diff options
Diffstat (limited to 'science')
104 files changed, 2754 insertions, 1589 deletions
diff --git a/science/ALPSCore/Makefile b/science/ALPSCore/Makefile index 66f4445bcda5..8f5d7cc38f2d 100644 --- a/science/ALPSCore/Makefile +++ b/science/ALPSCore/Makefile @@ -12,8 +12,6 @@ COMMENT= Generic algorithms and utilities for condensed matter physics LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE.TXT -BROKEN_FreeBSD_10= error: no matching function for call to 'deserialize' - LIB_DEPENDS= libboost_system.so:devel/boost-libs \ libhdf5.so:science/hdf5 \ libsz.so:science/szip diff --git a/science/Makefile b/science/Makefile index e8cab4244152..22e846e50b86 100644 --- a/science/Makefile +++ b/science/Makefile @@ -33,7 +33,6 @@ SUBDIR += avogadrolibs SUBDIR += bagel SUBDIR += bddsolve - SUBDIR += bft SUBDIR += bodr SUBDIR += brian SUBDIR += buddy @@ -50,6 +49,7 @@ SUBDIR += chrono SUBDIR += clhep SUBDIR += clipper + SUBDIR += code_saturne SUBDIR += colt SUBDIR += coordgenlibs SUBDIR += coot @@ -65,11 +65,11 @@ SUBDIR += dlib-cpp SUBDIR += dlpoly-classic SUBDIR += eccodes - SUBDIR += ecs SUBDIR += elk SUBDIR += epte SUBDIR += erd SUBDIR += erkale + SUBDIR += esys-particle SUBDIR += fastcap SUBDIR += fasthenry SUBDIR += fisicalab @@ -77,7 +77,6 @@ SUBDIR += fsom SUBDIR += fvcom SUBDIR += fvcom-mpi - SUBDIR += fvm SUBDIR += gabedit SUBDIR += gamess-us SUBDIR += gchemutils @@ -86,6 +85,7 @@ SUBDIR += ghemical SUBDIR += ghmm SUBDIR += gnudatalanguage + SUBDIR += gpaw-setups SUBDIR += gramps SUBDIR += grib_api SUBDIR += gromacs @@ -107,6 +107,7 @@ SUBDIR += kst2 SUBDIR += lammps SUBDIR += lamprop + SUBDIR += latte SUBDIR += libaec SUBDIR += libccp4 SUBDIR += libcint @@ -126,6 +127,7 @@ SUBDIR += libsvm SUBDIR += libsvm-python SUBDIR += libxc + SUBDIR += liggghts SUBDIR += linsmith SUBDIR += lm SUBDIR += luscus @@ -140,7 +142,6 @@ SUBDIR += mdynamix SUBDIR += medit SUBDIR += meep - SUBDIR += mei SUBDIR += metaf2xml SUBDIR += metaphysicl SUBDIR += minc2 @@ -154,7 +155,6 @@ SUBDIR += msms SUBDIR += multiwfn SUBDIR += namd - SUBDIR += ncs SUBDIR += netcdf SUBDIR += netcdf-cxx SUBDIR += netcdf-fortran diff --git a/science/avogadrolibs/Makefile b/science/avogadrolibs/Makefile index 5404a30daabd..ffa866fea09f 100644 --- a/science/avogadrolibs/Makefile +++ b/science/avogadrolibs/Makefile @@ -1,10 +1,13 @@ # $FreeBSD$ PORTNAME= avogadrolibs -DISTVERSION= 1.91.0-107 -DISTVERSIONSUFFIX= -g60c69b0 +DISTVERSION= 1.92.0 CATEGORIES= science +PATCH_SITES= https://github.com/${GH_ACCOUNT}/${PORTNAME}/commit/ +PATCHFILES= cf9d82575796d5fcabb153bdebde26843d81d83e.patch:-p1 \ + ea813f683cdd9865994c0ba94a24325e04b9f8fb.patch:-p1 \ + MAINTAINER= yuri@FreeBSD.org COMMENT= Avogadro2 libraries for chemical editor and visualization applications diff --git a/science/avogadrolibs/distinfo b/science/avogadrolibs/distinfo index 63f7049279f9..30ab9fc75c16 100644 --- a/science/avogadrolibs/distinfo +++ b/science/avogadrolibs/distinfo @@ -1,3 +1,7 @@ -TIMESTAMP = 1539886254 -SHA256 (OpenChemistry-avogadrolibs-1.91.0-107-g60c69b0_GH0.tar.gz) = 576868081a8e858ed8fa1eef0f84130ef1699391fa98bc1fd29f83116ca43c2f -SIZE (OpenChemistry-avogadrolibs-1.91.0-107-g60c69b0_GH0.tar.gz) = 2706803 +TIMESTAMP = 1541744180 +SHA256 (OpenChemistry-avogadrolibs-1.92.0_GH0.tar.gz) = b71d9f0034f2ea2ba648d812b0c6f1fee2d97ee0e3c7075258e63cfc2d68c473 +SIZE (OpenChemistry-avogadrolibs-1.92.0_GH0.tar.gz) = 2707322 +SHA256 (cf9d82575796d5fcabb153bdebde26843d81d83e.patch) = 54fdbab45cc8942e7f0e6dd47c451e3cad56a29b0224f385aee37b608bae8a99 +SIZE (cf9d82575796d5fcabb153bdebde26843d81d83e.patch) = 2665 +SHA256 (ea813f683cdd9865994c0ba94a24325e04b9f8fb.patch) = 6aea4b7e1163060db942f98b3d550e35f183233124db1b7f4d47c19038b02e75 +SIZE (ea813f683cdd9865994c0ba94a24325e04b9f8fb.patch) = 1398 diff --git a/science/avogadrolibs/pkg-plist b/science/avogadrolibs/pkg-plist index 8bf72d891da1..11f2b423d092 100644 --- a/science/avogadrolibs/pkg-plist +++ b/science/avogadrolibs/pkg-plist @@ -190,26 +190,26 @@ lib/cmake/avogadrolibs/FindLibArchive.cmake lib/cmake/avogadrolibs/Findlibmsym.cmake lib/libAvogadroCore.so lib/libAvogadroCore.so.1 -lib/libAvogadroCore.so.1.91.0 +lib/libAvogadroCore.so.1.92.0 lib/libAvogadroIO.so lib/libAvogadroIO.so.1 -lib/libAvogadroIO.so.1.91.0 +lib/libAvogadroIO.so.1.92.0 %%MOLEQUEUE%%lib/libAvogadroMoleQueue.so %%MOLEQUEUE%%lib/libAvogadroMoleQueue.so.1 -%%MOLEQUEUE%%lib/libAvogadroMoleQueue.so.1.91.0 +%%MOLEQUEUE%%lib/libAvogadroMoleQueue.so.1.92.0 %%QT5%%lib/libAvogadroQtGui.so %%QT5%%lib/libAvogadroQtGui.so.1 -%%QT5%%lib/libAvogadroQtGui.so.1.91.0 +%%QT5%%lib/libAvogadroQtGui.so.1.92.0 %%QT5%%lib/libAvogadroQtOpenGL.so %%QT5%%lib/libAvogadroQtOpenGL.so.1 -%%QT5%%lib/libAvogadroQtOpenGL.so.1.91.0 +%%QT5%%lib/libAvogadroQtOpenGL.so.1.92.0 %%QT5%%lib/libAvogadroQtPlugins.so %%QT5%%lib/libAvogadroQtPlugins.so.1 -%%QT5%%lib/libAvogadroQtPlugins.so.1.91.0 +%%QT5%%lib/libAvogadroQtPlugins.so.1.92.0 lib/libAvogadroQuantumIO.so lib/libAvogadroQuantumIO.so.1 -lib/libAvogadroQuantumIO.so.1.91.0 +lib/libAvogadroQuantumIO.so.1.92.0 %%OPENGL%%lib/libAvogadroRendering.so %%OPENGL%%lib/libAvogadroRendering.so.1 -%%OPENGL%%lib/libAvogadroRendering.so.1.91.0 +%%OPENGL%%lib/libAvogadroRendering.so.1.92.0 lib/liblibgwavi.a diff --git a/science/bagel/Makefile b/science/bagel/Makefile index 7a4b414a73ae..744620da9d1b 100644 --- a/science/bagel/Makefile +++ b/science/bagel/Makefile @@ -12,7 +12,6 @@ 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" -BROKEN_FreeBSD_10= /usr/include/c++/v1/memory:4004:35: error: no viable overloaded '='; __e->__weak_this_ = *this; LIB_DEPENDS= libboost_serialization.so:devel/boost-libs \ libcblas.so:math/cblas diff --git a/science/bft/Makefile b/science/bft/Makefile deleted file mode 100644 index f7d5cf90f33a..000000000000 --- a/science/bft/Makefile +++ /dev/null @@ -1,35 +0,0 @@ -# Created by: thierry@pompo.net -# $FreeBSD$ - -PORTNAME= bft -PORTVERSION= 1.1.5 -PORTREVISION= 1 -CATEGORIES= science parallel -MASTER_SITES= http://research.edf.com/fichiers/fckeditor/Commun/Innovation/logiciels/code_saturne/Releases/ -DISTNAME= ${PORTNAME}-${PORTVERSION:S/.//g} - -MAINTAINER= thierry@FreeBSD.org -COMMENT= Code_Saturne Base Functions and Types library - -LICENSE= LGPL21+ -LICENSE_FILE= ${WRKSRC}/COPYING - -WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION} - -USES= libtool zip -USE_LDCONFIG= yes -GNU_CONFIGURE= yes -INSTALL_TARGET= install-strip - -TESTSBIN= bft_test bft_mem_usage_test bft_printf_test - -pre-configure: - # No useful doc there - ${REINPLACE_CMD} -e 's|tests doc|tests|' ${WRKSRC}/Makefile.in - -do-test: -.for pg in ${TESTSBIN} - (cd ${WRKSRC}/tests; ./${pg} arg1 arg2) -.endfor - -.include <bsd.port.mk> diff --git a/science/bft/distinfo b/science/bft/distinfo deleted file mode 100644 index e2042788bb04..000000000000 --- a/science/bft/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -SHA256 (bft-115.zip) = 8af0134375140b7356c9b38ba2475fb57435a8cda5ace319ecc6c903e8d66e79 -SIZE (bft-115.zip) = 431032 diff --git a/science/bft/files/patch-src__bft_file.c b/science/bft/files/patch-src__bft_file.c deleted file mode 100644 index c8bb1ab9a613..000000000000 --- a/science/bft/files/patch-src__bft_file.c +++ /dev/null @@ -1,24 +0,0 @@ ---- src/bft_file.c.orig 2008-01-14 19:19:31.000000000 +0100 -+++ src/bft_file.c 2010-05-01 11:20:00.000000000 +0200 -@@ -106,6 +106,13 @@ - We redefine prototypes for gzseek() and gztell() ; - This is ugly, but should work with an unmodified Zlib (as of Zlib 1.2.1) */ - -+#if defined (__FreeBSD__) -+# if __FreeBSD_version < 900010 -+typedef long bft_z_off_t; -+# else -+typedef off_t bft_z_off_t; -+# endif -+#else - #if defined (BFT_SIZEOF_Z_OFF_T) - # if (BFT_SIZEOF_Z_OFF_T == BFT_SIZEOF_LONG) - typedef long bft_z_off_t; -@@ -119,6 +126,7 @@ - #else - typedef z_off_t bft_z_off_t; - #endif -+#endif - - typedef bft_z_off_t (bft_gzseek_t) (gzFile file, - bft_z_off_t offset, diff --git a/science/bft/files/patch-tests_Makefile.in b/science/bft/files/patch-tests_Makefile.in deleted file mode 100644 index 9584eaabb226..000000000000 --- a/science/bft/files/patch-tests_Makefile.in +++ /dev/null @@ -1,11 +0,0 @@ ---- tests/Makefile.in.orig 2011-07-11 11:05:15.000000000 +0200 -+++ tests/Makefile.in 2012-04-07 15:52:02.000000000 +0200 -@@ -261,7 +261,7 @@ - bft_mem_usage_test_SOURCES = bft_mem_usage_test.c - bft_mem_test_SOURCES = bft_mem_test.c - bft_printf_test_SOURCES = bft_printf_test.c --all: all-am -+all: $(check_PROGRAMS) - - .SUFFIXES: - .SUFFIXES: .c .lo .o .obj diff --git a/science/bft/pkg-descr b/science/bft/pkg-descr deleted file mode 100644 index 030afb56ebb0..000000000000 --- a/science/bft/pkg-descr +++ /dev/null @@ -1,5 +0,0 @@ -BFT stands for Base Functions and Types. -It is destined to be used by scientific codes (CFD) often using -some form of parallelism, especially MPI. - -WWW: https://www.code-saturne.org/ diff --git a/science/bft/pkg-plist b/science/bft/pkg-plist deleted file mode 100644 index ad61006af575..000000000000 --- a/science/bft/pkg-plist +++ /dev/null @@ -1,18 +0,0 @@ -bin/bft-config -include/bft_backtrace.h -include/bft_config.h -include/bft_config_priv.h -include/bft_error.h -include/bft_file.h -include/bft_fp_trap.h -include/bft_mem.h -include/bft_mem_usage.h -include/bft_printf.h -include/bft_sys_info.h -include/bft_timer.h -include/bft_version.h -lib/libbft.a -lib/libbft.so -lib/libbft.so.1 -lib/libbft.so.1.0.0 -man/man1/bft-config.1.gz diff --git a/science/chemps2/Makefile b/science/chemps2/Makefile index 0f56a1873479..35a07b3a5fbb 100644 --- a/science/chemps2/Makefile +++ b/science/chemps2/Makefile @@ -2,7 +2,7 @@ PORTNAME= CheMPS2 DISTVERSIONPREFIX= v -DISTVERSION= 1.8.8 +DISTVERSION= 1.8.9 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/chemps2/distinfo b/science/chemps2/distinfo index c145e6385e1d..31a5bdf98448 100644 --- a/science/chemps2/distinfo +++ b/science/chemps2/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1538104722 -SHA256 (SebWouters-CheMPS2-v1.8.8_GH0.tar.gz) = c64a0572d333c7c071c3ef59cd95eeb39abe766496cb28df184ce44bdb38f75c -SIZE (SebWouters-CheMPS2-v1.8.8_GH0.tar.gz) = 1249931 +TIMESTAMP = 1540879082 +SHA256 (SebWouters-CheMPS2-v1.8.9_GH0.tar.gz) = ccd4c0d9432759d97690bf37a0333440f93513960c62d1f75842f090406a224d +SIZE (SebWouters-CheMPS2-v1.8.9_GH0.tar.gz) = 1250010 diff --git a/science/clhep/Makefile b/science/clhep/Makefile index c8fa41f7291c..b036607ee278 100644 --- a/science/clhep/Makefile +++ b/science/clhep/Makefile @@ -13,8 +13,6 @@ COMMENT= Object-oriented toolkit for particle physics applications by CERN LICENSE= GPLv3 LGPL3 LICENSE_COMB= multi -BROKEN_FreeBSD_10= does not compile on clang3.4, requires 3.5+ - WRKSRC= ${WRKDIR}/${PORTVERSION}/${PORTNAME:tu} USES= cmake:outsource compiler:c++11-lang perl5 tar:tgz diff --git a/science/code_saturne/Makefile b/science/code_saturne/Makefile new file mode 100644 index 000000000000..e6152debd619 --- /dev/null +++ b/science/code_saturne/Makefile @@ -0,0 +1,96 @@ +# Created by: thierry@pompo.net +# $FreeBSD$ + +PORTNAME= code_saturne +PORTVERSION= 5.3.0 +DISTVERSIONPREFIX= v +CATEGORIES= science parallel + +MAINTAINER= thierry@FreeBSD.org +COMMENT= EDF's general purpose Computational Fluid Dynamics (CFD) software + +LICENSE= GPLv2 + +BUILD_DEPENDS= python:lang/python +LIB_DEPENDS= libsysinfo.so:devel/libsysinfo \ + libcgns.so:science/cgnslib \ + libhdf5.so:science/hdf5 \ + libomp.so:devel/openmp \ + libmedC.so:french/med +RUN_DEPENDS= xmgrace:math/grace \ + bash:shells/bash \ + xterm:x11/xterm + +USE_GITHUB= yes +GH_ACCOUNT= code-saturne + +USES= autoreconf bison fortran gettext gnome gmake iconv libtool \ + pyqt:5 python:2.7 shebangfix +USE_GNOME= libxml2 +USE_PYQT= core gui sip widgets xml_build +CPPFLAGS+= -I${LOCALBASE}/include -I${LOCALBASE}/include/libxml2 +GNU_CONFIGURE= yes +USE_LDCONFIG= yes + +OPTIONS_DEFINE= DOCS EXAMPLES ATLAS BATCH MPI +OPTIONS_DEFAULT= BATCH MPI METIS +OPTIONS_RADIO= METIS +OPTIONS_RADIO_METIS= METIS PARMETIS +ATLAS_USES= blaslapack:atlas +ATLAS_CONFIGURE_ON= --with-blas=yes --with-blas-type=ATLAS +BATCH_DESC= Use Torque to submit batches +BATCH_RUN_DEPENDS= pbs-config:sysutils/torque +MPI_LIB_DEPENDS= libmpi.so:net/mpich +MPI_CONFIGURE_WITH= mpi +METIS_LIB_DEPENDS= libmetis.so:math/metis +METIS_CONFIGURE_ON= --with-metis-include="${LOCALBASE}/include" +PARMETIS_LIB_DEPENDS= libparmetis.so:math/parmetis +PARMETIS_CONFIGURE_ON= --with-metis-include="${LOCALBASE}/include/parmetis" \ + --with-metis-lib="${LOCALBASE}/lib/parmetis" +PARMETIS_CONFIGURE_ENV= LIBS=-lexecinfo + +#TEST_TARGET= check + +.if defined(PACKAGE_BUILDING) +TERM= vt100 # Force for pointyhat to override su +.else +TERM?= vt100 # Default value needed for tput in jail or tinderbox +.endif + +.include <bsd.port.options.mk> + +.if ${ARCH} == "i386" +# /wrkdirs/usr/ports/science/code_saturne/work/code_saturne-5.3.0/src/apps/.libs +# /libsaturne.so: +# undefined reference to `__atomic_compare_exchange' +CONFIGURE_ARGS+= --disable-openmp +.endif + +.if ${PORT_OPTIONS:MDOCS} +USE_TEX= tex:build +BUILD_DEPENDS+= fig2dev:print/transfig \ + doxygen:devel/doxygen \ + dot:graphics/graphviz \ + sphinx-build:textproc/py-sphinx@${PY_FLAVOR} +ALL_TARGET= all pdf +DOCS= AUTHORS ChangeLog README +.endif + +pre-configure: + (cd ${WRKSRC} && ${LS} preprocessor/*/*.c src/*/*.c* | \ + ${GREP} -v user_examples > po/POTFILES.in) + ${FLEX} -o ${WRKSRC}/src/mei/mei_scanner.c ${WRKSRC}/src/mei/mei_scanner.l + ${LOCALBASE}/bin/bison --defines=${WRKSRC}/src/mei/mei_parser.h \ + -o ${WRKSRC}/src/mei/mei_parser.c ${WRKSRC}/src/mei/mei_parser.y + +post-install: +.if ${PORT_OPTIONS:MDOCS} + ${MKDIR} ${STAGEDIR}${DOCSDIR} + ${INSTALL_DATA} ${DOCS:C|^|${WRKSRC}/|} ${STAGEDIR}${DOCSDIR} +.endif +.if ${PORT_OPTIONS:MEXAMPLES} + ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} + cd ${WRKSRC}/examples && ${COPYTREE_SHARE} \* ${STAGEDIR}${EXAMPLESDIR} +.endif + +.include <bsd.port.mk> diff --git a/science/code_saturne/distinfo b/science/code_saturne/distinfo new file mode 100644 index 000000000000..8181668758dd --- /dev/null +++ b/science/code_saturne/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1541083916 +SHA256 (code-saturne-code_saturne-v5.3.0_GH0.tar.gz) = df1bd7784311842a3930bd2ab9490d261d7860c330ee0c3d6070c2b67e0d6734 +SIZE (code-saturne-code_saturne-v5.3.0_GH0.tar.gz) = 18872952 diff --git a/science/code_saturne/files/patch-libple_tests_Makefile.am b/science/code_saturne/files/patch-libple_tests_Makefile.am new file mode 100644 index 000000000000..4af4bea9b342 --- /dev/null +++ b/science/code_saturne/files/patch-libple_tests_Makefile.am @@ -0,0 +1,11 @@ +--- libple/tests/Makefile.am.orig 2018-10-26 17:43:02 UTC ++++ libple/tests/Makefile.am +@@ -33,7 +33,7 @@ check_PROGRAMS += ple_coupling_test + ple_coupling_test_SOURCES = ple_coupling_test.c + ple_coupling_test_CPPFLAGS = -I$(top_srcdir)/src $(MPI_CPPFLAGS) + ple_coupling_test_LDFLAGS = $(MPI_LDFLAGS) +-ple_coupling_test_LDADD = $(top_builddir)/src/libple.la $(MPI_LIBS) -lm ++ple_coupling_test_LDADD = $(top_builddir)/src/libple.la $(MPI_LIBS) $(INTLLIBS) -lm + endif + + # Uncomment for tests execution at "make check" diff --git a/science/code_saturne/pkg-descr b/science/code_saturne/pkg-descr new file mode 100644 index 000000000000..cdbbd01ed211 --- /dev/null +++ b/science/code_saturne/pkg-descr @@ -0,0 +1,11 @@ +Code_Saturne is EDF's general purpose Computational Fluid Dynamics (CFD) +software. + +The basic capabilities of Code_Saturne enable the handling of either +incompressible or expandable flows with or without heat transfer and turbulence. +Dedicated modules are available for specific physics such as radiative heat +transfer, combustion (gas, coal, heavy fuel oil, ...), magneto-hydrodynamics, +compressible flows, two-phase flows (Euler-Lagrange approach with two-way +coupling), or atmospheric flows. + +WWW: http://www.code-saturne.org/ diff --git a/science/code_saturne/pkg-plist b/science/code_saturne/pkg-plist new file mode 100644 index 000000000000..0695b9ef3e31 --- /dev/null +++ b/science/code_saturne/pkg-plist @@ -0,0 +1,1404 @@ +bin/code_saturne +bin/ple-config +etc/bash_completion.d/code_saturne +%%ETCDIR%%.cfg.template +include/code_saturne/alaste.mod +include/code_saturne/albase.mod +include/code_saturne/alstru.mod +include/code_saturne/atchem.mod +include/code_saturne/atimbr.mod +include/code_saturne/atincl.mod +include/code_saturne/atsoil.mod +include/code_saturne/bft_backtrace.h +include/code_saturne/bft_error.h +include/code_saturne/bft_mem.h +include/code_saturne/bft_mem_usage.h +include/code_saturne/bft_printf.h +include/code_saturne/cavitation.mod +include/code_saturne/cfpoin.mod +include/code_saturne/coincl.mod +include/code_saturne/cpincl.mod +include/code_saturne/cplsat.mod +include/code_saturne/cs_1d_wall_thermal.h +include/code_saturne/cs_1d_wall_thermal_check.h +include/code_saturne/cs_advection_field.h +include/code_saturne/cs_ale.h +include/code_saturne/cs_all_to_all.h +include/code_saturne/cs_array_reduce.h +include/code_saturne/cs_assert.h +include/code_saturne/cs_ast_coupling.h +include/code_saturne/cs_at_data_assim.h +include/code_saturne/cs_at_opt_interp.h +include/code_saturne/cs_at_plugin.h +include/code_saturne/cs_bad_cells_regularisation.h +include/code_saturne/cs_balance.h +include/code_saturne/cs_balance_by_zone.h +include/code_saturne/cs_base.h +include/code_saturne/cs_base_fortran.h +include/code_saturne/cs_basis_func.h +include/code_saturne/cs_benchmark.h +include/code_saturne/cs_blas.h +include/code_saturne/cs_block_dist.h +include/code_saturne/cs_block_to_part.h +include/code_saturne/cs_boundary_conditions.h +include/code_saturne/cs_boundary_zone.h +include/code_saturne/cs_c_bindings.mod +include/code_saturne/cs_calcium.h +include/code_saturne/cs_cdo_advection.h +include/code_saturne/cs_cdo_bc.h +include/code_saturne/cs_cdo_connect.h +include/code_saturne/cs_cdo_diffusion.h +include/code_saturne/cs_cdo_local.h +include/code_saturne/cs_cdo_main.h +include/code_saturne/cs_cdo_quantities.h +include/code_saturne/cs_cdo_time.h +include/code_saturne/cs_cdofb_ac.h +include/code_saturne/cs_cdofb_navsto.h +include/code_saturne/cs_cdofb_priv.h +include/code_saturne/cs_cdofb_scaleq.h +include/code_saturne/cs_cdofb_uzawa.h +include/code_saturne/cs_cdofb_vecteq.h +include/code_saturne/cs_cdovb_priv.h +include/code_saturne/cs_cdovb_scaleq.h +include/code_saturne/cs_cdovb_vecteq.h +include/code_saturne/cs_cdovcb_scaleq.h +include/code_saturne/cs_cf_bindings.mod +include/code_saturne/cs_cf_thermo.h +include/code_saturne/cs_coal_incl.mod +include/code_saturne/cs_combustion_model.h +include/code_saturne/cs_config.h +include/code_saturne/cs_control.h +include/code_saturne/cs_convection_diffusion.h +include/code_saturne/cs_coupling.h +include/code_saturne/cs_crystal_router.h +include/code_saturne/cs_ctwr.h 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+%%PORTDOCS%%%%DOCSDIR%%/refcard.pdf +%%PORTDOCS%%%%DOCSDIR%%/studymanager.pdf +%%PORTDOCS%%%%DOCSDIR%%/theory.pdf +%%PORTDOCS%%%%DOCSDIR%%/user.pdf +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/1-simple_junction/case1/case1.xml +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/1-simple_junction/mesh/downcomer.des +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/2-full_domain/case1/case1.xml +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/2-full_domain/case2/case2.xml +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/2-full_domain/case2/cs_user_boundary_conditions.f90 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/2-full_domain/case3/case3.xml +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/2-full_domain/case3/cs_user_boundary_conditions.f90 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/2-full_domain/mesh/downcomer.des +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/2-full_domain/mesh/fdc.des +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/2-full_domain/mesh/pic.des +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3-stratified_junction/case1/case1.xml +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3-stratified_junction/case1/cs_user_postprocess.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3-stratified_junction/mesh/sn_total.des +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/4-2Ddisks/case1/coupling_parameters.py +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/4-2Ddisks/case1/fluid/fluid-3rond2D-coupling.xml +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/4-2Ddisks/case1/fluid/fluid-3rond2D-coupling_restart.xml +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/4-2Ddisks/case1/fluid/fluid_3disks_alone.xml +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/4-2Ddisks/case1/solid/solid-alone.syd +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/4-2Ddisks/case1/solid/solid-coupling.syd +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/4-2Ddisks/case1/solid/solid-coupling_restart.syd +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/4-2Ddisks/mesh/fluid/3rond2d_fluide.des +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/4-2Ddisks/mesh/solid/3rond2d.des +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/4-2Ddisks/mesh/solid/3rond2d_syr40.dat +share/locale/fr/LC_MESSAGES/code_saturne.mo +share/locale/fr/LC_MESSAGES/ple.mo diff --git a/science/dalton/Makefile b/science/dalton/Makefile index ea10300332b1..7bfdc4ed96fd 100644 --- a/science/dalton/Makefile +++ b/science/dalton/Makefile @@ -2,8 +2,12 @@ PORTNAME= dalton DISTVERSION= 2016.2 +PORTREVISION= 1 CATEGORIES= science +PATCH_SITES= https://gitlab.com/${PORTNAME}/${PORTNAME}/commit/ +PATCHFILES= b838ac7be3bba7fe9bc0fdf81b20cde37a38f3c0.patch:-p1 + MAINTAINER= yuri@FreeBSD.org COMMENT= Powerful molecular electronic structure program for quantum chemistry diff --git a/science/dalton/distinfo b/science/dalton/distinfo index c818eaf35283..e14f24111a02 100644 --- a/science/dalton/distinfo +++ b/science/dalton/distinfo @@ -1,12 +1,10 @@ -TIMESTAMP = 1535867480 +TIMESTAMP = 1541354690 SHA256 (cstein-qfitlib-d931560_GH0.tar.gz) = db394ddc55e612d770104bf4cc23509c76645c2db9be360bb5c44d91f3a3b3e9 SIZE (cstein-qfitlib-d931560_GH0.tar.gz) = 20644 SHA256 (dftlibs-xcfun-177fcd96_GH0.tar.gz) = 101ea603ff5711a8c6427611244d4812edca678457dc23a62d1586df092c6d0c SIZE (dftlibs-xcfun-177fcd96_GH0.tar.gz) = 145555 SHA256 (dftlibs-xcint-2d1496f5_GH0.tar.gz) = d1f8dc0470fdea82af4aeb87e37df2017981ea3ddc9e9910e358aa261f3b3f1b SIZE (dftlibs-xcint-2d1496f5_GH0.tar.gz) = 77872 -SHA256 (PCMSolver-pcmsolver-v1.2.1_GH0.tar.gz) = aefaf84497a1c6157402ead46bb7bb32c919d15839906c6df85c9892c963b1c7 -SIZE (PCMSolver-pcmsolver-v1.2.1_GH0.tar.gz) = 98217947 SHA256 (dalton-dalton-130ffaa0613bb3af6cac766fc8183d6df7d68917_GL0.tar.gz) = a06b85d199039db5bd870588c7055ddd872e8624150be8c78f736ec2e5826296 SIZE (dalton-dalton-130ffaa0613bb3af6cac766fc8183d6df7d68917_GL0.tar.gz) = 33014691 SHA256 (dalton-gen1int-70d10a37390f4e42a90b2951cb3fec3e9a870d13_GL0.tar.gz) = 501bd7fe2a696beb9a2747d554724c7d9f8b9dd30119f6cc00470b5a2ce9cc10 @@ -15,3 +13,5 @@ SHA256 (dalton-efs-ffc1a2f137fa6e322143bf84be724d9b815e637b_GL0.tar.gz) = 235cf0 SIZE (dalton-efs-ffc1a2f137fa6e322143bf84be724d9b815e637b_GL0.tar.gz) = 193905 SHA256 (dalton-pelib-public-f679dfbc5d16cb91cb964320782d02fdb011b1f6_GL0.tar.gz) = c2f8abd5ae3ead95cd97abd196427426ffacad1669028ca02747bd86323a02a3 SIZE (dalton-pelib-public-f679dfbc5d16cb91cb964320782d02fdb011b1f6_GL0.tar.gz) = 51719 +SHA256 (b838ac7be3bba7fe9bc0fdf81b20cde37a38f3c0.patch) = 26ba9435a79aa96ce0a478dc39bead06b50a19ff02e409a3e0a45953e2a7081e +SIZE (b838ac7be3bba7fe9bc0fdf81b20cde37a38f3c0.patch) = 842 diff --git a/science/ecs/Makefile b/science/ecs/Makefile deleted file mode 100644 index d3fd0d3d840c..000000000000 --- a/science/ecs/Makefile +++ /dev/null @@ -1,77 +0,0 @@ -# Created by: thierry@pompo.net -# $FreeBSD$ - -PORTNAME= ecs -PORTVERSION= 2.0.4 -PORTREVISION= 6 -CATEGORIES= science -MASTER_SITES= http://code-saturne.org/releases/ - -MAINTAINER= thierry@FreeBSD.org -COMMENT= Code_Saturne Preprocessor - -LICENSE= GPLv2 - -BUILD_DEPENDS+= ${LOCALBASE}/lib/libscotch.a:cad/scotch -LIB_DEPENDS= libmed.so:french/med \ - libbft.so:science/bft \ - libhdf5.so:science/hdf5 \ - libcgns.so:science/cgnslib - -USES= gmake -USE_TEX= dvipsk -GNU_CONFIGURE= yes -CPPFLAGS+= -I${LOCALBASE}/include -LDFLAGS+= -L${LOCALBASE}/lib -CONFIGURE_ARGS= --with-bft=${LOCALBASE} \ - --with-hdf5=${LOCALBASE} \ - --with-cgns=${LOCALBASE} \ - --without-adf --without-ccm \ - --with-scotch=${LOCALBASE} \ - --with-med=${LOCALBASE} \ - --with-metis=${LOCALBASE} \ - --with-metis-include=${LOCALBASE}/include/metis -CONFIGURE_ENV= PTHREAD_LIBS=-lpthread - -OPTIONS_DEFINE= DOCS NLS -OPTIONS_SUB= yes - -NLS_USES= gettext iconv -NLS_CONFIGURE_ENABLE= nls - -DOCS_USE= TEX=tex:build -DOCS_BUILD_DEPENDS= fig2dev:print/transfig - -.include <bsd.port.options.mk> - -.if defined(WITH_DEBUG) -CONFIGURE_ARGS+= --enable-debug -.endif - -.if ${PORT_OPTIONS:MDOCS} -PORTDOCS= mi_ecs.pdf mt_ecs.pdf -MAKE_JOBS_UNSAFE=yes -.endif - -.include <bsd.port.pre.mk> - -.if exists(${LOCALBASE}/bin/kmetis) -# The regular metis is present, so we cannot depend on metis-edf -LIB_DEPENDS+= libmetis.so.1:math/metis4 -.else -# Prefer metis-edf to avoid conflict with Code_Aster -LIB_DEPENDS+= libmetis.so.2:math/metis-edf -.endif - -pre-configure: -.if ${PORT_OPTIONS:MDOCS} - ${REINPLACE_CMD} -e '/^SUBDIRS/s| po| po doc|' ${WRKSRC}/Makefile.in -.endif - -post-install: -.if ${PORT_OPTIONS:MDOCS} - ${MKDIR} ${STAGEDIR}${DOCSDIR} - ${INSTALL_DATA} ${PORTDOCS:S|^|${WRKSRC}/doc/|} ${STAGEDIR}${DOCSDIR} -.endif - -.include <bsd.port.post.mk> diff --git a/science/ecs/distinfo b/science/ecs/distinfo deleted file mode 100644 index 84a6ce2a58d8..000000000000 --- a/science/ecs/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -SHA256 (ecs-2.0.4.tar.gz) = fac2bbbf0ec3b34d7a87a1ca742adf8bfc2fbb4875a3bc277a16ef5bf5831be9 -SIZE (ecs-2.0.4.tar.gz) = 1191831 diff --git a/science/ecs/files/patch-configure b/science/ecs/files/patch-configure deleted file mode 100644 index 3e6753982644..000000000000 --- a/science/ecs/files/patch-configure +++ /dev/null @@ -1,11 +0,0 @@ ---- configure.orig 2015-05-05 08:41:58 UTC -+++ configure -@@ -12415,7 +12415,7 @@ have_scotch_header=no - have_scotch=no - - # Common library dependencies for SCOTCH --ecs_scotch_l0="-lm" -+ecs_scotch_l0="-lm $PTHREAD_LIBS" - ecs_scotch_l1="-lz -lm" - ecs_scotch_l2="-lm -lpthread" - ecs_scotch_l3="-lz -lm -lpthread" diff --git a/science/ecs/files/patch-doc_Makefile b/science/ecs/files/patch-doc_Makefile deleted file mode 100644 index 803be01ca865..000000000000 --- a/science/ecs/files/patch-doc_Makefile +++ /dev/null @@ -1,20 +0,0 @@ ---- doc/Makefile.orig 2012-07-05 16:54:45 UTC -+++ doc/Makefile -@@ -31,7 +31,7 @@ figures: - - - doc: -- @make pdf -+ @$(MAKE) pdf - - - pdf: -@@ -57,7 +57,7 @@ distclean: - - - install: -- @\mv $(TEX)/*.pdf . -+ @\cp $(TEX)/*.pdf . - - - help info aide: diff --git a/science/ecs/files/patch-src_appli_cs__partition.c b/science/ecs/files/patch-src_appli_cs__partition.c deleted file mode 100644 index 3049ec5f1fe5..000000000000 --- a/science/ecs/files/patch-src_appli_cs__partition.c +++ /dev/null @@ -1,10 +0,0 @@ ---- src/appli/cs_partition.c.orig 2012-07-05 16:54:42 UTC -+++ src/appli/cs_partition.c -@@ -117,6 +117,7 @@ void METIS_PartGraphKway(int *, idxtype - - #if defined(HAVE_SCOTCH) - -+#include <stdint.h> - #include <scotch.h> - - #endif diff --git a/science/ecs/pkg-descr b/science/ecs/pkg-descr deleted file mode 100644 index d97322ef9e5a..000000000000 --- a/science/ecs/pkg-descr +++ /dev/null @@ -1,4 +0,0 @@ -ECS means "Enveloppe Code Saturne". -This is the preprocessor used by the Code_Saturne and NEPTUNE_CDF codes. - -WWW: http://www.code-saturne.org/ diff --git a/science/ecs/pkg-plist b/science/ecs/pkg-plist deleted file mode 100644 index 6b122b67d80e..000000000000 --- a/science/ecs/pkg-plist +++ /dev/null @@ -1,9 +0,0 @@ -bin/cs_preprocess-config -bin/cs_preprocess -bin/cs_partition -bin/cs_io_dump -man/man1/cs_io_dump.1.gz -man/man1/cs_partition.1.gz -man/man1/cs_preprocess-config.1.gz -man/man1/cs_preprocess.1.gz -%%NLS%%share/locale/fr/LC_MESSAGES/cs_preprocess.mo diff --git a/science/erkale/Makefile b/science/erkale/Makefile index 1fb2588a1196..c7920bdbbff3 100644 --- a/science/erkale/Makefile +++ b/science/erkale/Makefile @@ -2,6 +2,7 @@ PORTNAME= erkale DISTVERSION= g20181009 +PORTREVISION= 1 CATEGORIES= science DIST_SUBDIR= ${PORTNAME}${PKGNAMESUFFIX} diff --git a/science/esys-particle/Makefile b/science/esys-particle/Makefile new file mode 100644 index 000000000000..fd2629be9630 --- /dev/null +++ b/science/esys-particle/Makefile @@ -0,0 +1,25 @@ +# $FreeBSD$ + +PORTNAME= esys-particle +DISTVERSION= 2.3.5 +CATEGORIES= science +MASTER_SITES= https://launchpad.net/esys-particle/trunk/${DISTVERSION}/+download/ +DISTNAME= ESyS-Particle-${DISTVERSION} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Particle-based numerical modelling software + +LICENSE= APACHE20 + +LIB_DEPENDS= libboost_system.so:devel/boost-libs \ + libmpi.so:net/mpich + +USES= cmake:outsource fortran +USE_LDCONFIG= yes + +LDFLAGS+= ${LOCALBASE}/lib/libboost_filesystem.so + +pre-build: + @${ECHO} "static int s_bzr_revision=-1;" > ${WRKSRC}/bzrversion.h + +.include <bsd.port.mk> diff --git a/science/esys-particle/distinfo b/science/esys-particle/distinfo new file mode 100644 index 000000000000..f9d0dc5d5eb9 --- /dev/null +++ b/science/esys-particle/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1541392871 +SHA256 (ESyS-Particle-2.3.5.tar.gz) = 97f53fd0056c8f90771e1e2ff91bcea67a419bc68fcd91c68f7df76339680888 +SIZE (ESyS-Particle-2.3.5.tar.gz) = 8197209 diff --git a/science/esys-particle/files/patch-CMakeLists.txt b/science/esys-particle/files/patch-CMakeLists.txt new file mode 100644 index 000000000000..97f2e0b56b98 --- /dev/null +++ b/science/esys-particle/files/patch-CMakeLists.txt @@ -0,0 +1,22 @@ +--- CMakeLists.txt.orig 2017-01-06 06:14:00 UTC ++++ CMakeLists.txt +@@ -2,8 +2,8 @@ PROJECT(Esys C CXX) + CMAKE_MINIMUM_REQUIRED(VERSION 2.8) + + +-FIND_PACKAGE(Boost COMPONENTS system filesystem python thread REQUIRED) +-INCLUDE(FindPythonLibs) ++FIND_PACKAGE(Boost COMPONENTS system filesystem thread REQUIRED) ++#INCLUDE(FindPythonLibs) + + INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}) + INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/Foundation) +@@ -25,7 +25,7 @@ ADD_SUBDIRECTORY("${CMAKE_SOURCE_DIR}/To + ADD_SUBDIRECTORY("${CMAKE_SOURCE_DIR}/ntable") + ADD_SUBDIRECTORY("${CMAKE_SOURCE_DIR}/tml") + ADD_SUBDIRECTORY("${CMAKE_SOURCE_DIR}/ppa/src") +-ADD_SUBDIRECTORY("${CMAKE_SOURCE_DIR}/Python") ++#ADD_SUBDIRECTORY("${CMAKE_SOURCE_DIR}/Python") + + + ADD_SUBDIRECTORY("${CMAKE_SOURCE_DIR}/Parallel") diff --git a/science/esys-particle/files/patch-Geometry_SphAggGougeBlock.hpp b/science/esys-particle/files/patch-Geometry_SphAggGougeBlock.hpp new file mode 100644 index 000000000000..5206377f0713 --- /dev/null +++ b/science/esys-particle/files/patch-Geometry_SphAggGougeBlock.hpp @@ -0,0 +1,11 @@ +--- Geometry/SphAggGougeBlock.hpp.orig 2018-11-05 04:51:07 UTC ++++ Geometry/SphAggGougeBlock.hpp +@@ -36,7 +36,7 @@ namespace esys { + void SphAggGougeBlock::visitParticles(TmplVisitor& visitor) const + { + GougeBlock3D::visitParticles(visitor); +- for(vector<SBG_ptr>::iterator it = m_grainParticleGen.begin(); ++ for(auto it = m_grainParticleGen.begin(); + it != m_grainParticleGen.end(); + it++) + { diff --git a/science/esys-particle/files/patch-Tools_StressCalculator_Contact.cpp b/science/esys-particle/files/patch-Tools_StressCalculator_Contact.cpp new file mode 100644 index 000000000000..84fe9a0d33f3 --- /dev/null +++ b/science/esys-particle/files/patch-Tools_StressCalculator_Contact.cpp @@ -0,0 +1,11 @@ +--- Tools/StressCalculator/Contact.cpp.orig 2018-11-05 04:44:17 UTC ++++ Tools/StressCalculator/Contact.cpp +@@ -18,7 +18,7 @@ namespace esys + namespace lsm + { + bool ParticleData::s_is3d = true; +- const double ParticleData::FOUR_THIRDS_PI = ((4.0/3.0)*M_PIl); ++ const double ParticleData::FOUR_THIRDS_PI = ((4.0/3.0)*M_PI); + } + } + diff --git a/science/esys-particle/files/patch-Tools_dump2vtk_frame__vtk.cpp b/science/esys-particle/files/patch-Tools_dump2vtk_frame__vtk.cpp new file mode 100644 index 000000000000..28c517c68025 --- /dev/null +++ b/science/esys-particle/files/patch-Tools_dump2vtk_frame__vtk.cpp @@ -0,0 +1,11 @@ +--- Tools/dump2vtk/frame_vtk.cpp.orig 2018-11-05 04:45:11 UTC ++++ Tools/dump2vtk/frame_vtk.cpp +@@ -1276,7 +1276,7 @@ void writeMeshFile(const string& infilen + string header,skip; + int numMeshIG; + +- while (datafile >> header != NULL){ ++ while (datafile >> header){ + if (header == "TMIG"){ + datafile >> numMeshIG; + for(int ni=0;ni<numMeshIG;ni++){ diff --git a/science/esys-particle/pkg-descr b/science/esys-particle/pkg-descr new file mode 100644 index 000000000000..abbb8592e1b6 --- /dev/null +++ b/science/esys-particle/pkg-descr @@ -0,0 +1,9 @@ +ESyS-Particle is Open Source Software for particle-based numerical modelling +using the Discrete Element Method (DEM); a widely adapted technique for +modelling processes involving large deformations, granular flow and/or +fragmentation. ESyS-Particle is best suited for execution on parallel +supercomputers, clusters or multi-core PCs running a Linux-based operating +system. The C++ DEM simulation engine implements spatial domain decomposition +via the Message Passing Interface (MPI). + +WWW: http://www.esys-particle.org/wiki/ diff --git a/science/esys-particle/pkg-plist b/science/esys-particle/pkg-plist new file mode 100644 index 000000000000..8da97b057ffe --- /dev/null +++ b/science/esys-particle/pkg-plist @@ -0,0 +1,19 @@ +bin/dump2geo +bin/dump2vtk +bin/fcconv +bin/fracextract +bin/grainextract +bin/raw2tostress +bin/rotextract +bin/strainextract +lib/libFields.so +lib/libFoundation.so +lib/libGeometry.so +lib/libModel.so +lib/libParallel.so +lib/libTmlComm.so +lib/libTmlMessage.so +lib/libTmlType.so +lib/liblibppa.so +lib/libntable.so +lib/libpis.so diff --git a/science/fvm/Makefile b/science/fvm/Makefile deleted file mode 100644 index 285dad7c0bb8..000000000000 --- a/science/fvm/Makefile +++ /dev/null @@ -1,58 +0,0 @@ -# Created by: thierry@pompo.net -# $FreeBSD$ - -PORTNAME= fvm -PORTVERSION= 0.15.5 -PORTREVISION= 10 -CATEGORIES= science parallel -MASTER_SITES= http://code-saturne.org/releases/ - -MAINTAINER= thierry@FreeBSD.org -COMMENT= Code_Saturne Finite Volume Mesh - -LICENSE= LGPL21 - -LIB_DEPENDS= libmed.so:french/med \ - libbft.so:science/bft \ - libhdf5.so:science/hdf5 \ - libcgns.so:science/cgnslib - -USES= libtool -USE_LDCONFIG= yes -GNU_CONFIGURE= yes -CONFIGURE_ARGS= --with-bft=${LOCALBASE} \ - --with-hdf5=${LOCALBASE} \ - --with-cgns=${LOCALBASE} \ - --with-med=${LOCALBASE} -INSTALL_TARGET= install-strip - -.if defined(WITH_OPENMPI) -BUILD_DEPENDS+= ${LOCALBASE}/mpi/openmpi/bin/mpicc:net/openmpi -RUN_DEPENDS+= ${LOCALBASE}/mpi/openmpi/bin/mpirun:net/openmpi -CONFIGURE_ARGS+= --with-mpi=${LOCALBASE}/mpi/openmpi -.else -BUILD_DEPENDS+= ${LOCALBASE}/bin/mpicc:net/mpich -RUN_DEPENDS+= ${LOCALBASE}/bin/mpirun:net/mpich -CONFIGURE_ARGS+= --with-mpi=${LOCALBASE} -# Do not directly depend on Fortran, but FFLAGS needed to link with mpich -USES+= fortran -.endif - -.if defined(WITH_DEBUG) -CONFIGURE_ARGS+= --enable-debug -.endif - -TESTSBIN= fvm_file_test fvm_interface_test fvm_selector_postfix_test fvm_selector_test - -pre-configure: - ${REINPLACE_CMD} -e 's|-lmpich|-lmpich -lmpl|' \ - ${WRKSRC}/${CONFIGURE_SCRIPT} - # No useful doc there - ${REINPLACE_CMD} -e 's|tests doc|tests|' ${WRKSRC}/Makefile.in - -regression-test: -.for pg in ${TESTSBIN} - (cd ${WRKSRC}/tests; ./${pg}) -.endfor - -.include <bsd.port.mk> diff --git a/science/fvm/distinfo b/science/fvm/distinfo deleted file mode 100644 index fee73c406ecb..000000000000 --- a/science/fvm/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -SHA256 (fvm-0.15.5.tar.gz) = b926d740636ba5b334ef5c199d2bdd1393c427c4df00f8a64a4f3c559cfdad28 -SIZE (fvm-0.15.5.tar.gz) = 732825 diff --git a/science/fvm/files/patch-tests_Makefile.in b/science/fvm/files/patch-tests_Makefile.in deleted file mode 100644 index 00360f3a5962..000000000000 --- a/science/fvm/files/patch-tests_Makefile.in +++ /dev/null @@ -1,11 +0,0 @@ ---- tests/Makefile.in.orig 2011-07-11 11:17:01.000000000 +0200 -+++ tests/Makefile.in 2012-04-07 16:46:12.000000000 +0200 -@@ -300,7 +300,7 @@ - @HAVE_MPI_TRUE@fvm_coupling_test_LDADD = $(top_builddir)/src/libfvm_coupl.la \ - @HAVE_MPI_TRUE@ @BFT_LIBS@ @MPI_LIBS@ - --all: all-am -+all: $(check_PROGRAMS) - - .SUFFIXES: - .SUFFIXES: .c .lo .o .obj diff --git a/science/fvm/pkg-descr b/science/fvm/pkg-descr deleted file mode 100644 index faa5fd5b2723..000000000000 --- a/science/fvm/pkg-descr +++ /dev/null @@ -1,5 +0,0 @@ -FVM stands for Finite Volume Mesh. -It is intended to provide finite volume mesh I/O and some other services such -as interpolation, possibly in parallel using MPI. - -WWW: https://www.code-saturne.org/ diff --git a/science/fvm/pkg-plist b/science/fvm/pkg-plist deleted file mode 100644 index 0a3b743bfc46..000000000000 --- a/science/fvm/pkg-plist +++ /dev/null @@ -1,38 +0,0 @@ -bin/fvm-config -include/fvm_block_to_part.h -include/fvm_config.h -include/fvm_config_priv.h -include/fvm_coupling.h -include/fvm_defs.h -include/fvm_file.h -include/fvm_group.h -include/fvm_interface.h -include/fvm_io_num.h -include/fvm_locator.h -include/fvm_neighborhood.h -include/fvm_nodal.h -include/fvm_nodal_append.h -include/fvm_nodal_extract.h -include/fvm_nodal_extrude.h -include/fvm_nodal_from_desc.h -include/fvm_nodal_order.h -include/fvm_nodal_project.h -include/fvm_nodal_triangulate.h -include/fvm_order.h -include/fvm_parall.h -include/fvm_part_to_block.h -include/fvm_periodicity.h -include/fvm_point_location.h -include/fvm_selector.h -include/fvm_trace.h -include/fvm_triangulate.h -include/fvm_writer.h -lib/libfvm.a -lib/libfvm.so -lib/libfvm.so.0 -lib/libfvm.so.0.0.0 -lib/libfvm_coupl.a -lib/libfvm_coupl.so -lib/libfvm_coupl.so.0 -lib/libfvm_coupl.so.0.0.0 -man/man1/fvm-config.1.gz diff --git a/science/gpaw-setups/Makefile b/science/gpaw-setups/Makefile new file mode 100644 index 000000000000..7e3246ccef29 --- /dev/null +++ b/science/gpaw-setups/Makefile @@ -0,0 +1,24 @@ +# $FreeBSD$ + +PORTNAME= gpaw-setups +DISTVERSION= 0.9.11271 +CATEGORIES= science +MASTER_SITES= https://wiki.fysik.dtu.dk/gpaw-files/ + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Setups (data files) for py-gpaw, the DFT quantum chemistry software + +LICENSE= GPLv3+ +LICENSE_FILE= ${WRKSRC}/COPYING + +NO_BUILD= yes +NO_ARCH= yes + +do-install: + @${MKDIR} ${STAGEDIR}${DATADIR} + ${INSTALL_DATA} ${WRKSRC}/* ${STAGEDIR}${DATADIR} + # autoplist for potentials: 500+ files in DATADIR + @cd ${STAGEDIR}${PREFIX} && \ + ${FIND} ${DATADIR:S/^${PREFIX}\///} -type f >> ${TMPPLIST} + +.include <bsd.port.mk> diff --git a/science/gpaw-setups/distinfo b/science/gpaw-setups/distinfo new file mode 100644 index 000000000000..3d65e99d9d54 --- /dev/null +++ b/science/gpaw-setups/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1540854184 +SHA256 (gpaw-setups-0.9.11271.tar.gz) = 71083327cee250fc61e9a5f5b3907e55b457857b54629563509464cb54b02a97 +SIZE (gpaw-setups-0.9.11271.tar.gz) = 52601589 diff --git a/science/gpaw-setups/pkg-descr b/science/gpaw-setups/pkg-descr new file mode 100644 index 000000000000..e8778d2f6f81 --- /dev/null +++ b/science/gpaw-setups/pkg-descr @@ -0,0 +1,10 @@ +A setup is to the PAW method what a pseudo-potential is to the pseudo-potential +method. There are setups for the LDA, PBE, revPBE, RPBE and GLLBSC functionals. +The setups are stored as compressed XML specification for atomic PAW datasets +files. + +This package installs the setups into the default location, +$(PREFIX)/share/gpaw-setups. You can use the GPAW_SETUP_PATH environment +variable with py-gpaw to override this default location. + +WWW: https://wiki.fysik.dtu.dk/gpaw/setups/setups.html diff --git a/science/gromacs/Makefile b/science/gromacs/Makefile index 960210fbb33e..1ba776ac5b32 100644 --- a/science/gromacs/Makefile +++ b/science/gromacs/Makefile @@ -16,7 +16,7 @@ LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= boost-libs>=1.44:devel/boost-libs LIB_DEPENDS= libhwloc.so:devel/hwloc -USES= cmake:outsource fortran perl5 pkgconfig shebangfix +USES= cmake:outsource compiler:c++11-lang fortran perl5 pkgconfig shebangfix SHEBANG_FILES= admin/*.sh scripts/*.pl scripts/*.sh src/gromacs/selection/*.sh bash_CMD= ${SH} USE_GNOME= libxml2 diff --git a/science/hdf5-18/Makefile b/science/hdf5-18/Makefile index bec6c03d8441..cb7c7537b96a 100644 --- a/science/hdf5-18/Makefile +++ b/science/hdf5-18/Makefile @@ -2,12 +2,11 @@ # $FreeBSD$ PORTNAME= hdf5 -PORTVERSION= 1.8.20 # When PORTVERSION changes, please update french/med/files/patch-configure -PORTREVISION= 2 +PORTVERSION= 1.8.21 # When PORTVERSION changes, please update french/med/files/patch-configure CATEGORIES= science archivers graphics -MASTER_SITES= https://support.hdfgroup.org/ftp/HDF5/current18/src/ \ - http://support.hdfgroup.org/ftp/HDF5/current18/src/ \ - ftp://ftp.hdfgroup.org/HDF5/current18/src/ +MASTER_SITES= https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/${PORTNAME}-${PORTVERSION}/src/ \ + http://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/${PORTNAME}-${PORTVERSION}/src/ \ + ftp://ftp.hdfgroup.org/HDF5/releases/hdf5-1.8/${PORTNAME}-${PORTVERSION}/src/ PKGNAMESUFFIX= -18 MAINTAINER= thierry@FreeBSD.org diff --git a/science/hdf5-18/distinfo b/science/hdf5-18/distinfo index 75865c544ec2..c94096ef1d50 100644 --- a/science/hdf5-18/distinfo +++ b/science/hdf5-18/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1512312358 -SHA256 (hdf5-1.8.20.tar.bz2) = a4f2db7e0a078aa324f64e0216a80731731f73025367fa94d158c9b1d3fbdf6f -SIZE (hdf5-1.8.20.tar.bz2) = 10170195 +TIMESTAMP = 1541674750 +SHA256 (hdf5-1.8.21.tar.bz2) = e5b1b1dee44a64b795a91c3321ab7196d9e0871fe50d42969761794e3899f40d +SIZE (hdf5-1.8.21.tar.bz2) = 6872822 diff --git a/science/hdf5-18/pkg-plist b/science/hdf5-18/pkg-plist index c08ec344a321..12adce530109 100644 --- a/science/hdf5-18/pkg-plist +++ b/science/hdf5-18/pkg-plist @@ -19,6 +19,7 @@ bin/h5stat-18 bin/h5unjam-18 include/hdf5-18/H5AbstractDs.h include/hdf5-18/H5ACpublic.h +include/hdf5-18/H5AcreatProp.h include/hdf5-18/H5api_adpt.h include/hdf5-18/H5Apublic.h include/hdf5-18/H5ArrayType.h @@ -65,6 +66,7 @@ include/hdf5-18/H5Include.h include/hdf5-18/H5IntType.h include/hdf5-18/H5Ipublic.h include/hdf5-18/H5LaccProp.h +include/hdf5-18/H5LcreatProp.h include/hdf5-18/H5Library.h include/hdf5-18/H5Location.h include/hdf5-18/H5Lpublic.h @@ -83,6 +85,7 @@ include/hdf5-18/H5PTpublic.h include/hdf5-18/H5Rpublic.h include/hdf5-18/H5Spublic.h include/hdf5-18/H5StrType.h +include/hdf5-18/H5StrcreatProp.h include/hdf5-18/H5TBpublic.h include/hdf5-18/H5Tpublic.h include/hdf5-18/H5VarLenType.h @@ -133,32 +136,32 @@ lib/libhdf5-18.la lib/libhdf5-18.settings lib/libhdf5-18.so lib/libhdf5-18.so.10 -lib/libhdf5-18.so.10.3.1 +lib/libhdf5-18.so.10.3.2 lib/libhdf5-18_cpp.a lib/libhdf5-18_cpp.la lib/libhdf5-18_cpp.so -lib/libhdf5-18_cpp.so.15 -lib/libhdf5-18_cpp.so.15.0.0 +lib/libhdf5-18_cpp.so.16 +lib/libhdf5-18_cpp.so.16.0.0 %%FORTRAN%%lib/libhdf5-18_fortran.a %%FORTRAN%%lib/libhdf5-18_fortran.la %%FORTRAN%%lib/libhdf5-18_fortran.so %%FORTRAN%%lib/libhdf5-18_fortran.so.10 -%%FORTRAN%%lib/libhdf5-18_fortran.so.10.0.5 +%%FORTRAN%%lib/libhdf5-18_fortran.so.10.0.6 lib/libhdf5-18_hl.a lib/libhdf5-18_hl.la lib/libhdf5-18_hl.so lib/libhdf5-18_hl.so.10 -lib/libhdf5-18_hl.so.10.2.1 +lib/libhdf5-18_hl.so.10.2.2 lib/libhdf5-18_hl_cpp.a lib/libhdf5-18_hl_cpp.la lib/libhdf5-18_hl_cpp.so lib/libhdf5-18_hl_cpp.so.11 -lib/libhdf5-18_hl_cpp.so.11.1.1 +lib/libhdf5-18_hl_cpp.so.11.1.2 %%FORTRAN%%lib/libhdf5-18hl_fortran.a %%FORTRAN%%lib/libhdf5-18hl_fortran.la %%FORTRAN%%lib/libhdf5-18hl_fortran.so %%FORTRAN%%lib/libhdf5-18hl_fortran.so.10 -%%FORTRAN%%lib/libhdf5-18hl_fortran.so.10.0.4 +%%FORTRAN%%lib/libhdf5-18hl_fortran.so.10.0.5 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/README %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/chunks.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/compound.cpp diff --git a/science/kalzium/Makefile b/science/kalzium/Makefile index a12be4b6c2fb..1815be7453e1 100644 --- a/science/kalzium/Makefile +++ b/science/kalzium/Makefile @@ -2,19 +2,21 @@ PORTNAME= kalzium DISTVERSION= ${KDE_APPLICATIONS_VERSION} +PORTREVISION= 2 CATEGORIES= science kde kde-applications MAINTAINER= kde@FreeBSD.org COMMENT= Periodic table of elements for KDE 4 LIB_DEPENDS= libopenbabel.so:science/openbabel \ - libavogadro.so:science/avogadro + libAvogadroCore.so:science/avogadrolibs BUILD_DEPENDS= ${LOCALBASE}/lib/ocaml/facile/facile.a:math/facile \ ${LOCALBASE}/libdata/pkgconfig/chemical-mime-data.pc:science/chemical-mime-data RUN_DEPENDS= ${LOCALBASE}/libdata/pkgconfig/chemical-mime-data.pc:science/chemical-mime-data -USES= cmake:outsource gettext kde:5 pkgconfig qt:5 tar:xz -USE_KDE= auth archive bookmarks codecs completion config configwidgets \ +USES= cmake:outsource desktop-file-utils gettext kde:5 pkgconfig qt:5 tar:xz +USE_GL= gl glew glu +USE_KDE= auth archive attica bookmarks codecs completion config configwidgets \ coreaddons crash doctools ecm emoticons guiaddons i18n \ iconthemes itemmodels itemviews jobwidgets js kdelibs4support \ khtml kio newstuff notifications parts plotting service solid \ @@ -22,7 +24,7 @@ USE_KDE= auth archive bookmarks codecs completion config configwidgets \ xmlgui USE_OCAML= yes NO_OCAML_RUNDEPENDS= yes -USE_QT= core dbus gui network opengl printsupport qml quick script svg \ +USE_QT= concurrent core dbus declarative gui network opengl printsupport script svg \ widgets xml \ buildtools_build qmake_build diff --git a/science/kalzium/distinfo b/science/kalzium/distinfo index b587d918660d..db803033c20a 100644 --- a/science/kalzium/distinfo +++ b/science/kalzium/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1539116194 -SHA256 (KDE/applications/18.08.2/kalzium-18.08.2.tar.xz) = 50e7194db4b6d2b9123dd4907e6fb642a6061a0d3188e10cda274126cdc26a61 -SIZE (KDE/applications/18.08.2/kalzium-18.08.2.tar.xz) = 24378012 +TIMESTAMP = 1541484467 +SHA256 (KDE/applications/18.08.3/kalzium-18.08.3.tar.xz) = 4b3b91fb86b2d97efc7ca8c3037f33101d402df7dd2fe311b12a87468e8a6b5c +SIZE (KDE/applications/18.08.3/kalzium-18.08.3.tar.xz) = 24377636 diff --git a/science/kalzium/pkg-plist b/science/kalzium/pkg-plist index 6427aa1db1dd..d9184ae07838 100644 --- a/science/kalzium/pkg-plist +++ b/science/kalzium/pkg-plist @@ -11,6 +11,9 @@ include/libkdeedu/parser.h include/libkdeedu/psetables.h include/libkdeedu/spectrum.h include/libkdeedu/spectrumparser.h +lib/libcompoundviewer.so +lib/libcompoundviewer.so.5 +lib/libcompoundviewer.so.5.0.0 lib/libscience.so lib/libscience.so.5 lib/libscience.so.5.0.0 diff --git a/science/lammps/Makefile b/science/lammps/Makefile index 99f2e2764a0d..70f2982c1068 100644 --- a/science/lammps/Makefile +++ b/science/lammps/Makefile @@ -1,7 +1,8 @@ # $FreeBSD$ PORTNAME= lammps -PORTVERSION= ${GH_TAGNAME:C/stable_([0-9]{1,2})([A-Z][a-z][a-z])([0-9]{4})/\3.\2.\1/S/Jan/01/S/Feb/02/S/Mar/03/S/Apr/04/S/May/05/S/Jun/06/S/Jul/07/S/Aug/08/S/Sep/09/S/Oct/10/S/Nov/11/S/Dec/12/} +PORTVERSION= ${GH_TAGNAME:C/(stable|patch)_([0-9]{1,2})([A-Z][a-z][a-z])([0-9]{4})/\4.\3.\2/S/Jan/01/S/Feb/02/S/Mar/03/S/Apr/04/S/May/05/S/Jun/06/S/Jul/07/S/Aug/08/S/Sep/09/S/Oct/10/S/Nov/11/S/Dec/12/} +PORTREVISION= 2 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -10,24 +11,63 @@ COMMENT= Classical molecular dynamics code with a focus on materials modeling LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE -LIB_DEPENDS= libpng16.so:graphics/png \ - libmpi_cxx.so:net/openmpi +CONFLICTS_BUILD= ga # conflicts with include/error.h, already fixed in the head -USES= cmake:outsource eigen:3 jpeg shebangfix +USES= blaslapack:openblas cmake:outsource,noninja eigen:3 fortran shebangfix USE_GITHUB= yes GH_TAGNAME= stable_22Aug2018 SHEBANG_GLOB= *.sh *.bash SHEBANG_FILES= lib/kokkos/bin/nvcc_wrapper CMAKE_SOURCE_PATH= ${WRKSRC}/cmake +CMAKE_ARGS= -DBLA_VENDOR:STRING="OpenBLAS" -OPTIONS_DEFINE= FFMPEG -OPTIONS_DEFAULT= FFMPEG +OPTIONS_DEFINE= JPEG PNG GZIP FFMPEG VORONOI LATTE +OPTIONS_GROUP= PARALLEL +OPTIONS_GROUP_PARALLEL= MPI OPENMP +OPTIONS_DEFAULT= MPI OPENMP JPEG PNG GZIP FFMPEG VORONOI LATTE +PARALLEL_DESC= Enable parallelizations: + +MPI_CMAKE_BOOL= BUILD_MPI +MPI_LIB_DEPENDS= libmpi.so:net/openmpi + +OPENMP_CMAKE_BOOL= BUILD_OMP +OPENMP_LIB_DEPENDS= libomp.so:devel/openmp FFMPEG_BUILD_DEPENDS= ffmpeg:multimedia/ffmpeg FFMPEG_RUN_DEPENDS= ffmpeg:multimedia/ffmpeg +JPEG_CMAKE_BOOL= WITH_JPEG +JPEG_USES= jpeg + +PNG_CMAKE_BOOL= WITH_PNG +PNG_LIB_DEPENDS= libpng16.so:graphics/png + +GZIP_CMAKE_BOOL= WITH_GZIP + +FFMPEG_CMAKE_BOOL= WITH_FFMPEG + +VORONOI_DESC= Use voro++, Voronoi tessellation package +VORONOI_CMAKE_BOOL= PKG_VORONOI +LIB_DEPENDS= libvoro++.so:science/voro++ + +LATTE_DESC= Use LATTE package +LATTE_CMAKE_BOOL= PKG_LATTE +LATTE_LIB_DEPENDS= liblatte.so:science/latte + +# use clang from ports because cmake can't find OpenMP with base clang, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=223678 +LLVM_VER= 60 +BUILD_DEPENDS+= clang${LLVM_VER}:devel/llvm${LLVM_VER} +CPP= clang-cpp${LLVM_VER} +CC= clang${LLVM_VER} +CXX= clang++${LLVM_VER} + +MAKE_ARGS= VERBOSE=1 + +post-patch: + @${REINPLACE_CMD} 's|SHELL = /bin/bash|SHELL = ${LOCALBASE}/bin/bash|' ${WRKSRC}/src/Makefile + post-patch-FFMPEG-off: - @${REINPLACE_CMD} 's|find_program(FFMPEG_EXECUTABLE|#&|' ${WRKSRC}/CMakeLists.txt + @${REINPLACE_CMD} 's|find_program(FFMPEG_EXECUTABLE|#&|' ${WRKSRC}/cmake/CMakeLists.txt .include <bsd.port.mk> diff --git a/science/lammps/distinfo b/science/lammps/distinfo index 57f11abc5c11..9bbfb9aafdfe 100644 --- a/science/lammps/distinfo +++ b/science/lammps/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1536211844 +TIMESTAMP = 1540967816 SHA256 (lammps-lammps-2018.08.22-stable_22Aug2018_GH0.tar.gz) = 78e7b389523d2fd5243a6f2daab72667907980d31bee22e44b64122c3afc9f04 SIZE (lammps-lammps-2018.08.22-stable_22Aug2018_GH0.tar.gz) = 108761541 diff --git a/science/latte/Makefile b/science/latte/Makefile new file mode 100644 index 000000000000..d218af9617d8 --- /dev/null +++ b/science/latte/Makefile @@ -0,0 +1,44 @@ +# $FreeBSD$ + +PORTNAME= latte +DISTVERSIONPREFIX= v +DISTVERSION= 1.2.1 +CATEGORIES= science + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Quantum chemistry: Density functional tight binding molecular dynamics + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE_GPL-2.0 + +USES= blaslapack:openblas cmake:outsource,noninja fortran shebangfix +SHEBANG_FILES= tests/run_test.sh +USE_GITHUB= yes +GH_ACCOUNT= lanl +GH_PROJECT= ${PORTNAME:tu} +USE_LDCONFIG= yes + +CMAKE_SOURCE_PATH= ${WRKSRC}/cmake +CMAKE_ON= BUILD_SHARED_LIBS +CMAKE_ARGS= -DBLA_VENDOR:STRING="OpenBLAS" + +OPTIONS_DEFINE= DBCSR OPENMP MPI # TODO PROGRESS needs to be ported +OPTIONS_DEFAULT= OPENMP MPI + +DBCSR_DESC= Use distributed block compressed sparse row matrix library +DBCSR_CMAKE_BOOL= DBCSR_OPT +DBCSR_LIB_DEPENDS= libdbcsr.so:math/dbcsr +DBCSR_BROKEN= see https://github.com/lanl/LATTE/issues/92 + +OPENMP_CMAKE_BOOL= OPENMP +OPENMP_LIB_DEPENDS= libomp.so:devel/openmp + +MPI_CMAKE_BOOL= DO_MPI +MPI_LIB_DEPENDS= libmpi.so:net/openmpi +MPI_LDFLAGS= ${LOCALBASE}/mpi/openmpi/lib/libmpi_mpifh.so +MPI_PLIST_FILES= bin/LATTE_MPI_DOUBLE +MPI_PLIST_FILES_OFF= bin/LATTE_DOUBLE + +PLIST_FILES= lib/liblatte.so + +.include <bsd.port.mk> diff --git a/science/latte/distinfo b/science/latte/distinfo new file mode 100644 index 000000000000..bf4e2adc38d3 --- /dev/null +++ b/science/latte/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1540963082 +SHA256 (lanl-LATTE-v1.2.1_GH0.tar.gz) = 343f28174365bd2185ff957038ac727d33659ef1bdf82f11af5603af3d943f2c +SIZE (lanl-LATTE-v1.2.1_GH0.tar.gz) = 6673701 diff --git a/science/latte/pkg-descr b/science/latte/pkg-descr new file mode 100644 index 000000000000..9508cb84585a --- /dev/null +++ b/science/latte/pkg-descr @@ -0,0 +1,12 @@ +A molecular dynamics package based around self-consistent-charge density +functional tight binding theory. + +Features: +* Forces computed at the SCC-DFTB level. +* Provides forces and the potential component of the total energy. +* Integrates the electronic degrees of freedom (XL) (provides charges). +* Solves the electronic structure of the system. +* Several solvers such as SP2, Truncated SP2, Chebyshev polynomial + expansion, etc. + +WWW: https://github.com/lanl/LATTE diff --git a/science/libint2/Makefile b/science/libint2/Makefile index 93bd2ee4d167..320a71b683ed 100644 --- a/science/libint2/Makefile +++ b/science/libint2/Makefile @@ -15,8 +15,6 @@ COMMENT= Evaluate the integrals in modern atomic and molecular theory LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE -BROKEN_FreeBSD_10= /usr/include/c++/v1/memory:4004:35: error: no viable overloaded '=': __e->__weak_this_ = *this; - LIB_DEPENDS= libboost_system.so:devel/boost-libs \ libgmpxx.so:math/gmp diff --git a/science/liggghts/Makefile b/science/liggghts/Makefile new file mode 100644 index 000000000000..48aa7f48320c --- /dev/null +++ b/science/liggghts/Makefile @@ -0,0 +1,40 @@ +# $FreeBSD$ + +PORTNAME= liggghts +DISTVERSION= 3.8.0 +PORTREVISION= 1 +CATEGORIES= science + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Discrete element method particle simulation software + +LICENSE= GPLv2 +LICENSE_FILE= ${WRKSRC}/../LICENSE + +BUILD_DEPENDS= gsed:textproc/gsed +LIB_DEPENDS= libexpat.so:textproc/expat2 \ + libfreetype.so:print/freetype2 \ + libmpi.so:net/openmpi \ + libpng16.so:graphics/png \ + libtiff.so:graphics/tiff \ + libvtkViewsCore-8.1.so:math/vtk8 + +USES= compiler:c++17-lang cmake:outsource fortran jpeg qt:5 +USE_GITHUB= yes +GH_ACCOUNT= CFDEMproject +GH_PROJECT= ${PORTNAME:tu}-PUBLIC +USE_XORG= ice sm x11 xext xt +USE_QT= core gui sql widgets qmake_build buildtools_build +USE_LDCONFIG= yes + +CMAKE_ARGS= -DMPI_C_COMPILER:FILEPATH="${LOCALBASE}/mpi/openmpi/bin/mpicc" -DMPI_CXX_COMPILER:FILEPATH="${LOCALBASE}/mpi/openmpi/bin/mpicxx" \ + -DVTK_DIR:FILEPATH="${LOCALBASE}/lib/cmake/vtk-8.1" + +WRKSRC_SUBDIR= src + +CFLAGS+= -fPIC +CXXFLAGS+= -fPIC + +BINARY_ALIAS= sed=gsed + +.include <bsd.port.mk> diff --git a/science/liggghts/distinfo b/science/liggghts/distinfo new file mode 100644 index 000000000000..bc32d19b2eb5 --- /dev/null +++ b/science/liggghts/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1541105259 +SHA256 (CFDEMproject-LIGGGHTS-PUBLIC-3.8.0_GH0.tar.gz) = 9cb2e6596f584463ac2f80e3ff7b9588b7e3638c44324635b6329df87b90ab03 +SIZE (CFDEMproject-LIGGGHTS-PUBLIC-3.8.0_GH0.tar.gz) = 35989481 diff --git a/science/liggghts/files/patch-CMakeLists.txt b/science/liggghts/files/patch-CMakeLists.txt new file mode 100644 index 000000000000..eae36a292121 --- /dev/null +++ b/science/liggghts/files/patch-CMakeLists.txt @@ -0,0 +1,77 @@ +--- CMakeLists.txt.orig 2017-11-30 09:34:53 UTC ++++ CMakeLists.txt +@@ -47,9 +47,9 @@ ENDIF() + ADD_LIBRARY(liggghts_obj OBJECT ${SOURCES}) + ADD_DEPENDENCIES(liggghts_obj GenerateHeaders) + +-ADD_LIBRARY(liggghts_static STATIC $<TARGET_OBJECTS:liggghts_obj>) +-SET_TARGET_PROPERTIES(liggghts_static PROPERTIES OUTPUT_NAME liggghts) +-SET_PROPERTY(TARGET liggghts_static PROPERTY PUBLIC_HEADER ${HEADERS}) ++#ADD_LIBRARY(liggghts_static STATIC $<TARGET_OBJECTS:liggghts_obj>) ++#SET_TARGET_PROPERTIES(liggghts_static PROPERTIES OUTPUT_NAME liggghts) ++#SET_PROPERTY(TARGET liggghts_static PROPERTY PUBLIC_HEADER ${HEADERS}) + + ADD_LIBRARY(liggghts_shared SHARED $<TARGET_OBJECTS:liggghts_obj>) + SET_TARGET_PROPERTIES(liggghts_shared PROPERTIES OUTPUT_NAME liggghts) +@@ -67,7 +67,7 @@ FIND_PACKAGE(VTK NO_MODULE) + IF(VTK_FOUND) + INCLUDE(${VTK_USE_FILE}) + ADD_DEFINITIONS(-DLAMMPS_VTK) +- TARGET_LINK_LIBRARIES(liggghts_static ${VTK_LIBRARIES}) ++ #TARGET_LINK_LIBRARIES(liggghts_static ${VTK_LIBRARIES}) + TARGET_LINK_LIBRARIES(liggghts_shared ${VTK_LIBRARIES}) + TARGET_LINK_LIBRARIES(liggghts_bin ${VTK_LIBRARIES}) + MESSAGE(STATUS "Found VTK") +@@ -82,7 +82,7 @@ FIND_PACKAGE(JPEG) + IF(JPEG_FOUND) + INCLUDE_DIRECTORIES(${JPEG_INCLUDE_DIR}) + ADD_DEFINITIONS(-DLAMMPS_JPEG) +- TARGET_LINK_LIBRARIES(liggghts_static jpeg) ++ #TARGET_LINK_LIBRARIES(liggghts_static jpeg) + TARGET_LINK_LIBRARIES(liggghts_shared jpeg) + TARGET_LINK_LIBRARIES(liggghts_bin jpeg) + ELSE(JPEG_FOUND) +@@ -95,25 +95,25 @@ FIND_PACKAGE(MPI) + + IF(MPI_FOUND) + INCLUDE_DIRECTORIES(${MPI_INCLUDE_PATH}) +- TARGET_LINK_LIBRARIES(liggghts_static ${MPI_LIBRARIES}) ++ #TARGET_LINK_LIBRARIES(liggghts_static ${MPI_LIBRARIES}) + TARGET_LINK_LIBRARIES(liggghts_shared ${MPI_LIBRARIES}) + TARGET_LINK_LIBRARIES(liggghts_bin ${MPI_LIBRARIES}) + + IF(MPI_COMPILE_FLAGS) +- SET_TARGET_PROPERTIES(liggghts_static PROPERTIES COMPILE_FLAGS "${MPI_COMPILE_FLAGS}") ++ #SET_TARGET_PROPERTIES(liggghts_static PROPERTIES COMPILE_FLAGS "${MPI_COMPILE_FLAGS}") + SET_TARGET_PROPERTIES(liggghts_shared PROPERTIES COMPILE_FLAGS "${MPI_COMPILE_FLAGS}") + SET_TARGET_PROPERTIES(liggghts_bin PROPERTIES COMPILE_FLAGS "${MPI_COMPILE_FLAGS}") + ENDIF() + + IF(MPI_LINK_FLAGS) +- SET_TARGET_PROPERTIES(liggghts_static PROPERTIES LINK_FLAGS "${MPI_LINK_FLAGS}") ++ #SET_TARGET_PROPERTIES(liggghts_static PROPERTIES LINK_FLAGS "${MPI_LINK_FLAGS}") + SET_TARGET_PROPERTIES(liggghts_shared PROPERTIES LINK_FLAGS "${MPI_LINK_FLAGS}") + SET_TARGET_PROPERTIES(liggghts_bin PROPERTIES LINK_FLAGS "${MPI_LINK_FLAGS}") + ENDIF() + ELSE(MPI_FOUND) + MESSAGE(STATUS "MPI NOT found! Using MPI Stubs instead.") + ADD_SUBDIRECTORY(STUBS) +- TARGET_LINK_LIBRARIES(liggghts_static mpi_stubs) ++ #TARGET_LINK_LIBRARIES(liggghts_static mpi_stubs) + TARGET_LINK_LIBRARIES(liggghts_shared mpi_stubs) + TARGET_LINK_LIBRARIES(liggghts_bin mpi_stubs) + ENDIF(MPI_FOUND) +@@ -128,11 +128,11 @@ ENDIF(MPI_FOUND) + # RUNTIME DESTINATION bin + # LIBRARY DESTINATION lib) + +-install(TARGETS liggghts_bin liggghts_static liggghts_shared ++install(TARGETS liggghts_bin liggghts_shared + RUNTIME DESTINATION bin + LIBRARY DESTINATION lib + ARCHIVE DESTINATION lib +- PUBLIC_HEADER DESTINATION include) ++ PUBLIC_HEADER DESTINATION include/liggghts) + IF (WIN32) + install(DIRECTORY WINDOWS DESTINATION include) + ENDIF() diff --git a/science/liggghts/files/patch-finish.cpp b/science/liggghts/files/patch-finish.cpp new file mode 100644 index 000000000000..fd27979c4b65 --- /dev/null +++ b/science/liggghts/files/patch-finish.cpp @@ -0,0 +1,11 @@ +--- finish.cpp.orig 2018-11-02 06:42:25 UTC ++++ finish.cpp +@@ -719,7 +719,7 @@ void Finish::end(int flag) + + nneighfull = 0; + if (m < neighbor->old_nrequest) { +- if (neighbor->lists[m]->numneigh > 0) { ++ if (neighbor->lists[m]->numneigh) { // see https://www.cfdem.com/forums/error-non-const-lvalue-reference-type-basicostringstream-cannot-bind-temporary-type + int inum = neighbor->lists[m]->inum; + int *ilist = neighbor->lists[m]->ilist; + int *numneigh = neighbor->lists[m]->numneigh; diff --git a/science/liggghts/files/patch-math__vector.h b/science/liggghts/files/patch-math__vector.h new file mode 100644 index 000000000000..4c96ce457e1a --- /dev/null +++ b/science/liggghts/files/patch-math__vector.h @@ -0,0 +1,38 @@ +--- math_vector.h.orig 2018-11-02 06:51:37 UTC ++++ math_vector.h +@@ -94,7 +94,7 @@ inline void vec_neg(vector &dest) { + dest[2] = -dest[2]; } + + inline void vec_norm(vector &dest) { // a/|a| +- register double f = sqrt(vec_dot(dest, dest)); ++ double f = sqrt(vec_dot(dest, dest)); + dest[0] /= f; + dest[1] /= f; + dest[2] /= f; } +@@ -222,7 +222,7 @@ inline void form_subtr(shape &dest, form + dest[3] -= src[3]; dest[4] -= src[4]; dest[5] -= src[5]; } + + inline int form_inv(form &m_inv, form &m) { // m^-1 +- register double det = form_det(m); ++ double det = form_det(m); + if (fzero(det)) return 0; + m_inv[0] = (m[1]*m[2]-m[3]*m[3])/det; + m_inv[1] = (m[0]*m[2]-m[4]*m[4])/det; +@@ -377,7 +377,7 @@ inline void form4_unit(form4 &dest) { + dest[0] = dest[1] = dest[2] = dest[3] = 1.0; } + + inline double form4_det(form4 &m) { +- register double f = m[6]*m[7]-m[5]*m[8]; ++ double f = m[6]*m[7]-m[5]*m[8]; + return m[0]*( + m[1]*(m[2]*m[3]-m[4]*m[4])+ + m[5]*(2.0*m[4]*m[7]-m[2]*m[5])-m[3]*m[7]*m[7])+f*f+ +@@ -387,7 +387,7 @@ inline double form4_det(form4 &m) { + m[9]*(m[4]*m[4]-m[2]*m[3])); } + + inline int form4_inv(form4 &m_inv, form4 &m) { +- register double det = form4_det(m); ++ double det = form4_det(m); + if (fzero(det)) return 0; + m_inv[0] = (m[1]*(m[2]*m[3]-m[4]*m[4])+ + m[5]*(2.0*m[4]*m[7]-m[2]*m[5])-m[3]*m[7]*m[7])/det; diff --git a/science/liggghts/files/patch-pair.cpp b/science/liggghts/files/patch-pair.cpp new file mode 100644 index 000000000000..4e1a7db54aef --- /dev/null +++ b/science/liggghts/files/patch-pair.cpp @@ -0,0 +1,20 @@ +--- pair.cpp.orig 2018-11-02 06:56:59 UTC ++++ pair.cpp +@@ -566,7 +566,7 @@ void Pair::init_tables_disp(double cut_l + } + + rsq = rsq_lookup.f; +- register double x2 = g2*rsq, a2 = 1.0/x2; ++ double x2 = g2*rsq, a2 = 1.0/x2; + x2 = a2*exp(-x2); + + rdisptable[i] = rsq_lookup.f; +@@ -612,7 +612,7 @@ void Pair::init_tables_disp(double cut_l + if (rsq_lookup.f < (cut_lj_globalsq = cut_lj_global * cut_lj_global)) { + rsq_lookup.f = cut_lj_globalsq; + +- register double x2 = g2*rsq, a2 = 1.0/x2; ++ double x2 = g2*rsq, a2 = 1.0/x2; + x2 = a2*exp(-x2); + f_tmp = g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq; + e_tmp = g6*((a2+1.0)*a2+0.5)*x2; diff --git a/science/liggghts/files/patch-utils.h b/science/liggghts/files/patch-utils.h new file mode 100644 index 000000000000..31adc450fe7e --- /dev/null +++ b/science/liggghts/files/patch-utils.h @@ -0,0 +1,15 @@ +--- utils.h.orig 2018-11-02 06:39:45 UTC ++++ utils.h +@@ -67,7 +67,11 @@ namespace Utils { + + inline std::string int_to_string(int a) + { +- return static_cast< std::ostringstream & >(( std::ostringstream() << std::dec << a ) ).str(); ++ // see https://www.cfdem.com/forums/error-non-const-lvalue-reference-type-basicostringstream-cannot-bind-temporary-type ++ // return static_cast< std::ostringstream & >(( std::ostringstream() << std::dec << a ) ).str(); ++ std::ostringstream ss; ++ ss << std::dec << a; ++ return ss.str(); + } + + inline std::string double_to_string(double dbl) diff --git a/science/liggghts/pkg-descr b/science/liggghts/pkg-descr new file mode 100644 index 000000000000..d1f50855ddd8 --- /dev/null +++ b/science/liggghts/pkg-descr @@ -0,0 +1,21 @@ +LIGGGHTS stands for LAMMPS improved for general granular and granular heat +transfer simulations. + +LAMMPS is a classical molecular dynamics simulator. It is widely used in the +field of Molecular Dynamics. Thanks to physical and algorithmic analogies, +LAMMPS is a very good platform for DEM simulations. LAMMPS offers a GRANULAR +package to perform these kind of simulations. LIGGGHTS aims to improve those +capability with the goal to apply it to industrial applications. + +The features added in LIGGGHTS with respect to the original LAMMPS distribution +comprise: +* Import and handling of complex wall geometries from CAD +* A moving mesh feature to account for moving geometry +* Re-write of contact force formulation, including optional cohesional and + rolling friction forces +* Heat conduction between particles in contact +* Improved particle insertion based on surface and volume meshes +* A "template" mechanism to account for particle non-uniformity +* More features added in the meantime and upcoming, see here. + +WWW: https://www.cfdem.com/liggghts-open-source-discrete-element-method-particle-simulation-code diff --git a/science/liggghts/pkg-plist b/science/liggghts/pkg-plist new file mode 100644 index 000000000000..b86a3b0abb72 --- /dev/null +++ b/science/liggghts/pkg-plist @@ -0,0 +1,448 @@ +bin/liggghts +include/liggghts/abstract_mesh.h +include/liggghts/accelerator_cuda.h +include/liggghts/accelerator_omp.h +include/liggghts/angle.h +include/liggghts/angle_hybrid.h +include/liggghts/associative_pointer_array.h +include/liggghts/associative_pointer_array_I.h +include/liggghts/atom.h +include/liggghts/atom_masks.h +include/liggghts/atom_vec.h +include/liggghts/atom_vec_atomic.h +include/liggghts/atom_vec_charge.h +include/liggghts/atom_vec_convexhull.h +include/liggghts/atom_vec_ellipsoid.h +include/liggghts/atom_vec_full.h +include/liggghts/atom_vec_hybrid.h +include/liggghts/atom_vec_line.h +include/liggghts/atom_vec_molecular.h +include/liggghts/atom_vec_sph.h +include/liggghts/atom_vec_sph_var.h +include/liggghts/atom_vec_sphere.h +include/liggghts/atom_vec_superquadric.h +include/liggghts/atom_vec_tri.h +include/liggghts/bond.h +include/liggghts/bond_harmonic.h +include/liggghts/bond_hybrid.h +include/liggghts/bounding_box.h +include/liggghts/cfd_datacoupling.h +include/liggghts/cfd_datacoupling_file.h +include/liggghts/cfd_datacoupling_mpi.h +include/liggghts/cfd_datacoupling_simple.h +include/liggghts/cfd_regionmodel.h +include/liggghts/cfd_regionmodel_none.h +include/liggghts/change_box.h +include/liggghts/citeme.h +include/liggghts/cohesion_model_base.h +include/liggghts/cohesion_model_easo_capillary_viscous.h +include/liggghts/cohesion_model_sjkr.h +include/liggghts/cohesion_model_sjkr2.h +include/liggghts/cohesion_model_washino_capillary_viscous.h +include/liggghts/comm.h +include/liggghts/comm_I.h +include/liggghts/compute.h +include/liggghts/compute_atom_molecule.h +include/liggghts/compute_bond_local.h +include/liggghts/compute_centro_atom.h +include/liggghts/compute_cluster_atom.h +include/liggghts/compute_cna_atom.h +include/liggghts/compute_com.h +include/liggghts/compute_com_molecule.h +include/liggghts/compute_contact_atom.h +include/liggghts/compute_contact_atom_gran.h +include/liggghts/compute_coord_atom.h +include/liggghts/compute_displace_atom.h +include/liggghts/compute_erotate.h +include/liggghts/compute_erotate_asphere.h +include/liggghts/compute_erotate_multisphere.h +include/liggghts/compute_erotate_sphere.h +include/liggghts/compute_erotate_sphere_atom.h +include/liggghts/compute_erotate_superquadric.h +include/liggghts/compute_group_group.h +include/liggghts/compute_gyration.h +include/liggghts/compute_gyration_molecule.h +include/liggghts/compute_inertia_molecule.h +include/liggghts/compute_ke.h +include/liggghts/compute_ke_atom.h +include/liggghts/compute_ke_multisphere.h +include/liggghts/compute_msd.h +include/liggghts/compute_msd_molecule.h +include/liggghts/compute_nparticles_tracer_region.h +include/liggghts/compute_pair_gran_local.h +include/liggghts/compute_pe.h +include/liggghts/compute_pe_atom.h +include/liggghts/compute_pressure.h +include/liggghts/compute_property_atom.h +include/liggghts/compute_property_local.h +include/liggghts/compute_property_molecule.h +include/liggghts/compute_rdf.h +include/liggghts/compute_reduce.h +include/liggghts/compute_reduce_region.h +include/liggghts/compute_rigid.h +include/liggghts/compute_slice.h +include/liggghts/compute_stress_atom.h +include/liggghts/compute_temp.h +include/liggghts/contact_interface.h +include/liggghts/contact_model_base.h +include/liggghts/contact_model_constants.h +include/liggghts/contact_models.h +include/liggghts/container.h +include/liggghts/container_base.h +include/liggghts/container_base_I.h +include/liggghts/create_atoms.h +include/liggghts/create_box.h +include/liggghts/custom_value_tracker.h +include/liggghts/custom_value_tracker_I.h +include/liggghts/debug_liggghts.h +include/liggghts/delete_atoms.h +include/liggghts/delete_bonds.h +include/liggghts/dihedral.h +include/liggghts/dihedral_hybrid.h +include/liggghts/displace_atoms.h +include/liggghts/domain.h +include/liggghts/domain_I.h +include/liggghts/domain_definitions.h +include/liggghts/domain_wedge.h +include/liggghts/domain_wedge_dummy.h +include/liggghts/dump.h +include/liggghts/dump_atom_vtk.h +include/liggghts/dump_custom.h +include/liggghts/dump_custom_vtk.h +include/liggghts/dump_custom_vtm.h +include/liggghts/dump_decomposition_vtk.h +include/liggghts/dump_euler_vtk.h +include/liggghts/dump_image.h +include/liggghts/dump_local.h +include/liggghts/dump_local_gran.h +include/liggghts/dump_local_gran_vtk.h +include/liggghts/dump_mesh.h +include/liggghts/dump_mesh_stl.h +include/liggghts/dump_mesh_vtk.h +include/liggghts/dump_mesh_vtm.h +include/liggghts/dump_movie.h +include/liggghts/dump_particle.h +include/liggghts/dump_vtk.h +include/liggghts/dump_xyz.h +include/liggghts/error.h +include/liggghts/error_special.h +include/liggghts/finish.h +include/liggghts/fix.h +include/liggghts/fix_adapt.h +include/liggghts/fix_addforce.h +include/liggghts/fix_ave_atom.h +include/liggghts/fix_ave_correlate.h +include/liggghts/fix_ave_euler.h +include/liggghts/fix_ave_histo.h +include/liggghts/fix_ave_spatial.h +include/liggghts/fix_ave_time.h +include/liggghts/fix_aveforce.h +include/liggghts/fix_base_liggghts.h +include/liggghts/fix_box_relax.h +include/liggghts/fix_buoyancy.h +include/liggghts/fix_calculate_energy_wall.h +include/liggghts/fix_cfd_coupling.h +include/liggghts/fix_cfd_coupling_convection.h +include/liggghts/fix_cfd_coupling_convection_impl.h +include/liggghts/fix_cfd_coupling_convection_species.h +include/liggghts/fix_cfd_coupling_force.h +include/liggghts/fix_cfd_coupling_force_implicit.h +include/liggghts/fix_check_timestep_gran.h +include/liggghts/fix_check_timestep_sph.h +include/liggghts/fix_contact_atom_counter.h +include/liggghts/fix_contact_atom_counter_dummy.h +include/liggghts/fix_contact_atom_counter_wall.h +include/liggghts/fix_contact_atom_counter_wall_dummy.h +include/liggghts/fix_contact_history.h +include/liggghts/fix_contact_history_mesh.h +include/liggghts/fix_contact_history_mesh_I.h +include/liggghts/fix_contact_property_atom.h +include/liggghts/fix_contact_property_atom_wall.h +include/liggghts/fix_continuum_weighted.h +include/liggghts/fix_deform.h +include/liggghts/fix_deform_check.h +include/liggghts/fix_diam_max.h +include/liggghts/fix_drag.h +include/liggghts/fix_dt_reset.h +include/liggghts/fix_dummy.h +include/liggghts/fix_dummy2.h +include/liggghts/fix_efield.h +include/liggghts/fix_enforce2d.h +include/liggghts/fix_external.h +include/liggghts/fix_fiber_spring_simple.h +include/liggghts/fix_freeze.h +include/liggghts/fix_gravity.h +include/liggghts/fix_heat_gran.h +include/liggghts/fix_heat_gran_conduction.h +include/liggghts/fix_insert.h +include/liggghts/fix_insert_pack.h +include/liggghts/fix_insert_rate_region.h +include/liggghts/fix_insert_stream.h +include/liggghts/fix_insert_stream_predefined.h +include/liggghts/fix_lb_coupling_onetoone.h +include/liggghts/fix_lineforce.h +include/liggghts/fix_massflow_mesh.h +include/liggghts/fix_massflow_mesh_sieve.h +include/liggghts/fix_mesh.h +include/liggghts/fix_mesh_surface.h +include/liggghts/fix_minimize.h +include/liggghts/fix_mixing.h +include/liggghts/fix_momentum.h +include/liggghts/fix_move.h +include/liggghts/fix_move_mesh.h +include/liggghts/fix_multicontact_halfspace.h +include/liggghts/fix_multisphere.h +include/liggghts/fix_multisphere_break.h +include/liggghts/fix_multisphere_comm_I.h +include/liggghts/fix_neighlist_mesh.h +include/liggghts/fix_nve.h +include/liggghts/fix_nve_asphere.h +include/liggghts/fix_nve_asphere_base.h +include/liggghts/fix_nve_asphere_noforce.h +include/liggghts/fix_nve_limit.h +include/liggghts/fix_nve_line.h +include/liggghts/fix_nve_noforce.h +include/liggghts/fix_nve_sph.h +include/liggghts/fix_nve_sph_stationary.h +include/liggghts/fix_nve_sphere.h +include/liggghts/fix_nve_superquadric.h +include/liggghts/fix_particledistribution_discrete.h +include/liggghts/fix_planeforce.h +include/liggghts/fix_print.h +include/liggghts/fix_property_atom.h +include/liggghts/fix_property_atom_region_tracer.h +include/liggghts/fix_property_atom_tracer.h +include/liggghts/fix_property_atom_tracer_stream.h +include/liggghts/fix_property_global.h +include/liggghts/fix_read_restart.h +include/liggghts/fix_region_variable.h +include/liggghts/fix_relax_contacts.h +include/liggghts/fix_remove.h +include/liggghts/fix_respa.h +include/liggghts/fix_rigid.h +include/liggghts/fix_scalar_transport_equation.h +include/liggghts/fix_setforce.h +include/liggghts/fix_sph.h +include/liggghts/fix_sph_density_continuity.h +include/liggghts/fix_sph_density_corr.h +include/liggghts/fix_sph_density_summation.h +include/liggghts/fix_sph_pressure.h +include/liggghts/fix_spring.h +include/liggghts/fix_spring_rg.h +include/liggghts/fix_spring_self.h +include/liggghts/fix_store.h +include/liggghts/fix_store_force.h +include/liggghts/fix_store_state.h +include/liggghts/fix_template_multiplespheres.h +include/liggghts/fix_template_multisphere.h +include/liggghts/fix_template_sphere.h +include/liggghts/fix_template_superquadric.h +include/liggghts/fix_viscous.h +include/liggghts/fix_wall.h +include/liggghts/fix_wall_gran.h +include/liggghts/fix_wall_gran_base.h +include/liggghts/fix_wall_region.h +include/liggghts/fix_wall_region_sph.h +include/liggghts/fix_wall_sph.h +include/liggghts/force.h +include/liggghts/general_container.h +include/liggghts/general_container_I.h +include/liggghts/global_properties.h +include/liggghts/granular_pair_style.h +include/liggghts/granular_styles.h +include/liggghts/granular_wall.h +include/liggghts/group.h +include/liggghts/histogram.h +include/liggghts/image.h +include/liggghts/improper.h +include/liggghts/improper_hybrid.h +include/liggghts/info.h +include/liggghts/input.h +include/liggghts/input_mesh_tet.h +include/liggghts/input_mesh_tri.h +include/liggghts/input_multisphere.h +include/liggghts/integrate.h +include/liggghts/irregular.h +include/liggghts/kspace.h +include/liggghts/lammps.h +include/liggghts/lattice.h +include/liggghts/library.h +include/liggghts/library_cfd_coupling.h +include/liggghts/lmptype.h +include/liggghts/lmpwindows.h +include/liggghts/math_complex.h +include/liggghts/math_const.h +include/liggghts/math_extra.h +include/liggghts/math_extra_liggghts.h +include/liggghts/math_extra_liggghts_nonspherical.h +include/liggghts/math_extra_liggghts_superquadric.h +include/liggghts/math_special.h +include/liggghts/math_vector.h +include/liggghts/memory.h +include/liggghts/memory_ns.h +include/liggghts/mesh_module.h +include/liggghts/mesh_module_liquidtransfer.h +include/liggghts/mesh_module_stress.h +include/liggghts/mesh_module_stress_servo.h +include/liggghts/mesh_mover.h +include/liggghts/mesh_mover_linear.h +include/liggghts/mesh_mover_rotation.h +include/liggghts/min.h +include/liggghts/min_cg.h +include/liggghts/min_linesearch.h +include/liggghts/minimize.h +include/liggghts/modified_andrew.h +include/liggghts/modify.h +include/liggghts/mpi_liggghts.h +include/liggghts/multi_node_mesh.h +include/liggghts/multi_node_mesh_I.h +include/liggghts/multi_node_mesh_parallel.h +include/liggghts/multi_node_mesh_parallel_I.h +include/liggghts/multi_node_mesh_parallel_buffer_I.h +include/liggghts/multi_vector_container.h +include/liggghts/multisphere.h +include/liggghts/multisphere_I.h +include/liggghts/multisphere_parallel.h +include/liggghts/multisphere_parallel_I.h +include/liggghts/my_page.h +include/liggghts/my_pool_chunk.h +include/liggghts/neigh_bond.h +include/liggghts/neigh_derive.h +include/liggghts/neigh_dummy.h +include/liggghts/neigh_full.h +include/liggghts/neigh_gran.h +include/liggghts/neigh_half_bin.h +include/liggghts/neigh_half_multi.h +include/liggghts/neigh_half_nsq.h +include/liggghts/neigh_list.h +include/liggghts/neigh_mlg_dummy.h +include/liggghts/neigh_modify.h +include/liggghts/neigh_multi_level_grid.h +include/liggghts/neigh_request.h +include/liggghts/neigh_respa.h +include/liggghts/neighbor.h +include/liggghts/normal_model_base.h +include/liggghts/normal_model_edinburgh.h +include/liggghts/normal_model_edinburgh_stiffness.h +include/liggghts/normal_model_hertz.h +include/liggghts/normal_model_hertz_stiffness.h +include/liggghts/normal_model_hooke.h +include/liggghts/normal_model_hooke_hysteresis.h +include/liggghts/normal_model_hooke_stiffness.h +include/liggghts/normal_model_luding.h +include/liggghts/normal_model_thornton_ning.h +include/liggghts/os_specific.h +include/liggghts/output.h +include/liggghts/pack.h +include/liggghts/pair.h +include/liggghts/pair_gran.h +include/liggghts/pair_gran_base.h +include/liggghts/pair_gran_proxy.h +include/liggghts/pair_hybrid.h +include/liggghts/pair_hybrid_overlay.h +include/liggghts/pair_line_lj.h +include/liggghts/pair_soft.h +include/liggghts/pair_sph.h +include/liggghts/pair_sph_artvisc_tenscorr.h +include/liggghts/particleToInsert.h +include/liggghts/particleToInsertSuperquadric.h +include/liggghts/particleToInsert_multisphere.h +include/liggghts/pointers.h +include/liggghts/primitive_wall.h +include/liggghts/primitive_wall_definitions.h +include/liggghts/probability_distribution.h +include/liggghts/procmap.h +include/liggghts/properties.h +include/liggghts/property_registry.h +include/liggghts/random.h +include/liggghts/random_mars.h +include/liggghts/random_park.h +include/liggghts/read_data.h +include/liggghts/read_dump.h +include/liggghts/read_restart.h +include/liggghts/reader.h +include/liggghts/reader_native.h +include/liggghts/reader_xyz.h +include/liggghts/region.h +include/liggghts/region_block.h +include/liggghts/region_cone.h +include/liggghts/region_cylinder.h +include/liggghts/region_intersect.h +include/liggghts/region_mesh_tet.h +include/liggghts/region_mesh_tet_I.h +include/liggghts/region_neighbor_list.h +include/liggghts/region_neighbor_list_I.h +include/liggghts/region_neighbor_list_base.h +include/liggghts/region_neighbor_list_definitions.h +include/liggghts/region_plane.h +include/liggghts/region_prism.h +include/liggghts/region_sphere.h +include/liggghts/region_union.h +include/liggghts/region_wedge.h +include/liggghts/replicate.h +include/liggghts/respa.h +include/liggghts/rolling_model_base.h +include/liggghts/rolling_model_cdt.h +include/liggghts/rolling_model_epsd.h +include/liggghts/rolling_model_epsd2.h +include/liggghts/rolling_model_epsd3.h +include/liggghts/rolling_model_luding.h +include/liggghts/rotate.h +include/liggghts/run.h +include/liggghts/run_time.h +include/liggghts/scalar_container.h +include/liggghts/set.h +include/liggghts/settings.h +include/liggghts/signal_handling.h +include/liggghts/sort_buffer.h +include/liggghts/special.h +include/liggghts/sph_kernel_cubicspline.h +include/liggghts/sph_kernel_cubicspline2D.h +include/liggghts/sph_kernel_spiky.h +include/liggghts/sph_kernel_spiky2D.h +include/liggghts/sph_kernel_wendland.h +include/liggghts/sph_kernel_wendland2D.h +include/liggghts/sph_kernels.h +include/liggghts/string_liggghts.h +include/liggghts/suffix.h +include/liggghts/superquadric.h +include/liggghts/surface_mesh.h +include/liggghts/surface_mesh_I.h +include/liggghts/surface_mesh_feature_remove.h +include/liggghts/surface_mesh_feature_remove_I.h +include/liggghts/surface_model_base.h +include/liggghts/surface_model_default.h +include/liggghts/surface_model_multicontact.h +include/liggghts/surface_model_superquadric.h +include/liggghts/tangential_model_base.h +include/liggghts/tangential_model_history.h +include/liggghts/tangential_model_luding_tn.h +include/liggghts/tangential_model_no_history.h +include/liggghts/tet_mesh.h +include/liggghts/tet_mesh_I.h +include/liggghts/thermo.h +include/liggghts/timer.h +include/liggghts/tracking_mesh.h +include/liggghts/tracking_mesh_I.h +include/liggghts/tri_line.h +include/liggghts/tri_mesh.h +include/liggghts/tri_mesh_I.h +include/liggghts/tri_mesh_I_superquadric.h +include/liggghts/tri_mesh_deform.h +include/liggghts/tri_mesh_planar.h +include/liggghts/tri_mesh_planar_I.h +include/liggghts/universe.h +include/liggghts/update.h +include/liggghts/utils.h +include/liggghts/variable.h +include/liggghts/vector_container.h +include/liggghts/vector_liggghts.h +include/liggghts/velocity.h +include/liggghts/verlet.h +include/liggghts/version.h +include/liggghts/volume_mesh.h +include/liggghts/volume_mesh_I.h +include/liggghts/write_data.h +include/liggghts/write_dump.h +include/liggghts/write_restart.h +lib/libliggghts.so diff --git a/science/mei/Makefile b/science/mei/Makefile deleted file mode 100644 index 3a9700021bc8..000000000000 --- a/science/mei/Makefile +++ /dev/null @@ -1,31 +0,0 @@ -# Created by: thierry@pompo.net -# $FreeBSD$ - -PORTNAME= mei -PORTVERSION= 1.0.4 -PORTREVISION= 1 -CATEGORIES= science parallel -MASTER_SITES= http://code-saturne.org/releases/ - -MAINTAINER= thierry@FreeBSD.org -COMMENT= Code_Saturne Mathematical Expression Interpreter - -LICENSE= LGPL21 - -LIB_DEPENDS= libbft.so:science/bft -BUILD_DEPENDS= swig3.0:devel/swig30 - -USES= libtool python:2.7 -USE_LDCONFIG= yes -GNU_CONFIGURE= yes -CONFIGURE_ENV= ac_cv_path_PYEXE=${PYTHON_CMD} -CONFIGURE_ARGS= --with-bft=${LOCALBASE} -INSTALL_TARGET= install-strip -BINARY_ALIAS= swig=swig3.0 - -do-test: - (cd ${WRKSRC}/tests && \ - ${MAKE_CMD} check && \ - ./mei_test ) - -.include <bsd.port.mk> diff --git a/science/mei/distinfo b/science/mei/distinfo deleted file mode 100644 index 6a563710c51d..000000000000 --- a/science/mei/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -SHA256 (mei-1.0.4.tar.gz) = 9f8aeaf8d36afd185723ea1e8765f950720e3db5e4078ea5f239a20e2a1bec47 -SIZE (mei-1.0.4.tar.gz) = 484410 diff --git a/science/mei/files/patch-tests_Makefile.in b/science/mei/files/patch-tests_Makefile.in deleted file mode 100644 index c72fa1d619b0..000000000000 --- a/science/mei/files/patch-tests_Makefile.in +++ /dev/null @@ -1,11 +0,0 @@ ---- tests/Makefile.in.orig 2011-07-20 17:26:55.000000000 +0200 -+++ tests/Makefile.in 2012-04-18 19:51:56.000000000 +0200 -@@ -526,7 +526,7 @@ - - - # Uncomment for tests execution at "make check" --#TESTS=$(check_PROGRAMS) -+TESTS=$(check_PROGRAMS) - - # Check Python module after installation - # diff --git a/science/mei/pkg-descr b/science/mei/pkg-descr deleted file mode 100644 index ff5f079b3883..000000000000 --- a/science/mei/pkg-descr +++ /dev/null @@ -1,4 +0,0 @@ -MEI stands for Mathematical Expression Interpreter. -It is intended to provide interpretation of mathematical formula in a string. - -WWW: http://www.code-saturne.org/ diff --git a/science/mei/pkg-plist b/science/mei/pkg-plist deleted file mode 100644 index f8da7b329d43..000000000000 --- a/science/mei/pkg-plist +++ /dev/null @@ -1,16 +0,0 @@ -bin/mei-config -include/mei_evaluate.h -include/mei_hash_table.h -include/mei_node.h -lib/libmei.a -lib/libmei.so -lib/libmei.so.0 -lib/libmei.so.0.0.0 -%%PYTHON_SITELIBDIR%%/mei/_mei.a -%%PYTHON_SITELIBDIR%%/mei/_mei.so -%%PYTHON_SITELIBDIR%%/mei/_mei.so.0 -%%PYTHON_SITELIBDIR%%/mei/_mei.so.0.0.0 -%%PYTHON_SITELIBDIR%%/mei/mei.py -%%PYTHON_SITELIBDIR%%/mei/mei.pyc -%%PYTHON_SITELIBDIR%%/mei/mei.pyo -man/man1/mei-config.1.gz diff --git a/science/ncs/Makefile b/science/ncs/Makefile deleted file mode 100644 index c95fb6f23f81..000000000000 --- a/science/ncs/Makefile +++ /dev/null @@ -1,121 +0,0 @@ -# Created by: thierry@pompo.net -# $FreeBSD$ - -PORTNAME= ncs -PORTVERSION= 2.0.8 -PORTREVISION= 6 -CATEGORIES= science parallel -MASTER_SITES= http://code-saturne.org/releases/ - -MAINTAINER= thierry@FreeBSD.org -COMMENT= Code_Saturne Kernel - -LICENSE= GPLv2 - -BROKEN= conflicting dependencies - -BUILD_DEPENDS= cs_preprocess:science/ecs -LIB_DEPENDS= libbft.so:science/bft \ - libcgns.so:science/cgnslib \ - libfvm.so:science/fvm \ - libhdf5.so:science/hdf5 \ - libmedC.so:french/med \ - libmei.so:science/mei -RUN_DEPENDS= xmgrace:math/grace \ - bash:shells/bash \ - xterm:x11/xterm \ - cs_preprocess:science/ecs - -USES= fortran gettext gmake iconv libtool pyqt:4 python:2.7 shebangfix -USE_GNOME= libxml2 -USE_PYQT= core xml_build -SHEBANG_FILES= bin/runcase.in -CPPFLAGS+= -I${LOCALBASE}/include -I${LOCALBASE}/include/libxml2 -GNU_CONFIGURE= yes -CONFIGURE_ENV= MPI_LIBS="${MPI_LIBS}" \ - PYEXE="${PYTHON_CMD}" -CONFIGURE_ARGS= --with-blas-libs="${BLASLIB} ${LAPACKLIB}" -MAKE_ENV= NOM_ARCH=${OPSYS} CS_MPI_PATH=${MPI_HOME}/bin \ - PTHREAD_LIBS=-lpthread TERM=${TERM} \ - MPI_HOME=${MPI_HOME} MPI_LIBS="${MPI_LIBS}" -USE_LDCONFIG= yes - -FORTRANLIBDIR= `${DIRNAME} \\`${FC} -print-libgcc-file-name\\`` -FORTRANLIBDIR2= `${DIRNAME} \\`${FC} -print-libgcc-file-name\\``/../../../ - -OPTIONS_DEFINE= DOCS EXAMPLES BATCH -BATCH_DESC= Use Torque to submit batches -BATCH_CONFIGURE_WITH= batch=PBS -BATCH_LIB_DEPENDS= libtorque.so:sysutils/torque - -OPTIONS_RADIO= BLAS -OPTIONS_RADIO_BLAS= REFERENCE ATLAS -OPTIONS_DEFAULT= REFERENCE - -REFERENCE_DESC= Blas / Lapack -REFERENCE_USES= blaslapack:netlib - -ATLAS_DESC= ATLAS -ATLAS_USES= blaslapack:atlas - -.include <bsd.port.options.mk> - -.if ${PORT_OPTIONS:MREFERENCE} -CONFIGURE_ARGS+= --with-blas-type=BLAS -.else -CONFIGURE_ARGS+= --with-blas-type=ATLAS -.endif - -.if defined(PACKAGE_BUILDING) -TERM= vt100 # Force for pointyhat to override su -.else -TERM?= vt100 # Default value needed for tput in jail or tinderbox -.endif - -SUB_DIRS= data include src users -BIN_SCRIPTS= autovalid check_mesh compiler_version cree_sat cs.exe gracehst \ - grp info_cs lance_install rang_mpi.sh -BIN_DATAS= Makefile SaturneGUI autovalid.xml cs_profile lance lance.help \ - macros_FreeBSD.mk - -.if defined(WITH_OPENMPI) -MPI_HOME= ${LOCALBASE}/mpi/openmpi -BUILD_DEPENDS+= ${MPI_HOME}/bin/mpicc:net/openmpi -RUN_DEPENDS+= ${MPI_HOME}/bin/mpirun:net/openmpi -MPI_LIBS= -lmpi -lorte -lopal -.else -MPI_HOME= ${LOCALBASE} -BUILD_DEPENDS+= ${MPI_HOME}/bin/mpicc:net/mpich2 -RUN_DEPENDS+= ${MPI_HOME}/bin/mpirun:net/mpich2 -MPI_LIBS= -lmpich -lmpl -lpthread -.endif - -.if ${PORT_OPTIONS:MDOCS} -USE_TEX= tex:build -BUILD_DEPENDS+= fig2dev:print/transfig -ALL_TARGET= all pdf -INSTALL_TARGET= install install-pdf -DOCS= AUTHORS COMPATIBILITY ChangeLog README -.endif - -RUN_DEPENDS+= xpdf:graphics/xpdf - -pre-everything:: - @${ECHO_MSG} - @${ECHO_MSG} "By default ncs is built with MPICH2, but you can set WITH_OPENMPI" - @${ECHO_MSG} "if you prefer." - @${ECHO_MSG} - -post-install: - @cd ${STAGEDIR}${PREFIX}/lib && ${STRIP_CMD} libsaturne.so* libsyrcs.so* libsyrcs.so* - @${REINPLACE_CMD} -i '' -e 's|^#!.*|#!${PYTHON_CMD}|' ${STAGEDIR}${PREFIX}/bin/code_saturne -.if ${PORT_OPTIONS:MDOCS} - ${MKDIR} ${STAGEDIR}${DOCSDIR} - ${INSTALL_DATA} ${DOCS:C|^|${WRKSRC}/|} ${STAGEDIR}${DOCSDIR} -.endif -.if ${PORT_OPTIONS:MEXAMPLES} - ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} - cd ${WRKSRC}/examples && ${COPYTREE_SHARE} \* ${STAGEDIR}${EXAMPLESDIR} -.endif - -.include <bsd.port.mk> diff --git a/science/ncs/distinfo b/science/ncs/distinfo deleted file mode 100644 index 52baf8234c8f..000000000000 --- a/science/ncs/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -SHA256 (ncs-2.0.8.tar.gz) = 5a363e716d0ad225d3de52169b846bb3885f3e4eb82c1074cdd1086e4b1fdf80 -SIZE (ncs-2.0.8.tar.gz) = 10840408 diff --git a/science/ncs/files/patch-config_cs_auto_flags.sh b/science/ncs/files/patch-config_cs_auto_flags.sh deleted file mode 100644 index c3a00b58c7b1..000000000000 --- a/science/ncs/files/patch-config_cs_auto_flags.sh +++ /dev/null @@ -1,11 +0,0 @@ ---- config/cs_auto_flags.sh.orig 2012-08-08 00:11:29.000000000 +0200 -+++ config/cs_auto_flags.sh 2014-09-14 14:45:51.000000000 +0200 -@@ -214,8 +214,6 @@ - gcc-3*|gcc-4.[01234]*) - ;; - *) -- cflags_default_opt="$cflags_default_opt -fexcess-precision=fast" -- cflags_default_hot="$cflags_default_hot -fexcess-precision=fast" - ;; - esac - diff --git a/science/ncs/files/patch-configure b/science/ncs/files/patch-configure deleted file mode 100644 index 1f518f391255..000000000000 --- a/science/ncs/files/patch-configure +++ /dev/null @@ -1,20 +0,0 @@ ---- configure.orig 2013-04-16 15:44:44.000000000 +0200 -+++ configure 2014-09-14 14:20:18.000000000 +0200 -@@ -21736,7 +21736,7 @@ - PYTHON_EXE=none - fi - --if test "x${PYTHON_EXE}" == "xnone" ; then -+if test "x${PYTHON_EXE}" = "xnone" ; then - cs_python="/usr/bin/env python" - # Extract the first word of "python", so it can be a program name with args. - set dummy python; ac_word=$2 -@@ -22073,7 +22073,7 @@ - fi - - # Test for PyQt4 --if test "x$have_gui" == "xyes" ; then -+if test "x$have_gui" = "xyes" ; then - - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for PyQt4 version >= 4.3" >&5 - $as_echo_n "checking for PyQt4 version >= 4.3... " >&6; } diff --git a/science/ncs/files/patch-src_base_tremai.c b/science/ncs/files/patch-src_base_tremai.c deleted file mode 100644 index 2896bc829f3e..000000000000 --- a/science/ncs/files/patch-src_base_tremai.c +++ /dev/null @@ -1,10 +0,0 @@ ---- src/base/tremai.c.orig 2011-04-11 18:26:06.000000000 +0200 -+++ src/base/tremai.c 2014-03-26 23:51:58.000000000 +0100 -@@ -45,6 +45,7 @@ - #include <string.h> - - #if defined(HAVE_SYS_RESOURCE_H) -+#include <sys/types.h> - #include <sys/resource.h> - #endif - diff --git a/science/ncs/pkg-descr b/science/ncs/pkg-descr deleted file mode 100644 index e0e25df25161..000000000000 --- a/science/ncs/pkg-descr +++ /dev/null @@ -1,19 +0,0 @@ -Code Saturne is a system designed to solve the Navier-Stokes equations in the -cases of 2D, 2D axisymmetric or 3D flows. Its main module is designed for the -simulation of flows which may be steady or unsteady, laminar or turbulent, -incompressible or potentially dilatable, isothermal or not. -Scalars and turbulent fluctuations of scalars can be taken into account. The -code includes specific modules, referred to as "specific physics", for the -treatment of lagrangian particle tracking, semi-transparent radiative transfer, -gas combustion, pulverised coal combustion, electricity effects (Joule effect -and electric arcs) and compressible flows. The code also includes an engineering -module, Matisse, for the simulation of nuclear waste surface storage. - -Code_Saturne relies on a finite volume discretisation and allows the use of -various mesh types which may be hybrid (containing several kinds of elements) -and may have structural non-conformities (hanging nodes). - -NCS means "Noyau Code Saturne", i.e. "Code Saturne Kernel". This is the -numerical solver. - -WWW: http://www.code-saturne.org/ diff --git a/science/ncs/pkg-plist b/science/ncs/pkg-plist deleted file mode 100644 index 3e008ce5912f..000000000000 --- a/science/ncs/pkg-plist +++ /dev/null @@ -1,885 +0,0 @@ -bin/code_saturne -bin/cs_solver -etc/bash_completion.d/code_saturne -include/alaste.h -include/albase.h -include/alstru.h -include/atincl.h -include/cfpoin.h -include/coincl.h -include/cpincl.h -include/cplsat.h -include/cs_ale.h -include/cs_ast_coupling.h -include/cs_base.h -include/cs_benchmark.h -include/cs_blas.h -include/cs_boundary_conditions.h -include/cs_calcium.h -include/cs_config.h -include/cs_coupling.h -include/cs_ctwr.h -include/cs_ctwr_air_props.h -include/cs_ctwr_halo.h -include/cs_ctwr_mesh.h -include/cs_ext_neighborhood.h -include/cs_gradient.h -include/cs_grid.h -include/cs_gui.h -include/cs_gui_boundary_conditions.h -include/cs_gui_conjugate_heat_transfer.h -include/cs_gui_matisse.h -include/cs_gui_mobile_mesh.h -include/cs_gui_particles.h -include/cs_gui_radiative_transfer.h -include/cs_gui_specific_physics.h -include/cs_gui_util.h -include/cs_gui_variables.h -include/cs_halo.h -include/cs_io.h -include/cs_join.h -include/cs_join_intersect.h -include/cs_join_merge.h -include/cs_join_mesh.h -include/cs_join_perio.h -include/cs_join_post.h -include/cs_join_set.h -include/cs_join_split.h -include/cs_join_update.h -include/cs_join_util.h -include/cs_lagr.h -include/cs_lagr_perio.h -include/cs_matrix.h -include/cs_mesh.h -include/cs_mesh_coherency.h -include/cs_mesh_connect.h -include/cs_mesh_halo.h -include/cs_mesh_quality.h -include/cs_mesh_quantities.h -include/cs_mesh_solcom.h -include/cs_mesh_warping.h -include/cs_multigrid.h -include/cs_numbering.h -include/cs_opts.h -include/cs_parall.h -include/cs_perio.h -include/cs_post.h -include/cs_preprocessor_data.h -include/cs_prototypes.h -include/cs_proxy_comm.h -include/cs_renumber.h -include/cs_restart.h -include/cs_sat_coupling.h -include/cs_search.h -include/cs_selector.h -include/cs_sles.h -include/cs_sort.h -include/cs_syr3_comm.h -include/cs_syr3_coupling.h -include/cs_syr3_messages.h -include/cs_syr4_coupling.h -include/cs_syr_coupling.h -include/cs_tpar1d.h -include/cs_ventil.h -include/cstnum.h -include/cstphy.h -include/ctincl.h -include/dimens.h -include/dimfbr.h -include/elincl.h -include/entsor.h -include/fuincl.h -include/ihmpre.h -include/lagdim.h -include/lagpar.h -include/lagran.h -include/matiss.h -include/mltgrd.h -include/numvar.h -include/optcal.h -include/parall.h -include/paramx.h -include/period.h -include/pointe.h -include/ppcpfu.h -include/ppincl.h -include/ppppar.h -include/ppthch.h -include/radiat.h -include/tcpumx.h -include/tremai.h -include/vector.h -include/vortex.h -%%PYTHON_SITELIBDIR%%/ncs/Base/BrowserForm.py -%%PYTHON_SITELIBDIR%%/ncs/Base/BrowserForm.pyc -%%PYTHON_SITELIBDIR%%/ncs/Base/BrowserForm.pyo -%%PYTHON_SITELIBDIR%%/ncs/Base/BrowserView.py 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-%%DATADIR%%/users/cplv/uscpiv.f90 -%%DATADIR%%/users/cplv/uscpl1.f90 -%%DATADIR%%/users/cplv/uscplc.f90 -%%DATADIR%%/users/ctwr/usctcl.f90 -%%DATADIR%%/users/ctwr/usctdz.f90 -%%DATADIR%%/users/ctwr/uscti1.f90 -%%DATADIR%%/users/ctwr/usctiv.f90 -%%DATADIR%%/users/elec/uselcl.f90 -%%DATADIR%%/users/elec/uselen.f90 -%%DATADIR%%/users/elec/useli1.f90 -%%DATADIR%%/users/elec/useliv.f90 -%%DATADIR%%/users/elec/uselph.f90 -%%DATADIR%%/users/elec/uselrc.f90 -%%DATADIR%%/users/elec/usetcl.f90 -%%DATADIR%%/users/fuel/usfucl.f90 -%%DATADIR%%/users/fuel/usfui1.f90 -%%DATADIR%%/users/fuel/usfuiv.f90 -%%DATADIR%%/users/lagr/uslabo.f90 -%%DATADIR%%/users/lagr/usladp.f90 -%%DATADIR%%/users/lagr/uslaed.f90 -%%DATADIR%%/users/lagr/uslaen.f90 -%%DATADIR%%/users/lagr/uslafe.f90 -%%DATADIR%%/users/lagr/uslag1.f90 -%%DATADIR%%/users/lagr/uslag2.f90 -%%DATADIR%%/users/lagr/uslain.f90 -%%DATADIR%%/users/lagr/uslapr.f90 -%%DATADIR%%/users/lagr/uslaru.f90 -%%DATADIR%%/users/lagr/uslast.f90 -%%DATADIR%%/users/lagr/uslatc.f90 -%%DATADIR%%/users/lagr/uslatp.f90 -%%DATADIR%%/users/pprt/usppmo.f90 -%%DATADIR%%/users/rayt/usray1.f90 -%%DATADIR%%/users/rayt/usray2.f90 -%%DATADIR%%/users/rayt/usray3.f90 -%%DATADIR%%/users/rayt/usray4.f90 -%%DATADIR%%/users/rayt/usray5.f90 diff --git a/science/nwchem/Makefile b/science/nwchem/Makefile index 0d361d7960f4..215f04a5a125 100644 --- a/science/nwchem/Makefile +++ b/science/nwchem/Makefile @@ -1,8 +1,7 @@ # $FreeBSD$ PORTNAME= nwchem -DISTVERSION= 6.8.1-release-144 -DISTVERSIONSUFFIX= -gb1062ed2c +PORTVERSION= 6.8.1.20181107 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -13,29 +12,29 @@ LICENSE_NAME= Educational Community License (ECL) 2.0 LICENSE_FILE= ${WRKSRC}/../LICENSE.TXT LICENSE_PERMS= dist-mirror dist-sell pkg-mirror pkg-sell auto-accept -BROKEN_i386= Compiling basis.F... f951: sorry, unimplemented: 64-bit mode not compiled in - BUILD_DEPENDS= bash:shells/bash LIB_DEPENDS= libblas.so:math/blas \ libga.so:devel/ga \ libmpich.so:net/mpich -USES= fortran gmake shebangfix +USES= fortran gmake ${ARCH_64BIT:S/^$/perl5/:S/64//} shebangfix SHEBANG_FILES= ../contrib/distro-tools/build_* ../contrib/add_* SHEBANG_GLOB= *.sh USE_GITHUB= yes GH_ACCOUNT= nwchemgit +GH_TAGNAME= master-oct22_2018-21-gd3913ef8b USE_PERL5= build MAKEFILE= GNUmakefile -MAKE_ENV= NWCHEM_TOP=${WRKSRC}/.. NWCHEM_MODULES=all NWCHEM_LONG_PATHS=Y NWCHEM_TARGET=LINUX64 USE_MPI=Y USE_INTERNALBLAS=Y EXTERNAL_GA_PATH=${LOCALBASE} \ +ARCH_64BIT= ${ARCH:C/.*64.*/64/:S/${ARCH}//} +MAKE_ENV= NWCHEM_TOP=${WRKSRC}/.. NWCHEM_MODULES=all NWCHEM_LONG_PATHS=Y NWCHEM_TARGET=LINUX${ARCH_64BIT} USE_MPI=Y USE_INTERNALBLAS=Y EXTERNAL_GA_PATH=${LOCALBASE} \ BLAS_SIZE=4 USE_64TO32=y SUB_FILES= nwchemrc WRKSRC_SUBDIR= src -BINARY_ALIAS= gcc=${CC} +BINARY_ALIAS= gcc=${CC} gfortran=gfortran${GCC_DEFAULT} post-extract: @${RM} ${WRKSRC}/atomscf/src.orig @@ -50,7 +49,7 @@ pre-build: do-install: ${INSTALL_DATA} ${WRKDIR}/nwchemrc ${STAGEDIR}${PREFIX}/etc/nwchemrc - ${INSTALL_PROGRAM} ${WRKSRC}/../bin/LINUX64/${PORTNAME} ${STAGEDIR}${PREFIX}/bin/${PORTNAME} + ${INSTALL_PROGRAM} ${WRKSRC}/../bin/LINUX${ARCH_64BIT}/${PORTNAME} ${STAGEDIR}${PREFIX}/bin/${PORTNAME} cd ${WRKSRC}/basis && ${COPYTREE_SHARE} libraries ${STAGEDIR}${DATADIR} cd ${WRKSRC} && ${COPYTREE_SHARE} data ${STAGEDIR}${DATADIR} @${MKDIR} ${STAGEDIR}${DATADIR}/libraryps diff --git a/science/nwchem/distinfo b/science/nwchem/distinfo index 6013e4fa2594..86553ee13ab3 100644 --- a/science/nwchem/distinfo +++ b/science/nwchem/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1539024872 -SHA256 (nwchemgit-nwchem-6.8.1-release-144-gb1062ed2c_GH0.tar.gz) = 6f8534343e01d72adcc8bfce531fd8afa85ebddbdcac902df02e9d6ec1b7917e -SIZE (nwchemgit-nwchem-6.8.1-release-144-gb1062ed2c_GH0.tar.gz) = 165110453 +TIMESTAMP = 1541645398 +SHA256 (nwchemgit-nwchem-6.8.1.20181107-master-oct22_2018-21-gd3913ef8b_GH0.tar.gz) = d496c76782299224ce42e944c69df6b5b1a8b1b9a20b18bacd7045c6228e9571 +SIZE (nwchemgit-nwchem-6.8.1.20181107-master-oct22_2018-21-gd3913ef8b_GH0.tar.gz) = 166929038 diff --git a/science/nwchem/pkg-plist b/science/nwchem/pkg-plist index fc0d6237d4ff..dabc4a7516cf 100644 --- a/science/nwchem/pkg-plist +++ b/science/nwchem/pkg-plist @@ -1253,6 +1253,7 @@ etc/nwchemrc %%DATADIR%%/libraryps/development_psps/Pa %%DATADIR%%/libraryps/development_psps/Pm %%DATADIR%%/libraryps/development_psps/Pr +%%DATADIR%%/libraryps/development_psps/Pt %%DATADIR%%/libraryps/development_psps/Pu %%DATADIR%%/libraryps/development_psps/Rf %%DATADIR%%/libraryps/development_psps/Rg diff --git a/science/pulseview/Makefile b/science/pulseview/Makefile index 7837f4633fc7..1acc4e2c1b6f 100644 --- a/science/pulseview/Makefile +++ b/science/pulseview/Makefile @@ -2,8 +2,7 @@ # $FreeBSD$ PORTNAME= pulseview -PORTVERSION= 0.4.0 -PORTREVISION= 3 +PORTVERSION= 0.4.1 CATEGORIES= science cad MASTER_SITES= http://sigrok.org/download/source/pulseview/ @@ -17,9 +16,10 @@ LIB_DEPENDS= libboost_thread.so:devel/boost-libs \ libsigrok.so:devel/libsigrok \ libsigrokdecode.so:devel/libsigrokdecode -USES= cmake compiler:c++14-lang desktop-file-utils pkgconfig qt:5 +USES= cmake compiler:c++14-lang desktop-file-utils gnome pkgconfig qt:5 USE_GNOME= glibmm glib20 libsigc++20 USE_QT= buildtools core gui qmake_build svg widgets + CMAKE_ARGS+= -DCMAKE_INSTALL_MANDIR:PATH=${MANPREFIX}/man \ -DDISABLE_WERROR:BOOL=TRUE INSTALLS_ICONS= yes diff --git a/science/pulseview/distinfo b/science/pulseview/distinfo index fb479849ca37..07fcf1741445 100644 --- a/science/pulseview/distinfo +++ b/science/pulseview/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1507723538 -SHA256 (pulseview-0.4.0.tar.gz) = 78f8291045c6f65b4827b12e83c8e68cea2d5e7268b15a51aaca9726c8100eb9 -SIZE (pulseview-0.4.0.tar.gz) = 226656 +TIMESTAMP = 1541193458 +SHA256 (pulseview-0.4.1.tar.gz) = 9ee7ce3dd1457c6a5f5e4e9c2469903a1f070ba077ea68535cc29ef1dfac6f2f +SIZE (pulseview-0.4.1.tar.gz) = 1342532 diff --git a/science/py-gpaw/Makefile b/science/py-gpaw/Makefile index ce685dff24f1..7a36c3ddf6cd 100644 --- a/science/py-gpaw/Makefile +++ b/science/py-gpaw/Makefile @@ -11,6 +11,7 @@ MAINTAINER= yuri@FreeBSD.org COMMENT= DFT and beyond within the projector-augmented wave method in chemistry LICENSE= GPLv3+ +LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= ${PYNUMPY} LIB_DEPENDS= libmpich.so:net/mpich \ @@ -21,10 +22,12 @@ RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}ase>0:science/py-ase@${PY_FLAVOR} \ ${PYNUMPY} USES= gettext-runtime localbase python shebangfix -GH_ACCOUNT= psychopy USE_PYTHON= distutils concurrent autoplist SHEBANG_FILES= tools/* +post-patch: + @${REINPLACE_CMD} "s|'/usr/local/|'${LOCALBASE}/|" ${WRKSRC}/gpaw/__init__.py + post-install: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/gpaw-python ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/_gpaw.so diff --git a/science/py-gpaw/pkg-message b/science/py-gpaw/pkg-message new file mode 100644 index 000000000000..53cae563283e --- /dev/null +++ b/science/py-gpaw/pkg-message @@ -0,0 +1,8 @@ +====================================================================== +You installed GPAW, the system for DFT computations in quantum +chemistry. + +In order to use this package you most likely need to also install +science/gpaw-setups that contains data files for electronic +configurations for many elements of the periodic table. +====================================================================== diff --git a/science/py-scikit-learn/Makefile b/science/py-scikit-learn/Makefile index 94c987a036f3..e21d60a78b04 100644 --- a/science/py-scikit-learn/Makefile +++ b/science/py-scikit-learn/Makefile @@ -10,6 +10,9 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= demon@FreeBSD.org COMMENT= Machine learning algorithms for python +LICENSE= BSD3CLAUSE +LICENSE_FILE= ${WRKSRC}/COPYING + BUILD_DEPENDS= ${PYNUMPY} \ ${PYTHON_SITELIBDIR}/scipy/version.py:science/py-scipy@${PY_FLAVOR} RUN_DEPENDS:= ${BUILD_DEPENDS} diff --git a/science/qmcpack/Makefile b/science/qmcpack/Makefile index 7d59112bb2dd..ed3a30131a3c 100644 --- a/science/qmcpack/Makefile +++ b/science/qmcpack/Makefile @@ -12,7 +12,6 @@ COMMENT= Many-body ab initio Quantum Monte Carlo code for quantum chemstry LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE -BROKEN_FreeBSD_10= error: use of undeclared identifier '__builtin_assume_aligned' BROKEN_i386= undefined reference to `__atomic_load' LIB_DEPENDS= libboost_system.so:devel/boost-libs \ diff --git a/science/sigrok-cli/Makefile b/science/sigrok-cli/Makefile index f73e3f58d567..1ac2ae46d51a 100644 --- a/science/sigrok-cli/Makefile +++ b/science/sigrok-cli/Makefile @@ -2,7 +2,7 @@ # $FreeBSD$ PORTNAME= sigrok-cli -PORTVERSION= 0.7.0 +PORTVERSION= 0.7.1 CATEGORIES= science cad MASTER_SITES= http://sigrok.org/download/source/sigrok-cli/ @@ -15,10 +15,15 @@ LIB_DEPENDS= libserialport.so:devel/libserialport \ libsigrok.so:devel/libsigrok \ libsigrokdecode.so:devel/libsigrokdecode -PLIST_FILES= bin/sigrok-cli man/man1/sigrok-cli.1.gz +USES= desktop-file-utils gettext-runtime gmake gnome pathfix \ + libtool pkgconfig GNU_CONFIGURE= yes -USES= gmake pathfix libtool pkgconfig MAKE_JOBS_UNSAFE= yes +INSTALLS_ICONS= yes + +PLIST_FILES= bin/sigrok-cli man/man1/sigrok-cli.1.gz \ + share/applications/org.sigrok.sigrok-cli.desktop \ + share/icons/hicolor/scalable/apps/sigrok-cli.svg .include <bsd.port.mk> diff --git a/science/sigrok-cli/distinfo b/science/sigrok-cli/distinfo index ec85f994132a..cd62a9747521 100644 --- a/science/sigrok-cli/distinfo +++ b/science/sigrok-cli/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1507722101 -SHA256 (sigrok-cli-0.7.0.tar.gz) = 5669d968c2de3dfc6adfda76e83789b6ba76368407c832438cef5e7099a65e1c -SIZE (sigrok-cli-0.7.0.tar.gz) = 210736 +TIMESTAMP = 1541192883 +SHA256 (sigrok-cli-0.7.1.tar.gz) = f52413429f47d457c333db0fd068416ab7a3f9e35ca76de8624dc5ac6fb07797 +SIZE (sigrok-cli-0.7.1.tar.gz) = 221754 diff --git a/science/simlib/Makefile b/science/simlib/Makefile index 8c10b255a929..4b30a3cf2605 100644 --- a/science/simlib/Makefile +++ b/science/simlib/Makefile @@ -24,7 +24,7 @@ NOT_FOR_ARCHS_REASON= contains not working ${ARCH}-dependent assembly code .include <bsd.port.options.mk> -.if ${OPSYS} == FreeBSD && ${OSVERSION} >= 1101000 +.if ${OPSYS} == FreeBSD # nm crashes during the build: # Assertion failed: (ddata->output.size > 0), function cpp_demangle_read_sname, file /usr/src/contrib/elftoolchain/libelftc/libelftc_dem_gnu3.c, line 2137. USE_BINUTILS= yes diff --git a/science/step/Makefile b/science/step/Makefile index f79cc9c77c43..ea2e92854579 100644 --- a/science/step/Makefile +++ b/science/step/Makefile @@ -2,6 +2,7 @@ PORTNAME= step DISTVERSION= ${KDE_APPLICATIONS_VERSION} +PORTREVISION= 1 CATEGORIES= science kde kde-applications MAINTAINER= kde@FreeBSD.org @@ -19,7 +20,7 @@ USE_KDE= attica auth bookmarks codecs completion config configwidgets \ kdelibs4support khtml kio newstuff notifications parts \ plotting service solid sonnet textwidgets unitconversion \ widgetsaddons windowsystem xmlgui -USE_QT= core dbus gui network opengl printsupport qml quick svg \ +USE_QT= core dbus declarative gui network opengl printsupport svg \ widgets xml \ buildtools_build qmake_build CXXFLAGS_powerpc64= -Wno-error=return-type diff --git a/science/step/distinfo b/science/step/distinfo index 474b8dd56487..febbd23e3cad 100644 --- a/science/step/distinfo +++ b/science/step/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1539116194 -SHA256 (KDE/applications/18.08.2/step-18.08.2.tar.xz) = b53031a4f57667291a571bcacd4f5387821cf7b50a506775ca7634532b77950b -SIZE (KDE/applications/18.08.2/step-18.08.2.tar.xz) = 860376 +TIMESTAMP = 1541484467 +SHA256 (KDE/applications/18.08.3/step-18.08.3.tar.xz) = 0ac40b5a65fe89aa57e866da9afda31c5a8b4a408cc94cc74f75b1f152cead1d +SIZE (KDE/applications/18.08.3/step-18.08.3.tar.xz) = 860260 diff --git a/science/triqs/Makefile b/science/triqs/Makefile index 0f90d60fc6f9..abdfd61820c8 100644 --- a/science/triqs/Makefile +++ b/science/triqs/Makefile @@ -12,7 +12,6 @@ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING.txt BROKEN= wrong LIB_DEPENDS -BROKEN_FreeBSD_10= fatal error: 'optional' file not found BROKEN_i386= error: no matching function for call to 'max': https://github.com/TRIQS/triqs/issues/596 BUILD_DEPENDS= boost-libs>=1.53:devel/boost-libs \ diff --git a/science/udunits/Makefile b/science/udunits/Makefile index 17eef9203b7b..4f108c3a3054 100644 --- a/science/udunits/Makefile +++ b/science/udunits/Makefile @@ -3,7 +3,7 @@ PORTNAME= udunits PORTVERSION= 2.2.26 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science math MASTER_SITES= ftp://ftp.unidata.ucar.edu/pub/udunits/ \ LOCAL/sunpoet diff --git a/science/voro++/Makefile b/science/voro++/Makefile index 1da9e97a4182..c61b5ee19294 100644 --- a/science/voro++/Makefile +++ b/science/voro++/Makefile @@ -1,7 +1,8 @@ # $FreeBSD$ PORTNAME= voro++ -PORTVERSION= 0.4.6 +DISTVERSION= 0.4.6 +PORTREVISION= 1 CATEGORIES= science MASTER_SITES= http://math.lbl.gov/voro++/download/dir/ @@ -12,18 +13,11 @@ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE USES= gmake +USE_LDCONFIG= yes -post-patch: - ${REINPLACE_CMD} \ - -e 's|CXX=|CXX?=|g' \ - -e 's|CFLAGS=|CFLAGS?=|g' \ - -e 's|PREFIX=.*|PREFIX?=|g' \ - ${WRKSRC}/config.mk - ${REINPLACE_CMD} \ - -e 's|$$(PREFIX)|$$(DESTDIR)$$(PREFIX)|g' \ - ${WRKSRC}/Makefile +CFLAGS+= -fPIC post-install: - ${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/voro++ + @${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/voro++ .include <bsd.port.mk> diff --git a/science/voro++/files/patch-Makefile b/science/voro++/files/patch-Makefile new file mode 100644 index 000000000000..0a2ea370d078 --- /dev/null +++ b/science/voro++/files/patch-Makefile @@ -0,0 +1,101 @@ +--- Makefile.orig 2013-10-17 17:54:13 UTC ++++ Makefile +@@ -12,7 +12,7 @@ include config.mk + # Build all of the executable files + all: + $(MAKE) -C src +- $(MAKE) -C examples ++ #$(MAKE) -C examples + + # Build the help files (with Doxygen) + help: +@@ -26,47 +26,48 @@ clean: + # Install the executable, man page, and shared library + install: + $(MAKE) -C src +- $(INSTALL) -d $(IFLAGS_EXEC) $(PREFIX)/bin +- $(INSTALL) -d $(IFLAGS_EXEC) $(PREFIX)/lib +- $(INSTALL) -d $(IFLAGS_EXEC) $(PREFIX)/man +- $(INSTALL) -d $(IFLAGS_EXEC) $(PREFIX)/man/man1 +- $(INSTALL) -d $(IFLAGS_EXEC) $(PREFIX)/include +- $(INSTALL) -d $(IFLAGS_EXEC) $(PREFIX)/include/voro++ +- $(INSTALL) $(IFLAGS_EXEC) src/voro++ $(PREFIX)/bin +- $(INSTALL) $(IFLAGS) man/voro++.1 $(PREFIX)/man/man1 +- $(INSTALL) $(IFLAGS) src/libvoro++.a $(PREFIX)/lib +- $(INSTALL) $(IFLAGS) src/voro++.hh $(PREFIX)/include/voro++ +- $(INSTALL) $(IFLAGS) src/c_loops.hh $(PREFIX)/include/voro++ +- $(INSTALL) $(IFLAGS) src/cell.hh $(PREFIX)/include/voro++ +- $(INSTALL) $(IFLAGS) src/common.hh $(PREFIX)/include/voro++ +- $(INSTALL) $(IFLAGS) src/config.hh $(PREFIX)/include/voro++ +- $(INSTALL) $(IFLAGS) src/container.hh $(PREFIX)/include/voro++ +- $(INSTALL) $(IFLAGS) src/container_prd.hh $(PREFIX)/include/voro++ +- $(INSTALL) $(IFLAGS) src/rad_option.hh $(PREFIX)/include/voro++ +- $(INSTALL) $(IFLAGS) src/pre_container.hh $(PREFIX)/include/voro++ +- $(INSTALL) $(IFLAGS) src/unitcell.hh $(PREFIX)/include/voro++ +- $(INSTALL) $(IFLAGS) src/v_base.hh $(PREFIX)/include/voro++ +- $(INSTALL) $(IFLAGS) src/v_compute.hh $(PREFIX)/include/voro++ +- $(INSTALL) $(IFLAGS) src/wall.hh $(PREFIX)/include/voro++ +- $(INSTALL) $(IFLAGS) src/worklist.hh $(PREFIX)/include/voro++ ++ $(INSTALL) -d $(IFLAGS_EXEC) $(DESTDIR)$(PREFIX)/bin ++ $(INSTALL) -d $(IFLAGS_EXEC) $(DESTDIR)$(PREFIX)/lib ++ $(INSTALL) -d $(IFLAGS_EXEC) $(DESTDIR)$(PREFIX)/man ++ $(INSTALL) -d $(IFLAGS_EXEC) $(DESTDIR)$(PREFIX)/man/man1 ++ $(INSTALL) -d $(IFLAGS_EXEC) $(DESTDIR)$(PREFIX)/include ++ $(INSTALL) -d $(IFLAGS_EXEC) $(DESTDIR)$(PREFIX)/include/voro++ ++ $(INSTALL) $(IFLAGS_EXEC) src/voro++ $(DESTDIR)$(PREFIX)/bin ++ $(INSTALL) $(IFLAGS) man/voro++.1 $(DESTDIR)$(PREFIX)/man/man1 ++ $(INSTALL) $(IFLAGS) src/libvoro++.a $(DESTDIR)$(PREFIX)/lib ++ $(INSTALL) $(IFLAGS) src/libvoro++.so $(DESTDIR)$(PREFIX)/lib ++ $(INSTALL) $(IFLAGS) src/voro++.hh $(DESTDIR)$(PREFIX)/include/voro++ ++ $(INSTALL) $(IFLAGS) src/c_loops.hh $(DESTDIR)$(PREFIX)/include/voro++ ++ $(INSTALL) $(IFLAGS) src/cell.hh $(DESTDIR)$(PREFIX)/include/voro++ ++ $(INSTALL) $(IFLAGS) src/common.hh $(DESTDIR)$(PREFIX)/include/voro++ ++ $(INSTALL) $(IFLAGS) src/config.hh $(DESTDIR)$(PREFIX)/include/voro++ ++ $(INSTALL) $(IFLAGS) src/container.hh $(DESTDIR)$(PREFIX)/include/voro++ ++ $(INSTALL) $(IFLAGS) src/container_prd.hh $(DESTDIR)$(PREFIX)/include/voro++ ++ $(INSTALL) $(IFLAGS) src/rad_option.hh $(DESTDIR)$(PREFIX)/include/voro++ ++ $(INSTALL) $(IFLAGS) src/pre_container.hh $(DESTDIR)$(PREFIX)/include/voro++ ++ $(INSTALL) $(IFLAGS) src/unitcell.hh $(DESTDIR)$(PREFIX)/include/voro++ ++ $(INSTALL) $(IFLAGS) src/v_base.hh $(DESTDIR)$(PREFIX)/include/voro++ ++ $(INSTALL) $(IFLAGS) src/v_compute.hh $(DESTDIR)$(PREFIX)/include/voro++ ++ $(INSTALL) $(IFLAGS) src/wall.hh $(DESTDIR)$(PREFIX)/include/voro++ ++ $(INSTALL) $(IFLAGS) src/worklist.hh $(DESTDIR)$(PREFIX)/include/voro++ + + # Uninstall the executable, man page, and shared library + uninstall: +- rm -f $(PREFIX)/bin/voro++ +- rm -f $(PREFIX)/man/man1/voro++.1 +- rm -f $(PREFIX)/lib/libvoro++.a +- rm -f $(PREFIX)/include/voro++/voro++.hh +- rm -f $(PREFIX)/include/voro++/c_loops.hh +- rm -f $(PREFIX)/include/voro++/cell.hh +- rm -f $(PREFIX)/include/voro++/common.hh +- rm -f $(PREFIX)/include/voro++/config.hh +- rm -f $(PREFIX)/include/voro++/container.hh +- rm -f $(PREFIX)/include/voro++/container_prd.hh +- rm -f $(PREFIX)/include/voro++/pre_container.hh +- rm -f $(PREFIX)/include/voro++/rad_option.hh +- rm -f $(PREFIX)/include/voro++/unitcell.hh +- rm -f $(PREFIX)/include/voro++/v_base.hh +- rm -f $(PREFIX)/include/voro++/v_compute.hh +- rm -f $(PREFIX)/include/voro++/wall.hh +- rm -f $(PREFIX)/include/voro++/worklist.hh +- rmdir $(PREFIX)/include/voro++ ++ rm -f $(DESTDIR)$(PREFIX)/bin/voro++ ++ rm -f $(DESTDIR)$(PREFIX)/man/man1/voro++.1 ++ rm -f $(DESTDIR)$(PREFIX)/lib/libvoro++.a ++ rm -f $(DESTDIR)$(PREFIX)/include/voro++/voro++.hh ++ rm -f $(DESTDIR)$(PREFIX)/include/voro++/c_loops.hh ++ rm -f $(DESTDIR)$(PREFIX)/include/voro++/cell.hh ++ rm -f $(DESTDIR)$(PREFIX)/include/voro++/common.hh ++ rm -f $(DESTDIR)$(PREFIX)/include/voro++/config.hh ++ rm -f $(DESTDIR)$(PREFIX)/include/voro++/container.hh ++ rm -f $(DESTDIR)$(PREFIX)/include/voro++/container_prd.hh ++ rm -f $(DESTDIR)$(PREFIX)/include/voro++/pre_container.hh ++ rm -f $(DESTDIR)$(PREFIX)/include/voro++/rad_option.hh ++ rm -f $(DESTDIR)$(PREFIX)/include/voro++/unitcell.hh ++ rm -f $(DESTDIR)$(PREFIX)/include/voro++/v_base.hh ++ rm -f $(DESTDIR)$(PREFIX)/include/voro++/v_compute.hh ++ rm -f $(DESTDIR)$(PREFIX)/include/voro++/wall.hh ++ rm -f $(DESTDIR)$(PREFIX)/include/voro++/worklist.hh ++ rmdir $(DESTDIR)$(PREFIX)/include/voro++ diff --git a/science/voro++/files/patch-config.mk b/science/voro++/files/patch-config.mk new file mode 100644 index 000000000000..04e78f8ecabb --- /dev/null +++ b/science/voro++/files/patch-config.mk @@ -0,0 +1,27 @@ +--- config.mk.orig 2013-10-17 17:54:13 UTC ++++ config.mk +@@ -8,20 +8,20 @@ + # the Makefiles. + + # C++ compiler +-CXX=g++ ++CXX?=g++ + + # Flags for the C++ compiler +-CFLAGS=-Wall -ansi -pedantic -O3 ++CFLAGS?=-Wall -ansi -pedantic -O3 + + # Relative include and library paths for compilation of the examples + E_INC=-I../../src + E_LIB=-L../../src + + # Installation directory +-PREFIX=/usr/local ++PREFIX?=/usr/local + + # Install command +-INSTALL=install ++INSTALL?=install + + # Flags for install command for executable + IFLAGS_EXEC=-m 0755 diff --git a/science/voro++/files/patch-src_Makefile b/science/voro++/files/patch-src_Makefile new file mode 100644 index 000000000000..41a7da0568d5 --- /dev/null +++ b/science/voro++/files/patch-src_Makefile @@ -0,0 +1,24 @@ +--- src/Makefile.orig 2013-10-17 17:54:13 UTC ++++ src/Makefile +@@ -13,7 +13,7 @@ objs=cell.o common.o container.o unitcel + src=$(patsubst %.o,%.cc,$(objs)) + + # Makefile rules +-all: libvoro++.a voro++ ++all: libvoro++.a libvoro++.so voro++ + + depend: + $(CXX) -MM $(src) >Makefile.dep +@@ -24,7 +24,11 @@ libvoro++.a: $(objs) + rm -f libvoro++.a + ar rs libvoro++.a $^ + +-voro++: libvoro++.a cmd_line.cc ++libvoro++.so: $(objs) ++ rm -f libvoro++.so ++ $(CXX) -shared $(LDFLAGS) -o libvoro++.so -Wl,-soname,libvoro++.so $^ ++ ++voro++: libvoro++.so cmd_line.cc + $(CXX) $(CFLAGS) -L. -o voro++ cmd_line.cc -lvoro++ + + %.o: %.cc diff --git a/science/voro++/pkg-descr b/science/voro++/pkg-descr index 85c4e6c242b2..65e2d5c0b3b5 100644 --- a/science/voro++/pkg-descr +++ b/science/voro++/pkg-descr @@ -1,9 +1,9 @@ Voro++ is a software library for carrying out three-dimensional computations -of the Voronoi tessellation. A distinguishing feature of the Voro++ library -is that it carries out cell-based calculations, computing the Voronoi cell -for each particle individually. It is particularly well-suited for -applications that rely on cell-based statistics, where features of Voronoi -cells (eg. volume, centroid, number of faces) can be used to analyze a -system of particles. +of the Voronoi tessellation. A distinguishing feature of the Voro++ library is +that it carries out cell-based calculations, computing the Voronoi cell for +each particle individually. It is particularly well-suited for applications +that rely on cell-based statistics, where features of Voronoi cells (eg. +volume, centroid, number of faces) can be used to analyze a system of +particles. WWW: http://math.lbl.gov/voro++/ diff --git a/science/voro++/pkg-plist b/science/voro++/pkg-plist index 56d9e585b6c1..ba46c2c064c4 100644 --- a/science/voro++/pkg-plist +++ b/science/voro++/pkg-plist @@ -14,4 +14,5 @@ include/voro++/voro++.hh include/voro++/wall.hh include/voro++/worklist.hh lib/libvoro++.a +lib/libvoro++.so man/man1/voro++.1.gz diff --git a/science/xcrysden/Makefile b/science/xcrysden/Makefile index 8f63d553cffc..1fa48b1ce780 100644 --- a/science/xcrysden/Makefile +++ b/science/xcrysden/Makefile @@ -2,7 +2,7 @@ PORTNAME= xcrysden DISTVERSION= 1.5.60 -PORTREVISION= 2 +PORTREVISION= 5 CATEGORIES= science MASTER_SITES= http://www.xcrysden.org/download/ @@ -15,11 +15,11 @@ LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libfftw3.so:math/fftw3 RUN_DEPENDS= bwidget>0:x11-toolkits/bwidget \ babel:science/openbabel \ - convert:graphics/ImageMagick \ + convert:graphics/ImageMagick6 \ ppmtompeg:graphics/netpbm \ xwd:x11/xwd -USES= fortran gmake localbase:ldflags tcl tk +USES= fortran gl gmake localbase:ldflags tcl tk USE_GL= gl glu USE_XORG= x11 xmu diff --git a/science/xcrysden/files/patch-F_gengeom.f b/science/xcrysden/files/patch-F_gengeom.f new file mode 100644 index 000000000000..b39ec84b710a --- /dev/null +++ b/science/xcrysden/files/patch-F_gengeom.f @@ -0,0 +1,17 @@ +Temporary fix for gcc8 breakage: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=232960 +Source: http://www.democritos.it/pipermail/xcrysden/2018-October/001929.html + +--- F/gengeom.f 2012-02-03 11:53:05.000000000 +0100 ++++ F/gengeom.f 2018-10-30 08:58:33.624408287 +0100 +@@ -905,9 +905,9 @@ + + SUBROUTINE GETCCOOR(A33,B33,BROW,X,Y,Z,XC,YC,ZC,NA,NATR) + include 'param.inc' +- REAL*8 B33(3,4),A33(3,3),RA(3,3),COOR(3),X(NATR),Y(NATR),Z(NATR), +- * XC(NAC,4),YC(NAC,4),ZC(NAC,4),RX(3) + INTEGER BROW ++ REAL*8 B33(3,BROW),A33(3,3),RA(3,3),COOR(3),X(NATR),Y(NATR), ++ * Z(NATR),XC(NAC,4),YC(NAC,4),ZC(NAC,4),RX(3) + + C ******** + C ATTENTION: HERE WE HAVE MULT. OFF "SAME-LAYING" ELEMENTS, |