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-rw-r--r--sci-chemistry/namd/files/namd-2.6-gentoo.patch107
-rw-r--r--sci-chemistry/namd/files/namd-2.7-gentoo.patch117
-rw-r--r--sci-chemistry/namd/files/namd-2.7-ldflags.patch41
-rw-r--r--sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch126
-rw-r--r--sci-chemistry/namd/files/namd-barrier-fix-gentoo.patch61
-rw-r--r--sci-chemistry/namd/files/namd-fftw-lib-gentoo.patch15
-rw-r--r--sci-chemistry/namd/files/namd-makefile-gentoo.patch88
-rw-r--r--sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch16
8 files changed, 0 insertions, 571 deletions
diff --git a/sci-chemistry/namd/files/namd-2.6-gentoo.patch b/sci-chemistry/namd/files/namd-2.6-gentoo.patch
deleted file mode 100644
index 9a71de8d3bd7..000000000000
--- a/sci-chemistry/namd/files/namd-2.6-gentoo.patch
+++ /dev/null
@@ -1,107 +0,0 @@
-diff -Naur NAMD_2.6_Source/Makefile NAMD_2.6_Source.new/Makefile
---- NAMD_2.6_Source/Makefile 2006-08-30 00:19:25.000000000 -0400
-+++ NAMD_2.6_Source.new/Makefile 2006-09-19 15:56:17.000000000 -0400
-@@ -232,10 +232,10 @@
- $(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/charm-5.9 $(COPTD)CMK_OPTIMIZE=1
-+CHARMLIB = /usr/lib
-
- # Libraries we may have changed
- LIBS = $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL)
-@@ -255,7 +255,7 @@
-
- # 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
-@@ -284,11 +284,6 @@
- $(CHARMOPTS) \
- -lm -o namd2
-
--charmrun: $(CHARM)/bin/charmrun # XXX
-- $(COPY) $(CHARM)/bin/charmrun $@
--
--windowsbinaries: namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe
--
- namd2.exe: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS)
- $(MAKEBUILDINFO)
- $(CHARMC) -verbose \
-@@ -309,9 +304,6 @@
- charmd_faceless.exe:
- $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe
-
--charmrun.exe:
-- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe
--
- psfgen: $(DSTDIR) $(SBOBJS)
- $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
-
-@@ -571,9 +563,7 @@
-
- DOC_FILES = README.txt announce.txt license.txt notes.txt
-
--RELEASE_FILES = flipdcd flipbinpdb psfgen charmrun namd2
--
--WIN32_RELEASE_FILES = namd2.exe psfgen.exe charmrun.exe charmd.exe charmd_faceless.exe $(TCLDLL)
-+RELEASE_FILES = flipdcd flipbinpdb psfgen namd2
-
- release: all
- $(ECHO) Creating release $(RELEASE_DIR_NAME)
-@@ -582,17 +572,9 @@
- 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 -Naur NAMD_2.6_Source/arch/Linux-i686.fftw NAMD_2.6_Source.new/arch/Linux-i686.fftw
---- NAMD_2.6_Source/arch/Linux-i686.fftw 2004-02-20 17:38:36.000000000 -0500
-+++ NAMD_2.6_Source.new/arch/Linux-i686.fftw 2006-09-19 15:52:32.000000000 -0400
-@@ -1,7 +1,7 @@
-
--FFTDIR=/Projects/namd2/fftw/linux
--FFTINCL=-I$(FFTDIR)/include -I$(HOME)/fftw/include
--FFTLIB=-L$(FFTDIR)/lib -L$(HOME)/fftw/lib -lsrfftw -lsfftw
-+#FFTDIR=/Projects/namd2/fftw/linux
-+FFTINCL=-I/usr/include
-+FFTLIB=-L/usr/lib -lsrfftw -lsfftw
- FFTFLAGS=-DNAMD_FFTW
- FFT=$(FFTINCL) $(FFTFLAGS)
-
-diff -Naur NAMD_2.6_Source/arch/Linux-i686.tcl NAMD_2.6_Source.new/arch/Linux-i686.tcl
---- NAMD_2.6_Source/arch/Linux-i686.tcl 2004-10-27 17:40:55.000000000 -0400
-+++ NAMD_2.6_Source.new/arch/Linux-i686.tcl 2006-09-19 15:56:45.000000000 -0400
-@@ -1,8 +1,8 @@
-
--TCLDIR=/Projects/namd2/tcl/linux
-+#TCLDIR=/Projects/namd2/tcl/linux
- #TCLDIR=$(HOME)/tcl/cray-xt3
--TCLINCL=-I$(TCLDIR)/include -I$(HOME)/tcl/include
--TCLLIB=-L$(TCLDIR)/lib -L$(HOME)/tcl/lib -ltcl8.3 -ldl
-+TCLINCL=-I/usr/include
-+TCLLIB=-L/usr/lib -L$(HOME)/tcl/lib -ltcl -ldl
- TCLFLAGS=-DNAMD_TCL -DUSE_NON_CONST
- TCL=$(TCLINCL) $(TCLFLAGS)
-
diff --git a/sci-chemistry/namd/files/namd-2.7-gentoo.patch b/sci-chemistry/namd/files/namd-2.7-gentoo.patch
deleted file mode 100644
index 28a580e3113c..000000000000
--- a/sci-chemistry/namd/files/namd-2.7-gentoo.patch
+++ /dev/null
@@ -1,117 +0,0 @@
-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 -ltcl -ldl
- TCLFLAGS=-DNAMD_TCL
- TCL=$(TCLINCL) $(TCLFLAGS)
-
diff --git a/sci-chemistry/namd/files/namd-2.7-ldflags.patch b/sci-chemistry/namd/files/namd-2.7-ldflags.patch
deleted file mode 100644
index 686eba83a2de..000000000000
--- a/sci-chemistry/namd/files/namd-2.7-ldflags.patch
+++ /dev/null
@@ -1,41 +0,0 @@
-diff --git a/Makefile b/Makefile
-index fd20f12..0821bed 100644
---- a/Makefile
-+++ b/Makefile
-@@ -339,7 +339,7 @@ all: $(BINARIES) $(LIBCUDARTSO)
-
- 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 commlib -language charm++ \
- $(BUILDINFO).o \
-@@ -394,23 +394,23 @@ charmrun.exe:
- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.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
-
- 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 $(SRCDIR)/dumpdcd.c
diff --git a/sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch b/sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch
deleted file mode 100644
index 898d6b5d0980..000000000000
--- a/sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch
+++ /dev/null
@@ -1,126 +0,0 @@
-diff -ur NAMD_2.7b2_Source.orig//arch/Linux-x86_64.fftw NAMD_2.7b2_Source//arch/Linux-x86_64.fftw
---- NAMD_2.7b2_Source.orig//arch/Linux-x86_64.fftw 2010-04-23 14:40:54.566510874 -0500
-+++ NAMD_2.7b2_Source//arch/Linux-x86_64.fftw 2010-04-23 14:41:08.106528893 -0500
-@@ -1,7 +1,7 @@
-
--FFTDIR=/Projects/namd2/fftw/linux-x86_64
-+FFTDIR=/usr
- FFTINCL=-I$(FFTDIR)/include
--FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw
-+FFTLIB=-L$(FFTDIR)/gentoo-libdir -lsrfftw -lsfftw
- FFTFLAGS=-DNAMD_FFTW
- FFT=$(FFTINCL) $(FFTFLAGS)
-
-diff -ur NAMD_2.7b2_Source.orig//arch/Linux-x86_64.tcl NAMD_2.7b2_Source//arch/Linux-x86_64.tcl
---- NAMD_2.7b2_Source.orig//arch/Linux-x86_64.tcl 2010-04-23 14:40:54.566510874 -0500
-+++ NAMD_2.7b2_Source//arch/Linux-x86_64.tcl 2010-04-23 14:41:08.106528893 -0500
-@@ -1,7 +1,7 @@
-
--TCLDIR=/Projects/namd2/tcl/linux-x86_64
-+TCLDIR=/usr
- TCLINCL=-I$(TCLDIR)/include
--TCLLIB=-L$(TCLDIR)/lib -ltcl8.3 -ldl
-+TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl
- TCLFLAGS=-DNAMD_TCL
- TCL=$(TCLINCL) $(TCLFLAGS)
-
-diff -ur NAMD_2.7b2_Source.orig//Make.charm NAMD_2.7b2_Source//Make.charm
---- NAMD_2.7b2_Source.orig//Make.charm 2010-04-23 14:40:54.556517020 -0500
-+++ NAMD_2.7b2_Source//Make.charm 2010-04-23 14:42:16.026530011 -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-6.1.3
-+CHARMBASE = /usr/include/charm-6.1.3
-
-Only in NAMD_2.7b2_Source/: Make.charm.~1~
-Only in NAMD_2.7b2_Source/: Make.charm.porig
-diff -ur NAMD_2.7b2_Source.orig//Makefile NAMD_2.7b2_Source//Makefile
---- NAMD_2.7b2_Source.orig//Makefile 2010-04-23 14:40:54.556517020 -0500
-+++ NAMD_2.7b2_Source//Makefile 2010-04-23 14:42:59.446523306 -0500
-@@ -300,10 +300,10 @@
- $(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)
-@@ -323,7 +323,7 @@
-
- # 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
-@@ -354,9 +354,6 @@
- $(CHARMOPTS) \
- -lm -o namd2
-
--charmrun: $(CHARM)/bin/charmrun # XXX
-- $(COPY) $(CHARM)/bin/charmrun $@
--
- $(LIBCUDARTSO):
- if [ -r $(CUDADIR)/lib64/$(LIBCUDARTSO) ]; then \
- $(COPY) $(CUDADIR)/lib64/$(LIBCUDARTSO) $@; \
-@@ -364,10 +361,6 @@
- $(COPY) $(CUDADIR)/lib/$(LIBCUDARTSO) $@; \
- fi
-
--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 \
-@@ -390,9 +383,6 @@
- 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
-
-@@ -716,9 +706,7 @@
-
- DOC_FILES = README.txt announce.txt license.txt notes.txt
-
--RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb psfgen charmrun namd2
--
--WINDOWS_RELEASE_FILES = $(WINDOWSBINARIES) $(TCLDLL)
-+RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb psfgen namd2
-
- release: all
- $(ECHO) Creating release $(RELEASE_DIR_NAME)
-@@ -727,17 +715,9 @@
- 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
-Only in NAMD_2.7b2_Source/: Makefile.porig
diff --git a/sci-chemistry/namd/files/namd-barrier-fix-gentoo.patch b/sci-chemistry/namd/files/namd-barrier-fix-gentoo.patch
deleted file mode 100644
index 40e8e68b5ba3..000000000000
--- a/sci-chemistry/namd/files/namd-barrier-fix-gentoo.patch
+++ /dev/null
@@ -1,61 +0,0 @@
-# patch to fix compile error on gcc-3.x
-
-diff -Naur NAMD_2.6b1_Source/src/BackEnd.C NAMD_2.6b1_Source_patched/src/BackEnd.C
---- NAMD_2.6b1_Source/src/BackEnd.C 2003-12-31 06:37:15.000000000 +0000
-+++ NAMD_2.6b1_Source_patched/src/BackEnd.C 2005-08-22 18:59:59.000000000 +0000
-@@ -162,7 +162,7 @@
- }
-
- // start QD and scheduler
--void BackEnd::barrier(void) {
-+void BackEnd::namd_barrier(void) {
- awaken();
- suspend();
- }
-diff -Naur NAMD_2.6b1_Source/src/BackEnd.h NAMD_2.6b1_Source_patched/src/BackEnd.h
---- NAMD_2.6b1_Source/src/BackEnd.h 2000-01-29 00:20:05.000000000 +0000
-+++ NAMD_2.6b1_Source_patched/src/BackEnd.h 2005-08-22 18:59:47.000000000 +0000
-@@ -17,7 +17,7 @@
-
- static void suspend(void); // Let message code run...
- static void awaken(void); // ...then return
-- static void barrier(void); // Let message code run, then return
-+ static void namd_barrier(void); // Let message code run, then return
- static void ExitSchedOn(int pe); // Tell a remote processor to stop
- // his scheduler
-
-diff -Naur NAMD_2.6b1_Source/src/ScriptTcl.C NAMD_2.6b1_Source_patched/src/ScriptTcl.C
---- NAMD_2.6b1_Source/src/ScriptTcl.C 2005-06-23 18:47:00.000000000 +0000
-+++ NAMD_2.6b1_Source_patched/src/ScriptTcl.C 2005-08-22 19:00:21.000000000 +0000
-@@ -56,7 +56,7 @@
- }
-
- void ScriptTcl::barrier() {
-- BackEnd::barrier();
-+ BackEnd::namd_barrier();
- }
-
- void ScriptTcl::initcheck() {
-diff -Naur NAMD_2.6b1_Source/src/main.C NAMD_2.6b1_Source_patched/src/main.C
---- NAMD_2.6b1_Source/src/main.C 2005-05-27 22:56:49.000000000 +0000
-+++ NAMD_2.6b1_Source_patched/src/main.C 2005-08-22 19:17:34.000000000 +0000
-@@ -67,7 +67,9 @@
-
- #ifndef NOHOSTNAME
- iout << iINFO <<
-- "Sending usage information to NAMD developers via UDP. Sent data is:\n"
-+ "Markus says: I don't want to send usage information \n"
-+ << endi;
-+ iout << iINFO << "to NAMD developers :) Data not sent is:\n"
- << endi;
-
- char sendbuf[TBSOFT_TRACK_MAXLEN];
-@@ -88,7 +90,7 @@
- sprintf(sendbuf, "1 %s %s %s %s %s %s %s",
- program, versionnum, platform, numcpus, miscinfo, host, user);
- iout << iINFO << sendbuf << "\n" << endi;
-- send_dgram(TBSOFT_TRACK_HOST, TBSOFT_TRACK_PORT, sendbuf, strlen(sendbuf));
-+ //send_dgram(TBSOFT_TRACK_HOST, TBSOFT_TRACK_PORT, sendbuf, strlen(sendbuf));
-
- #endif
- return 0;
diff --git a/sci-chemistry/namd/files/namd-fftw-lib-gentoo.patch b/sci-chemistry/namd/files/namd-fftw-lib-gentoo.patch
deleted file mode 100644
index 731ea2337e91..000000000000
--- a/sci-chemistry/namd/files/namd-fftw-lib-gentoo.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-# adjust paths for proper linking to fftw libs
-
---- NAMD_2.6b1_Source/arch/Linux-i686.fftw 2004-02-20 22:38:36.000000000 +0000
-+++ NAMD_2.6b1_Source_patched/arch/Linux-i686.fftw 2005-08-22 18:50:38.000000000 +0000
-@@ -1,7 +1,7 @@
-
--FFTDIR=/Projects/namd2/fftw/linux
--FFTINCL=-I$(FFTDIR)/include -I$(HOME)/fftw/include
--FFTLIB=-L$(FFTDIR)/lib -L$(HOME)/fftw/lib -lsrfftw -lsfftw
-+#FFTDIR=/Projects/namd2/fftw/linux
-+FFTINCL=-I/usr/include
-+FFTLIB=-L/usr/lib -lsrfftw -lsfftw
- FFTFLAGS=-DNAMD_FFTW
- FFT=$(FFTINCL) $(FFTFLAGS)
-
diff --git a/sci-chemistry/namd/files/namd-makefile-gentoo.patch b/sci-chemistry/namd/files/namd-makefile-gentoo.patch
deleted file mode 100644
index 4ee5822ccb8f..000000000000
--- a/sci-chemistry/namd/files/namd-makefile-gentoo.patch
+++ /dev/null
@@ -1,88 +0,0 @@
-# provide paths for charm++ provided includes/libraries/binaries
-
---- NAMD_2.6b1_Source-patched/Makefile 2005-07-22 18:50:58.000000000 +0000
-+++ NAMD_2.6b1_Source/Makefile 2005-09-30 02:28:35.000000000 +0000
-@@ -227,10 +227,10 @@
- $(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/charm-5.9 $(COPTD)CMK_OPTIMIZE=1
-+CHARMLIB = /usr/lib
-
- # Libraries we may have changed
- LIBS = $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL)
-@@ -250,7 +250,7 @@
-
- # 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
-@@ -279,10 +279,7 @@
- $(CHARMOPTS) \
- -lm -o namd2
-
--charmrun: $(CHARM)/bin/charmrun # XXX
-- $(COPY) $(CHARM)/bin/charmrun $@
--
--win32binaries: namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe
-+win32binaries: namd2.exe psfgen.exe charmd.exe charmd_faceless.exe
-
- namd2.exe: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS)
- $(MAKEBUILDINFO)
-@@ -304,9 +301,6 @@
- charmd_faceless.exe:
- $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe
-
--charmrun.exe:
-- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe
--
- psfgen: $(DSTDIR) $(SBOBJS)
- $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
-
-@@ -565,9 +559,9 @@
-
- DOC_FILES = README.txt announce.txt license.txt notes.txt
-
--RELEASE_FILES = namd2 psfgen charmrun flipdcd flipbinpdb
-+RELEASE_FILES = namd2 psfgen flipdcd flipbinpdb
-
--WIN32_RELEASE_FILES = namd2.exe psfgen.exe charmrun.exe charmd.exe charmd_faceless.exe $(TCLDLL)
-+WIN32_RELEASE_FILES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe $(TCLDLL)
-
- release: all
- $(ECHO) Creating release $(RELEASE_DIR_NAME)
-@@ -575,18 +569,18 @@
- cp $(RELEASE_FILES) $(RELEASE_DIR_NAME)
- for f in $(DOC_FILES); do cp .rootdir/$$f $(RELEASE_DIR_NAME); done
- cp -r .rootdir/lib $(RELEASE_DIR_NAME)
-- if [ -r $(CHARM)/bin/charmd ]; then \
-- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \
-+ if [ -r /usr/bin/charmd ]; then \
-+ $(COPY) /usr/bin/charmd $(RELEASE_DIR_NAME); \
- fi
-- if [ -r $(CHARM)/bin/charmd_faceless ]; then \
-- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \
-+ if [ -r /usr/bin/charmd_faceless ]; then \
-+ $(COPY) /usr/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
-- echo $(CHARM)
-+ echo /usr
-+ ls -l /usr/lib
-+ echo /usr
- file $(RELEASE_FILES)
-
- winrelease: winall
diff --git a/sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch b/sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch
deleted file mode 100644
index 0e6f0dd337e5..000000000000
--- a/sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-# adjust paths for proper linking to tcl libs
-
---- NAMD_2.6b1_Source/arch/Linux-i686.tcl 2004-10-27 21:40:55.000000000 +0000
-+++ NAMD_2.6b1_Source_patched/arch/Linux-i686.tcl 2005-09-14 20:50:14.000000000 +0000
-@@ -1,8 +1,8 @@
-
--TCLDIR=/Projects/namd2/tcl/linux
-+#TCLDIR=/Projects/namd2/tcl/linux
- #TCLDIR=$(HOME)/tcl/cray-xt3
--TCLINCL=-I$(TCLDIR)/include -I$(HOME)/tcl/include
--TCLLIB=-L$(TCLDIR)/lib -L$(HOME)/tcl/lib -ltcl8.3 -ldl
-+TCLINCL=-I/usr/include
-+TCLLIB=-L/usr/lib -L$(HOME)/tcl/lib -ltcl -ldl
- TCLFLAGS=-DNAMD_TCL -DUSE_NON_CONST
- TCL=$(TCLINCL) $(TCLFLAGS)
-