svn commit: r472353 - in head: . science science/abinit science/abinit/files

Yuri Victorovich yuri at FreeBSD.org
Thu Jun 14 05:49:42 UTC 2018 

Author: yuri
Date: Thu Jun 14 05:49:39 2018
New Revision: 472353
URL: https://svnweb.freebsd.org/changeset/ports/472353

Log:
  Re-add port: science/abinit: Full-featured atomic-scale first-principles simulation software
  
  I couldn't make MPI work, created a bug report.
  Will add DOCS and EXAMPLES options later.
  
  PR:		219025

Added:
  head/science/abinit/
     - copied from r366979, head/science/abinit/
  head/science/abinit/files/patch-Makefile.in   (contents, props changed)
  head/science/abinit/files/patch-src_02__clib_md5.c   (contents, props changed)
Deleted:
  head/science/abinit/files/makefile_macros
  head/science/abinit/files/patch-bindings_parser_ab_dtset_c.c
  head/science/abinit/files/patch-bindings_parser_parser.mk
  head/science/abinit/files/patch-config+m4+init.m4
  head/science/abinit/files/patch-config+optflags
  head/science/abinit/files/patch-config.mk.in
  head/science/abinit/files/patch-config_scripts_make-macros-autotools
  head/science/abinit/files/patch-configure
  head/science/abinit/files/patch-prereqs+linalg+linalg.mk
Modified:
  head/MOVED
  head/science/Makefile
  head/science/abinit/Makefile
  head/science/abinit/distinfo
  head/science/abinit/pkg-descr
  head/science/abinit/pkg-plist

Modified: head/MOVED
==============================================================================
--- head/MOVED	Thu Jun 14 03:27:00 2018	(r472352)
+++ head/MOVED	Thu Jun 14 05:49:39 2018	(r472353)
@@ -6750,7 +6750,6 @@ russian/prawda||2014-09-01|Not staged
 russian/pscyr||2014-09-01|Not staged
 russian/tac+ia||2014-09-01|Not staged
 science/2dhf||2014-09-01|Not staged
-science/abinit||2014-09-01|Not staged
 science/dtiquery||2014-09-01|Not staged
 science/elmer-hutiter||2014-09-01|Not staged
 science/elmerpost||2014-09-01|Not staged

Modified: head/science/Makefile
==============================================================================
--- head/science/Makefile	Thu Jun 14 03:27:00 2018	(r472352)
+++ head/science/Makefile	Thu Jun 14 05:49:39 2018	(r472353)
@@ -22,6 +22,7 @@
     SUBDIR += R-cran-snow
     SUBDIR += R-cran-som
     SUBDIR += R-cran-udunits2
+    SUBDIR += abinit
     SUBDIR += afni
     SUBDIR += aircraft-datcom
     SUBDIR += antioch

Modified: head/science/abinit/Makefile
==============================================================================
--- head/science/abinit/Makefile	Tue Sep  2 09:04:44 2014	(r366979)
+++ head/science/abinit/Makefile	Thu Jun 14 05:49:39 2018	(r472353)
@@ -2,87 +2,26 @@
 # $FreeBSD$
 
 PORTNAME=	abinit
-PORTVERSION=	5.7.3
-PORTREVISION=	16
+DISTVERSION=	8.8.2
 CATEGORIES=	science
-MASTER_SITES=	ftp://ftp.abinit.org/pub/abinitio/ABINIT_v${PORTVERSION}/
+MASTER_SITES=	https://www.abinit.org/sites/default/files/packages/
 
-MAINTAINER=	ports at FreeBSD.org
-COMMENT=	Abinit calculates electronic structure of systems
+MAINTAINER=	yuri at FreeBSD.org
+COMMENT=	Full-featured atomic-scale first-principles simulation software
 
-BUILD_DEPENDS=	python:${PORTSDIR}/lang/python \
-		${PYTHON_SITELIBDIR}/numarray/__init__.py:${PORTSDIR}/math/py-numarray
-LIB_DEPENDS=	libnetcdff.so:${PORTSDIR}/science/netcdf-fortran \
-		libgsl.so:${PORTSDIR}/math/gsl
+LICENSE=	GPLv3
+LICENSE_FILE=	${WRKSRC}/COPYING
 
-USES=		fortran gmake perl5
-USE_PYTHON=	yes
-USE_PERL5=	build
-USE_AUTOTOOLS=	autoconf automake
-CONFIGURE_ENV=	WGET=${TRUE}
-CONFIGURE_ARGS=	--disable-wannier90 --disable-bigdft --disable-etsf-io	\
-		--with-plugins-tardir=/dev/null				\
-		--with-netcdf-includes="-I${LOCALBASE}/include"		\
-		--enable-bindings --enable-gsl				\
-		--with-netcdf-libs="-L${LOCALBASE}/lib -lnetcdff -lnetcdf"
-CPPFLAGS+=	-I${LOCALBASE}/include
-LDFLAGS+=	-L${LOCALBASE}/lib
+ONLY_FOR_ARCHS=	amd64 i386
 
-OPTIONS_DEFINE=	DOCS EXAMPLES
+LIB_DEPENDS=	liblapack.so:math/lapack \
+		libblas.so:math/blas
+RUN_DEPENDS=	atompaw:science/atompaw
 
-NO_STAGE=	yes
-.include <bsd.port.options.mk>
+USES=		fortran gmake localbase:ldflags
+GNU_CONFIGURE=	yes
+CONFIGURE_ARGS=	--enable-shared --disable-static
 
-.if ${PORT_OPTIONS:MDOCS}
-USE_TEX=	latex:build dvipsk:build
-BUILD_DEPENDS+= gm4:${PORTSDIR}/devel/m4		\
-		markdown:${PORTSDIR}/textproc/markdown
-USE_GHOSTSCRIPT_BUILD=	yes
-.endif
-
-.if ${ARCH} == "ia64" || ${ARCH} == "powerpc" || ${ARCH} == "sparc64"
-MANUAL_PACKAGE_BUILD=	takes a tremendous amount of time to build on pointyhat nodes
-.endif
-
-.if exists(${LOCALBASE}/lib/libatlas.so) && !defined(WITH_BLAS)
-WITH_ATLAS=	yes
-.endif
-.if defined(WITH_ATLAS)
-LIB_DEPENDS+=	libatlas.so:${PORTSDIR}/math/atlas
-BLAS=		-lf77blas
-LAPACK=		-lalapack -lcblas
-.else
-LIB_DEPENDS+=	libblas.so:${PORTSDIR}/math/blas
-LIB_DEPENDS+=	liblapack.so:${PORTSDIR}/math/lapack
-BLAS=		-lblas
-LAPACK=		-llapack
-.endif
-
-pre-configure:
-.if ! ${PORT_OPTIONS:MDOCS}
-	${REINPLACE_CMD} -e '/^abinit_top_subdirs =/s| doc||' ${WRKSRC}/config/specs/other.cf
-.endif
-.if ! ${PORT_OPTIONS:MEXAMPLES}
-	${REINPLACE_CMD} -e '/^abinit_top_subdirs =/s| tests||' ${WRKSRC}/config/specs/other.cf
-.endif
-	(cd ${WRKSRC} && ./config/scripts/makemake)
-	${CHMOD} a+x ${WRKSRC}/bindings/parser/*.py
-
-post-build:
-	@(cd ${BUILD_WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} \
-		${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} libabinit)
-
-post-install:
-	${MKDIR} ${PREFIX}/include ${PREFIX}/lib
-.for lf in libabinip.a libabinis.a
-	${INSTALL_DATA} ${WRKSRC}/${lf} ${PREFIX}/lib
-.endfor
-.for lf in ab_dtset_c.h dtset_c.h dtset_c.static.h dtset_f90.inc dtset_py.h	\
-	ab_dtset_f90_get.f90
-	${INSTALL_DATA} ${WRKSRC}/bindings/parser/${lf} ${PREFIX}/include
-.endfor
-
-regression-test:
-	cd ${WRKSRC}/tests ; ${MAKE_CMD} tests_min
+FCFLAGS+=	-ffree-line-length-none
 
 .include <bsd.port.mk>

Modified: head/science/abinit/distinfo
==============================================================================
--- head/science/abinit/distinfo	Tue Sep  2 09:04:44 2014	(r366979)
+++ head/science/abinit/distinfo	Thu Jun 14 05:49:39 2018	(r472353)
@@ -1,2 +1,3 @@
-SHA256 (abinit-5.7.3.tar.gz) = caac56530ceaa5e16326fd4407adcd0b1aede07ded51017f3eb6a6a3696c2867
-SIZE (abinit-5.7.3.tar.gz) = 31683174
+TIMESTAMP = 1528909182
+SHA256 (abinit-8.8.2.tar.gz) = 15216703bd56a799a249a112b336d07d733627d3756487a4b1cb48ebb625c3e7
+SIZE (abinit-8.8.2.tar.gz) = 82546807

Added: head/science/abinit/files/patch-Makefile.in
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/abinit/files/patch-Makefile.in	Thu Jun 14 05:49:39 2018	(r472353)
@@ -0,0 +1,11 @@
+--- Makefile.in.orig	2018-06-14 05:16:42 UTC
++++ Makefile.in
+@@ -876,7 +876,7 @@ AM_DISTCHECK_CONFIGURE_FLAGS = \
+   @abi_ac_distcheck@ \
+   PYFLAGS="@PYFLAGS@ -B"
+ 
+-SUBDIRS = fallbacks src abichecks tests
++SUBDIRS = fallbacks src abichecks
+ 
+ # Additional files to clean
+ CLEANFILES = config.optim config.fc_info.tmp

Added: head/science/abinit/files/patch-src_02__clib_md5.c
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/abinit/files/patch-src_02__clib_md5.c	Thu Jun 14 05:49:39 2018	(r472353)
@@ -0,0 +1,11 @@
+--- src/02_clib/md5.c.orig	2017-02-28 12:02:53 UTC
++++ src/02_clib/md5.c
+@@ -47,7 +47,7 @@
+ #ifdef HAVE_MALLOC_MALLOC_H
+ #  include <malloc/malloc.h>
+ #else
+-#  include <malloc.h>
++#  include <stdlib.h>
+ #endif
+ 
+ #include "md5.h"

Modified: head/science/abinit/pkg-descr
==============================================================================
--- head/science/abinit/pkg-descr	Tue Sep  2 09:04:44 2014	(r366979)
+++ head/science/abinit/pkg-descr	Thu Jun 14 05:49:39 2018	(r472353)
@@ -1,7 +1,14 @@
-ABINIT is a package whose main program allows one to find
-the total energy, charge density and electronic structure of
-systems made of electrons and nulcei (molecules and periodic
-solids) within Density Functional Theory (DFT), using pseudo-
-potentials and a planewave basis.
+ABINIT is a package whose main program allows one to find the total energy,
+charge density and electronic structure of systems made of electrons and nuclei
+(molecules and periodic solids) within Density Functional Theory (DFT), using
+pseudopotentials and a planewave or wavelet basis. ABINIT also includes options
+to optimize the geometry according to the DFT forces and stresses, or to perform
+molecular dynamics simulations using these forces, or to generate dynamical
+matrices, Born effective charges, and dielectric tensors, based on
+Density-Functional Perturbation Theory, and many more properties. Excited states
+can be computed within the Many-Body Perturbation Theory (the GW approximation
+and the Bethe-Salpeter equation), and Time-Dependent Density Functional Theory
+(for molecules). In addition to the main ABINIT code, different utility programs
+are provided.
 
-WWW: http://www.abinit.org/
+WWW: https://www.abinit.org

Modified: head/science/abinit/pkg-plist
==============================================================================
--- head/science/abinit/pkg-plist	Tue Sep  2 09:04:44 2014	(r366979)
+++ head/science/abinit/pkg-plist	Thu Jun 14 05:49:39 2018	(r472353)
@@ -1,2407 +1,23 @@
-bin/abinetcdf
-bin/abinis
+bin/abinit
 bin/aim
 bin/anaddb
 bin/band2eps
+bin/bsepostproc
 bin/conducti
 bin/cut3d
-bin/lwf
+bin/dummy_tests
+bin/fftprof
+bin/fold2Bloch
+bin/ioprof
+bin/lapackprof
 bin/macroave
 bin/mrgddb
+bin/mrgdv
 bin/mrggkk
 bin/mrgscr
-bin/newsp
+bin/multibinit
 bin/optic
-include/ab_dtset_c.h
-include/ab_dtset_f90_get.f90
-include/dtset_c.h
-include/dtset_c.static.h
-include/dtset_f90.inc
-include/dtset_py.h
-lib/libabibase.a
-lib/libabinip.a
-lib/libabinis.a
-%%PORTDOCS%%%%DOCSDIR%%/README
-%%PORTDOCS%%%%DOCSDIR%%/build/README
-%%PORTDOCS%%%%DOCSDIR%%/build/adding-extlibs.tex
-%%PORTDOCS%%%%DOCSDIR%%/build/before-starting.tex
-%%PORTDOCS%%%%DOCSDIR%%/build/build-docs.mk
-%%PORTDOCS%%%%DOCSDIR%%/build/build-system-guide.pdf
-%%PORTDOCS%%%%DOCSDIR%%/build/build-system-guide.tex
-%%PORTDOCS%%%%DOCSDIR%%/build/configure-options.tex
-%%PORTDOCS%%%%DOCSDIR%%/build/contributors.tex
-%%PORTDOCS%%%%DOCSDIR%%/build/conventions.tex
-%%PORTDOCS%%%%DOCSDIR%%/build/extending-the-build-system.tex
-%%PORTDOCS%%%%DOCSDIR%%/build/overview.tex
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