/libbagel_prop.la asd/libbagel_asd.la asd/dmrg/libbagel_asd_dmrg.la asd/orbital/libbagel_asd_orbital.la asd/dimer/libbagel_dimer.la asd/multisite/libbagel_multisite.la ci/ciutil/libbagel_ciutil.la mat1e/libbagel_mat1e.la integral/libbagel_integral.la molecule/libbagel_molecule.la util/io/libbagel_io.la util/libbagel_util.la util/parallel/libbagel_parallel.la util/math/libbagel_math.la util/input/libbagel_input.la $(EXTRA_LIBS) + + lib_LTLIBRARIES = libbagel.la + libbagel_la_SOURCES = run_bagel.cc static.cc Property changes on: head/science/bagel/files/patch-src_Makefile.am ___________________________________________________________________ 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/bagel/pkg-descr =================================================================== --- head/science/bagel/pkg-descr (nonexistent) +++ head/science/bagel/pkg-descr (revision 480687) @@ -0,0 +1,7 @@ +BAGEL is a parallel electronic-structure program licensed under the GNU General +Public License. + +BAGEL is intended for use by researchers performing quantum chemistry +computations. + +WWW: https://nubakery.org/ Property changes on: head/science/bagel/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/bagel/pkg-plist =================================================================== --- head/science/bagel/pkg-plist (nonexistent) +++ head/science/bagel/pkg-plist (revision 480687) @@ -0,0 +1,63 @@ +bin/BAGEL +include/bagel.h +lib/libbagel.so +lib/libbagel.so.0 +lib/libbagel.so.0.0.0 +%%DATADIR%%/3-21g.json +%%DATADIR%%/6-31g.json +%%DATADIR%%/ano-rcc.json +%%DATADIR%%/aug-cc-pcv5z.json +%%DATADIR%%/aug-cc-pcvdz-dk.json +%%DATADIR%%/aug-cc-pcvdz.json +%%DATADIR%%/aug-cc-pcvqz-dk.json +%%DATADIR%%/aug-cc-pcvqz.json +%%DATADIR%%/aug-cc-pcvtz-dk.json +%%DATADIR%%/aug-cc-pcvtz.json +%%DATADIR%%/aug-cc-pv5z.json +%%DATADIR%%/aug-cc-pv6z.json +%%DATADIR%%/aug-cc-pvdz.json +%%DATADIR%%/aug-cc-pvqz.json +%%DATADIR%%/aug-cc-pvtz.json +%%DATADIR%%/aug-cc-pwcv5z.json +%%DATADIR%%/aug-cc-pwcvdz.json +%%DATADIR%%/aug-cc-pwcvqz.json +%%DATADIR%%/aug-cc-pwcvtz.json +%%DATADIR%%/cc-pcv5z.json +%%DATADIR%%/cc-pcvdz.json +%%DATADIR%%/cc-pcvqz.json +%%DATADIR%%/cc-pcvtz.json +%%DATADIR%%/cc-pv5z-jkfit.json +%%DATADIR%%/cc-pv5z-ri.json +%%DATADIR%%/cc-pv5z.json +%%DATADIR%%/cc-pv6z.json +%%DATADIR%%/cc-pvdz-dk.json +%%DATADIR%%/cc-pvdz-jkfit.json +%%DATADIR%%/cc-pvdz-ri.json +%%DATADIR%%/cc-pvdz.json +%%DATADIR%%/cc-pvqz-jkfit.json +%%DATADIR%%/cc-pvqz-ri.json +%%DATADIR%%/cc-pvqz.json +%%DATADIR%%/cc-pvtz-dk.json +%%DATADIR%%/cc-pvtz-jkfit.json +%%DATADIR%%/cc-pvtz-ri.json +%%DATADIR%%/cc-pvtz.json +%%DATADIR%%/complete.json +%%DATADIR%%/d-aug-cc-pv5z.json +%%DATADIR%%/d-aug-cc-pvdz.json +%%DATADIR%%/d-aug-cc-pvqz.json +%%DATADIR%%/d-aug-cc-pvtz.json +%%DATADIR%%/def2-SVP-2c-ecp.json +%%DATADIR%%/def2-SVP-ecp.json +%%DATADIR%%/ecp10mdf.json +%%DATADIR%%/ecp28mdf.json +%%DATADIR%%/ecp46mdf.json +%%DATADIR%%/ecp60mdf.json +%%DATADIR%%/ecp78mdf.json +%%DATADIR%%/lanl2dz-ecp.json +%%DATADIR%%/qzvpp-jkfit.json +%%DATADIR%%/qzvpp.json +%%DATADIR%%/sto-3g.json +%%DATADIR%%/svp-jkfit.json +%%DATADIR%%/svp.json +%%DATADIR%%/tzvpp-jkfit.json +%%DATADIR%%/tzvpp.json Property changes on: head/science/bagel/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