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ESMTPS id 4NK8Mp5ndXzHpY; Sat, 26 Nov 2022 11:17:26 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 2AQBHQbO070843; Sat, 26 Nov 2022 11:17:26 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 2AQBHQmB070842; Sat, 26 Nov 2022 11:17:26 GMT (envelope-from git) Date: Sat, 26 Nov 2022 11:17:26 GMT Message-Id: <202211261117.2AQBHQmB070842@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: c492d0dd0415 - main - science/psi4: New port: Open-source suite of ab initio quantum chemistry programs List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: c492d0dd0415418439ef92b8e13e72b3a9a24a23 Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=c492d0dd0415418439ef92b8e13e72b3a9a24a23 commit c492d0dd0415418439ef92b8e13e72b3a9a24a23 Author: Yuri Victorovich AuthorDate: 2022-11-26 11:00:33 +0000 Commit: Yuri Victorovich CommitDate: 2022-11-26 11:04:46 +0000 science/psi4: New port: Open-source suite of ab initio quantum chemistry programs --- science/Makefile | 1 + science/psi4/Makefile | 74 + science/psi4/distinfo | 3 + science/psi4/files/patch-CMakeLists.txt | 32 + .../patch-external_upstream_libxc_CMakeLists.txt | 8 + science/psi4/files/patch-psi4_CMakeLists.txt | 11 + .../psi4/files/patch-psi4_src_psi4_libpsio_open.cc | 14 + science/psi4/pkg-descr | 8 + science/psi4/pkg-plist | 5940 ++++++++++++++++++++ 9 files changed, 6091 insertions(+) diff --git a/science/Makefile b/science/Makefile index eea5525542a8..9599ad5c079a 100644 --- a/science/Makefile +++ b/science/Makefile @@ -265,6 +265,7 @@ SUBDIR += plumed SUBDIR += pnetcdf SUBDIR += precice + SUBDIR += psi4 SUBDIR += pulseview SUBDIR += py-DendroPy SUBDIR += py-GPy diff --git a/science/psi4/Makefile b/science/psi4/Makefile new file mode 100644 index 000000000000..a68a4f6e7fb9 --- /dev/null +++ b/science/psi4/Makefile @@ -0,0 +1,74 @@ +PORTNAME= psi4 +DISTVERSION= 1.6.1.20221122 +CATEGORIES= science # quantum-chemistry +EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Open-source suite of ab initio quantum chemistry programs +WWW= https://psicode.org/ + +LICENSE= LGPL3 +LICENSE_FILE= ${WRKSRC}/COPYING + +PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}gau2grid>0:math/py-gau2grid@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}qcelemental>0:science/py-qcelemental@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}qcengine>0:science/py-qcengine@${PY_FLAVOR} +BUILD_DEPENDS= boost-libs>0:devel/boost-libs \ + ${LOCALBASE}/include/pybind11/pybind11.h:devel/pybind11 \ + ${PY_DEPENDS} \ + libint2-psi4>0:science/libint2-psi4 # has to be this library +LIB_DEPENDS= libgg.so:math/gau2grid \ + libxc.so:science/libxc +RUN_DEPENDS= ${PY_DEPENDS} \ + libint2-psi4>0:science/libint2-psi4 + +USES= blaslapack:openblas cmake compiler:c++17-lang eigen:3 fortran localbase:ldflags python:3.8+ + +USE_GITHUB= yes +GH_TAGNAME= 0889d6d34 + +CMAKE_ARGS= -DLibxc_DIR=${LOCALBASE} \ + -DFREEBSD_PYTHON_VER=${PYTHON_VER} \ + -DPython_EXECUTABLE=${PYTHON_CMD} +CONFIGURE_ENV= FREEBSD_PYTHON_VER=${PYTHON_VER} + +LDFLAGS+= -lexecinfo # for backtrace_symbols + +TEST_ENV= ${MAKE_ENV} \ + PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}:${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/psi4/tests \ + PSIDATADIR=${STAGEDIR}${DATADIR} + +post-patch: + # correct the default data dir + @${REINPLACE_CMD} \ + -E 's|os.path.sep.join\(\[os.path.abspath\(os.path.dirname\(__file__\)\), "share", "psi4"\]\)|"${DATADIR}"|' \ + ${WRKSRC}/psi4/run_psi4.py + @${REINPLACE_CMD} \ + -E 's|from pathlib import Path|&; os.environ["PSIDATADIR"] = "${DATADIR}"|' \ + ${WRKSRC}/psi4/run_psi4.py + +do-install: # project fails to install itself into a stage directory due to a convoluted cmake code structure (DESTDIR isn't handled correctly) + # main + cd ${BUILD_WRKSRC}/stage && ${COPYTREE_SHARE} . ${STAGEDIR}${PREFIX} + ${FIND} ${STAGEDIR}${PREFIX} -name "*.pyc" -delete + # samples + cd ${WRKSRC} && ${COPYTREE_SHARE} samples ${STAGEDIR}${DATADIR} + ${FIND} ${STAGEDIR}${PREFIX} -name "example_psi4rc_file" -delete + # delete empty directories + ${FIND} ${STAGEDIR} -type d -empty -delete + # set executable flag + ${CHMOD} +x ${STAGEDIR}${PREFIX}/bin/psi4 + # move python module to a proper place + ${MKDIR} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} + ${MV} ${STAGEDIR}${PREFIX}/lib/psi4 ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} + ${RLN} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/psi4 ${STAGEDIR}${PREFIX}/lib/psi4 # for the path-calculating logic in psi4/__init__.py + # correct version number + @${REINPLACE_CMD} -i '' -e "s|__version__ = 'undefined'|__version__ = '${DISTVERSION}'|" \ + ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/psi4/metadata.py + @${REINPLACE_CMD} -i '' -e "s|__version_long = 'undefined+11'|__version_long = '${DISTVERSION}'|" \ + ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/psi4/metadata.py + +do-test: # based on https://psicode.org/psi4manual/master/build_planning.html#faq-minutetests - most tests fail due to path mismatches + @cd ${WRKSRC}/tests/isapt2 && ${SETENV} ${TEST_ENV} pytest + +.include diff --git a/science/psi4/distinfo b/science/psi4/distinfo new file mode 100644 index 000000000000..c7af4b750590 --- /dev/null +++ b/science/psi4/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1669450517 +SHA256 (psi4-psi4-1.6.1.20221122-0889d6d34_GH0.tar.gz) = 2ae56a29a2e6a9677ae6bcf0f302a22086427effee072c8fa58d0f12ee55cdef +SIZE (psi4-psi4-1.6.1.20221122-0889d6d34_GH0.tar.gz) = 44809685 diff --git a/science/psi4/files/patch-CMakeLists.txt b/science/psi4/files/patch-CMakeLists.txt new file mode 100644 index 000000000000..5d1335785a98 --- /dev/null +++ b/science/psi4/files/patch-CMakeLists.txt @@ -0,0 +1,32 @@ +--- CMakeLists.txt.orig 2022-11-22 21:26:37 UTC ++++ CMakeLists.txt +@@ -187,10 +190,14 @@ message(STATUS "Psi4 install: ${CMAKE_INSTALL_PREFIX}" + # * library: not at all + + set(Python_ADDITIONAL_VERSIONS 3.11 3.10 3.9 3.8) # adjust with CMake minimum FindPythonInterp ++ ++ + if(DEFINED ENV{LGTM_SRC}) +- find_package(Python 3.8 EXACT COMPONENTS Interpreter Development REQUIRED) ++ #find_package(Python ${FREEBSD_PYTHON_VER} EXACT COMPONENTS Interpreter Development REQUIRED) ++ find_package(Python $ENV{FREEBSD_PYTHON_VER} EXACT COMPONENTS Interpreter Development REQUIRED) + else() +- find_package(Python 3.8 COMPONENTS Interpreter Development NumPy REQUIRED) ++ #find_package(Python ${FREEBSD_PYTHON_VER} EXACT COMPONENTS Interpreter Development NumPy REQUIRED) ++ find_package(Python $ENV{FREEBSD_PYTHON_VER} EXACT COMPONENTS Interpreter Development NumPy REQUIRED) + endif() + message(STATUS "${Cyan}Found Python ${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}${ColourReset}: ${Python_EXECUTABLE} (found version ${Python_VERSION})") + +@@ -302,9 +309,10 @@ ExternalProject_Add(psi4-core + -DOpenMP_LIBRARY_DIRS=${OpenMP_LIBRARY_DIRS} + -DCMAKE_EXPORT_COMPILE_COMMANDS=ON + -DENABLE_CYTHONIZE=${ENABLE_CYTHONIZE} ++ -DFREEBSD_PYTHON_VER=${FREEBSD_PYTHON_VER} + CMAKE_CACHE_ARGS -DCMAKE_PREFIX_PATH:PATH=${CMAKE_PREFIX_PATH} +- USES_TERMINAL_BUILD 1 +- BUILD_ALWAYS 1) ++ #USES_TERMINAL_BUILD 1 ++ BUILD_ALWAYS 0) + + add_subdirectory(external/downstream) + add_subdirectory(doc) diff --git a/science/psi4/files/patch-external_upstream_libxc_CMakeLists.txt b/science/psi4/files/patch-external_upstream_libxc_CMakeLists.txt new file mode 100644 index 000000000000..937a01c59226 --- /dev/null +++ b/science/psi4/files/patch-external_upstream_libxc_CMakeLists.txt @@ -0,0 +1,8 @@ +--- external/upstream/libxc/CMakeLists.txt.orig 2022-11-24 03:25:13 UTC ++++ external/upstream/libxc/CMakeLists.txt +@@ -1,4 +1,4 @@ +-find_package(Libxc 5.1.2 CONFIG QUIET COMPONENTS C) ++find_package(Libxc CONFIG REQUIRED COMPONENTS C) + + if(${Libxc_FOUND}) + get_property(_loc TARGET Libxc::xc PROPERTY LOCATION) diff --git a/science/psi4/files/patch-psi4_CMakeLists.txt b/science/psi4/files/patch-psi4_CMakeLists.txt new file mode 100644 index 000000000000..da9639648d3f --- /dev/null +++ b/science/psi4/files/patch-psi4_CMakeLists.txt @@ -0,0 +1,11 @@ +--- psi4/CMakeLists.txt.orig 2022-11-24 05:29:32 UTC ++++ psi4/CMakeLists.txt +@@ -207,7 +207,7 @@ else() + message(STATUS "Disabled BrianQC") + endif() + +-find_package(Libxc 5.1.2 CONFIG REQUIRED COMPONENTS C) ++find_package(Libxc CONFIG REQUIRED COMPONENTS C) + get_property(_loc TARGET Libxc::xc PROPERTY LOCATION) + list(APPEND _addons ${_loc}) + message(STATUS "${Cyan}Using Libxc${ColourReset}: ${_loc} (version ${Libxc_VERSION})") diff --git a/science/psi4/files/patch-psi4_src_psi4_libpsio_open.cc b/science/psi4/files/patch-psi4_src_psi4_libpsio_open.cc new file mode 100644 index 000000000000..f997ef196883 --- /dev/null +++ b/science/psi4/files/patch-psi4_src_psi4_libpsio_open.cc @@ -0,0 +1,14 @@ +--- psi4/src/psi4/libpsio/open.cc.orig 2022-11-22 21:26:37 UTC ++++ psi4/src/psi4/libpsio/open.cc +@@ -41,6 +41,11 @@ + #include "psi4/libpsio/psio.h" + #include "psi4/libpsio/psio.hpp" + #include "psi4/psi4-dec.h" ++ ++#if defined(__FreeBSD__) ++#include ++#endif ++ + namespace psi { + + void PSIO::open(size_t unit, int status) { diff --git a/science/psi4/pkg-descr b/science/psi4/pkg-descr new file mode 100644 index 000000000000..a68f8e4cef9c --- /dev/null +++ b/science/psi4/pkg-descr @@ -0,0 +1,8 @@ +Psi4 is an open-source suite of ab initio quantum chemistry programs designed +for efficient, high-accuracy simulations of a variety of molecular properties. +We can routinely perform computations with more than 2500 basis functions +running serially or on multi-core machines. + +With computationally demanding portions written in C++, Pybind11 exports many +of the C++ classes into Python, and a flexible Python driver, Psi4 strives to +be friendly to both users and developers. diff --git a/science/psi4/pkg-plist b/science/psi4/pkg-plist new file mode 100644 index 000000000000..adce8cae69e7 --- /dev/null +++ b/science/psi4/pkg-plist @@ -0,0 +1,5940 @@ +bin/psi4 +include/psi4/lib3index/3index.h +include/psi4/lib3index/cholesky.h +include/psi4/lib3index/denominator.h +include/psi4/lib3index/dfhelper.h +include/psi4/lib3index/dftensor.h +include/psi4/libciomr/libciomr.h +include/psi4/libcubeprop/csg.h +include/psi4/libcubeprop/cubeprop.h +include/psi4/libdiis/diismanager.h +include/psi4/libdisp/dispersion.h +include/psi4/libdisp/dispersion_defines.h +include/psi4/libdpd/dpd.h +include/psi4/libdpd/dpdmospace.h +include/psi4/libfilesystem/path.h +include/psi4/libfock/PK_workers.h +include/psi4/libfock/PKmanagers.h +include/psi4/libfock/apps.h +include/psi4/libfock/cubature.h +include/psi4/libfock/dft_integrators.h +include/psi4/libfock/gridblocker.h +include/psi4/libfock/hamiltonian.h +include/psi4/libfock/jk.h +include/psi4/libfock/points.h +include/psi4/libfock/sap.h +include/psi4/libfock/solver.h +include/psi4/libfock/soscf.h +include/psi4/libfock/v.h +include/psi4/libfunctional/LibXCfunctional.h +include/psi4/libfunctional/functional.h +include/psi4/libfunctional/superfunctional.h +include/psi4/libiwl/config.h +include/psi4/libiwl/iwl.h +include/psi4/libiwl/iwl.hpp +include/psi4/libmints/3coverlap.h +include/psi4/libmints/angularmomentum.h +include/psi4/libmints/basisset.h +include/psi4/libmints/benchmark.h +include/psi4/libmints/cartesianiter.h +include/psi4/libmints/cdsalclist.h +include/psi4/libmints/coordentry.h +include/psi4/libmints/corrtab.h +include/psi4/libmints/dcd.h +include/psi4/libmints/deriv.h +include/psi4/libmints/dimension.h +include/psi4/libmints/dipole.h +include/psi4/libmints/ecpint.h +include/psi4/libmints/electricfield.h +include/psi4/libmints/electrostatic.h +include/psi4/libmints/element_to_Z.h +include/psi4/libmints/erd_eri.h +include/psi4/libmints/eri.h +include/psi4/libmints/extern.h +include/psi4/libmints/factory.h +include/psi4/libmints/fjt.h +include/psi4/libmints/gridblock.h +include/psi4/libmints/gshell.h +include/psi4/libmints/integral.h +include/psi4/libmints/integralparameters.h +include/psi4/libmints/kinetic.h +include/psi4/libmints/local.h +include/psi4/libmints/matrix.h +include/psi4/libmints/mcmurchiedavidson.h +include/psi4/libmints/mintshelper.h +include/psi4/libmints/molecule.h +include/psi4/libmints/multipolepotential.h +include/psi4/libmints/multipoles.h +include/psi4/libmints/multipolesymmetry.h +include/psi4/libmints/nabla.h +include/psi4/libmints/oeprop.h +include/psi4/libmints/onebody.h +include/psi4/libmints/orbitalspace.h +include/psi4/libmints/orthog.h +include/psi4/libmints/overlap.h +include/psi4/libmints/petitelist.h +include/psi4/libmints/pointgrp.h +include/psi4/libmints/potential.h +include/psi4/libmints/potentialint.h +include/psi4/libmints/psimath.h +include/psi4/libmints/quadrupole.h +include/psi4/libmints/rel_potential.h +include/psi4/libmints/shellpair.h +include/psi4/libmints/shellrotation.h +include/psi4/libmints/sieve.h +include/psi4/libmints/siminteri.h +include/psi4/libmints/sobasis.h +include/psi4/libmints/sointegral_onebody.h +include/psi4/libmints/sointegral_twobody.h +include/psi4/libmints/tracelessquadrupole.h +include/psi4/libmints/twobody.h +include/psi4/libmints/typedefs.h +include/psi4/libmints/vector.h 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