namd: bump to 2.8.

4 files changed, 170 insertions, 6 deletions

diff --git a/sci-chemistry/namd/Manifest b/sci-chemistry/namd/Manifest
index e9fe216..45c4bb0 100644
--- a/sci-chemistry/namd/Manifest
+++ b/sci-chemistry/namd/Manifest
@@ -3,11 +3,13 @@ AUX namd-2.7-gentoo.patch 4046 RMD160 a7d087c47088d9a8df8f804e023d1a882e281e74 S
 AUX namd-2.7-iml-dec.patch 520 RMD160 f8f33d8e10a7c6933369c3a6b857d44243bb1c74 SHA1 2edd740e3b6cb5514bde0c4742d0ca4bf6b98126 SHA256 6be7d0a3b4dff7fa39246e7ce49afb82ff508456ebbe3983e2def1202ebb3024
 AUX namd-2.7-ldflags.patch 1547 RMD160 bfaf2ca893168e1a652e75a186817d8149af94d8 SHA1 a0ce28bcc65e1cb7ff5c61723e602c26f5eef16b SHA256 ce2fd68cf2bf0c459c65caef4e71010b2ae5bf3c2c16770d44ca461291b9b924
 AUX namd-2.7_beta2-gentoo.patch 4409 RMD160 301bc17156f10a552eae4c2b3ed91ed2ea9fae6a SHA1 3cb0deb35e690156cf1a41e35482fab42480e3af SHA256 c56728dbf426540f9558db31f7e45cacc654112022f42917e715dbaa6c05373d
+AUX namd-2.8-gentoo.patch 4083 RMD160 736e9aed3da973b58f01bf57907bf307980b5354 SHA1 3916a0f8dce506e9dfcdf56c34e279eb1c578827 SHA256 c8e5c6b27d32098203709aa898f024b93de590b3a337682252a66cff5b100be5
+AUX namd-2.8-ldflags.patch 1735 RMD160 130707ed9c3b91ab069af350d7a5e703515287f6 SHA1 b07e95a2efe999102384da7e99ede609eac3ee14 SHA256 48ea2c9195001c537e013238950a53910c19705f8d4d9e5db9988e5f3fb73ae5
 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_2.7b2_Source.tar.gz 9094631 RMD160 ec2c46f6cdb582dca73ebdbd894a9827f2e276d9 SHA1 0acab2a3bb6fca67b767f02bf7d2d2045ce6c3b9 SHA256 5675eb08534a6e4ea7a59e52e949991b3ba42abd78b45a46976ac3d7ed3b8d67
-EBUILD namd-2.7_beta3.ebuild 2996 RMD160 a63b37e03be81128dcc411503bec610d73f5b828 SHA1 613157a497f34edb47733082afe0b53b221aad1d SHA256 e25afb54ca065f0657683088e9dd60543939808f95a22298c0caf71a58637b6d
+DIST NAMD_2.8_Source.tar.gz 8451502 RMD160 9a3e4122b29fecc273f56feb714681743d494674 SHA1 dcc7124665c44bfce7c4460415c854be97098233 SHA256 729e69c2a60866bc3c9e91c0266238dd8e6fad135693913e06853289be90a4cb
+EBUILD namd-2.8.ebuild 2988 RMD160 7104c858037aea16e52e51b4545d4029c81b7d4b SHA1 9f5b6723bdde5ef634c996fde5cdcc05f130ffeb SHA256 ab65d05d8b60431e8187204aeb3970293588a3f8b8c7ba92b71f2271372113c6
 MISC ChangeLog 2797 RMD160 050da7ba2120061612df6321b0ffd2e49c1ae9e6 SHA1 06d5dc422168a91e935ebd7d5596f4a474ce0c53 SHA256 05c0e8e730d8ba7cebcd8bb0435aa8980e686b908713cc340c222d0455ad8421
 MISC metadata.xml 282 RMD160 539a53475b01291eadb86c8c53a0fbc02b4a34d4 SHA1 7f42dcea44641b8a77ab9644791344ec6ed6c327 SHA256 3c1785eb4ab63774ed3a6b1bddd602ef24cd6795f690bb3289d5a980bca06349
diff --git a/sci-chemistry/namd/files/namd-2.8-gentoo.patch b/sci-chemistry/namd/files/namd-2.8-gentoo.patch
new file mode 100644
index 0000000..c4f2e0a
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-2.8-gentoo.patch
@@ -0,0 +1,120 @@
+diff -ur NAMD_2.8_Source.orig/Make.charm NAMD_2.8_Source/Make.charm
+--- NAMD_2.8_Source.orig/Make.charm	2011-07-30 13:11:21.052330641 -0500
++++ NAMD_2.8_Source/Make.charm	2011-07-30 13:13:16.412798831 -0500
+@@ -2,5 +2,5 @@
+ # The config script will override this setting if there is a directory
+ # called charm-6.3.2 or charm in the NAMD base directory.
+ 
+-CHARMBASE = /Projects/namd2/charm-6.3.2
++CHARMBASE = /usr/include/charm-6.2.1
+ 
+Only in NAMD_2.8_Source: Make.charm.~1~
+diff -ur NAMD_2.8_Source.orig/Makefile NAMD_2.8_Source/Makefile
+--- NAMD_2.8_Source.orig/Makefile	2011-07-30 13:11:21.052330641 -0500
++++ NAMD_2.8_Source/Makefile	2011-07-30 13:15:48.003410162 -0500
+@@ -323,10 +323,10 @@
+ 	$(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)
+@@ -346,7 +346,7 @@
+ 
+ # 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
+@@ -378,16 +378,9 @@
+ 	$(EXTRALINKLIBS) \
+ 	-lm -o namd2
+ 
+-charmrun: $(CHARM)/bin/charmrun # XXX
+-	$(COPY) $(CHARM)/bin/charmrun $@
+-
+ $(LIBCUDARTSO):
+ 	$(COPY) $(CUDASODIR)/$(LIBCUDARTSO) $@;
+ 
+-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 \
+@@ -410,9 +403,6 @@
+ 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
+ 
+@@ -630,9 +620,7 @@
+ 
+ DOC_FILES = README.txt announce.txt license.txt notes.txt
+ 
+-RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb psfgen charmrun namd2
+-
+-WINDOWS_RELEASE_FILES = $(LIBCUDARTSO) $(WINDOWSBINARIES) $(TCLDLL)
++RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb psfgen namd2
+ 
+ release: all
+ 	$(ECHO) Creating release $(RELEASE_DIR_NAME)
+@@ -643,17 +631,9 @@
+ 	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 -ur NAMD_2.8_Source.orig/arch/Linux-x86_64.fftw NAMD_2.8_Source/arch/Linux-x86_64.fftw
+--- NAMD_2.8_Source.orig/arch/Linux-x86_64.fftw	2011-07-30 13:11:21.052330641 -0500
++++ NAMD_2.8_Source/arch/Linux-x86_64.fftw	2011-07-30 13:12:25.242589102 -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) $(FFTFLAGS)
+ 
+diff -ur NAMD_2.8_Source.orig/arch/Linux-x86_64.tcl NAMD_2.8_Source/arch/Linux-x86_64.tcl
+--- NAMD_2.8_Source.orig/arch/Linux-x86_64.tcl	2011-07-30 13:11:21.052330641 -0500
++++ NAMD_2.8_Source/arch/Linux-x86_64.tcl	2011-07-30 13:12:25.242589102 -0500
+@@ -1,7 +1,7 @@
+ 
+-TCLDIR=/Projects/namd2/tcl/linux-x86_64
++TCLDIR=/usr
+ TCLINCL=-I$(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/files/namd-2.8-ldflags.patch b/sci-chemistry/namd/files/namd-2.8-ldflags.patch
new file mode 100644
index 0000000..272590d
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-2.8-ldflags.patch
@@ -0,0 +1,42 @@
+diff -ur NAMD_2.8_Source.orig/Makefile NAMD_2.8_Source/Makefile
+--- NAMD_2.8_Source.orig/Makefile	2011-07-30 13:17:02.513705293 -0500
++++ NAMD_2.8_Source/Makefile	2011-07-30 13:18:03.363943762 -0500
+@@ -362,7 +362,7 @@
+ 
+ namd2:	$(INCDIR) $(DSTDIR) $(OBJS) $(LIBS)
+ 	$(MAKEBUILDINFO)
+-	$(CHARMC) -verbose -ld++-option \
++	$(CHARMC) $(LDFLAGS) -verbose -ld++-option \
+ 	"$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \
+ 	-module NeighborLB -module HybridLB -module RefineLB -module GreedyLB -language charm++ \
+ 	$(BUILDINFO).o \
+@@ -404,7 +404,7 @@
+ 	$(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe
+ 
+ psfgen:	$(DSTDIR) $(SBOBJS) $(PLUGINOBJS)
+-	$(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
++	$(CC) $(SBCFLAGS) $(LDFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
+ 
+ psfgen.exe:	$(DSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL)
+ 	$(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
+@@ -413,17 +413,17 @@
+ 	$(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 $@
+ 
+ flipbinpdb:	$(SRCDIR)/flipbinpdb.c
+-	$(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipbinpdb.c || \
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipbinpdb.c || \
+ 	echo "#!/bin/sh\necho unavailable on this platform" > $@; \
+ 	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
diff --git a/sci-chemistry/namd/namd-2.7_beta3.ebuild b/sci-chemistry/namd/namd-2.8.ebuild
index 2ef08e4..b8d8d2b 100644
--- a/sci-chemistry/namd/namd-2.7_beta3.ebuild
+++ b/sci-chemistry/namd/namd-2.8.ebuild
@@ -9,7 +9,7 @@ LICENSE="namd"
 HOMEPAGE="http://www.ks.uiuc.edu/Research/namd/"
 
 MY_PN="NAMD"
-MY_PV="2.7b2"
+MY_PV="2.8"
 
 SRC_URI="${MY_PN}_${MY_PV}_Source.tar.gz"
 
@@ -51,10 +51,10 @@ src_unpack() {
 
 	# apply a few small fixes to make NAMD compile and
 	# link to the proper libraries
-	epatch "${FILESDIR}"/namd-2.7_beta2-gentoo.patch
-	epatch "${FILESDIR}"/namd-2.7-ldflags.patch
+	epatch "${FILESDIR}"/namd-2.8-gentoo.patch
+	epatch "${FILESDIR}"/namd-2.8-ldflags.patch
 	epatch "${FILESDIR}"/namd-2.7-iml-dec.patch
-	sed -e "s:charm-6.1.3:charm-${CHARM_VERSION}:" \
+	sed -e "s:charm-6.2.1:charm-${CHARM_VERSION}:" \
 		Make.charm || \
 		die