diff --git a/science/Makefile b/science/Makefile index 66209aa09188..15122fd8e7a1 100644 --- a/science/Makefile +++ b/science/Makefile @@ -1,361 +1,362 @@ COMMENT = Scientific ports SUBDIR += 2d-rewriter SUBDIR += ALPSCore SUBDIR += InsightToolkit SUBDIR += PETSc SUBDIR += R-cran-AMORE SUBDIR += R-cran-DCluster SUBDIR += R-cran-Epi SUBDIR += R-cran-FAdist 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 += agrum SUBDIR += aircraft-datcom SUBDIR += antioch SUBDIR += apbs SUBDIR += atompaw SUBDIR += avogadro2 SUBDIR += avogadrolibs SUBDIR += axom SUBDIR += bagel SUBDIR += bddsolve SUBDIR += berkeleygw SUBDIR += bodr SUBDIR += buddy SUBDIR += cdcl SUBDIR += cdf SUBDIR += cdk 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 += code_saturne SUBDIR += colt SUBDIR += conduit SUBDIR += coordgenlibs SUBDIR += cp2k SUBDIR += cp2k-data SUBDIR += crf++ SUBDIR += dakota SUBDIR += dalton SUBDIR += dcl SUBDIR += devisor SUBDIR += dftbplus SUBDIR += dkh SUBDIR += dlib-cpp SUBDIR += drawxtl SUBDIR += dvc SUBDIR += eccodes SUBDIR += elk SUBDIR += elmerfem SUBDIR += epte SUBDIR += erd SUBDIR += ergo SUBDIR += erkale SUBDIR += erkale-pseudopotentials SUBDIR += fastcap SUBDIR += fasthenry SUBDIR += fastjet SUBDIR += fisicalab SUBDIR += frontistr SUBDIR += fsom SUBDIR += fvcom SUBDIR += fvcom-mpi SUBDIR += gabedit SUBDIR += gamess-us SUBDIR += gchemutils SUBDIR += gdma SUBDIR += getdp SUBDIR += ghemical SUBDIR += ghmm SUBDIR += gnudatalanguage SUBDIR += gpaw-setups SUBDIR += gramps SUBDIR += grib_api SUBDIR += gromacs SUBDIR += gsmc SUBDIR += gtamsanalyzer SUBDIR += h5utils SUBDIR += h5z-zfp SUBDIR += harminv SUBDIR += hdf SUBDIR += hdf5 SUBDIR += hdf5-18 SUBDIR += healpix SUBDIR += hepmc3 SUBDIR += highfive SUBDIR += hypre SUBDIR += iboview SUBDIR += isaac-cfd SUBDIR += jdftx SUBDIR += jmol SUBDIR += jstrack SUBDIR += kalzium SUBDIR += kim-api SUBDIR += kst2 SUBDIR += lammps SUBDIR += lamprop SUBDIR += latte SUBDIR += libaec SUBDIR += libccp4 SUBDIR += libcint SUBDIR += libctl SUBDIR += libecpint SUBDIR += libefp SUBDIR += libgeodecomp SUBDIR += libghemical SUBDIR += libgridxc SUBDIR += libint SUBDIR += libint2 SUBDIR += libkml SUBDIR += liblinear SUBDIR += libmsym SUBDIR += liboglappth SUBDIR += libquantum SUBDIR += libssm SUBDIR += libsvm SUBDIR += libsvm-python SUBDIR += libvdwxc SUBDIR += libxc SUBDIR += liggghts SUBDIR += luscus SUBDIR += madness SUBDIR += maeparser SUBDIR += massxpert SUBDIR += mbdyn SUBDIR += mcstas SUBDIR += mcstas-comps SUBDIR += mcxtrace SUBDIR += mcxtrace-comps SUBDIR += mdynamix SUBDIR += medit SUBDIR += metaphysicl SUBDIR += minc2 SUBDIR += mmdb2 SUBDIR += mmtf-cpp SUBDIR += mol2ps SUBDIR += molgif SUBDIR += molscript SUBDIR += molsketch SUBDIR += mpb SUBDIR += mpqc SUBDIR += msms SUBDIR += multiwfn SUBDIR += namd SUBDIR += nest SUBDIR += netcdf SUBDIR += netcdf-cxx SUBDIR += netcdf-fortran SUBDIR += nifticlib SUBDIR += nwchem SUBDIR += nwchem-data SUBDIR += octopus SUBDIR += openbabel SUBDIR += openkim SUBDIR += openkim-models SUBDIR += opensim-core SUBDIR += opensph SUBDIR += opsin 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-WebService-Elevation-USGS SUBDIR += p5-Mcstas-Tools SUBDIR += p5-PerlMol SUBDIR += p5-Physics-Unit SUBDIR += packmol SUBDIR += pagmo2 SUBDIR += paje SUBDIR += pcmsolver SUBDIR += plumed SUBDIR += pnetcdf SUBDIR += pulseview SUBDIR += py-DendroPy SUBDIR += py-GPy SUBDIR += py-GPyOpt SUBDIR += py-MDAnalysis SUBDIR += py-MDAnalysisTests SUBDIR += py-OpenFermion SUBDIR += py-PyFR SUBDIR += py-SimpleSpectral SUBDIR += py-abipy SUBDIR += py-access SUBDIR += py-asdf SUBDIR += py-ase SUBDIR += py-avogadrolibs SUBDIR += py-cdo SUBDIR += py-chainer SUBDIR += py-chainer-chemistry SUBDIR += py-chempy SUBDIR += py-coards SUBDIR += py-dipy SUBDIR += py-dlib SUBDIR += py-eccodes SUBDIR += py-esda SUBDIR += py-geolinks SUBDIR += py-geomet SUBDIR += py-geometer SUBDIR += py-geometric SUBDIR += py-gpaw SUBDIR += py-gsd SUBDIR += py-h5json SUBDIR += py-h5py SUBDIR += py-inequality SUBDIR += py-jupyter_jsmol SUBDIR += py-kim-query SUBDIR += py-kinematics SUBDIR += py-kliff SUBDIR += py-liac-arff SUBDIR += py-libpysal SUBDIR += py-lifelines SUBDIR += py-mdp SUBDIR += py-mmtf-python SUBDIR += py-molmod SUBDIR += py-moltemplate SUBDIR += py-netCDF4 SUBDIR += py-netcdf-flattener SUBDIR += py-nibabel SUBDIR += py-nilearn SUBDIR += py-obspy SUBDIR += py-oddt SUBDIR += py-openpiv SUBDIR += py-paida SUBDIR += py-paramz SUBDIR += py-phono3py SUBDIR += py-phonopy SUBDIR += py-pupynere SUBDIR += py-pyaixi SUBDIR += py-pycsw SUBDIR += py-pydicom SUBDIR += py-pygeodesy SUBDIR += py-pygeometa SUBDIR += py-pygmo2 SUBDIR += py-pymatgen SUBDIR += py-pymol SUBDIR += py-pyosf SUBDIR += py-pysal + SUBDIR += py-pyscf SUBDIR += py-pyteomics SUBDIR += py-qcelemental SUBDIR += py-qcengine SUBDIR += py-qspin SUBDIR += py-quantities SUBDIR += py-rmf SUBDIR += py-rmsd SUBDIR += py-ruffus SUBDIR += py-scikit-fuzzy SUBDIR += py-scikit-learn SUBDIR += py-scikit-optimize SUBDIR += py-scikit-sparse SUBDIR += py-scimath SUBDIR += py-scipy SUBDIR += py-scoria SUBDIR += py-segregation SUBDIR += py-segyio SUBDIR += py-skrebate SUBDIR += py-spaghetti SUBDIR += py-spglib SUBDIR += py-tensorflow SUBDIR += py-tobler SUBDIR += py-veusz SUBDIR += pybrain SUBDIR += pynn SUBDIR += qbox SUBDIR += qcl SUBDIR += qiskit-aer SUBDIR += qmcpack SUBDIR += quantum-espresso SUBDIR += quantum-espresso-pseudopotentials 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 += scidavis SUBDIR += segyio SUBDIR += shelxle SUBDIR += siesta SUBDIR += sigrok-cli SUBDIR += sigrok-firmware SUBDIR += sigrok-firmware-fx2lafw SUBDIR += sigrok-firmware-utils SUBDIR += silo SUBDIR += simbody SUBDIR += simgrid SUBDIR += simint SUBDIR += simlib SUBDIR += simsmith SUBDIR += smoldyn SUBDIR += sparta SUBDIR += spglib SUBDIR += step SUBDIR += svmlight SUBDIR += szip SUBDIR += teem SUBDIR += tfel SUBDIR += tfel-edf SUBDIR += thermofun SUBDIR += tinker SUBDIR += udunits SUBDIR += v_sim SUBDIR += vipster SUBDIR += vmd SUBDIR += voro++ SUBDIR += votca SUBDIR += wannier90 SUBDIR += wwplot SUBDIR += wxmacmolplt SUBDIR += xcfun SUBDIR += xcrysden SUBDIR += xdrawchem SUBDIR += xtb SUBDIR += yoda .include diff --git a/science/py-pyscf/Makefile b/science/py-pyscf/Makefile new file mode 100644 index 000000000000..ba862012ec8e --- /dev/null +++ b/science/py-pyscf/Makefile @@ -0,0 +1,40 @@ +PORTNAME= pyscf +DISTVERSIONPREFIX= v +DISTVERSION= 2.0.0a-103 +DISTVERSIONSUFFIX= -ga81f201c4 +CATEGORIES= science python +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Python module for quantum chemistry + +LICENSE= BSD2CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE + +PY_DEPENDS= ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR} +BUILD_DEPENDS= ${PY_DEPENDS} \ + cmake:devel/cmake \ + gmake:devel/gmake +LIB_DEPENDS= libcint.so:science/libcint \ + libxc.so:science/libxc \ + libxcfun.so:science/xcfun +RUN_DEPENDS= ${PY_DEPENDS} + +USES= fortran blaslapack:openblas compiler:c++11-lang python +USE_PYTHON= distutils autoplist +USE_GITHUB= yes + +POST_PLIST= fix-plist + +post-install: + @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/pyscf/lib/lib*.so + +fix-plist: + @${REINPLACE_CMD} -e 's|.*pyscf_lib_placeholder.so$$||' ${TMPPLIST} + +do-test: install + @${PYTHON_CMD} ${FILESDIR}/test.py + +.include diff --git a/science/py-pyscf/distinfo b/science/py-pyscf/distinfo new file mode 100644 index 000000000000..b7ec60ae09cc --- /dev/null +++ b/science/py-pyscf/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1622919502 +SHA256 (pyscf-pyscf-v2.0.0a-103-ga81f201c4_GH0.tar.gz) = 590c37cf2a206548f3eaec3c8458f034b8e56053e510906e5a9c05ba5d1c0569 +SIZE (pyscf-pyscf-v2.0.0a-103-ga81f201c4_GH0.tar.gz) = 9510408 diff --git a/science/py-pyscf/files/patch-pyscf_lib_CMakeLists.txt b/science/py-pyscf/files/patch-pyscf_lib_CMakeLists.txt new file mode 100644 index 000000000000..1174b9fb17f1 --- /dev/null +++ b/science/py-pyscf/files/patch-pyscf_lib_CMakeLists.txt @@ -0,0 +1,22 @@ +--- pyscf/lib/CMakeLists.txt.orig 2021-06-05 19:22:32 UTC ++++ pyscf/lib/CMakeLists.txt +@@ -138,7 +138,7 @@ set(C_LINK_TEMPLATE " -o ") + + include(ExternalProject) +-option(BUILD_LIBCINT "Using libcint for analytical gaussian integral" ON) ++option(BUILD_LIBCINT "Using libcint for analytical gaussian integral" OFF) + option(WITH_F12 "Compling F12 integrals" ON) + if(BUILD_LIBCINT) + if(NOT EXISTS "${PROJECT_SOURCE_DIR}/deps/include/cint.h") +@@ -164,8 +164,8 @@ endif() + + option(ENABLE_LIBXC "Using libxc for XC functional library" ON) + option(ENABLE_XCFUN "Using xcfun for XC functional library" ON) +-option(BUILD_LIBXC "Download and build libxc library" ON) +-option(BUILD_XCFUN "Download and build xcfun library" ON) ++option(BUILD_LIBXC "Download and build libxc library" OFF) ++option(BUILD_XCFUN "Download and build xcfun library" OFF) + + if(NOT DISABLE_DFT) + add_subdirectory(dft) diff --git a/science/py-pyscf/files/test.py b/science/py-pyscf/files/test.py new file mode 100644 index 000000000000..89ce2cc2eccf --- /dev/null +++ b/science/py-pyscf/files/test.py @@ -0,0 +1,4 @@ +from pyscf import gto, scf +mol = gto.M(atom='H 0 0 0; H 0 0 1.2', basis='cc-pvdz') +mf = scf.RHF(mol) +mf.kernel() diff --git a/science/py-pyscf/pkg-descr b/science/py-pyscf/pkg-descr new file mode 100644 index 000000000000..68196e180664 --- /dev/null +++ b/science/py-pyscf/pkg-descr @@ -0,0 +1,6 @@ +PyMOL is a Python-enhanced molecular graphics tool. It excels at +3D visualization of proteins, small molecules, density, surfaces, +and trajectories. It also includes molecular editing, ray tracing, +and movies. Open Source PyMOL is free to everyone! + +WWW: https://www.pymol.org/