diff --git a/science/Makefile b/science/Makefile index 64432059faa6..eccba75fb10f 100644 --- a/science/Makefile +++ b/science/Makefile @@ -1,551 +1,552 @@ COMMENT = Scientific ports SUBDIR += 2d-rewriter SUBDIR += ALPSCore SUBDIR += ChipmunkPhysics SUBDIR += InsightToolkit SUBDIR += InsightToolkit501 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-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 += acados SUBDIR += afni SUBDIR += agrum SUBDIR += aircraft-datcom + SUBDIR += amrex SUBDIR += antioch SUBDIR += apbs SUBDIR += arbor SUBDIR += ascent SUBDIR += atompaw SUBDIR += avogadro2 SUBDIR += avogadrolibs SUBDIR += axom SUBDIR += bagel SUBDIR += bddsolve SUBDIR += berkeleygw SUBDIR += bodr SUBDIR += bout++ SUBDIR += bout++-merging-filaments SUBDIR += buddy SUBDIR += cantera SUBDIR += cardioid 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 += conduit SUBDIR += coordgenlibs SUBDIR += cp2k SUBDIR += cp2k-data SUBDIR += cpcmx SUBDIR += csvtk SUBDIR += dakota SUBDIR += dalton SUBDIR += dd_package SUBDIR += devisor SUBDIR += dftbplus SUBDIR += dftd3 SUBDIR += dftd4 SUBDIR += dimod SUBDIR += dirac SUBDIR += dkh SUBDIR += dlib-cpp SUBDIR += drawxtl SUBDIR += dssp 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 += fleur SUBDIR += frontistr SUBDIR += fsom SUBDIR += fvcom SUBDIR += fvcom-mpi SUBDIR += gabedit SUBDIR += gamess-us SUBDIR += gbtolib SUBDIR += gchemutils SUBDIR += gcp SUBDIR += gdma SUBDIR += geant4 SUBDIR += gemmi SUBDIR += getdp SUBDIR += ghemical SUBDIR += ghmm SUBDIR += gnudatalanguage SUBDIR += gpaw-setups SUBDIR += gramps SUBDIR += gromacs SUBDIR += gsmc SUBDIR += h5utils SUBDIR += h5z-zfp SUBDIR += harminv SUBDIR += hdf SUBDIR += hdf5 SUBDIR += hdf5-110 SUBDIR += hdf5-18 SUBDIR += hdf5-21 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 += kst SUBDIR += lammps SUBDIR += lamprop SUBDIR += latte SUBDIR += libaec SUBDIR += libccp4 SUBDIR += libcifpp SUBDIR += libcint SUBDIR += libctl SUBDIR += libecpint SUBDIR += libefp SUBDIR += libgetar SUBDIR += libghemical SUBDIR += libgridxc SUBDIR += libint SUBDIR += libint2 SUBDIR += libint2-psi4 SUBDIR += libkml SUBDIR += liblinear SUBDIR += libmbd SUBDIR += libminc SUBDIR += libmsym SUBDIR += libnegf SUBDIR += liboglappth SUBDIR += libpsml SUBDIR += libquantum SUBDIR += libssm SUBDIR += libsvm SUBDIR += libsvm-python SUBDIR += libvdwxc SUBDIR += libxc SUBDIR += liggghts SUBDIR += linearelasticity SUBDIR += linux-ai-ml-env SUBDIR += linux-zotero SUBDIR += luscus SUBDIR += m-aneos SUBDIR += madness SUBDIR += maeparser SUBDIR += massxpert SUBDIR += mbdyn SUBDIR += mcpl SUBDIR += mcstas SUBDIR += mcstas-comps SUBDIR += mctc-lib SUBDIR += mcxtrace SUBDIR += mcxtrace-comps SUBDIR += mdynamix SUBDIR += medit SUBDIR += meep SUBDIR += metaphysicl SUBDIR += minc-tools SUBDIR += mmdb2 SUBDIR += mmg SUBDIR += mmtf-cpp SUBDIR += mol2ps SUBDIR += molgif SUBDIR += molscript SUBDIR += molsketch SUBDIR += moltui SUBDIR += mopac SUBDIR += mp2d SUBDIR += mpb SUBDIR += mpqc SUBDIR += mrchem SUBDIR += mrcpp SUBDIR += msms SUBDIR += mstore SUBDIR += multicharge SUBDIR += multiwfn SUBDIR += mutationpp SUBDIR += namd SUBDIR += ncrystal SUBDIR += neko SUBDIR += nest SUBDIR += netcdf SUBDIR += netcdf-cxx SUBDIR += netcdf-fortran SUBDIR += nifticlib SUBDIR += nlcglib SUBDIR += numsa SUBDIR += nwchem SUBDIR += nwchem-data SUBDIR += ocean SUBDIR += octopus SUBDIR += openbabel SUBDIR += openems SUBDIR += openkim-models SUBDIR += openmc SUBDIR += openmodelica SUBDIR += openmolcas SUBDIR += openmx SUBDIR += opensim-core SUBDIR += opensph SUBDIR += opsin SUBDIR += optench SUBDIR += orthanc SUBDIR += orthanc-dicomweb SUBDIR += orthanc-mysql SUBDIR += orthanc-postgresql SUBDIR += orthanc-webviewer 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-OpenSMILES 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-Coordinates-Transform 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 += parthenon SUBDIR += pastix SUBDIR += pcmsolver SUBDIR += phonopy SUBDIR += plumed SUBDIR += pnetcdf SUBDIR += polytope SUBDIR += precice SUBDIR += psi4 SUBDIR += pulseview SUBDIR += py-GPy SUBDIR += py-GPyOpt SUBDIR += py-HepMC3 SUBDIR += py-HofstadterTools 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-arbor SUBDIR += py-arch 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-boutdata SUBDIR += py-boututils SUBDIR += py-cdo SUBDIR += py-cfgrib 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-web SUBDIR += py-coards SUBDIR += py-corner SUBDIR += py-dftbplus SUBDIR += py-dftd4 SUBDIR += py-dimod SUBDIR += py-dipy SUBDIR += py-dlib SUBDIR += py-dwave-cloud-client SUBDIR += py-dwave-gate 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-optimization 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-emmet-core 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-gwlearn SUBDIR += py-h5json SUBDIR += py-h5netcdf SUBDIR += py-h5py SUBDIR += py-h5pyd SUBDIR += py-hdmf SUBDIR += py-hiPhive SUBDIR += py-hoomd-blue SUBDIR += py-icet SUBDIR += py-igor2 SUBDIR += py-inequality SUBDIR += py-ipygany SUBDIR += py-jupyter_jsmol SUBDIR += py-kim-query SUBDIR += py-kimpy SUBDIR += py-kinematics SUBDIR += py-kliff SUBDIR += py-klusta SUBDIR += py-kpLib SUBDIR += py-liac-arff SUBDIR += py-libgetar SUBDIR += py-libpysal SUBDIR += py-lifelines SUBDIR += py-mdp SUBDIR += py-mercantile SUBDIR += py-meshio SUBDIR += py-mmcif SUBDIR += py-mmtf-python SUBDIR += py-mne SUBDIR += py-molmod SUBDIR += py-morphio SUBDIR += py-mp-api SUBDIR += py-mpcontribs-client SUBDIR += py-mplhep SUBDIR += py-mplhep-data SUBDIR += py-mrchem SUBDIR += py-ncrystal SUBDIR += py-neo SUBDIR += py-netCDF4 SUBDIR += py-netcdf-flattener SUBDIR += py-nglview SUBDIR += py-nibabel SUBDIR += py-nixio SUBDIR += py-obspy SUBDIR += py-oddt SUBDIR += py-openEMS SUBDIR += py-openbabel SUBDIR += py-openpiv SUBDIR += py-optking SUBDIR += py-paida SUBDIR += py-paramz SUBDIR += py-penaltymodel SUBDIR += py-periodictable SUBDIR += py-phono3py SUBDIR += py-phonopy SUBDIR += py-phonors SUBDIR += py-plumed SUBDIR += py-pnetcdf SUBDIR += py-probeinterface SUBDIR += py-pupynere SUBDIR += py-py3Dmol SUBDIR += py-pyaixi SUBDIR += py-pyberny SUBDIR += py-pycsw SUBDIR += py-pydicom SUBDIR += py-pydoe SUBDIR += py-pygeodesy SUBDIR += py-pygeometa SUBDIR += py-pygmo2 SUBDIR += py-pyked SUBDIR += py-pymatgen SUBDIR += py-pymatgen-analysis-alloys SUBDIR += py-pymatgen-core SUBDIR += py-pymbd SUBDIR += py-pymol SUBDIR += py-pynrrd SUBDIR += py-pynwb SUBDIR += py-pyosf SUBDIR += py-pyphot SUBDIR += py-pyprecice SUBDIR += py-pyqubo SUBDIR += py-pysal SUBDIR += py-pyscf SUBDIR += py-pyteomics SUBDIR += py-qcelemental SUBDIR += py-qcengine SUBDIR += py-qcmanybody SUBDIR += py-qiskit SUBDIR += py-qspin SUBDIR += py-quantities SUBDIR += py-rmf SUBDIR += py-rmsd SUBDIR += py-ruffus SUBDIR += py-sarpy 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-seekpath SUBDIR += py-segregation SUBDIR += py-segyio SUBDIR += py-signac SUBDIR += py-sklearn-pandas SUBDIR += py-skrebate SUBDIR += py-spaghetti SUBDIR += py-spglib SUBDIR += py-spml SUBDIR += py-symfc SUBDIR += py-tensorflow SUBDIR += py-thewalrus SUBDIR += py-tobler SUBDIR += py-trainstation SUBDIR += py-trx-python SUBDIR += py-tweedledum SUBDIR += py-vedo SUBDIR += py-veusz SUBDIR += py-xbout SUBDIR += pybrain SUBDIR += pynn SUBDIR += q SUBDIR += qbox SUBDIR += qcl SUBDIR += qiskit-aer SUBDIR += qmcpack SUBDIR += qt6-quick3dphysics 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-netcdf SUBDIR += salome-configuration SUBDIR += salome-kernel SUBDIR += scidavis SUBDIR += sciplot SUBDIR += seacas 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 += spheral SUBDIR += step SUBDIR += sz3 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 .include diff --git a/science/amrex/Makefile b/science/amrex/Makefile new file mode 100644 index 000000000000..4a55340a0da1 --- /dev/null +++ b/science/amrex/Makefile @@ -0,0 +1,37 @@ +PORTNAME= amrex +DISTVERSION= 26.06 +CATEGORIES= science + +MAINTAINER= yuri@FreeBSD.org +COMMENT= AMReX: Software Framework for Block Structured AMR +WWW= https://amrex-codes.github.io/index.html \ + https://github.com/AMReX-Codes/amrex + +LICENSE= APACHE20 + +USES= cmake:testing compiler:c++20-lang mpi:openmpi perl5 python shebangfix +USE_PERL5= build +USE_LDCONFIG= yes + +USE_GITHUB= yes +GH_ACCOUNT= AMReX-Codes + +SHEBANG_GLOB= *.pl *.py +SHEBANG_FILES= Tools/C_scripts/mkdep + +CMAKE_ON= BUILD_SHARED_LIBS +CMAKE_OFF= AMReX_ENABLE_TESTS + +CMAKE_TESTING_ON= AMReX_ENABLE_TESTS + +BINARY_ALIAS= mpiexec=${MPIEXEC} + +OPTIONS_DEFINE= PLOTFILE_TOOLS +OPTIONS_DEFAULT= PLOTFILE_TOOLS + +PLOTFILE_TOOLS_DESC= Enable Plotfile tools # project fails to build/indtall additional executables when this option is enabled +PLOTFILE_TOOLS_CMAKE_ON= AMReX_PLOTFILE_TOOLS + +# tests as of 26.06: 100% tests passed, 0 tests failed out of 67 + +.include diff --git a/science/amrex/distinfo b/science/amrex/distinfo new file mode 100644 index 000000000000..2e6c59ccab42 --- /dev/null +++ b/science/amrex/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1782756742 +SHA256 (AMReX-Codes-amrex-26.06_GH0.tar.gz) = 822e4d69777ababb2caafadefb88dbdd144111d056fe693a566c820ab0b9b8e6 +SIZE (AMReX-Codes-amrex-26.06_GH0.tar.gz) = 9427515 diff --git a/science/amrex/pkg-descr b/science/amrex/pkg-descr new file mode 100644 index 000000000000..82ba80fd7953 --- /dev/null +++ b/science/amrex/pkg-descr @@ -0,0 +1,6 @@ +AMReX is a software framework designed to accelerate scientific discovery for +applications solving partial differential equations on block-structured meshes. +Its massively parallel adaptive mesh refinement (AMR) algorithms focus +computational resources and allow scalable performance on heterogeneous +architectures so that scientists can efficiently resolve details in large +simulations. diff --git a/science/amrex/pkg-plist b/science/amrex/pkg-plist new file mode 100644 index 000000000000..6c9bdab58a42 --- /dev/null +++ b/science/amrex/pkg-plist @@ -0,0 +1,372 @@ +include/AMReX.H +include/AMReX_ANSIEscCode.H +include/AMReX_AlgPartition.H +include/AMReX_AlgVecUtil.H +include/AMReX_AlgVector.H +include/AMReX_Algebra.H +include/AMReX_Algorithm.H +include/AMReX_Amr.H +include/AMReX_AmrCore.H +include/AMReX_AmrCoreFwd.H +include/AMReX_AmrFwd.H +include/AMReX_AmrLevel.H +include/AMReX_AmrMesh.H +include/AMReX_AmrParGDB.H +include/AMReX_AmrParticles.H +include/AMReX_Any.H +include/AMReX_Arena.H +include/AMReX_Array.H +include/AMReX_Array4.H +include/AMReX_ArrayLim.H +include/AMReX_ArrayOfStructs.H +include/AMReX_AsyncOut.H +include/AMReX_AuxBoundaryData.H +include/AMReX_BArena.H +include/AMReX_BCRec.H +include/AMReX_BCUtil.H +include/AMReX_BC_TYPES.H +include/AMReX_BLBackTrace.H +include/AMReX_BLFort.H +include/AMReX_BLProfiler.H +include/AMReX_BLassert.H +include/AMReX_BackgroundThread.H +include/AMReX_BaseFab.H +include/AMReX_BaseFabUtility.H +include/AMReX_BaseFwd.H +include/AMReX_BinIterator.H +include/AMReX_BlockMutex.H +include/AMReX_BndryData.H +include/AMReX_BndryRegister.H +include/AMReX_BoundCond.H +include/AMReX_BoundaryFwd.H +include/AMReX_Box.H +include/AMReX_BoxArray.H +include/AMReX_BoxDomain.H +include/AMReX_BoxIterator.H +include/AMReX_BoxList.H +include/AMReX_CArena.H +include/AMReX_CONSTANTS.H +include/AMReX_COORDSYS_3D_C.H +include/AMReX_COORDSYS_C.H +include/AMReX_CSR.H +include/AMReX_CTOParallelForImpl.H +include/AMReX_Cluster.H +include/AMReX_Concepts.H +include/AMReX_Config.H +include/AMReX_Config_3D.H +include/AMReX_ConstexprFor.H +include/AMReX_CoordSys.H +include/AMReX_CudaGraph.H +include/AMReX_DataAllocator.H +include/AMReX_Demangle.H +include/AMReX_DenseBins.H +include/AMReX_Derive.H +include/AMReX_Dim3.H +include/AMReX_DistributionMapping.H +include/AMReX_EdgeFluxRegister.H +include/AMReX_Enum.H +include/AMReX_ErrorList.H +include/AMReX_Exception.H +include/AMReX_Extension.H +include/AMReX_Extrapolater.H +include/AMReX_FACopyDescriptor.H +include/AMReX_FArrayBox.H +include/AMReX_FBI.H +include/AMReX_FEIntegrator.H +include/AMReX_FPC.H +include/AMReX_FabArray.H +include/AMReX_FabArrayBase.H +include/AMReX_FabArrayCommI.H +include/AMReX_FabArrayUtility.H +include/AMReX_FabConv.H +include/AMReX_FabDataType.H +include/AMReX_FabFactory.H +include/AMReX_FabSet.H +include/AMReX_FilCC_3D_C.H +include/AMReX_FilCC_C.H +include/AMReX_FilFC_3D_C.H +include/AMReX_FilFC_C.H +include/AMReX_FilND_C.H +include/AMReX_FileSystem.H +include/AMReX_FillPatchUtil.H +include/AMReX_FillPatchUtil_I.H +include/AMReX_FillPatcher.H +include/AMReX_FluxReg_3D_C.H +include/AMReX_FluxReg_C.H +include/AMReX_FluxRegister.H +include/AMReX_ForkJoin.H +include/AMReX_Functional.H +include/AMReX_GMRES.H +include/AMReX_GMRES_MLMG.H +include/AMReX_GMRES_MV.H +include/AMReX_Geometry.H +include/AMReX_Gpu.H +include/AMReX_GpuAllocators.H +include/AMReX_GpuAssert.H +include/AMReX_GpuAsyncArray.H +include/AMReX_GpuAtomic.H +include/AMReX_GpuBuffer.H +include/AMReX_GpuComplex.H +include/AMReX_GpuContainers.H +include/AMReX_GpuControl.H +include/AMReX_GpuDevice.H 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