From 0fb71e0215ed52863e462cccef73c01aff44d43d Mon Sep 17 00:00:00 2001
From: V3n3RiX <venerix@redcorelinux.org>
Date: Mon, 18 Dec 2017 15:11:02 +0000
Subject: gentoo resync : 18.12.2017

---
 sci-chemistry/namd/files/namd-2.10-gentoo.patch |   2 +-
 sci-chemistry/namd/files/namd-2.9-gentoo.patch  | 151 ------------------------
 2 files changed, 1 insertion(+), 152 deletions(-)
 delete mode 100644 sci-chemistry/namd/files/namd-2.9-gentoo.patch

(limited to 'sci-chemistry/namd/files')

diff --git a/sci-chemistry/namd/files/namd-2.10-gentoo.patch b/sci-chemistry/namd/files/namd-2.10-gentoo.patch
index e578c131c36d..ffef6dc3ad68 100644
--- a/sci-chemistry/namd/files/namd-2.10-gentoo.patch
+++ b/sci-chemistry/namd/files/namd-2.10-gentoo.patch
@@ -22,7 +22,7 @@ diff -Naur NAMD_2.10_Source.orig/arch/Linux-x86_64.tcl NAMD_2.10_Source/arch/Lin
  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
++#TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl -lpthread
  TCLFLAGS=-DNAMD_TCL
  TCL=$(TCLINCL) $(TCLFLAGS)
  
diff --git a/sci-chemistry/namd/files/namd-2.9-gentoo.patch b/sci-chemistry/namd/files/namd-2.9-gentoo.patch
deleted file mode 100644
index 583cc52645df..000000000000
--- a/sci-chemistry/namd/files/namd-2.9-gentoo.patch
+++ /dev/null
@@ -1,151 +0,0 @@
-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)
- 
-- 
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