moved to gx86

6 files changed, 0 insertions, 306 deletions

diff --git a/sci-chemistry/namd/ChangeLog b/sci-chemistry/namd/ChangeLog
deleted file mode 100644
index 09bd2cde4..000000000
--- a/sci-chemistry/namd/ChangeLog
+++ /dev/null
@@ -1,20 +0,0 @@
-# ChangeLog for sci-chemistry/namd
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-  18 Oct 2013; Christoph Junghans <ottxor@gentoo.org> namd-2.9.ebuild:
-  fixed deps
-
-  14 Oct 2013; Nicolas Bock <nicolasbock@gmail.com> namd-2.9.ebuild:
-  sci-chemistry/namd-2.9: Some cleanup in ebuild.
-
-  02 Oct 2013; Nicolas Bock <nicolasbock@gmail.com> namd-2.9.ebuild:
-  sci-chemistry/namd-2.9: Fixed ebuild  The build needs charm using static-libs.
-
-*namd-2.9 (14 Sep 2013)
-
-  14 Sep 2013; Nicolas Bock <nicolasbock@gmail.com>
-  +files/namd-2.7-iml-dec.patch, +files/namd-2.9-gentoo.patch, +metadata.xml,
-  +namd-2.9.ebuild:
-  sci-chemistry/namd-2.9: Version bump; ported patches from namd-2.7_beta2-r1
-  and bumped EAPI to 5.
diff --git a/sci-chemistry/namd/Manifest b/sci-chemistry/namd/Manifest
deleted file mode 100644
index 738c167a3..000000000
--- a/sci-chemistry/namd/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST NAMD_2.9_Source.tar.gz 8814042 SHA256 9ba6a1f87d4600a62847728d7c223295be214f9a72b5bb62552f74d644108424 SHA512 0644814a2799b560d9dcf807ba0047325bc9f0a26e3831b0465d95180784f038d69595e036daac85d59cd919c92d11a0343031975d99deb1fa3052c8a649bdd6 WHIRLPOOL 5494ccb2ee2f2792fe52ad7dcfe6da9d11453f0a9b0859d30698dea56b00d92fae73465967f82bd708abee5cd4ff50b0a6ffde86451e859e2f515af203e09286
diff --git a/sci-chemistry/namd/files/namd-2.7-iml-dec.patch b/sci-chemistry/namd/files/namd-2.7-iml-dec.patch
deleted file mode 100644
index e5ee3bd6c..000000000
--- a/sci-chemistry/namd/files/namd-2.7-iml-dec.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-diff --git a/src/flipbinpdb.c b/src/flipbinpdb.c
-index 94b71ba..01a2529 100644
---- a/src/flipbinpdb.c
-+++ b/src/flipbinpdb.c
-@@ -9,6 +9,7 @@
- #include <sys/mman.h>
- #include <fcntl.h>
- #include <stdio.h>
-+#include <stdlib.h>
- 
- #ifndef MAP_FILE
- #define MAP_FILE 0
-diff --git a/src/flipdcd.c b/src/flipdcd.c
-index 8ec85b7..1c23433 100644
---- a/src/flipdcd.c
-+++ b/src/flipdcd.c
-@@ -13,6 +13,7 @@
- #include <sys/mman.h>
- #include <fcntl.h>
- #include <stdio.h>
-+#include <stdlib.h>
- 
- #ifndef MAP_FILE
- #define MAP_FILE 0
diff --git a/sci-chemistry/namd/files/namd-2.9-gentoo.patch b/sci-chemistry/namd/files/namd-2.9-gentoo.patch
deleted file mode 100644
index 583cc5264..000000000
--- a/sci-chemistry/namd/files/namd-2.9-gentoo.patch
+++ /dev/null
@@ -1,151 +0,0 @@
-diff -Naur NAMD_2.9_Source.original/Make.charm NAMD_2.9_Source/Make.charm
---- NAMD_2.9_Source.original/Make.charm	2012-02-29 19:12:11.000000000 -0700
-+++ NAMD_2.9_Source/Make.charm	2013-09-13 21:23:26.000000000 -0600
-@@ -2,5 +2,5 @@
- # The config script will override this setting if there is a directory
- # called charm-6.4.0 or charm in the NAMD base directory.
- 
--CHARMBASE = /Projects/namd2/charm-6.4.0
-+CHARMBASE = /usr/include/charm-6.4.0
- 
-diff -Naur NAMD_2.9_Source.original/Makefile NAMD_2.9_Source/Makefile
---- NAMD_2.9_Source.original/Makefile	2012-04-27 09:53:24.000000000 -0600
-+++ NAMD_2.9_Source/Makefile	2013-09-13 21:30:15.000000000 -0600
-@@ -344,10 +344,10 @@
- 	$(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
- #CHARM_MODULES = -module msa -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB
- #MSA = -DCHARM_HAS_MSA
-@@ -370,7 +370,7 @@
- 
- # Add new executables here.
- 
--BINARIES = namd2 psfgen sortreplicas charmrun flipdcd flipbinpdb
-+BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb
- 
- # This should be rebuilt at every compile, but not on Win32.
- BUILDINFO = $(DSTDIR)/buildinfo
-@@ -386,7 +386,7 @@
- 
- namd2:	$(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS)
- 	$(MAKEBUILDINFO)
--	$(CHARMC) -verbose -ld++-option \
-+	$(CHARMC) $(LDFLAGS) -verbose -ld++-option \
- 	"$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \
- 	"$(CHARM_MODULES)" -language charm++ \
- 	$(BUILDINFO).o \
-@@ -402,16 +402,9 @@
- 	$(EXTRALINKLIBS) \
- 	-lm -o namd2
- 
--charmrun: $(CHARM)/bin/charmrun # XXX
--	$(COPY) $(CHARM)/bin/charmrun $@
--
- $(LIBCUDARTSO):
- 	$(COPY) $(CUDASODIR)/$(LIBCUDARTSO) $@;
- 
--WINDOWSBINARIES = namd2.exe psfgen.exe sortreplicas.exe
--# WINDOWSBINARIES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe
--windowsbinaries: $(WINDOWSBINARIES)
--
- namd2.exe:  $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS) $(TCLDLL)
- 	$(MAKEBUILDINFO)
- 	$(CHARMC) -verbose \
-@@ -434,11 +427,8 @@
- 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
-@@ -456,7 +446,7 @@
- 	$(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 $@
- 
-@@ -466,7 +456,7 @@
- 	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
-@@ -665,9 +655,7 @@
- 
- 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)
-@@ -678,17 +666,9 @@
- 	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 -Naur NAMD_2.9_Source.original/arch/Linux-x86_64.fftw NAMD_2.9_Source/arch/Linux-x86_64.fftw
---- NAMD_2.9_Source.original/arch/Linux-x86_64.fftw	2009-02-21 21:16:04.000000000 -0700
-+++ NAMD_2.9_Source/arch/Linux-x86_64.fftw	2013-09-13 20:55:02.000000000 -0600
-@@ -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) $(FFTFLAGS)
- 
-diff -Naur NAMD_2.9_Source.original/arch/Linux-x86_64.tcl NAMD_2.9_Source/arch/Linux-x86_64.tcl
---- NAMD_2.9_Source.original/arch/Linux-x86_64.tcl	2011-06-17 14:38:43.000000000 -0600
-+++ NAMD_2.9_Source/arch/Linux-x86_64.tcl	2013-09-13 20:56:30.000000000 -0600
-@@ -1,9 +1,9 @@
- 
- #TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64
--TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64-threaded
-+TCLDIR=/usr
- TCLINCL=-I$(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 --git a/sci-chemistry/namd/metadata.xml b/sci-chemistry/namd/metadata.xml
deleted file mode 100644
index e42d0af60..000000000
--- a/sci-chemistry/namd/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<herd>sci-chemistry</herd>
-</pkgmetadata>
diff --git a/sci-chemistry/namd/namd-2.9.ebuild b/sci-chemistry/namd/namd-2.9.ebuild
deleted file mode 100644
index 1be231a7a..000000000
--- a/sci-chemistry/namd/namd-2.9.ebuild
+++ /dev/null
@@ -1,105 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-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"
-
-DEPEND="
-	app-shells/tcsh
-	|| ( >=sys-cluster/charm-6.5.1-r2 <=sys-cluster/charm-6.5.1-r1[static-libs] )
-	sci-libs/fftw:2.1
-	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}/${MY_PN}_${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 "${FILESDIR}"/namd-2.9-gentoo.patch
-	epatch "${FILESDIR}"/namd-2.7-iml-dec.patch
-	sed \
-		-e "s:charm-.\+:charm-${CHARM_VERSION}:" \
-		-i Make.charm || die
-
-	# Remove charm distribution. We don't need it.
-	rm -f charm-6.4.0.tar || die
-
-	# proper compiler and cflags
-	sed \
-		-e "s/g++/$(tc-getCXX)/" \
-		-e "s/gcc/$(tc-getCC)/" \
-		-e "s/CXXOPTS = -O3 -m64 -fexpensive-optimizations -ffast-math/CXXOPTS = ${CXXFLAGS}/" \
-		-e "s/COPTS = -O3 -m64 -fexpensive-optimizations -ffast-math/COPTS = ${CFLAGS}/" \
-		-i arch/${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/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.fftw || die
-	sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.tcl || die
-}
-
-src_configure() {
-	# configure
-	./config ${NAMD_ARCH} --charm-arch . || die
-}
-
-src_compile() {
-	# build namd
-	cd "${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
-}