version bump

(Portage version: 2.2.14/cvs/Linux x86_64, signed Manifest commit with key C2000586)

3 files changed, 237 insertions, 2 deletions

diff --git a/sci-chemistry/namd/ChangeLog b/sci-chemistry/namd/ChangeLog
index 901dce286e4a..5e92658dfcff 100644
--- a/sci-chemistry/namd/ChangeLog
+++ b/sci-chemistry/namd/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/namd
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/ChangeLog,v 1.20 2013/12/13 19:39:42 nicolasbock Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/ChangeLog,v 1.21 2015/03/07 01:18:22 ottxor Exp $
+
+*namd-2.10 (07 Mar 2015)
+
+  07 Mar 2015; Christoph Junghans <ottxor@gentoo.org>
+  +files/namd-2.10-gentoo.patch, +namd-2.10.ebuild:
+  version bump
 
   13 Dec 2013; Nicolas Bock <nicolasbock@gentoo.org> metadata.xml:
   sci-chemistry/namd: Updated maintainer email to gentoo.org
diff --git a/sci-chemistry/namd/files/namd-2.10-gentoo.patch b/sci-chemistry/namd/files/namd-2.10-gentoo.patch
new file mode 100644
index 000000000000..e578c131c36d
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-2.10-gentoo.patch
@@ -0,0 +1,124 @@
+diff -Naur NAMD_2.10_Source.orig/arch/Linux-x86_64.fftw NAMD_2.10_Source/arch/Linux-x86_64.fftw
+--- NAMD_2.10_Source.orig/arch/Linux-x86_64.fftw	2015-03-06 17:53:44.170416075 -0700
++++ NAMD_2.10_Source/arch/Linux-x86_64.fftw	2015-03-06 17:54:46.641162629 -0700
+@@ -1,7 +1,7 @@
+ 
+-FFTDIR=/Projects/namd2/fftw/linux-x86_64
++FFTDIR=/usr
+ FFTINCL=-I$(FFTDIR)/include
+-FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw
++FFTLIB=-L$(FFTDIR)/gentoo-libdir -lsrfftw -lsfftw
+ FFTFLAGS=-DNAMD_FFTW
+ FFT=$(FFTINCL) $(FFTFLAGS)
+ 
+diff -Naur NAMD_2.10_Source.orig/arch/Linux-x86_64.tcl NAMD_2.10_Source/arch/Linux-x86_64.tcl
+--- NAMD_2.10_Source.orig/arch/Linux-x86_64.tcl	2015-03-06 17:53:44.170416075 -0700
++++ NAMD_2.10_Source/arch/Linux-x86_64.tcl	2015-03-06 17:54:46.641162629 -0700
+@@ -1,9 +1,9 @@
+ 
+ #TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64
+-TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64-threaded
++TCLDIR=/usr
+ TCLINCL=-I$(TCLDIR)/include
+ #TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl
+-TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl -lpthread
++TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl -lpthread
+ TCLFLAGS=-DNAMD_TCL
+ TCL=$(TCLINCL) $(TCLFLAGS)
+ 
+diff -Naur NAMD_2.10_Source.orig/Makefile NAMD_2.10_Source/Makefile
+--- NAMD_2.10_Source.orig/Makefile	2015-03-06 17:53:44.170416075 -0700
++++ NAMD_2.10_Source/Makefile	2015-03-06 18:01:32.645966590 -0700
+@@ -389,10 +389,10 @@
+ 	$(DSTDIR)/stringhash.o
+ 
+ # definitions for Charm routines
+-CHARMC = $(CHARM)/bin/charmc
+-CHARMXI = $(CHARM)/bin/charmc
+-CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1
+-CHARMLIB = $(CHARM)/lib
++CHARMC = /usr/bin/charmc
++CHARMXI = /usr/bin/charmc
++CHARMINC = /usr/include/gentoo-charm $(COPTD)CMK_OPTIMIZE=1
++CHARMLIB = /usr/gentoo-libdir
+ CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB -module CkMulticast
+ #CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB
+ #CHARM_MODULES = -module msa -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB
+@@ -418,7 +418,7 @@
+ 
+ # Add new executables here.
+ 
+-BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb charmrun
++BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb
+ 
+ # This should be rebuilt at every compile, but not on Win32.
+ BUILDINFO = $(DSTDIR)/buildinfo
+@@ -434,7 +434,7 @@
+ 
+ namd2:	$(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS)
+ 	$(MAKEBUILDINFO)
+-	$(CHARMC) -verbose -ld++-option \
++	$(CHARMC) $(LDFLAGS) -verbose -ld++-option \
+ 	'$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS) $(CXXMICOPTS)' \
+ 	"$(CHARM_MODULES)" -language charm++ \
+ 	$(BUILDINFO).o \
+@@ -484,11 +484,8 @@
+ charmd_faceless.exe:
+ 	$(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe
+ 
+-charmrun.exe:
+-	$(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe
+-
+ psfgen:	$(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS)
+-	$(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
++	$(CC) $(SBCFLAGS) $(LDFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
+ 
+ psfgen.exe:	$(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL)
+ 	$(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
+@@ -506,7 +503,7 @@
+ 	$(CC) $(CFLAGS) -o diffbinpdb $(SRCDIR)/diffbinpdb.c -lm
+ 
+ flipdcd:	$(SRCDIR)/flipdcd.c
+-	$(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \
+ 	echo "#!/bin/sh\necho unavailable on this platform" > $@; \
+ 	chmod +x $@
+ 
+@@ -516,7 +513,7 @@
+ 	chmod +x $@
+ 
+ fixdcd:	$(SRCDIR)/fixdcd.c
+-	$(CC) $(CFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c
+ 
+ dumpdcd:	$(SRCDIR)/dumpdcd.c
+ 	$(CC) $(CFLAGS) -o dumpdcd $(SRCDIR)/dumpdcd.c
+@@ -711,9 +708,7 @@
+ 
+ DOC_FILES = README.txt announce.txt license.txt notes.txt
+ 
+-RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen charmrun namd2
+-
+-WINDOWS_RELEASE_FILES = $(LIBCUDARTSO) $(WINDOWSBINARIES) $(TCLDLL)
++RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen namd2
+ 
+ release: all
+ 	$(ECHO) Creating release $(RELEASE_DIR_NAME)
+@@ -724,17 +719,9 @@
+ 	for f in `find $(RELEASE_DIR_NAME)/lib -name CVS`; do \
+ 	  /bin/rm -rf $$f; \
+ 	done
+-	if [ -r $(CHARM)/bin/charmd ]; then \
+-	  $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \
+-	fi
+-	if [ -r $(CHARM)/bin/charmd_faceless ]; then \
+-	  $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \
+-	fi
+ 	chmod -R a+rX $(RELEASE_DIR_NAME)
+ 	tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME)
+ 	gzip $(RELEASE_DIR_NAME).tar
+-	echo $(CHARM)
+-	ls -l $(CHARM)/lib
+ 	-for f in $(RELEASE_FILES); do echo $$f; $(LDD) $(RELEASE_DIR_NAME)/$$f; done
+ 
+ winrelease: winall
diff --git a/sci-chemistry/namd/namd-2.10.ebuild b/sci-chemistry/namd/namd-2.10.ebuild
new file mode 100644
index 000000000000..e85b7f3b1ede
--- /dev/null
+++ b/sci-chemistry/namd/namd-2.10.ebuild
@@ -0,0 +1,105 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/namd-2.10.ebuild,v 1.1 2015/03/07 01:18:22 ottxor Exp $
+
+EAPI=5
+
+inherit eutils multilib toolchain-funcs flag-o-matic
+
+DESCRIPTION="A powerful and highly parallelized molecular dynamics code"
+LICENSE="namd"
+HOMEPAGE="http://www.ks.uiuc.edu/Research/namd/"
+
+MY_PN="NAMD"
+
+SRC_URI="${MY_PN}_${PV}_Source.tar.gz"
+
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+RESTRICT="fetch"
+
+RDEPEND="
+	>=sys-cluster/charm-6.5.1-r2
+	sci-libs/fftw:3.0
+	dev-lang/tcl"
+
+DEPEND="${RDEPEND}
+	app-shells/tcsh"
+
+NAMD_ARCH="Linux-x86_64-g++"
+
+NAMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD"
+
+S="${WORKDIR}/${MY_PN}_${PV}_Source"
+
+pkg_nofetch() {
+	echo
+	einfo "Please download ${MY_PN}_${PV}_Source.tar.gz from"
+	einfo "${NAMD_DOWNLOAD}"
+	einfo "after agreeing to the license and then move it to"
+	einfo "${DISTDIR}"
+	einfo "Be sure to select the ${PV} version!"
+	echo
+}
+
+src_prepare() {
+	CHARM_VERSION=$(best_version sys-cluster/charm | cut -d- -f3)
+
+	# apply a few small fixes to make NAMD compile and
+	# link to the proper libraries
+	epatch "${FILESDIR}"/namd-2.10-gentoo.patch
+	epatch "${FILESDIR}"/namd-2.7-iml-dec.patch
+	sed \
+		-e "/CHARMBASE =/s:= .*:= /usr/bin/charm-${CHARM_VERSION}:" \
+		-i Make.charm || die
+
+	# Remove charm distribution. We don't need it.
+	rm -f charm-*.tar
+
+	# proper compiler and cflags
+	sed \
+		-e "s/g++.*/$(tc-getCXX)/" \
+		-e "s/gcc.*/$(tc-getCC)/" \
+		-e "s/CXXOPTS = .*/CXXOPTS = ${CXXFLAGS} ${LDFLAGS}/" \
+		-e "s/COPTS = .*/COPTS = ${CFLAGS} ${LDFLAGS}/" \
+		-i arch/${NAMD_ARCH}.arch || die
+
+	sed \
+		-e "s/gentoo-libdir/$(get_libdir)/g" \
+		-e "s/gentoo-charm/charm-${CHARM_VERSION}/g" \
+		-i Makefile || die "Failed gentooizing Makefile."
+	sed -e "s@/lib@/$(get_libdir)@g" -e '/FFTDIR=/s@=.*@=/usr@' -i arch/Linux-x86_64.fftw3 || die
+	sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.tcl || die
+}
+
+src_configure() {
+	# configure
+	./config ${NAMD_ARCH} --with-fftw3 --charm-arch . || die
+}
+
+src_compile() {
+	# build namd
+	cd "${S}/${NAMD_ARCH}"
+	emake
+}
+
+src_install() {
+	dodoc announce.txt license.txt notes.txt
+	cd "${S}/${NAMD_ARCH}"
+
+	# the binaries
+	dobin ${PN}2 psfgen flipbinpdb flipdcd
+}
+
+pkg_postinst() {
+	echo
+	einfo "For detailed instructions on how to run and configure"
+	einfo "NAMD please consults the extensive documentation at"
+	einfo "http://www.ks.uiuc.edu/Research/namd/"
+	einfo "and the NAMD tutorials available at"
+	einfo "http://www.ks.uiuc.edu/Training/Tutorials/"
+	einfo "Have fun :)"
+	echo
+}