Latest version for testing. If anyone wants to modify and test on x86 please feel free :)

Package-Manager: portage-2.1.6.13/cvs/Linux x86_64

5 files changed, 238 insertions, 6 deletions

diff --git a/sci-chemistry/namd/ChangeLog b/sci-chemistry/namd/ChangeLog
index fb127c9e28aa..9e3175e03b0f 100644
--- a/sci-chemistry/namd/ChangeLog
+++ b/sci-chemistry/namd/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-chemistry/namd
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/ChangeLog,v 1.7 2008/06/03 02:12:24 mr_bones_ Exp $
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/ChangeLog,v 1.8 2009/06/08 02:39:18 je_fro Exp $
+
+*namd-2.7 (08 Jun 2009)
+
+  08 Jun 2009; Jeff Gardner <je_fro@gentoo.org> namd-2.6.ebuild,
+  +namd-2.7.ebuild, +files/namd-2.7-gentoo.patch:
+  Latest version for testing. If anyone wants to modify and test on x86
+  please feel free :)
 
   03 Jun 2008; Michael Sterrett <mr_bones_@gentoo.org> namd-2.6.ebuild:
   remove reference to app-shells/csh which has been removed
diff --git a/sci-chemistry/namd/Manifest b/sci-chemistry/namd/Manifest
index 0684ec323577..5b53f7b27733 100644
--- a/sci-chemistry/namd/Manifest
+++ b/sci-chemistry/namd/Manifest
@@ -1,9 +1,12 @@
 AUX namd-2.6-gentoo.patch 3650 RMD160 e7cc7fa0e20b01295d6f7c83211f961720e8beaa SHA1 f5525811cc092c5125be93cdce0e8c4e22fbee38 SHA256 55fad22d757d83d786b279a50a724499fb915767ade827895d686df16fa829d9
+AUX namd-2.7-gentoo.patch 4046 RMD160 a7d087c47088d9a8df8f804e023d1a882e281e74 SHA1 333fe98dcfb54736f192f3baa82280dcab1fbd21 SHA256 9416859fa9f065f3f269441cbbb44d4f627b71c8cba29ba9e6765c08dae3611f
 AUX namd-barrier-fix-gentoo.patch 2362 RMD160 c6b045a0f2ec9f29bf7f98db7a71c1533f2a20d3 SHA1 5d42ef58f08914ecdf4afe735345ff1264389544 SHA256 f0186fada88b387c0681095174be336d61b2968197d223c15c840c1ca96e4992
 AUX namd-fftw-lib-gentoo.patch 528 RMD160 bb776e58497f0ec672bf5fc9ef22d0717d8c27ad SHA1 b8ca7a0521900bd9dbf725d9ce7ed809ff2d1aa0 SHA256 04528fd52f70cccbba1ccf844b97b256a35f9b1b85ca3ef8a56b4c9308b22696
 AUX namd-makefile-gentoo.patch 2804 RMD160 e52934e5a1aa7ed34e270dc11e780b1bdef3011d SHA1 22d5bd779a280c1287c936dd855f8359fa7b1b4e SHA256 f3945ae8fff113286847d61a00d5a749b1c3a00b65394085e56ff47a0a209250
 AUX namd-tcl-lib-gentoo.patch 576 RMD160 0992dd4103b97baed85e66a8d4fc04c3991bedd1 SHA1 f1cc944b14f7f77785f1a914d3d50f44d9929aec SHA256 7a57497410f5791b1b9fa0535e66137bd1b4c5008e0253c7467bc40af7b6ac01
 DIST NAMD_2.6_Source.tar.gz 8963319 RMD160 186f79322226a20398031618011104a666237298 SHA1 3b3d83fdc54a520cb6c59b34cde03c9f74d2f443 SHA256 bf353ff13eae18b5a8dc33d79d295e9fe73fb87482858309b7695ce3e24f0d0b
-EBUILD namd-2.6.ebuild 2260 RMD160 d902ae892b41ebf777cf8dcdaeb8c6b0605a1628 SHA1 5a34fa5a7696d981b477c89ec3c7ab4a6bc3c3bd SHA256 9dc25c1fe085fbfe18ece0bad1f826078d72e8a3a228f3b1df6af328f097986e
-MISC ChangeLog 1505 RMD160 8ae53121b16caafb03cf2a3445854639fe3738ff SHA1 1a93bce6cc2016623f21840808f089649fa8c2e3 SHA256 14037ee5e01ab1457a5971265f8cd7d435ea2b5c75a41d4de48186893fc1c455
+DIST NAMD_2.7b1_Source.tar.gz 26302404 RMD160 ccb73606d3f0724c55ce022aa130656444825f5e SHA1 955e096a6c70e1e7786d10334bec3cae1eb4fff6 SHA256 cf48b659667fe9e03af27c8d434567525e924ebd08c801321c71361a8f166b2e
+EBUILD namd-2.6.ebuild 2276 RMD160 6d4583a35fb4d805f2062b2df9b7e9c8bc5bf139 SHA1 04b549e5825b8c0a069e5b157fda2905d10c2a8b SHA256 796fe9827679ed51df1f08ea0e25bba6cc316ffd99d5381cf3a8ebc06c7b4adc
+EBUILD namd-2.7.ebuild 2663 RMD160 21be6839941c2218d66502c3b4426354e7d264fa SHA1 71dd1f79ad88bddca1c2fd0029e7d07a74f3d183 SHA256 834b65c877679084faef28f01ea532f0ddbcbfab70ba1b91d922cc13bfd45197
+MISC ChangeLog 1737 RMD160 36758e08171cef146a77af07d4f933ae4001a091 SHA1 f258801df6be68820f9f2f5ef3622d6fc0f9b38a SHA256 55e44132e7f8f17f6e26c3ad95dbd08c283357ff217421ec0e52b55976aae0c7
 MISC metadata.xml 282 RMD160 539a53475b01291eadb86c8c53a0fbc02b4a34d4 SHA1 7f42dcea44641b8a77ab9644791344ec6ed6c327 SHA256 3c1785eb4ab63774ed3a6b1bddd602ef24cd6795f690bb3289d5a980bca06349
diff --git a/sci-chemistry/namd/files/namd-2.7-gentoo.patch b/sci-chemistry/namd/files/namd-2.7-gentoo.patch
new file mode 100644
index 000000000000..733ee8eacc04
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-2.7-gentoo.patch
@@ -0,0 +1,117 @@
+diff -aurN NAMD_2.7b1_Source.orig/Make.charm NAMD_2.7b1_Source/Make.charm
+--- NAMD_2.7b1_Source.orig/Make.charm	2009-06-07 15:15:11.000000000 -0500
++++ NAMD_2.7b1_Source/Make.charm	2009-06-07 15:15:11.000000000 -0500
+@@ -2,5 +2,5 @@
+ # The config script will override this setting if there is a directory
+ # called charm-6.1 or charm in the NAMD base directory.
+ 
+-CHARMBASE = /Projects/namd2/charm-6.1
++CHARMBASE = /usr/include/charm-6.1.2
+ 
+diff -aurN NAMD_2.7b1_Source.orig/Makefile NAMD_2.7b1_Source/Makefile
+--- NAMD_2.7b1_Source.orig/Makefile	2009-06-07 15:15:11.000000000 -0500
++++ NAMD_2.7b1_Source/Makefile	2009-06-07 15:15:11.000000000 -0500
+@@ -297,10 +297,10 @@
+ 	$(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
+ 
+ # Libraries we may have changed
+ LIBS = $(CUDAOBJS) $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL)
+@@ -320,7 +320,7 @@
+ 
+ # Add new executables here.
+ 
+-BINARIES = namd2 psfgen charmrun flipdcd flipbinpdb
++BINARIES = namd2 psfgen flipdcd flipbinpdb
+ 
+ # This should be rebuilt at every compile, but not on Win32.
+ BUILDINFO = $(DSTDIR)/buildinfo
+@@ -351,14 +351,6 @@
+ 	$(CHARMOPTS) \
+ 	-lm -o namd2
+ 
+-charmrun: $(CHARM)/bin/charmrun # XXX
+-	$(COPY) $(CHARM)/bin/charmrun $@
+-
+-WINDOWSBINARIES = namd2.exe psfgen.exe
+-# WINDOWSBINARIES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe
+-
+-windowsbinaries: $(WINDOWSBINARIES)
+-
+ namd2.exe:  $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) $(TCLDLL)
+ 	$(MAKEBUILDINFO)
+ 	$(CHARMC) -verbose \
+@@ -381,9 +373,6 @@
+ charmd_faceless.exe:
+ 	$(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe
+ 
+-charmrun.exe:
+-	$(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe
+-
+ psfgen:	$(DSTDIR) $(SBOBJS) $(PLUGINOBJS)
+ 	$(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
+ 
+@@ -700,9 +689,7 @@
+ 
+ DOC_FILES = README.txt announce.txt license.txt notes.txt
+ 
+-RELEASE_FILES = flipdcd flipbinpdb psfgen charmrun namd2
+-
+-WINDOWS_RELEASE_FILES = $(WINDOWSBINARIES) $(TCLDLL)
++RELEASE_FILES = flipdcd flipbinpdb psfgen namd2
+ 
+ release: all
+ 	$(ECHO) Creating release $(RELEASE_DIR_NAME)
+@@ -711,17 +698,9 @@
+ 	for f in $(DOC_FILES); do cp .rootdir/$$f $(RELEASE_DIR_NAME); done
+ 	cp -r .rootdir/lib $(RELEASE_DIR_NAME)
+ 	/bin/rm -rf $(RELEASE_DIR_NAME)/lib/CVS $(RELEASE_DIR_NAME)/lib/*/CVS
+-	if [ -r $(CHARM)/bin/charmd ]; then \
+-	  $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \
+-	fi
+-	if [ -r $(CHARM)/bin/charmd_faceless ]; then \
+-	  $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \
+-	fi
+ 	chmod -R a+rX $(RELEASE_DIR_NAME)
+ 	tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME)
+ 	gzip $(RELEASE_DIR_NAME).tar
+-	echo $(CHARM)
+-	ls -l $(CHARM)/lib
+ 	-for f in $(RELEASE_FILES); do echo $$f; $(LDD) $$f; done
+ 
+ winrelease: winall
+diff -aurN NAMD_2.7b1_Source.orig/arch/Linux-x86_64.fftw NAMD_2.7b1_Source/arch/Linux-x86_64.fftw
+--- NAMD_2.7b1_Source.orig/arch/Linux-x86_64.fftw	2009-06-07 15:15:11.000000000 -0500
++++ NAMD_2.7b1_Source/arch/Linux-x86_64.fftw	2009-06-07 15:15:11.000000000 -0500
+@@ -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) $(FFTFLAGS)
+ 
+diff -aurN NAMD_2.7b1_Source.orig/arch/Linux-x86_64.tcl NAMD_2.7b1_Source/arch/Linux-x86_64.tcl
+--- NAMD_2.7b1_Source.orig/arch/Linux-x86_64.tcl	2009-06-07 15:15:11.000000000 -0500
++++ NAMD_2.7b1_Source/arch/Linux-x86_64.tcl	2009-06-07 18:25:07.000000000 -0500
+@@ -1,7 +1,7 @@
+ 
+-TCLDIR=/Projects/namd2/tcl/linux-x86_64
++TCLDIR=/usr
+ TCLINCL=-I$(TCLDIR)/include
+-TCLLIB=-L$(TCLDIR)/lib -ltcl8.3 -ldl
++TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl
+ TCLFLAGS=-DNAMD_TCL
+ TCL=$(TCLINCL) $(TCLFLAGS)
+ 
diff --git a/sci-chemistry/namd/namd-2.6.ebuild b/sci-chemistry/namd/namd-2.6.ebuild
index 40f66cde6402..d419fd3e5e14 100644
--- a/sci-chemistry/namd/namd-2.6.ebuild
+++ b/sci-chemistry/namd/namd-2.6.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/namd-2.6.ebuild,v 1.2 2008/06/03 02:12:24 mr_bones_ Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/namd-2.6.ebuild,v 1.3 2009/06/08 02:39:18 je_fro Exp $
 
 inherit eutils toolchain-funcs flag-o-matic
 
@@ -25,6 +25,8 @@ DEPEND="app-shells/tcsh
 	=sci-libs/fftw-2*
 	=dev-lang/tcl-8.4*"
 
+RDEPEND=${DEPEND}
+
 CHARM="charm-5.9"
 NAMD_ARCH="Linux-i686-g++"
 
diff --git a/sci-chemistry/namd/namd-2.7.ebuild b/sci-chemistry/namd/namd-2.7.ebuild
new file mode 100644
index 000000000000..fc6e0cc9951b
--- /dev/null
+++ b/sci-chemistry/namd/namd-2.7.ebuild
@@ -0,0 +1,103 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/namd-2.7.ebuild,v 1.1 2009/06/08 02:39:18 je_fro Exp $
+
+inherit eutils 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"
+MY_PV="2.7b1"
+
+SRC_URI="${MY_PN}_${MY_PV}_Source.tar.gz"
+
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+RESTRICT="fetch"
+
+DEPEND="|| ( app-shells/csh
+			app-shells/tcsh )
+	virtual/libc
+	sys-cluster/charm
+	=sci-libs/fftw-2*
+	dev-lang/tcl"
+
+RDEPEND=${DEPEND}
+
+NAMD_ARCH="Linux-x86_64-g++"
+
+NAMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD"
+
+S="${WORKDIR}/${MY_PN}_${MY_PV}_Source"
+
+pkg_nofetch() {
+	echo
+	einfo "Please download ${MY_PN}_${MY_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 ${MY_PV} version!"
+	echo
+}
+
+src_unpack() {
+	unpack ${A}
+	cd "${WORKDIR}"
+# apply a few small fixes to make NAMD compile and
+	# link to the proper libraries
+	epatch "${FILESDIR}"/namd-2.7-gentoo.patch
+	cd "${S}"
+	# proper compiler and cflags
+	sed -e "s/g++/$(tc-getCXX)/" \
+		-e "s/CXXOPTS = -O3 -m64 -fexpensive-optimizations -ffast-math/CXXOPTS = ${CXXFLAGS}/" \
+		-e "s/gcc/$(tc-getCC)/" \
+		-e "s/COPTS = -O3 -m64 -fexpensive-optimizations -ffast-math/COPTS = ${CFLAGS}/" \
+		-i arch/${NAMD_ARCH}.arch || \
+		die "Failed to setup ${NAMD_ARCH}.arch"
+
+	sed -e "s/gentoo-libdir/$(get_libdir)/g" \
+		-e "s/gentoo-charm/charm-6.1.2/g" \
+		-i Makefile || die "Failed gentooizing Makefile."
+	sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.fftw || \
+		die "Failed gentooizing Linux-x86_64.fftw."
+	sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.tcl || \
+		die "Failed gentooizing Linux-x86_64.tcl."
+
+	# configure
+	./config ${NAMD_ARCH}
+}
+
+src_compile() {
+	# build namd
+	cd "${S}/${NAMD_ARCH}"
+	emake || die "Failed to build namd"
+}
+
+src_install() {
+	cd "${S}/${NAMD_ARCH}"
+
+	# the binaries
+	dobin ${PN}2 psfgen flipbinpdb flipdcd || \
+		die "Failed to install binaries"
+
+	cd "${S}"
+
+	# some docs
+	dodoc announce.txt license.txt notes.txt || \
+		die "Failed to install docs"
+}
+
+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
+}