1 files changed, 105 insertions, 0 deletions
diff --git a/sci-chemistry/namd/files/namd-2.6-gentoo-amd64.patch b/sci-chemistry/namd/files/namd-2.6-gentoo-amd64.patch
new file mode 100644
index 0000000..9d65e51
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-2.6-gentoo-amd64.patch
@@ -0,0 +1,105 @@
+diff -aurN NAMD_2.6_Source-orig/Makefile NAMD_2.6_Source/Makefile
+--- NAMD_2.6_Source-orig/Makefile	2007-08-24 13:35:35.659265380 -0500
++++ NAMD_2.6_Source/Makefile	2007-08-24 13:42:09.933733803 -0500
+@@ -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-9999 $(COPTD)CMK_OPTIMIZE=1
++CHARMLIB = /usr/lib64
+ 
+ # 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 -aurN NAMD_2.6_Source-orig/arch/Linux-amd64.fftw NAMD_2.6_Source/arch/Linux-amd64.fftw
+--- NAMD_2.6_Source-orig/arch/Linux-amd64.fftw	2007-08-24 13:35:35.663265610 -0500
++++ NAMD_2.6_Source/arch/Linux-amd64.fftw	2007-08-24 13:43:45.623186828 -0500
+@@ -1,7 +1,6 @@
+ 
+-FFTDIR=/Projects/namd2/fftw/linux-amd64
+-FFTINCL=-I$(FFTDIR)/include -I$(HOME)/fftw/include
+-FFTLIB=-L$(FFTDIR)/lib -L$(HOME)/fftw/lib -lsrfftw -lsfftw
++FFTINCL=-I/usr/include 
++FFTLIB=-L/usr/lib64 -lsrfftw -lsfftw
+ FFTFLAGS=-DNAMD_FFTW
+ FFT=$(FFTINCL) $(FFTFLAGS)
+ 
+diff -aurN NAMD_2.6_Source-orig/arch/Linux-amd64.tcl NAMD_2.6_Source/arch/Linux-amd64.tcl
+--- NAMD_2.6_Source-orig/arch/Linux-amd64.tcl	2007-08-24 13:35:35.663265610 -0500
++++ NAMD_2.6_Source/arch/Linux-amd64.tcl	2007-08-24 13:46:44.921404457 -0500
+@@ -1,7 +1,6 @@
+ 
+-TCLDIR=/Projects/namd2/tcl/linux-amd64
+-TCLINCL=-I$(TCLDIR)/include -I$(HOME)/tcl/include
+-TCLLIB=-L$(TCLDIR)/lib -L$(HOME)/tcl/lib -ltcl8.3 -ldl
+-TCLFLAGS=-DNAMD_TCL
++TCLINCL=-I/usr/include 
++TCLLIB=-L/usr/lib64 -L$(HOME)/tcl/lib -ltcl -ldl
++TCLFLAGS=-DNAMD_TCL -DUSE_NON_CONST
+ TCL=$(TCLINCL) $(TCLFLAGS)
+