gentoo-overlay/sci-chemistry/namd/files/namd-2.7-gentoo.patch

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)