diff --git a/science/tinker/Makefile b/science/tinker/Makefile index c5b9b72ff278..a62f2268609b 100644 --- a/science/tinker/Makefile +++ b/science/tinker/Makefile @@ -1,96 +1,95 @@ PORTNAME= tinker -DISTVERSION= 8.11.3 -PORTREVISION= 1 +DISTVERSION= 25.3 CATEGORIES= science MASTER_SITES= https://dasher.wustl.edu/tinker/downloads/ MAINTAINER= yuri@FreeBSD.org COMMENT= General purpose molecular modelling package WWW= https://dasher.wustl.edu/tinker/ LICENSE= TINKER LICENSE_NAME= TINKER license agreement LICENSE_FILE= ${WRKSRC}/doc/license.pdf LICENSE_PERMS= auto-accept # internal academic purposes only, no commercial use LIB_DEPENDS= libfftw3.so:math/fftw3 USES= fortran gmake WRKSRC= ${WRKDIR}/${PORTNAME} BUILD_WRKSRC= ${WRKSRC}/source INSTALL_WRKSRC= ${WRKSRC}/source MAKE_ENV= HAVE_G2C=yes MAKE_ARGS= RANLIB=ranlib BINDIR=${STAGEDIR}${PREFIX}/bin LIBS="${LOCALBASE}/lib/libfftw3.a ${LOCALBASE}/lib/libfftw3_threads.a" MAKEFILE= ${WRKSRC}/make/Makefile EXTRACT_AFTER_ARGS=--exclude fftw --exclude windows --exclude macosx SUB_FILES= pkg-message BINARY_ALIAS= gfortran=gfortran${GCC_DEFAULT} OPTIONS_DEFINE= NATIVE OPTIMIZED_FFLAGS DOCS EXAMPLES OPTIONS_DEFINE_amd64= SIMD OPTIONS_DEFINE_i386= SIMD NATIVE_MAKE_ARGS= PORT_SIMD_FLAGS+="-march=native" OPTIMIZED_FFLAGS_DESC= Fortran compilation optimizations SIMD_MAKE_ARGS= PORT_SIMD_FLAGS+="-msse -msse2 -mssse3" PORTDOCS= * PORTEXAMPLES= * .include .if ${PORT_OPTIONS:MOPTIMIZED_FFLAGS} FFLAGS+= -O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations .if (${ARCH} == "i386") FFLAGS+= -mfancy-math-387 -malign-double .endif # i386 .endif # OPTIMIZED_FFLAGS post-extract: @${RM} ${BUILD_WRKSRC}/*.c @${RM} ${WRKSRC}/other/eopbend.orig # remove bundled linux libraries @${RM} ${WRKSRC}/lib/linux/* post-patch: @${REINPLACE_CMD} -i '' 's|\.\./bin/|${STAGEDIR}${PREFIX}/bin/|' ${BUILD_WRKSRC}/../bench/bench*.run post-install: @${MKDIR} ${STAGEDIR}${DATADIR} @${MKDIR} ${STAGEDIR}${DATADIR}/params cd ${WRKSRC}/params && ${INSTALL_DATA} * ${STAGEDIR}${DATADIR}/params @${MKDIR} ${STAGEDIR}${DATADIR}/test cd ${WRKSRC}/test && ${INSTALL_DATA} * ${STAGEDIR}${DATADIR}/test post-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} cd ${WRKSRC}/doc && ${INSTALL_DATA} 0README *.pdf ${STAGEDIR}${DOCSDIR} post-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} cd ${WRKSRC}/example && ${INSTALL_DATA} \ 0README *.make *.dyn *.int *.frac *.key *.seq *.pdb *.xyz \ ${STAGEDIR}${EXAMPLESDIR} do-test: ${RM} -r ${WRKSRC}/bin ${LN} -s ${STAGEDIR}${PREFIX}/bin ${WRKSRC}/bin cd ${WRKSRC}/test && \ for test_run in *.run; do \ ${ECHO} "Running test $${test_run} ..." && \ ./$${test_run} && \ ${ECHO} "Test $${test_run} suceeded"; \ done benchmarks: stage .for n in 1 2 3 4 5 6 7 8 9 @cd ${BUILD_WRKSRC}/../bench && ./bench${n}.run .endfor .include diff --git a/science/tinker/distinfo b/science/tinker/distinfo index 6c20209908c4..7ca60014bed4 100644 --- a/science/tinker/distinfo +++ b/science/tinker/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1719188902 -SHA256 (tinker-8.11.3.tar.gz) = 8dfbc9fb8f26742d91139187657e2c905744b0243538f81b75bc04cdc2606ff7 -SIZE (tinker-8.11.3.tar.gz) = 73256260 +TIMESTAMP = 1753634645 +SHA256 (tinker-25.3.tar.gz) = d536f1d4d0d7d4394b3b3d88a52cf12ed3489312ac2ad9c6ce4d198bd681e36c +SIZE (tinker-25.3.tar.gz) = 80772142 diff --git a/science/tinker/pkg-plist b/science/tinker/pkg-plist index 286fc0abcadd..b0f9367ade44 100644 --- a/science/tinker/pkg-plist +++ b/science/tinker/pkg-plist @@ -1,223 +1,231 @@ bin/alchemy bin/analyze bin/anneal bin/arcedit bin/bar bin/correlate bin/critical bin/crystal bin/diffuse bin/distgeom bin/document bin/dynamic bin/freefix bin/gda bin/intedit bin/intxyz bin/minimize bin/minirot bin/minrigid bin/mol2xyz bin/molxyz bin/monte bin/newton bin/newtrot bin/nucleic bin/optimize bin/optirot bin/optrigid bin/path bin/pdbxyz bin/polarize bin/poledit bin/potential bin/prmedit bin/protein bin/pss bin/pssrigid bin/pssrot bin/radial bin/saddle bin/scan bin/sniffer bin/spacefill bin/spectrum bin/superpose bin/testgrad bin/testhess bin/testpair bin/testpol bin/testrot bin/testsurf bin/testvir bin/timer bin/timerot bin/torsfit bin/valence bin/vibbig bin/vibrate bin/vibrot bin/xtalfit bin/xtalmin bin/xyzedit bin/xyzint bin/xyzmol2 bin/xyzpdb %%DATADIR%%/params/0README +%%DATADIR%%/params/amber14sb.prm +%%DATADIR%%/params/amber19sb.prm %%DATADIR%%/params/amber94.prm %%DATADIR%%/params/amber96.prm %%DATADIR%%/params/amber98.prm %%DATADIR%%/params/amber99.prm %%DATADIR%%/params/amber99sb.prm %%DATADIR%%/params/amoeba04.prm %%DATADIR%%/params/amoeba09.prm %%DATADIR%%/params/amoebabio-hfc23.prm %%DATADIR%%/params/amoebabio09.prm %%DATADIR%%/params/amoebabio18.prm %%DATADIR%%/params/amoebail22.prm %%DATADIR%%/params/amoebanuc17.prm %%DATADIR%%/params/amoebaplus.prm %%DATADIR%%/params/amoebapro04.prm %%DATADIR%%/params/amoebapro13.prm %%DATADIR%%/params/basic.prm %%DATADIR%%/params/charmm19.prm %%DATADIR%%/params/charmm22.prm -%%DATADIR%%/params/charmm22cmap.prm +%%DATADIR%%/params/charmm27.prm +%%DATADIR%%/params/charmm36.prm %%DATADIR%%/params/dang.prm %%DATADIR%%/params/hippo19.prm %%DATADIR%%/params/hoch.prm %%DATADIR%%/params/iwater.prm %%DATADIR%%/params/mm2.prm %%DATADIR%%/params/mm3.prm %%DATADIR%%/params/mm3pro.prm -%%DATADIR%%/params/mmff.prm -%%DATADIR%%/params/oplsaa.prm +%%DATADIR%%/params/mmff94.prm +%%DATADIR%%/params/mmff94s.prm +%%DATADIR%%/params/oplsaa08.prm %%DATADIR%%/params/oplsaal.prm %%DATADIR%%/params/oplsua.prm %%DATADIR%%/params/smoothaa.prm %%DATADIR%%/params/smoothua.prm %%DATADIR%%/params/uwater.prm %%DATADIR%%/params/water03.prm %%DATADIR%%/params/water14.prm %%DATADIR%%/params/water21.prm %%DATADIR%%/params/water22.prm %%DATADIR%%/test/0README %%DATADIR%%/test/anion.dat %%DATADIR%%/test/anion.dyn0 %%DATADIR%%/test/anion.key %%DATADIR%%/test/anion.log %%DATADIR%%/test/anion.run %%DATADIR%%/test/anion.xyz %%DATADIR%%/test/argon.1st %%DATADIR%%/test/argon.key %%DATADIR%%/test/argon.log %%DATADIR%%/test/argon.run %%DATADIR%%/test/cation.ckey %%DATADIR%%/test/cation.cxyz %%DATADIR%%/test/cation.log %%DATADIR%%/test/cation.rkey %%DATADIR%%/test/cation.run %%DATADIR%%/test/cation.rxyz %%DATADIR%%/test/clean.make %%DATADIR%%/test/cluster.dat %%DATADIR%%/test/cluster.key %%DATADIR%%/test/cluster.log %%DATADIR%%/test/cluster.run %%DATADIR%%/test/cluster.xyz %%DATADIR%%/test/crambin.key %%DATADIR%%/test/crambin.log %%DATADIR%%/test/crambin.pdb %%DATADIR%%/test/crambin.run %%DATADIR%%/test/cyclohexane.boat %%DATADIR%%/test/cyclohexane.chair %%DATADIR%%/test/cyclohexane.key %%DATADIR%%/test/cyclohexane.log %%DATADIR%%/test/cyclohexane.run %%DATADIR%%/test/dhfr.dyn %%DATADIR%%/test/dhfr.key %%DATADIR%%/test/dhfr.log %%DATADIR%%/test/dhfr.run %%DATADIR%%/test/dhfr.xyz %%DATADIR%%/test/dialanine.key %%DATADIR%%/test/dialanine.log %%DATADIR%%/test/dialanine.run %%DATADIR%%/test/dialanine.xyz %%DATADIR%%/test/enkephalin.dat %%DATADIR%%/test/enkephalin.key %%DATADIR%%/test/enkephalin.log %%DATADIR%%/test/enkephalin.run %%DATADIR%%/test/ethanol.000 %%DATADIR%%/test/ethanol.020 %%DATADIR%%/test/ethanol.040 %%DATADIR%%/test/ethanol.060 %%DATADIR%%/test/ethanol.080 %%DATADIR%%/test/ethanol.100 %%DATADIR%%/test/ethanol.120 %%DATADIR%%/test/ethanol.140 %%DATADIR%%/test/ethanol.160 %%DATADIR%%/test/ethanol.180 %%DATADIR%%/test/ethanol.dat %%DATADIR%%/test/ethanol.key %%DATADIR%%/test/ethanol.log %%DATADIR%%/test/ethanol.run %%DATADIR%%/test/ethanol.xyz %%DATADIR%%/test/formamide.cell %%DATADIR%%/test/formamide.dat %%DATADIR%%/test/formamide.key %%DATADIR%%/test/formamide.log %%DATADIR%%/test/formamide.run %%DATADIR%%/test/gpcr.blk %%DATADIR%%/test/gpcr.key %%DATADIR%%/test/gpcr.log %%DATADIR%%/test/gpcr.run %%DATADIR%%/test/gpcr.xyz %%DATADIR%%/test/helix.1st %%DATADIR%%/test/helix.key %%DATADIR%%/test/helix.log %%DATADIR%%/test/helix.run %%DATADIR%%/test/ice.key %%DATADIR%%/test/ice.log %%DATADIR%%/test/ice.run %%DATADIR%%/test/ice.xyz %%DATADIR%%/test/ifabp.dat %%DATADIR%%/test/ifabp.key %%DATADIR%%/test/ifabp.log %%DATADIR%%/test/ifabp.run %%DATADIR%%/test/ifabp.xyz %%DATADIR%%/test/liquid.amoeba %%DATADIR%%/test/liquid.aplus %%DATADIR%%/test/liquid.hippo %%DATADIR%%/test/liquid.kamoeba %%DATADIR%%/test/liquid.kaplus %%DATADIR%%/test/liquid.khippo %%DATADIR%%/test/liquid.log %%DATADIR%%/test/liquid.run %%DATADIR%%/test/methanol.dat %%DATADIR%%/test/methanol.dma %%DATADIR%%/test/methanol.key %%DATADIR%%/test/methanol.log %%DATADIR%%/test/methanol.run %%DATADIR%%/test/nitrogen.arc %%DATADIR%%/test/nitrogen.key %%DATADIR%%/test/nitrogen.log %%DATADIR%%/test/nitrogen.run %%DATADIR%%/test/nitrogen.xyz %%DATADIR%%/test/polyala.dat %%DATADIR%%/test/polyala.key %%DATADIR%%/test/polyala.log %%DATADIR%%/test/polyala.run +%%DATADIR%%/test/pyridine.dat +%%DATADIR%%/test/pyridine.log +%%DATADIR%%/test/pyridine.run +%%DATADIR%%/test/pyridine.xyz %%DATADIR%%/test/salt.cell %%DATADIR%%/test/salt.key %%DATADIR%%/test/salt.log %%DATADIR%%/test/salt.run %%DATADIR%%/test/vasopressin.key %%DATADIR%%/test/vasopressin.log %%DATADIR%%/test/vasopressin.run %%DATADIR%%/test/vasopressin.xyz %%DATADIR%%/test/water.amoeba %%DATADIR%%/test/water.hippo %%DATADIR%%/test/water.log %%DATADIR%%/test/water.pot %%DATADIR%%/test/water.run %%DATADIR%%/test/water.tip3p %%DATADIR%%/test/water.xyz