Index: head/science/Makefile =================================================================== --- head/science/Makefile (revision 479262) +++ head/science/Makefile (revision 479263) @@ -1,277 +1,278 @@ # $FreeBSD$ # COMMENT = Scientific ports SUBDIR += 2d-rewriter SUBDIR += ALPSCore SUBDIR += InsightToolkit SUBDIR += MOOSE-neural-simulator SUBDIR += PETSc SUBDIR += R-cran-AMORE SUBDIR += R-cran-DCluster SUBDIR += R-cran-Epi SUBDIR += R-cran-bayesm SUBDIR += R-cran-cmprsk SUBDIR += R-cran-e1071 SUBDIR += R-cran-eco SUBDIR += R-cran-epicalc SUBDIR += R-cran-etm SUBDIR += R-cran-fastICA SUBDIR += R-cran-kernlab SUBDIR += R-cran-snow SUBDIR += R-cran-som SUBDIR += R-cran-udunits2 SUBDIR += abinit SUBDIR += afni SUBDIR += aircraft-datcom SUBDIR += antioch SUBDIR += atom SUBDIR += atompaw SUBDIR += avogadro SUBDIR += bddsolve SUBDIR += bft SUBDIR += bodr SUBDIR += brian SUBDIR += buddy SUBDIR += cdcl SUBDIR += cdf SUBDIR += cdo SUBDIR += cgnslib SUBDIR += cgribex SUBDIR += checkmol SUBDIR += chemical-mime-data SUBDIR += chemps2 SUBDIR += chemtool SUBDIR += chemtool-devel SUBDIR += chrono SUBDIR += clhep SUBDIR += clipper SUBDIR += colt SUBDIR += coot SUBDIR += cp2k SUBDIR += crf++ SUBDIR += dalton SUBDIR += datawarrior SUBDIR += dcl SUBDIR += devisor SUBDIR += dft_tools SUBDIR += dkh SUBDIR += dlib-cpp SUBDIR += dlpoly-classic SUBDIR += eccodes SUBDIR += ecs SUBDIR += epte SUBDIR += erd SUBDIR += fastcap SUBDIR += fasthenry SUBDIR += fisicalab SUBDIR += fleur SUBDIR += fsom SUBDIR += fvcom SUBDIR += fvcom-mpi SUBDIR += fvm SUBDIR += gabedit SUBDIR += gchemutils SUBDIR += gdma SUBDIR += getdp SUBDIR += ghemical SUBDIR += ghmm SUBDIR += gnudatalanguage SUBDIR += gramps SUBDIR += grib_api SUBDIR += gromacs SUBDIR += gsmc SUBDIR += gtamsanalyzer SUBDIR += gwyddion SUBDIR += h5utils SUBDIR += harminv SUBDIR += hdf SUBDIR += hdf5 SUBDIR += hdf5-18 SUBDIR += hypre SUBDIR += iboview SUBDIR += isaac-cfd SUBDIR += jdftx SUBDIR += jstrack SUBDIR += kalzium SUBDIR += kalzium-kde4 SUBDIR += kst2 SUBDIR += lammps SUBDIR += lamprop SUBDIR += libaec SUBDIR += libccp4 SUBDIR += libcint SUBDIR += libctl SUBDIR += libefp SUBDIR += libgeodecomp SUBDIR += libghemical SUBDIR += libgridxc SUBDIR += libint SUBDIR += libint2 SUBDIR += libkml SUBDIR += liblinear SUBDIR += liboglappth SUBDIR += libquantum SUBDIR += libssm SUBDIR += libsvm SUBDIR += libsvm-python SUBDIR += libxc SUBDIR += linsmith SUBDIR += madness SUBDIR += massxpert SUBDIR += mbdyn SUBDIR += mcstas SUBDIR += mcstas-comps SUBDIR += mcxtrace SUBDIR += mcxtrace-comps SUBDIR += mdynamix SUBDIR += medit SUBDIR += meep SUBDIR += mei SUBDIR += metaf2xml SUBDIR += metaphysicl SUBDIR += minc2 SUBDIR += mmdb2 SUBDIR += mol2ps SUBDIR += mpb SUBDIR += mpqc SUBDIR += multiwfn + SUBDIR += namd SUBDIR += ncs SUBDIR += netcdf SUBDIR += netcdf-cxx SUBDIR += netcdf-fortran SUBDIR += nifticlib SUBDIR += nwchem SUBDIR += octopus SUBDIR += openbabel SUBDIR += openkim SUBDIR += openstructure SUBDIR += p5-Algorithm-SVMLight SUBDIR += p5-Chemistry-3DBuilder SUBDIR += p5-Chemistry-Bond-Find SUBDIR += p5-Chemistry-Canonicalize SUBDIR += p5-Chemistry-Elements SUBDIR += p5-Chemistry-File-MDLMol SUBDIR += p5-Chemistry-File-Mopac SUBDIR += p5-Chemistry-File-PDB SUBDIR += p5-Chemistry-File-SLN SUBDIR += p5-Chemistry-File-SMARTS SUBDIR += p5-Chemistry-File-SMILES SUBDIR += p5-Chemistry-File-VRML SUBDIR += p5-Chemistry-File-XYZ SUBDIR += p5-Chemistry-FormulaPattern SUBDIR += p5-Chemistry-InternalCoords SUBDIR += p5-Chemistry-Isotope SUBDIR += p5-Chemistry-MacroMol SUBDIR += p5-Chemistry-MidasPattern SUBDIR += p5-Chemistry-Mok SUBDIR += p5-Chemistry-Mol SUBDIR += p5-Chemistry-Pattern SUBDIR += p5-Chemistry-Reaction SUBDIR += p5-Chemistry-Ring SUBDIR += p5-Geo-BUFR SUBDIR += p5-Geo-Coordinates-Converter SUBDIR += p5-Geo-Coordinates-Converter-iArea SUBDIR += p5-Geo-ReadGRIB SUBDIR += p5-Geo-WebService-Elevation-USGS SUBDIR += p5-Mcstas-Tools SUBDIR += p5-PerlMol SUBDIR += p5-Physics-Unit SUBDIR += paje SUBDIR += paraview SUBDIR += pcmsolver SUBDIR += pnetcdf SUBDIR += psychopy SUBDIR += pulseview SUBDIR += py-DendroPy SUBDIR += py-MDAnalysis SUBDIR += py-MDAnalysisTests SUBDIR += py-OpenFermion SUBDIR += py-PyQuante SUBDIR += py-ScientificPython SUBDIR += py-SimpleSpectral SUBDIR += py-abipy SUBDIR += py-ase SUBDIR += py-cdo SUBDIR += py-coards SUBDIR += py-dlib SUBDIR += py-gpaw SUBDIR += py-gsd SUBDIR += py-h5py SUBDIR += py-hcluster SUBDIR += py-kinematics SUBDIR += py-mdp SUBDIR += py-mlpy SUBDIR += py-mmtf-python SUBDIR += py-netCDF4 SUBDIR += py-obspy SUBDIR += py-openpiv SUBDIR += py-paida SUBDIR += py-pupynere SUBDIR += py-pyaixi SUBDIR += py-pydicom SUBDIR += py-pymatgen SUBDIR += py-pymol SUBDIR += py-pyosf SUBDIR += py-pysal SUBDIR += py-pyteomics SUBDIR += py-pyteomics.biolccc SUBDIR += py-qspin SUBDIR += py-quantities SUBDIR += py-rmf SUBDIR += py-scikit-fuzzy SUBDIR += py-scikit-learn SUBDIR += py-scikit-sparse SUBDIR += py-scimath SUBDIR += py-scipy SUBDIR += py-scoria SUBDIR += py-spglib SUBDIR += py-veusz SUBDIR += py-ws2300 SUBDIR += pybrain SUBDIR += pycdf SUBDIR += pynn SUBDIR += qbox SUBDIR += qcl SUBDIR += qmcpack SUBDIR += qtresistors SUBDIR += quantum-espresso SUBDIR += qwalk SUBDIR += rdkit SUBDIR += rmf SUBDIR += rubygem-ai4r SUBDIR += rubygem-cdo SUBDIR += rubygem-rgeo SUBDIR += rubygem-rgeo-geojson SUBDIR += rubygem-rgeo-proj4 SUBDIR += rubygem-rgeo-shapefile SUBDIR += rubygem-ruby-dcl SUBDIR += rubygem-ruby-netcdf SUBDIR += siesta SUBDIR += sigrok-cli SUBDIR += sigrok-firmware SUBDIR += sigrok-firmware-fx2lafw SUBDIR += sigrok-firmware-utils SUBDIR += silo SUBDIR += simlib SUBDIR += simsmith SUBDIR += spglib SUBDIR += step SUBDIR += step-kde4 SUBDIR += svmlight SUBDIR += szip SUBDIR += teem SUBDIR += tfel SUBDIR += triqs SUBDIR += udunits SUBDIR += v_sim SUBDIR += vmd SUBDIR += voro++ SUBDIR += wannier90 SUBDIR += xcrysden SUBDIR += xdrawchem SUBDIR += xfce4-equake-plugin SUBDIR += xmakemol .include Index: head/science/namd/Makefile =================================================================== --- head/science/namd/Makefile (nonexistent) +++ head/science/namd/Makefile (revision 479263) @@ -0,0 +1,81 @@ +# $FreeBSD$ + +PORTNAME= namd +DISTVERSION= 2-12-211 +DISTVERSIONSUFFIX= -gfdf7ea56 +CATEGORIES= science + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Computer software for molecular dynamics simulation + +LICENSE= NAMD_MOLECULAR_DYNAMICS_LICENSE +LICENSE_NAME= NAMD Molecular Dynamics Software +LICENSE_FILE= ${WRKSRC}/license.txt +LICENSE_PERMS= auto-accept dist-mirror pkg-mirror + +ONLY_FOR_ARCHS= amd64 i386 +ONLY_FOR_ARCHS_REASON= Not clear if it can be built on other architectures +BROKEN_i386= need to fix the fft library handling + +FETCH_DEPENDS= git:devel/git +BUILD_DEPENDS= bash:shells/bash \ + ${LOCALBASE}/include/fftw3.h:math/fftw3 +LIB_DEPENDS= libck.so:net/charm \ + libfftw3f.so:math/fftw3-float + +USES= fortran gmake localbase:ldflags python:build shebangfix tcl +SHEBANG_FILES= config + +GIT_URL= https://charm.cs.illinois.edu/gerrit/namd.git + +ARCH_STR= Linux-${ARCH:S/amd64/x86_64/:S/i386/x86/}-g++ +ARCH_STR_CHARM= linux${ARCH:S/amd64/64/:S/i386/32/} + +PATCH_WRKSRC= ${WRKSRC} +BUILD_WRKSRC= ${WRKSRC}/${ARCH_STR} + +CFLAGS+= -D_NO_MALLOC_H -D_NO_ALLOCA_H +CXXFLAGS+= -D_NO_MALLOC_H -D_NO_ALLOCA_H + +BINARY_ALIAS= gcc=${CC} g++=${CXX} + +PLIST_FILES= bin/flipbinpdb \ + bin/flipdcd \ + bin/namd2 \ + bin/psfgen \ + bin/sortreplicas + +local-makesum: # Workaround: the generic 'make makesum' is broken when custom do-fetch is defined: it calls ${SCRIPTSDIR}/do-fetch.sh. + @${MAKE} distclean fetch makesum + +do-fetch: + @if [ "${FORCE_FETCH_ALL}" = "true" ] || ! [ -f "${DISTDIR}/${DIST_SUBDIR}/${DISTNAME}${EXTRACT_SUFX}" ]; then \ + ${MKDIR} ${DISTDIR}/${DIST_SUBDIR} && \ + cd ${DISTDIR}/${DIST_SUBDIR} && \ + git clone -q ${GIT_URL} ${PORTNAME}-${DISTVERSIONFULL} && \ + (cd ${PORTNAME}-${DISTVERSIONFULL} && git reset -q --hard ${DISTVERSIONFULL} && ${RM} -r .git) && \ + ${FIND} ${PORTNAME}-${DISTVERSIONFULL} -and -exec ${TOUCH} -h -d 1970-01-01T00:00:00Z {} \; && \ + ${FIND} ${PORTNAME}-${DISTVERSIONFULL} -print0 | LC_ALL=C ${SORT} -z | \ + ${TAR} czf ${PORTNAME}-${DISTVERSIONFULL}${EXTRACT_SUFX} --format=bsdtar --uid 0 --gid 0 --options gzip:!timestamp --no-recursion --null -T - && \ + ${RM} -r ${PORTNAME}-${DISTVERSIONFULL}; \ + fi + +do-configure: + @cd ${WRKSRC} && ${ECHO} "CHARMBASE=${LOCALBASE}" > Make.config + @cd ${WRKSRC} && ./config ${ARCH_STR} --charm-arch multicore-${ARCH_STR_CHARM} ${ARCH:S/amd64/--with-fftw3/:S/${ARCH}//} + @${REINPLACE_CMD} 's|CHARMBASE = .*|CHARMBASE = ${LOCALBASE}|' ${WRKSRC}/Make.charm + @${REINPLACE_CMD} '\ + s|FFTDIR=.*|FFTDIR=${LOCALBASE}|; \ + s|-lsfftw|-lfft3f|; \ + s|-lsrfftw|-lrfft3f|; \ + s|TCLDIR=.*|TCLDIR=${LOCALBASE}/include/tcl8.6|; \ + s|TCLINCL=.*|TCLINCL=-I${LOCALBASE}/include/tcl8.6|; \ + s|TCLLIB=.*|TCLLIB=-L${LOCALBASE}/lib -ltcl86 -lpthread|' \ + ${WRKSRC}/arch/Linux* + +do-install: +.for e in namd2 flipbinpdb flipdcd psfgen sortreplicas + ${INSTALL_PROGRAM} ${BUILD_WRKSRC}/${e} ${STAGEDIR}${PREFIX}/bin +.endfor + +.include Property changes on: head/science/namd/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/namd/distinfo =================================================================== --- head/science/namd/distinfo (nonexistent) +++ head/science/namd/distinfo (revision 479263) @@ -0,0 +1,3 @@ +TIMESTAMP = 1536445358 +SHA256 (namd-2-12-211-gfdf7ea56.tar.gz) = 2ab3a98f7cc9fa997088502aa87ad8cfe9218b35d4b783b7370a5d5d49f7fe15 +SIZE (namd-2-12-211-gfdf7ea56.tar.gz) = 8278948 Property changes on: head/science/namd/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/namd/files/patch-Makefile =================================================================== --- head/science/namd/files/patch-Makefile (nonexistent) +++ head/science/namd/files/patch-Makefile (revision 479263) @@ -0,0 +1,11 @@ +--- Makefile.orig 1970-01-01 00:00:00 UTC ++++ Makefile +@@ -435,7 +435,7 @@ LIBS = $(CUDAOBJS) $(PLUGINLIB) $(SBLIB) + + # CXX is platform dependent + CXXBASEFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(FMM) $(COPTI)$(PLUGININCDIR) $(COPTI)$(COLVARSINCDIR) $(COPTD)STATIC_PLUGIN $(TCL) $(PYTHON) $(FFT) $(CUDA) $(MIC) $(MEMOPT) $(CCS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF) $(EXTRAINCS) $(MSA) $(CKLOOP) +-CXXFLAGS = $(CXXBASEFLAGS) $(CXXOPTS) ++CXXFLAGS += $(CXXBASEFLAGS) $(CXXOPTS) + CXXMICFLAGS = $(CXXBASEFLAGS) $(CXXOPTS) $(CXXMICOPTS) + CXXTHREADFLAGS = $(CXXBASEFLAGS) $(CXXTHREADOPTS) + CXXSIMPARAMFLAGS = $(CXXBASEFLAGS) $(CXXSIMPARAMOPTS) Property changes on: head/science/namd/files/patch-Makefile ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/namd/files/patch-config =================================================================== --- head/science/namd/files/patch-config (nonexistent) +++ head/science/namd/files/patch-config (revision 479263) @@ -0,0 +1,11 @@ +--- config.orig 2018-09-07 20:23:43 UTC ++++ config +@@ -582,7 +582,7 @@ function error_exists { + if [ -n "$CHARM_OPTS" ]; then + echo "CHARMOPTS = $CHARM_OPTS" >> Make.config + fi +- echo 'CHARM = $(CHARMBASE)/$(CHARMARCH)' >> Make.config ++ echo 'CHARM = $(CHARMBASE)' >> Make.config + ARCH_SUFFIX="" + [[ "$CHARM_ARCH" == *-scyld* ]] && ARCH_SUFFIX=${ARCH_SUFFIX}-Scyld + if [[ "$CHARM_ARCH" == *-clustermatic* ]]; then Property changes on: head/science/namd/files/patch-config ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/namd/pkg-descr =================================================================== --- head/science/namd/pkg-descr (nonexistent) +++ head/science/namd/pkg-descr (revision 479263) @@ -0,0 +1,8 @@ +NAMD is computer software for molecular dynamics simulation, written using the +Charm++ parallel programming model. It is noted for its parallel efficiency and +is often used to simulate large systems (millions of atoms). It has been +developed by the collaboration of the Theoretical and Computational Biophysics +Group (TCB) and the Parallel Programming Laboratory (PPL) at the University of +Illinois at Urbana-Champaign. + +WWW: https://www.ks.uiuc.edu/Research/namd/ Property changes on: head/science/namd/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property