Index: head/science/Makefile =================================================================== --- head/science/Makefile (revision 467682) +++ head/science/Makefile (revision 467683) @@ -1,228 +1,229 @@ # $FreeBSD$ # 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 += afni SUBDIR += aircraft-datcom + SUBDIR += antioch 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 += clhep SUBDIR += colt SUBDIR += crf++ SUBDIR += dcl SUBDIR += devisor SUBDIR += dkh SUBDIR += dlpoly-classic SUBDIR += ecs SUBDIR += epte SUBDIR += erd SUBDIR += fastcap SUBDIR += fasthenry SUBDIR += fisicalab SUBDIR += fsom SUBDIR += fvcom SUBDIR += fvcom-mpi SUBDIR += fvm 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 += hs-bio SUBDIR += hypre SUBDIR += iboview SUBDIR += isaac-cfd SUBDIR += jstrack SUBDIR += kalzium SUBDIR += kalzium-kde4 SUBDIR += kst2 SUBDIR += lamprop SUBDIR += libaec SUBDIR += libcint SUBDIR += libctl SUBDIR += libefp SUBDIR += libgeodecomp SUBDIR += libghemical SUBDIR += libint SUBDIR += libkml SUBDIR += liblinear SUBDIR += liboglappth SUBDIR += libquantum SUBDIR += libsvm SUBDIR += libsvm-python SUBDIR += libxc SUBDIR += linsmith SUBDIR += massxpert SUBDIR += mbdyn SUBDIR += mcstas SUBDIR += mcstas-comps SUBDIR += mcxtrace SUBDIR += medit SUBDIR += meep SUBDIR += mei SUBDIR += metaf2xml SUBDIR += metaphysicl SUBDIR += minc2 SUBDIR += mol2ps SUBDIR += mpb SUBDIR += mpqc SUBDIR += mpqc-mpich SUBDIR += ncs SUBDIR += netcdf SUBDIR += netcdf-cxx SUBDIR += netcdf-fortran SUBDIR += nifticlib SUBDIR += openbabel SUBDIR += openkim SUBDIR += orthanc SUBDIR += orthanc-dicomweb SUBDIR += orthanc-postgresql SUBDIR += orthanc-webviewer 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-OpenFermion SUBDIR += py-cdo SUBDIR += py-coards SUBDIR += py-h5py SUBDIR += py-hcluster SUBDIR += py-mdp SUBDIR += py-mlpy SUBDIR += py-netCDF4 SUBDIR += py-obspy SUBDIR += py-openpiv SUBDIR += py-paida SUBDIR += py-pupynere SUBDIR += py-pyaixi SUBDIR += py-pydicom SUBDIR += py-pymol SUBDIR += py-pyosf SUBDIR += py-pysal SUBDIR += py-pyteomics SUBDIR += py-pyteomics.biolccc SUBDIR += py-qspin SUBDIR += py-quantities SUBDIR += py-scikit-fuzzy SUBDIR += py-scikit-learn SUBDIR += py-scikit-sparse SUBDIR += py-scimath SUBDIR += py-scipy SUBDIR += py-scoria SUBDIR += py-tensorflow SUBDIR += py-veusz SUBDIR += py-ws2300 SUBDIR += pybrain SUBDIR += pycdf SUBDIR += pynn SUBDIR += qcl SUBDIR += qtresistors SUBDIR += rdkit 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 += step SUBDIR += step-kde4 SUBDIR += svmlight SUBDIR += szip SUBDIR += tfel SUBDIR += udunits SUBDIR += v_sim SUBDIR += vmd SUBDIR += voro++ SUBDIR += xfce4-equake-plugin SUBDIR += xmakemol .include Index: head/science/antioch/Makefile =================================================================== --- head/science/antioch/Makefile (nonexistent) +++ head/science/antioch/Makefile (revision 467683) @@ -0,0 +1,36 @@ +# $FreeBSD$ + +PORTNAME= antioch +DISTVERSIONPREFIX= v +DISTVERSION= 0.4.0-156 +DISTVERSIONSUFFIX= -g90ffa43 +CATEGORIES= science + +MAINTAINER= yuri@FreeBSD.org +COMMENT= C++ Chemical Kinetics, Thermodynaimics, and Transport Library + +LICENSE= LGPL21 +LICENSE_FILE= ${WRKSRC}/COPYING + +BUILD_DEPENDS= ${LOCALBASE}/include/metaphysicl/metaphysicl_version.h:science/metaphysicl \ + ${LOCALBASE}/include/viennacl/vector.hpp:math/viennacl +LIB_DEPENDS= libgsl.so:math/gsl \ + libOpenCL.so:devel/ocl-icd + +USES= autoreconf eigen:3 gmake libtool localbase +USE_GITHUB= yes +GH_ACCOUNT= libantioch +GNU_CONFIGURE= yes +USE_LDCONFIG= yes + +CONFIGURE_ARGS= --disable-static \ + --enable-eigen --with-eigen-include=${LOCALBASE}/include/eigen3 \ + --enable-opencl \ + --with-metaphysicl=${LOCALBASE} \ + --with-viennacl=${LOCALBASE}/include \ + --with-gsl=${LOCALBASE} + +post-install: + @${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/libantioch.so.0.0.0 + +.include Property changes on: head/science/antioch/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/antioch/distinfo =================================================================== --- head/science/antioch/distinfo (nonexistent) +++ head/science/antioch/distinfo (revision 467683) @@ -0,0 +1,3 @@ +TIMESTAMP = 1524017800 +SHA256 (libantioch-antioch-v0.4.0-156-g90ffa43_GH0.tar.gz) = 22fe4d70fbc9c9abe3f5a0dcca9ea4e7f78d0b3ebf2b1af08a68bafcda0d43ff +SIZE (libantioch-antioch-v0.4.0-156-g90ffa43_GH0.tar.gz) = 767056 Property changes on: head/science/antioch/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/antioch/files/patch-Makefile.am =================================================================== --- head/science/antioch/files/patch-Makefile.am (nonexistent) +++ head/science/antioch/files/patch-Makefile.am (revision 467683) @@ -0,0 +1,11 @@ +--- Makefile.am.orig 2018-04-18 06:06:18 UTC ++++ Makefile.am +@@ -4,7 +4,7 @@ include $(top_srcdir)/doxygen/aminclude. + AUTOMAKE_OPTIONS = foreign + ACLOCAL_AMFLAGS = -I m4 -I m4/common + +-SUBDIRS = src test doxygen share examples ++SUBDIRS = src test doxygen share + EXTRA_DIST = CHANGES LICENSE COPYING share + + # Eliminate .svn directories in dist tarball Property changes on: head/science/antioch/files/patch-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/antioch/files/patch-configure.ac =================================================================== --- head/science/antioch/files/patch-configure.ac (nonexistent) +++ head/science/antioch/files/patch-configure.ac (revision 467683) @@ -0,0 +1,13 @@ +--- configure.ac.orig 2018-04-18 05:44:31 UTC ++++ configure.ac +@@ -265,8 +265,8 @@ AC_SUBST(ANTIOCH_STAMPED_FILES) + # to make it $datadir/antioch_default_files + # then we define the default files + # Need to make sure to have the `/` at the end +-ANTIOCH_DEFAULT_FILES_SOURCE_PATH_TMP=$TOP_SEARCH_DIR/share/antioch_default_files/ +-ANTIOCH_DEFAULT_FILES_INSTALL_PATH_TMP=$prefix/share/antioch_default_files/ ++ANTIOCH_DEFAULT_FILES_SOURCE_PATH_TMP=$TOP_SEARCH_DIR/share/antioch/default_files/ ++ANTIOCH_DEFAULT_FILES_INSTALL_PATH_TMP=$prefix/share/antioch/default_files/ + ANTIOCH_SHARE_XML_INPUT_FILES_SOURCE_PATH_TMP=$TOP_SEARCH_DIR/share/xml_inputs/ + ANTIOCH_SHARE_XML_INPUT_FILES_INSTALL_PATH_TMP=$prefix/share/xml_inputs/ + ANTIOCH_TESTING_INPUT_FILES_PATH_TMP=$TOP_SEARCH_DIR/test/input_files/ Property changes on: head/science/antioch/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/antioch/files/patch-share_Makefile.am =================================================================== --- head/science/antioch/files/patch-share_Makefile.am (nonexistent) +++ head/science/antioch/files/patch-share_Makefile.am (revision 467683) @@ -0,0 +1,15 @@ +--- share/Makefile.am.orig 2018-04-13 14:56:50 UTC ++++ share/Makefile.am +@@ -1,10 +1,10 @@ + aclocaldir = $(prefix)/share/aclocal + aclocal_DATA = $(top_srcdir)/share/aclocal/* + +-antioch_default_filesdir = $(prefix)/share/antioch_default_files ++antioch_default_filesdir = $(prefix)/share/antioch/default_files + antioch_default_files_DATA = $(top_srcdir)/share/antioch_default_files/* + +-xml_inputsdir = $(prefix)/share/xml_inputs ++xml_inputsdir = $(prefix)/share/antioch/xml_inputs + xml_inputs_DATA = $(top_srcdir)/share/xml_inputs/* + + EXTRA_DIST = $(aclocal_DATA) Property changes on: head/science/antioch/files/patch-share_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/antioch/pkg-descr =================================================================== --- head/science/antioch/pkg-descr (nonexistent) +++ head/science/antioch/pkg-descr (revision 467683) @@ -0,0 +1,6 @@ +A New Templated Implementation Of Chemistry for Hydrodynamics (Antioch) was +initiated to centralize work within the realm of hypersonic aerodynamics, +based on the libMesh finite element library. It's features include +thread-safety and high performance. + +WWW: https://libantioch.github.io/ Property changes on: head/science/antioch/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/antioch/pkg-plist =================================================================== --- head/science/antioch/pkg-plist (nonexistent) +++ head/science/antioch/pkg-plist (revision 467683) @@ -0,0 +1,160 @@ +bin/antioch_version +include/antioch/antioch_asserts.h +include/antioch/antioch_exceptions.h +include/antioch/antioch_numeric_type_instantiate_macro.h +include/antioch/antioch_version.h +include/antioch/arrhenius_rate.h +include/antioch/arrhenius_rate_test_helper.h +include/antioch/arrhenius_rate_vector_test_base.h +include/antioch/ascii_parser.h +include/antioch/ascii_parser_instantiation_macro.h +include/antioch/berthelot_rate.h +include/antioch/berthelothercourtessen_rate.h +include/antioch/binary_diffusion_base.h +include/antioch/blottner_parsing.h +include/antioch/blottner_parsing_instantiate_macro.h +include/antioch/blottner_viscosity.h +include/antioch/cea_curve_fit.h +include/antioch/cea_evaluator.h +include/antioch/cea_mixture.h +include/antioch/cea_mixture_ascii_parsing.h +include/antioch/cea_mixture_ascii_parsing_instantiate_macro.h +include/antioch/cea_mixture_parsing.h +include/antioch/chemical_mixture.h +include/antioch/chemical_species.h +include/antioch/chemkin_definitions.h +include/antioch/chemkin_parser.h +include/antioch/cmath_shims.h +include/antioch/conductivity_traits.h +include/antioch/constant_lewis_diffusivity.h +include/antioch/constant_lewis_diffusivity_building.h +include/antioch/constant_rate.h +include/antioch/converter.h +include/antioch/default_filename.h +include/antioch/diffusion_traits.h +include/antioch/duplicate_reaction.h +include/antioch/eigen_utils.h +include/antioch/eigen_utils_decl.h +include/antioch/elementary_reaction.h +include/antioch/eucken_thermal_conductivity.h +include/antioch/eucken_thermal_conductivity_building.h +include/antioch/falloff_reaction.h +include/antioch/falloff_threebody_reaction.h +include/antioch/gsl_spliner.h +include/antioch/gsl_spliner_impl.h +include/antioch/gsl_spliner_policy.h +include/antioch/gsl_spliner_shim.h +include/antioch/gsl_spliner_test_base.h +include/antioch/hercourtessen_rate.h +include/antioch/ideal_gas_micro_thermo.h +include/antioch/input_utils.h +include/antioch/insi.h +include/antioch/kinetics_conditions.h +include/antioch/kinetics_enum.h +include/antioch/kinetics_evaluator.h +include/antioch/kinetics_parsing.h +include/antioch/kinetics_theory_thermal_conductivity.h +include/antioch/kinetics_theory_thermal_conductivity_building.h +include/antioch/kinetics_theory_viscosity.h +include/antioch/kinetics_theory_viscosity_building.h +include/antioch/kinetics_type.h +include/antioch/kooij_rate.h +include/antioch/lennard_jones_potential.h +include/antioch/lindemann_falloff.h +include/antioch/macro_micro_thermo_base.h +include/antioch/math_constants.h +include/antioch/metaphysicl_utils.h +include/antioch/metaphysicl_utils_decl.h +include/antioch/metaprogramming.h +include/antioch/metaprogramming_decl.h +include/antioch/mixture_averaged_transport_evaluator.h +include/antioch/mixture_averaged_transport_mixture.h +include/antioch/mixture_conductivity.h +include/antioch/mixture_diffusion.h +include/antioch/mixture_transport_base.h +include/antioch/mixture_viscosity.h +include/antioch/molecular_binary_diffusion.h +include/antioch/nasa7_curve_fit.h +include/antioch/nasa7_mixture_vector_test_base.h +include/antioch/nasa7_thermo_test_base.h +include/antioch/nasa9_curve_fit.h +include/antioch/nasa9_mixture_vector_test_base.h +include/antioch/nasa9_thermo_test_base.h +include/antioch/nasa_curve_fit_base.h +include/antioch/nasa_evaluator.h +include/antioch/nasa_mixture.h +include/antioch/nasa_mixture_ascii_parsing.h +include/antioch/nasa_mixture_parsing.h +include/antioch/nasa_mixture_parsing_instantiate_macro.h +include/antioch/nasa_test_helper.h +include/antioch/parser_base.h +include/antioch/parsing_enum.h +include/antioch/particle_flux.h +include/antioch/photochemical_rate.h +include/antioch/physical_constants.h +include/antioch/reaction.h +include/antioch/reaction_enum.h +include/antioch/reaction_parsing.h +include/antioch/reaction_rate_test_base.h +include/antioch/reaction_rate_vector_test_base.h +include/antioch/reaction_set.h +include/antioch/read_reaction_set_data.h +include/antioch/read_reaction_set_data_instantiate_macro.h +include/antioch/read_reaction_set_data_xml.h +include/antioch/rotational_relaxation.h +include/antioch/sigma_bin_converter.h +include/antioch/siprefix.h +include/antioch/species_conductivity_base.h +include/antioch/species_diffusion_base.h +include/antioch/species_parsing.h +include/antioch/species_parsing_instantiation_macro.h +include/antioch/species_viscosity_base.h +include/antioch/stat_mech_thermo.h +include/antioch/stockmayer_potential.h +include/antioch/string_utils.h +include/antioch/sutherland_parsing.h +include/antioch/sutherland_parsing_instantiate_macro.h +include/antioch/sutherland_viscosity.h +include/antioch/temp_cache.h +include/antioch/testing_utils.h +include/antioch/thermo_vector_test_base.h +include/antioch/threebody_reaction.h +include/antioch/tinyxml2.h +include/antioch/tinyxml2_imp.h +include/antioch/transport_mixture.h +include/antioch/transport_species.h +include/antioch/transport_species_ascii_parsing.h +include/antioch/transport_species_parsing.h +include/antioch/troe_falloff.h +include/antioch/unit_base.h +include/antioch/unit_defs.h +include/antioch/unit_store.h +include/antioch/units.h +include/antioch/valarray_utils.h +include/antioch/valarray_utils_decl.h +include/antioch/vanthoff_rate.h +include/antioch/vector_utils.h +include/antioch/vector_utils_decl.h +include/antioch/vexcl_utils.h +include/antioch/vexcl_utils_decl.h +include/antioch/wilke_evaluator.h +include/antioch/wilke_mixture.h +include/antioch/xml_parser.h +include/antioch/xml_parser_instantiation_macro.h +include/antioch_config.h +lib/libantioch.so +lib/libantioch.so.0 +lib/libantioch.so.0.0.0 +libdata/pkgconfig/antioch.pc +share/aclocal/antioch.m4 +%%DATADIR%%/default_files/antioch_default_blottner_coefficient.dat +%%DATADIR%%/default_files/antioch_default_chemical_mixture.dat +%%DATADIR%%/default_files/antioch_default_chemical_species.dat +%%DATADIR%%/default_files/antioch_default_electronic_data.dat +%%DATADIR%%/default_files/antioch_default_sutherland_coefficient.dat +%%DATADIR%%/default_files/antioch_default_thermo_data.dat +%%DATADIR%%/default_files/antioch_default_thermo_data_NASA7.dat +%%DATADIR%%/default_files/antioch_default_transport_species_data.dat +%%DATADIR%%/default_files/antioch_default_vibrational_data.dat +%%DATADIR%%/xml_inputs/gri30.xml +%%DATADIR%%/xml_inputs/nasa9_thermo.xml Property changes on: head/science/antioch/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