proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

15 files changed, 1091 insertions, 0 deletions

diff --git a/sci-chemistry/namd/Manifest b/sci-chemistry/namd/Manifest
new file mode 100644
index 000000000000..80b19cddaea7
--- /dev/null
+++ b/sci-chemistry/namd/Manifest
@@ -0,0 +1,2 @@
+DIST NAMD_2.10_Source.tar.gz 9200234 SHA256 a5282c172524c2fbe6b9ba56f2de8c84f1093405c914ffbc70442dd0dd4e4289 SHA512 3712a03841fad76c502ac4e41469162ff78e6152560d0f6855d61d2b5583241a661e2a3e7446029b56a6f6f1100f25cb51b2c3df6571542397961d3bb625bc92 WHIRLPOOL b97e47c1d73d505620c26a2eca2e2e91807ebeff19e8820d9be7ea6ddd84c59cd5839846a18a2615ae993a1a6fc22b90e5080cf9d8a72aa412f6b81354e0f284
+DIST NAMD_2.9_Source.tar.gz 8814042 SHA256 9ba6a1f87d4600a62847728d7c223295be214f9a72b5bb62552f74d644108424 SHA512 0644814a2799b560d9dcf807ba0047325bc9f0a26e3831b0465d95180784f038d69595e036daac85d59cd919c92d11a0343031975d99deb1fa3052c8a649bdd6 WHIRLPOOL 5494ccb2ee2f2792fe52ad7dcfe6da9d11453f0a9b0859d30698dea56b00d92fae73465967f82bd708abee5cd4ff50b0a6ffde86451e859e2f515af203e09286
diff --git a/sci-chemistry/namd/files/namd-2.10-gentoo.patch b/sci-chemistry/namd/files/namd-2.10-gentoo.patch
new file mode 100644
index 000000000000..e578c131c36d
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-2.10-gentoo.patch
@@ -0,0 +1,124 @@
+diff -Naur NAMD_2.10_Source.orig/arch/Linux-x86_64.fftw NAMD_2.10_Source/arch/Linux-x86_64.fftw
+--- NAMD_2.10_Source.orig/arch/Linux-x86_64.fftw	2015-03-06 17:53:44.170416075 -0700
++++ NAMD_2.10_Source/arch/Linux-x86_64.fftw	2015-03-06 17:54:46.641162629 -0700
+@@ -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) $(FFTFLAGS)
+ 
+diff -Naur NAMD_2.10_Source.orig/arch/Linux-x86_64.tcl NAMD_2.10_Source/arch/Linux-x86_64.tcl
+--- NAMD_2.10_Source.orig/arch/Linux-x86_64.tcl	2015-03-06 17:53:44.170416075 -0700
++++ NAMD_2.10_Source/arch/Linux-x86_64.tcl	2015-03-06 17:54:46.641162629 -0700
+@@ -1,9 +1,9 @@
+ 
+ #TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64
+-TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64-threaded
++TCLDIR=/usr
+ TCLINCL=-I$(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 -Naur NAMD_2.10_Source.orig/Makefile NAMD_2.10_Source/Makefile
+--- NAMD_2.10_Source.orig/Makefile	2015-03-06 17:53:44.170416075 -0700
++++ NAMD_2.10_Source/Makefile	2015-03-06 18:01:32.645966590 -0700
+@@ -389,10 +389,10 @@
+ 	$(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 -module CkMulticast
+ #CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB
+ #CHARM_MODULES = -module msa -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB
+@@ -418,7 +418,7 @@
+ 
+ # Add new executables here.
+ 
+-BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb charmrun
++BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb
+ 
+ # This should be rebuilt at every compile, but not on Win32.
+ BUILDINFO = $(DSTDIR)/buildinfo
+@@ -434,7 +434,7 @@
+ 
+ namd2:	$(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS)
+ 	$(MAKEBUILDINFO)
+-	$(CHARMC) -verbose -ld++-option \
++	$(CHARMC) $(LDFLAGS) -verbose -ld++-option \
+ 	'$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS) $(CXXMICOPTS)' \
+ 	"$(CHARM_MODULES)" -language charm++ \
+ 	$(BUILDINFO).o \
+@@ -484,11 +484,8 @@
+ 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
+@@ -506,7 +503,7 @@
+ 	$(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 $@
+ 
+@@ -516,7 +513,7 @@
+ 	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
+@@ -711,9 +708,7 @@
+ 
+ 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)
+@@ -724,17 +719,9 @@
+ 	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 --git a/sci-chemistry/namd/files/namd-2.6-gentoo.patch b/sci-chemistry/namd/files/namd-2.6-gentoo.patch
new file mode 100644
index 000000000000..9a71de8d3bd7
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-2.6-gentoo.patch
@@ -0,0 +1,107 @@
+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
new file mode 100644
index 000000000000..28a580e3113c
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-2.7-gentoo.patch
@@ -0,0 +1,117 @@
+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-iml-dec.patch b/sci-chemistry/namd/files/namd-2.7-iml-dec.patch
new file mode 100644
index 000000000000..e5ee3bd6c818
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-2.7-iml-dec.patch
@@ -0,0 +1,24 @@
+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-2.7-ldflags.patch b/sci-chemistry/namd/files/namd-2.7-ldflags.patch
new file mode 100644
index 000000000000..686eba83a2de
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-2.7-ldflags.patch
@@ -0,0 +1,41 @@
+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
new file mode 100644
index 000000000000..898d6b5d0980
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch
@@ -0,0 +1,126 @@
+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-2.9-gentoo.patch b/sci-chemistry/namd/files/namd-2.9-gentoo.patch
new file mode 100644
index 000000000000..583cc52645df
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-2.9-gentoo.patch
@@ -0,0 +1,151 @@
+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/files/namd-barrier-fix-gentoo.patch b/sci-chemistry/namd/files/namd-barrier-fix-gentoo.patch
new file mode 100644
index 000000000000..40e8e68b5ba3
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-barrier-fix-gentoo.patch
@@ -0,0 +1,61 @@
+# 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
new file mode 100644
index 000000000000..731ea2337e91
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-fftw-lib-gentoo.patch
@@ -0,0 +1,15 @@
+# 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
new file mode 100644
index 000000000000..4ee5822ccb8f
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-makefile-gentoo.patch
@@ -0,0 +1,88 @@
+# 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 $(RELEASE_FILES)
+ 
+ winrelease: winall
diff --git a/sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch b/sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch
new file mode 100644
index 000000000000..0e6f0dd337e5
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch
@@ -0,0 +1,16 @@
+# adjust paths for proper linking to tcl libs 
+
+--- NAMD_2.6b1_Source/arch/Linux-i686.tcl	2004-10-27 21:40:55.000000000 +0000
++++ NAMD_2.6b1_Source_patched/arch/Linux-i686.tcl	2005-09-14 20:50:14.000000000 +0000
+@@ -1,8 +1,8 @@
+ 
+-TCLDIR=/Projects/namd2/tcl/linux
++#TCLDIR=/Projects/namd2/tcl/linux
+ #TCLDIR=$(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)
+ 
diff --git a/sci-chemistry/namd/metadata.xml b/sci-chemistry/namd/metadata.xml
new file mode 100644
index 000000000000..c73650100bed
--- /dev/null
+++ b/sci-chemistry/namd/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-chemistry</herd>
+	<maintainer>
+		<email>nicolasbock@gentoo.org</email>
+		<name>Nicolas Bock</name>
+	</maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/namd/namd-2.10.ebuild b/sci-chemistry/namd/namd-2.10.ebuild
new file mode 100644
index 000000000000..05e3fd7275dd
--- /dev/null
+++ b/sci-chemistry/namd/namd-2.10.ebuild
@@ -0,0 +1,105 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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"
+
+RDEPEND="
+	>=sys-cluster/charm-6.5.1-r2
+	sci-libs/fftw:3.0
+	dev-lang/tcl:0="
+
+DEPEND="${RDEPEND}
+	app-shells/tcsh"
+
+NAMD_ARCH="Linux-x86_64-g++"
+
+NAMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD"
+
+S="${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 "${FILESDIR}"/namd-2.10-gentoo.patch
+	epatch "${FILESDIR}"/namd-2.7-iml-dec.patch
+	sed \
+		-e "/CHARMBASE =/s:= .*:= /usr/bin/charm-${CHARM_VERSION}:" \
+		-i Make.charm || die
+
+	# Remove charm distribution. We don't need it.
+	rm -f charm-*.tar
+
+	# proper compiler and cflags
+	sed \
+		-e "s/g++.*/$(tc-getCXX)/" \
+		-e "s/gcc.*/$(tc-getCC)/" \
+		-e "s/CXXOPTS = .*/CXXOPTS = ${CXXFLAGS} ${LDFLAGS}/" \
+		-e "s/COPTS = .*/COPTS = ${CFLAGS} ${LDFLAGS}/" \
+		-i arch/${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@/lib@/$(get_libdir)@g" -e '/FFTDIR=/s@=.*@=/usr@' -i arch/Linux-x86_64.fftw3 || die
+	sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.tcl || die
+}
+
+src_configure() {
+	# configure
+	./config ${NAMD_ARCH} --with-fftw3 --charm-arch . || die
+}
+
+src_compile() {
+	# build namd
+	cd "${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
+}
diff --git a/sci-chemistry/namd/namd-2.9-r1.ebuild b/sci-chemistry/namd/namd-2.9-r1.ebuild
new file mode 100644
index 000000000000..feeba40a7c45
--- /dev/null
+++ b/sci-chemistry/namd/namd-2.9-r1.ebuild
@@ -0,0 +1,105 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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"
+
+RDEPEND="
+	>=sys-cluster/charm-6.5.1-r2
+	sci-libs/fftw:3.0
+	dev-lang/tcl:0="
+
+DEPEND="${RDEPEND}
+	app-shells/tcsh"
+
+NAMD_ARCH="Linux-x86_64-g++"
+
+NAMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD"
+
+S="${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 = .*/CXXOPTS = ${CXXFLAGS} ${LDFLAGS}/" \
+		-e "s/COPTS = .*/COPTS = ${CFLAGS} ${LDFLAGS}/" \
+		-i arch/${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@/lib@/$(get_libdir)@g" -e '/FFTDIR=/s@=.*@=/usr@' -i arch/Linux-x86_64.fftw3 || die
+	sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.tcl || die
+}
+
+src_configure() {
+	# configure
+	./config ${NAMD_ARCH} --with-fftw3 --charm-arch . || die
+}
+
+src_compile() {
+	# build namd
+	cd "${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
+}