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

(Portage version: 2.1.6.13/cvs/Linux x86_64)

4 files changed, 233 insertions, 4 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/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
+}