diff --git a/science/Makefile b/science/Makefile index d03c526d0235..eea5525542a8 100644 --- a/science/Makefile +++ b/science/Makefile @@ -1,490 +1,491 @@ COMMENT = Scientific ports SUBDIR += 2d-rewriter SUBDIR += ALPSCore SUBDIR += ChipmunkPhysics SUBDIR += InsightToolkit SUBDIR += InsightToolkit501 SUBDIR += InsightToolkit521 SUBDIR += PETSc 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-ks 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 += ascent SUBDIR += atompaw SUBDIR += avogadro2 SUBDIR += avogadrolibs SUBDIR += axom SUBDIR += bagel SUBDIR += bddsolve SUBDIR += berkeleygw SUBDIR += bodr SUBDIR += buddy SUBDIR += cantera SUBDIR += cardioid SUBDIR += cdcl SUBDIR += cdf SUBDIR += cdk SUBDIR += cdo SUBDIR += cgnslib SUBDIR += cgribex SUBDIR += checkmol SUBDIR += chemical-mime-data SUBDIR += chemicalfun SUBDIR += chemps2 SUBDIR += chemtool SUBDIR += chemtool-devel SUBDIR += chimes-calculator SUBDIR += chrono SUBDIR += cif-tools SUBDIR += clhep SUBDIR += clipper SUBDIR += code_saturne SUBDIR += colt SUBDIR += conduit SUBDIR += coordgenlibs SUBDIR += cp2k SUBDIR += cp2k-data SUBDIR += crf++ SUBDIR += csvtk SUBDIR += dakota SUBDIR += dalton SUBDIR += dcl SUBDIR += dd_package SUBDIR += devisor SUBDIR += dftbplus SUBDIR += dftd4 SUBDIR += dimod SUBDIR += dirac SUBDIR += dkh SUBDIR += dlib-cpp SUBDIR += drawxtl SUBDIR += dssp SUBDIR += dvc SUBDIR += dwave-preprocessing SUBDIR += dynare SUBDIR += eccodes SUBDIR += elk SUBDIR += elmerfem SUBDIR += epte SUBDIR += erd SUBDIR += ergo SUBDIR += erkale SUBDIR += erkale-pseudopotentials SUBDIR += fastcap SUBDIR += fasthenry SUBDIR += fastjet SUBDIR += feff10 SUBDIR += fisicalab SUBDIR += fleur SUBDIR += frontistr SUBDIR += fsom SUBDIR += fvcom SUBDIR += fvcom-mpi SUBDIR += gabedit SUBDIR += gamess-us SUBDIR += gbtolib SUBDIR += gchemutils SUBDIR += gdma SUBDIR += gemmi 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 += hdf5-110 SUBDIR += hdf5-18 SUBDIR += healpix SUBDIR += helfem SUBDIR += hepmc3 SUBDIR += highfive SUBDIR += hypre SUBDIR += iboview SUBDIR += isaac-cfd SUBDIR += jdftx SUBDIR += jmol SUBDIR += jstrack SUBDIR += kalzium SUBDIR += kim-api SUBDIR += kplib SUBDIR += kst2 SUBDIR += lammps SUBDIR += lamprop SUBDIR += latte SUBDIR += libaec SUBDIR += libccp4 SUBDIR += libcifpp SUBDIR += libcint SUBDIR += libctl SUBDIR += libecpint SUBDIR += libefp SUBDIR += libgeodecomp SUBDIR += libgetar SUBDIR += libghemical SUBDIR += libgridxc SUBDIR += libint SUBDIR += libint2 + SUBDIR += libint2-psi4 SUBDIR += libkml SUBDIR += liblinear SUBDIR += libmbd SUBDIR += libmsym SUBDIR += libnegf SUBDIR += liboglappth SUBDIR += libquantum SUBDIR += libssm SUBDIR += libsvm SUBDIR += libsvm-python SUBDIR += libtensorflow1 SUBDIR += libvdwxc SUBDIR += libxc SUBDIR += liggghts SUBDIR += linux-zotero SUBDIR += luscus SUBDIR += madness SUBDIR += maeparser SUBDIR += massxpert SUBDIR += mbdyn SUBDIR += mcstas SUBDIR += mcstas-comps SUBDIR += mctc-lib SUBDIR += mcxtrace SUBDIR += mcxtrace-comps SUBDIR += mdynamix SUBDIR += medit SUBDIR += meep SUBDIR += mercantile SUBDIR += metaphysicl SUBDIR += minc2 SUBDIR += mmdb2 SUBDIR += mmtf-cpp SUBDIR += mol2ps SUBDIR += molgif SUBDIR += molscript SUBDIR += molsketch SUBDIR += mopac SUBDIR += mpb SUBDIR += mpqc SUBDIR += mrchem SUBDIR += mrcpp SUBDIR += msms SUBDIR += mstore SUBDIR += multicharge SUBDIR += multiwfn SUBDIR += namd SUBDIR += nest SUBDIR += netcdf SUBDIR += netcdf-cxx SUBDIR += netcdf-fortran SUBDIR += nifticlib SUBDIR += nlcglib SUBDIR += nwchem SUBDIR += nwchem-data SUBDIR += ocean SUBDIR += octopus SUBDIR += openbabel SUBDIR += openems SUBDIR += openkim-models SUBDIR += openmc SUBDIR += openmolcas SUBDIR += openmx SUBDIR += opensim-core SUBDIR += opensph SUBDIR += opsin SUBDIR += orthanc SUBDIR += orthanc-dicomweb SUBDIR += orthanc-mysql SUBDIR += orthanc-postgresql SUBDIR += orthanc-webviewer 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-Calc 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 += paraview SUBDIR += pastix SUBDIR += pcmsolver SUBDIR += phonopy SUBDIR += plumed SUBDIR += pnetcdf SUBDIR += precice SUBDIR += pulseview SUBDIR += py-DendroPy SUBDIR += py-GPy SUBDIR += py-GPyOpt SUBDIR += py-MDAnalysis SUBDIR += py-MDAnalysisTests SUBDIR += py-OpenFermion SUBDIR += py-OpenFermion-Dirac SUBDIR += py-OpenFermion-PySCF SUBDIR += py-OpenMC SUBDIR += py-PubChemPy SUBDIR += py-PyFR SUBDIR += py-PyNE SUBDIR += py-SimpleSpectral SUBDIR += py-abipy SUBDIR += py-access SUBDIR += py-asap3 SUBDIR += py-asdf SUBDIR += py-asdf-standard SUBDIR += py-asdf-transform-schemas SUBDIR += py-ase SUBDIR += py-atomium SUBDIR += py-avogadrolibs SUBDIR += py-cdo SUBDIR += py-chainer SUBDIR += py-chainer-chemistry SUBDIR += py-chempy SUBDIR += py-cirq-aqt SUBDIR += py-cirq-core SUBDIR += py-cirq-google SUBDIR += py-cirq-ionq SUBDIR += py-cirq-pasqal SUBDIR += py-cirq-rigetti SUBDIR += py-coards SUBDIR += py-dimod SUBDIR += py-dipy SUBDIR += py-dlib SUBDIR += py-dwave-cloud-client SUBDIR += py-dwave-greedy SUBDIR += py-dwave-hybrid SUBDIR += py-dwave-inspector SUBDIR += py-dwave-neal SUBDIR += py-dwave-networkx SUBDIR += py-dwave-ocean-sdk SUBDIR += py-dwave-preprocessing SUBDIR += py-dwave-samplers SUBDIR += py-dwave-system SUBDIR += py-dwave-tabu SUBDIR += py-dwavebinarycsp SUBDIR += py-earthpy SUBDIR += py-eccodes SUBDIR += py-esda SUBDIR += py-fresnel SUBDIR += py-gemmi 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-hiphive SUBDIR += py-hoomd-blue SUBDIR += py-inequality SUBDIR += py-jupyter_jsmol SUBDIR += py-kim-query SUBDIR += py-kimpy SUBDIR += py-kinematics SUBDIR += py-kliff SUBDIR += py-kpLib SUBDIR += py-liac-arff SUBDIR += py-libgetar SUBDIR += py-libpysal SUBDIR += py-lifelines SUBDIR += py-mdp SUBDIR += py-meshio SUBDIR += py-mmcif SUBDIR += py-mmtf-python SUBDIR += py-molmod SUBDIR += py-moltemplate SUBDIR += py-mrchem SUBDIR += py-netCDF4 SUBDIR += py-netcdf-flattener SUBDIR += py-nibabel SUBDIR += py-nilearn SUBDIR += py-obspy SUBDIR += py-oddt SUBDIR += py-openbabel SUBDIR += py-openpiv SUBDIR += py-paida SUBDIR += py-paramz SUBDIR += py-penaltymodel SUBDIR += py-phono3py SUBDIR += py-phonopy SUBDIR += py-pupynere SUBDIR += py-py3Dmol SUBDIR += py-pyaixi SUBDIR += py-pyberny SUBDIR += py-pycsw SUBDIR += py-pydicom SUBDIR += py-pygeodesy SUBDIR += py-pygeometa SUBDIR += py-pygmo2 SUBDIR += py-pyked SUBDIR += py-pymatgen SUBDIR += py-pymbd SUBDIR += py-pymol SUBDIR += py-pyosf SUBDIR += py-pyprecice SUBDIR += py-pyqubo SUBDIR += py-pysal SUBDIR += py-pyscf SUBDIR += py-pyteomics SUBDIR += py-qcelemental SUBDIR += py-qcengine SUBDIR += py-qiskit SUBDIR += py-qiskit-aer SUBDIR += py-qiskit-experiments SUBDIR += py-qiskit-finance SUBDIR += py-qiskit-ibm-experiment SUBDIR += py-qiskit-ibm-provider SUBDIR += py-qiskit-ibmq-provider SUBDIR += py-qiskit-nature SUBDIR += py-qiskit-optimization SUBDIR += py-qiskit-terra 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-sdf SUBDIR += py-segregation SUBDIR += py-segyio SUBDIR += py-sklearn-pandas SUBDIR += py-skrebate SUBDIR += py-spaghetti SUBDIR += py-spglib SUBDIR += py-tensorflow SUBDIR += py-thewalrus SUBDIR += py-tobler SUBDIR += py-trainstation SUBDIR += py-tweedledum SUBDIR += py-veusz SUBDIR += pybrain SUBDIR += pynn SUBDIR += q SUBDIR += qbox SUBDIR += qcl SUBDIR += qiskit-aer SUBDIR += qmcpack SUBDIR += quantum-espresso SUBDIR += quantum-espresso-pseudopotentials SUBDIR += quantum-jet 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 += sciplot SUBDIR += segyio SUBDIR += serac SUBDIR += shelxle SUBDIR += siconos 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 += simple-dftd3 SUBDIR += simsmith SUBDIR += sirius SUBDIR += smoldyn SUBDIR += sparta SUBDIR += spglib SUBDIR += step SUBDIR += svmlight SUBDIR += tblite SUBDIR += teem SUBDIR += tfel SUBDIR += tfel-edf SUBDIR += thermofun SUBDIR += tinker SUBDIR += trilinos SUBDIR += ttk SUBDIR += tweedledum SUBDIR += udunits SUBDIR += ukrmol+ 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 SUBDIR += zotero SUBDIR += zx .include diff --git a/science/libint2-psi4/Makefile b/science/libint2-psi4/Makefile new file mode 100644 index 000000000000..ae4617206194 --- /dev/null +++ b/science/libint2-psi4/Makefile @@ -0,0 +1,35 @@ +PORTNAME= libint2-psi4 +DISTVERSION= 0.1 +CATEGORIES= science +MASTER_SITES= https://github.com/loriab/libint/releases/download/v${DISTVERSION}/ +DISTFILES= Libint2-export-5-4-3-6-5-4_mm4f12ob2.tgz + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Evaluate the integrals in modern atomic and molecular theory (psi4) +WWW= https://github.com/evaleev/libint + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/COPYING + +LIB_DEPENDS= libboost_system.so:devel/boost-libs \ + libgmpxx.so:math/gmp + +USES= cmake:testing eigen:3 python:build +USE_LDCONFIG= yes + +WRKSRC= ${WRKDIR}/libint-2.7.1 + +CMAKE_ARGS= -DLIBINT2_SHGAUSS_ORDERING=gaussian \ + -DPython_EXECUTABLE=${PYTHON_CMD} +CMAKE_ON= BUILD_SHARED_LIBS \ + REQUIRE_CXX_API +CMAKE_OFF= ENABLE_FORTRAN \ + REQUIRE_CXX_API_COMPILED + +CONFLICTS= libint2 + +post-configure: # workaround for clang hanging on unity_1935_cxx.cxx, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=265809 + @cd ${BUILD_WRKSRC} && \ + ${SED} -e 's|%%BUILD_WRKSRC%%|${BUILD_WRKSRC}|g ; s|%%WRKDIR%%|${WRKDIR}|g' < ${FILESDIR}/build.patch | tee p | ${PATCH} + +.include diff --git a/science/libint2-psi4/distinfo b/science/libint2-psi4/distinfo new file mode 100644 index 000000000000..f4f0dd6c9ea4 --- /dev/null +++ b/science/libint2-psi4/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1669405977 +SHA256 (Libint2-export-5-4-3-6-5-4_mm4f12ob2.tgz) = 2e1e4560992185ac0fbc74c53bc80476115ef9d0af60c9ad64c510ebe6235584 +SIZE (Libint2-export-5-4-3-6-5-4_mm4f12ob2.tgz) = 313090742 diff --git a/science/libint2-psi4/files/build.patch b/science/libint2-psi4/files/build.patch new file mode 100644 index 000000000000..305c55ea670b --- /dev/null +++ b/science/libint2-psi4/files/build.patch @@ -0,0 +1,13 @@ +- workaround for clang hanging on unity_1935_cxx.cxx, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=265809 + +--- build.ninja.orig 2022-11-25 16:11:30.230881000 -0800 ++++ build.ninja 2022-11-25 16:10:18.165198000 -0800 +@@ -890,7 +890,7 @@ + build CMakeFiles/int-obj.dir/Unity/unity_1935_cxx.cxx.o: CXX_COMPILER__int-obj_Release %%BUILD_WRKSRC%%/CMakeFiles/int-obj.dir/Unity/unity_1935_cxx.cxx || cmake_object_order_depends_target_int-obj + DEFINES = -D__COMPILING_LIBINT2=1 + DEP_FILE = CMakeFiles/int-obj.dir/Unity/unity_1935_cxx.cxx.o.d +- FLAGS = -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC ++ FLAGS = -pipe -fstack-protector-strong -fno-strict-aliasing -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC + INCLUDES = -I%%BUILD_WRKSRC%%/include -I%%WRKDIR%%/libint-2.7.1/src -I%%WRKDIR%%/libint-2.7.1/include -I%%WRKDIR%%/libint-2.7.1/include/libint2 + OBJECT_DIR = CMakeFiles/int-obj.dir + OBJECT_FILE_DIR = CMakeFiles/int-obj.dir/Unity diff --git a/science/libint2-psi4/pkg-descr b/science/libint2-psi4/pkg-descr new file mode 100644 index 000000000000..7f60d82c3859 --- /dev/null +++ b/science/libint2-psi4/pkg-descr @@ -0,0 +1,4 @@ +Libint is a library for evaluating ERI (electron replusion integral) +over Cartesian Gaussian fuctions for modern atomic and molecular theory. + +Spacial build for science/psi4. diff --git a/science/libint2-psi4/pkg-plist b/science/libint2-psi4/pkg-plist new file mode 100644 index 000000000000..9fda97e6afb9 --- /dev/null +++ b/science/libint2-psi4/pkg-plist @@ -0,0 +1,163 @@ +include/libint2.h +include/libint2.hpp +include/libint2/GenericContract.h +include/libint2/GenericGaussDeriv.h +include/libint2/GenericGaussDeriv.impl.h +include/libint2/GenericScale.h +include/libint2/ITR_xs_xs.h +include/libint2/OSVRR_sx_sx.h +include/libint2/OSVRR_sx_sx_deriv.h +include/libint2/OSVRR_xs_xs.h +include/libint2/OSVRR_xs_xs_deriv.h +include/libint2/VRR_GTG_1d_xx_xx.h +include/libint2/VRR_GTG_1d_xx_xx_vec.h +include/libint2/VRR_r12kg12_xs_xs.h +include/libint2/atom.h +include/libint2/basis.h +include/libint2/boys.h +include/libint2/boys_cheb7.h +include/libint2/boys_cheb7_v2.h +include/libint2/boys_fwd.h +include/libint2/braket.h +include/libint2/cartesian.h +include/libint2/cgshell_ordering.h +include/libint2/cgshellinfo.h +include/libint2/chemistry/elements.h +include/libint2/chemistry/sto3g_atomic_density.h +include/libint2/config.h +include/libint2/config2.h +include/libint2/cxxapi.h +include/libint2/deriv_iter.h +include/libint2/deriv_map.h +include/libint2/diis.h +include/libint2/engine.h +include/libint2/engine.impl.h +include/libint2/initialize.h +include/libint2/lcao/1body.h +include/libint2/lcao/molden.h +include/libint2/libint2_iface.h +include/libint2/libint2_iface_internal.h +include/libint2/libint2_params.h +include/libint2/libint2_types.h +include/libint2/numeric.h +include/libint2/shell.h +include/libint2/shgshell_ordering.h +include/libint2/solidharmonics.h +include/libint2/statics_definition.h +include/libint2/tenno_cheb.h +include/libint2/tenno_cheb15.h +include/libint2/tensor.h +include/libint2/tests/unit/fixture.h +include/libint2/util/any.h +include/libint2/util/array_adaptor.h +include/libint2/util/compressed_pair.h +include/libint2/util/cxxstd.h +include/libint2/util/deprecated.h +include/libint2/util/generated/libint2_iface.h +include/libint2/util/generated/libint2_params.h +include/libint2/util/generated/libint2_types.h +include/libint2/util/intpart_iter.h 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