science/psi4: New port: Open-source suite of ab initio quantum chemis…

…try programs

science/Makefile

@@ -265,6 +265,7 @@
     SUBDIR += plumed
     SUBDIR += pnetcdf
     SUBDIR += precice
+    SUBDIR += psi4
     SUBDIR += pulseview
     SUBDIR += py-DendroPy
     SUBDIR += py-GPy

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 <bsd.port.mk>

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

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)

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)

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})")

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 <sys/stat.h>
++#endif
++
+ namespace psi {
+
+ void PSIO::open(size_t unit, int status) {

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.