Index: head/science/Makefile =================================================================== --- head/science/Makefile (revision 478990) +++ head/science/Makefile (revision 478991) @@ -1,274 +1,275 @@ # $FreeBSD$ # 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 += 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 += medit SUBDIR += meep SUBDIR += mei SUBDIR += metaf2xml SUBDIR += metaphysicl SUBDIR += minc2 SUBDIR += mmdb2 SUBDIR += mol2ps SUBDIR += mpb SUBDIR += mpqc SUBDIR += multiwfn 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/cp2k/Makefile =================================================================== --- head/science/cp2k/Makefile (nonexistent) +++ head/science/cp2k/Makefile (revision 478991) @@ -0,0 +1,55 @@ +# $FreeBSD$ + +PORTNAME= cp2k +DISTVERSION= 6.1 +CATEGORIES= science +MASTER_SITES= SF/${PORTNAME}/ + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Quantum chemistry and solid state physics software package + +LICENSE= GPLv2+ + +LIB_DEPENDS= libblas.so:math/blas \ + libfftw3.so:math/fftw3 \ + liblapack.so:math/lapack + +USES= fortran gmake python:build tar:bz2 + +MAKEFILE= ${WRKSRC}/makefiles/Makefile +MAKE_ARGS= XARCH=FreeBSD-${NOLIBINT}libint-gfortran VERSION=${VERSION} FC=gfortran${GCC_DEFAULT} CC=${CC} LD=gfortran${GCC_DEFAULT} + +BUILD_WRKSRC= ${WRKSRC}/.build +INSTALL_WRKSRC= ${BUILD_WRKSRC} + +BINARY_ALIAS= python=${PYTHON_CMD} + +OPTIONS_DEFINE= LIBINT +OPTIONS_SINGLE= MULTIPROCESSING +OPTIONS_SINGLE_MULTIPROCESSING= SERIAL OPENMP # for the complete list see "3a. ARCH files" in https://www.cp2k.org/howto:compile +OPTIONS_DEFAULT= LIBINT SERIAL +MULTIPROCESSING_DESC= Multiprocessing + +LIBINT_DESC= Use libint to evaluate integrals +LIBINT_VARS_OFF= NOLIBINT=no +LIBINT_LIB_DEPENDS= libint.so:science/libint + +SERIAL_DESC= Single core (no multiprocessing) +SERIAL_VARS= VERSION=sopt + +OPENMP_VARS= VERSION=ssmp +OPENMP_LIB_DEPENDS= libomp.so:devel/openmp +OPENMP_BROKEN= undefined reference to `dfftw_plan_with_nthreads_': https://github.com/cp2k/cp2k/issues/12 (need OPENMP=on in math/fftw3 ?) + +PLIST_FILES= bin/${PORTNAME} + +post-patch: + @${REINPLACE_CMD} 's|^LIBS.*=.*|& ${LDFLAGS}|' ${WRKSRC}/arch/FreeBSD-* + +pre-build: + @${MKDIR} ${BUILD_WRKSRC} + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/exe/*/${PORTNAME}.* ${STAGEDIR}${PREFIX}/bin/${PORTNAME} + +.include Property changes on: head/science/cp2k/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/cp2k/distinfo =================================================================== --- head/science/cp2k/distinfo (nonexistent) +++ head/science/cp2k/distinfo (revision 478991) @@ -0,0 +1,3 @@ +TIMESTAMP = 1536086561 +SHA256 (cp2k-6.1.tar.bz2) = af803558e0a6b9e9d9ce8a3ab955ba32bacd179922455424e061c82c9fefa34b +SIZE (cp2k-6.1.tar.bz2) = 55139278 Property changes on: head/science/cp2k/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/cp2k/files/patch-makefiles_Makefile =================================================================== --- head/science/cp2k/files/patch-makefiles_Makefile (nonexistent) +++ head/science/cp2k/files/patch-makefiles_Makefile (revision 478991) @@ -0,0 +1,96 @@ +--- makefiles/Makefile.orig 2018-09-04 19:11:12 UTC ++++ makefiles/Makefile +@@ -11,7 +11,7 @@ SHELL = /bin/sh + # also works fine + # + CP2KHOME := $(abspath $(PWD)/..) +-ARCH := local ++XARCH := local + export VERSION=sopt + + MAKEFILE := $(CP2KHOME)/makefiles/Makefile +@@ -25,7 +25,7 @@ PRETTYOBJDIR := $(CP2KHOME)/obj/prettifi + DOXIFYOBJDIR := $(CP2KHOME)/obj/doxified + TOOLSRC := $(CP2KHOME)/tools + SRCDIR := $(CP2KHOME)/src +-EXEDIR := $(MAINEXEDIR)/$(ARCH) ++EXEDIR := $(MAINEXEDIR)/$(XARCH) + REVISION := $(shell $(CP2KHOME)/tools/build_utils/get_revision_number $(SRCDIR)) + + +@@ -39,10 +39,10 @@ EXE_NAMES := $(basename $(notdir $(ALL_E + # this only happens on stage 3 and 4 + ifneq ($(ONEVERSION),) + MODDEPS = "lower" +-include $(CP2KHOME)/arch/$(ARCH).$(ONEVERSION) +-LIBDIR := $(MAINLIBDIR)/$(ARCH)/$(ONEVERSION) +-OBJDIR := $(MAINOBJDIR)/$(ARCH)/$(ONEVERSION) +-TSTDIR := $(MAINTSTDIR)/$(ARCH)/$(ONEVERSION) ++include $(CP2KHOME)/arch/$(XARCH).$(ONEVERSION) ++LIBDIR := $(MAINLIBDIR)/$(XARCH)/$(ONEVERSION) ++OBJDIR := $(MAINOBJDIR)/$(XARCH)/$(ONEVERSION) ++TSTDIR := $(MAINTSTDIR)/$(XARCH)/$(ONEVERSION) + ifeq ($(NVCC),) + EXE_NAMES := $(basename $(notdir $(filter-out %.cu, $(ALL_EXE_FILES)))) + endif +@@ -130,7 +130,7 @@ all: dirs makedep + + # foreground testing, compilation happens in do_regtest + test: dirs +- cd $(TSTDIR); $(TOOLSRC)/regtesting/do_regtest -nosvn -quick -arch $(ARCH) -version $(ONEVERSION) -cp2kdir ../../../ $(TESTOPTS) ++ cd $(TSTDIR); $(TOOLSRC)/regtesting/do_regtest -nosvn -quick -arch $(XARCH) -version $(ONEVERSION) -cp2kdir ../../../ $(TESTOPTS) + + # background testing, compilation happens here + testbg: dirs makedep all +@@ -191,7 +191,7 @@ $(LIBDIR)/libcp2k$(ARCHIVE_EXT) : $(ALL_ + + testbg: + @echo "testing: $(ONEVERSION) : full log in $(TSTDIR)/regtest.log " +- @$(TOOLSRC)/regtesting/do_regtest -nobuild -nosvn -arch $(ARCH) -version $(ONEVERSION) -cp2kdir ../../../ $(TESTOPTS) >& $(TSTDIR)/regtest.log ++ @$(TOOLSRC)/regtesting/do_regtest -nobuild -nosvn -arch $(XARCH) -version $(ONEVERSION) -cp2kdir ../../../ $(TESTOPTS) >& $(TSTDIR)/regtest.log + @cat `grep 'regtesting location error_summary file:' $(TSTDIR)/regtest.log | awk '{print $$NF}'` + @cat `grep 'regtesting location summary file:' $(TSTDIR)/regtest.log | awk '{print $$NF}'` + @grep "Number of FAILED tests 0" $(TSTDIR)/regtest.log >& /dev/null +@@ -244,9 +244,9 @@ define get_extensions + endef + clean: + rm -rf $(LIBCUSMM_ABS_DIR)/libcusmm.cu $(LIBCUSMM_ABS_DIR)/libcusmm_part*.cu +- @echo rm -rf $(foreach v, $(VERSION), $(MAINOBJDIR)/$(ARCH)/$(v)) +- @$(foreach v, $(VERSION), $(foreach ext, $(call get_extensions, $(MAINOBJDIR)/$(ARCH)/$(v)/), $(shell rm -rf $(MAINOBJDIR)/$(ARCH)/$(v)/*.$(ext)))) +- rm -rf $(foreach v, $(VERSION), $(MAINLIBDIR)/$(ARCH)/$(v)) ++ @echo rm -rf $(foreach v, $(VERSION), $(MAINOBJDIR)/$(XARCH)/$(v)) ++ @$(foreach v, $(VERSION), $(foreach ext, $(call get_extensions, $(MAINOBJDIR)/$(XARCH)/$(v)/), $(shell rm -rf $(MAINOBJDIR)/$(XARCH)/$(v)/*.$(ext)))) ++ rm -rf $(foreach v, $(VERSION), $(MAINLIBDIR)/$(XARCH)/$(v)) + OTHER_HELP += "clean : Remove intermediate object and mod files, but not the libraries and executables, for given ARCH and VERSION" + + execlean: +@@ -258,16 +258,16 @@ OTHER_HELP += "execlean : Remove the exe + # Use this if you want to fully rebuild an executable (for a given compiler and or VERSION) + # + realclean: clean execlean +- rm -rf $(foreach v, $(VERSION), $(MAINOBJDIR)/$(ARCH)/$(v)) +- rm -rf $(foreach v, $(VERSION), $(MAINLIBDIR)/$(ARCH)/$(v)) ++ rm -rf $(foreach v, $(VERSION), $(MAINOBJDIR)/$(XARCH)/$(v)) ++ rm -rf $(foreach v, $(VERSION), $(MAINLIBDIR)/$(XARCH)/$(v)) + OTHER_HELP += "realclean : Remove all files for given ARCH and VERSION" + + testclean: +- rm -rf $(foreach v, $(VERSION), $(MAINTSTDIR)/$(ARCH)/$(v)/TEST-*) ++ rm -rf $(foreach v, $(VERSION), $(MAINTSTDIR)/$(XARCH)/$(v)/TEST-*) + OTHER_HELP += "testclean : Remove all TEST-* files for given ARCH and VERSION" + + testrealclean: testclean +- rm -rf $(foreach v, $(VERSION), $(MAINTSTDIR)/$(ARCH)/$(v)/LAST-*) ++ rm -rf $(foreach v, $(VERSION), $(MAINTSTDIR)/$(XARCH)/$(v)/LAST-*) + OTHER_HELP += "testrealclean : Remove all LAST-* and TEST-* files for given ARCH and VERSION" + + # +@@ -426,7 +426,7 @@ endif + + # some practical variables for the build + ifeq ($(CPPSHELL),) +-CPPSHELL := -D__COMPILE_ARCH="\"$(ARCH)\""\ ++CPPSHELL := -D__COMPILE_ARCH="\"$(XARCH)\""\ + -D__COMPILE_DATE="\"$(shell date)\""\ + -D__COMPILE_HOST="\"$(shell hostname)\""\ + -D__COMPILE_REVISION="\"$(strip $(REVISION))\""\ Property changes on: head/science/cp2k/files/patch-makefiles_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/cp2k/pkg-descr =================================================================== --- head/science/cp2k/pkg-descr (nonexistent) +++ head/science/cp2k/pkg-descr (revision 478991) @@ -0,0 +1,12 @@ +CP2K is a quantum chemistry and solid state physics software package that can +perform atomistic simulations of solid state, liquid, molecular, periodic, +material, crystal, and biological systems. CP2K provides a general framework for +different modeling methods such as DFT using the mixed Gaussian and plane waves +approaches GPW and GAPW. Supported theory levels include DFTB, LDA, GGA, MP2, +RPA, semi-empirical methods (AM1, PM3, PM6, RM1, MNDO, ...), and classical force +fields (AMBER, CHARMM, ...). CP2K can do simulations of molecular dynamics, +metadynamics, Monte Carlo, Ehrenfest dynamics, vibrational analysis, core level +spectroscopy, energy minimization, and transition state optimization using NEB +or dimer method. + +WWW: https://www.cp2k.org/ Property changes on: head/science/cp2k/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