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

3 files changed, 304 insertions, 0 deletions

diff --git a/sci-chemistry/gamess/files/gamess-20110811.1.gentoo.patch b/sci-chemistry/gamess/files/gamess-20110811.1.gentoo.patch
new file mode 100644
index 000000000000..7bf5797bf513
--- /dev/null
+++ b/sci-chemistry/gamess/files/gamess-20110811.1.gentoo.patch
@@ -0,0 +1,263 @@
+diff -urN gamess.orig/comp gamess/comp
+--- gamess.orig/comp	2011-08-11 17:37:48.000000000 +0200
++++ gamess/comp	2011-10-11 15:17:23.349829478 +0200
+@@ -1444,7 +1444,7 @@
+ #   g77 does not support FORTRAN logical units above 99, or 128 bit math.
+ #
+    case g77:
+-   set OPT = '-O2'
++   set gentoo-OPT = '-O2'
+    if ($MODULE == ormas1) set OPT='-O2 -fno-move-all-movables' # RH9, g77 3.3
+    if ($MODULE == zheev)  set OPT='-O0'  # defensive compiling
+    if (($MODULE == qeigen) || ($MODULE == int2c)) then
+@@ -1474,7 +1474,7 @@
+ #      -std=legacy  suppresses warnings about use of f77 constructs.
+ #
+    case gfortran:
+-   set OPT='-O2'
++   set gentoo-OPT = '-O2'
+    if ($MODULE == zheev)  set OPT='-O0'  # defensive compiling
+    if ($MODULE == pcmcv2) set OPT='-O1'  # EFP+CPCM, ala Francois, v4.1.2
+    if (($MODULE == qeigen) || ($MODULE == int2c)) then
+@@ -1500,7 +1500,7 @@
+ #    optimizations in 32 bit mode, as a function of the ifort version.
+ #
+    case ifort:
+-   set OPT = '-O3'
++   set gentoo-OPT = '-O2'
+    if ($MODULE == delocl) set OPT='-O0'  # from Cheol
+    if ($MODULE == prpamm) set OPT='-O0'  # for exam13
+    if ($MODULE == zheev)  set OPT='-O0'
+@@ -1617,7 +1617,7 @@
+    case gfortran:
+ #           -finit-real=<zero|inf|-inf|nan>  could be interesting debug opt
+ #           -fno-automatic forces static storage of all local variables
+-      set OPT='-O2'
++      set gentoo-OPT = '-O2'
+       if (".$GMS_DEBUG_FLAGS" != .) set OPT="$GMS_DEBUG_FLAGS"
+       if ($MODULE == zheev)  set OPT='-O0'  # defensive compiling
+       if (($MODULE == qeigen) || ($MODULE == int2c)) then
+@@ -1648,7 +1648,7 @@
+ #     -WB means warn but don't fail on out-of-bounds array references
+ #     -ftz flushes underflow results to zero
+ #
+-      set OPT = '-O2'
++      set gentoo-OPT = '-O2'
+       if (".$GMS_DEBUG_FLAGS" != .) set OPT="$GMS_DEBUG_FLAGS"
+ #       alas, I'm so tired of hearing about so many versions failing to
+ #       diagonalize, that this time critical code is run w/o optimization.
+diff -urN gamess.orig/compall gamess/compall
+--- gamess.orig/compall	2011-05-17 22:53:33.000000000 +0200
++++ gamess/compall	2011-10-11 12:13:30.041087251 +0200
+@@ -84,12 +84,11 @@
+    endif
+ endif
+ if ($TARGET == linux32)      set extraflags='-DLINUX32'
+-if ($TARGET == linux64)      then
++if ($TARGET == linux64) then
++	set chip=`uname -m`
+ #      Ubuntu uses the non-standard -m flag, its -p replies "unknown"
+-                         set chip=`uname -p`
+-   if ($chip == unknown) set chip=`uname -m`
+-   if ($chip == x86_64) set extraflags='-DLINUX64 -m64'
+-   if ($chip == ia64)   set extraflags='-DLINUX64'  # this always 64 bits
++   	if ($chip == x86_64) set extraflags='-DLINUX64 -m64'
++   	if ($chip == ia64)   set extraflags='-DLINUX64'  # this always 64 bits
+ endif
+ if ($TARGET == mac32)        set extraflags='-DLINUX32'
+ if ($TARGET == mac64)    set extraflags='-DLINUX64 -m64 -I/usr/include/malloc'
+diff -urN gamess.orig/ddi/compddi gamess/ddi/compddi
+--- gamess.orig/ddi/compddi	2011-02-15 21:31:30.000000000 +0100
++++ gamess/ddi/compddi	2011-10-11 12:23:45.513796580 +0200
+@@ -634,7 +634,7 @@
+ 
+      set FORTRAN=$GMS_FORTRAN   # might be g77, gfortran, ifort, pgf77, f2c
+ 
+-     set CC = 'gcc'
++     set gentoo-CC = 'gcc'
+      set CFLAGS = "-DLINUX -O3 -fstrict-aliasing -I./"
+      set CLIBS  = "-lpthread"
+ 
+@@ -687,7 +687,7 @@
+                              set ARCH='-m64'
+      if (`uname -p` == ia64) set ARCH=''
+ 
+-     set CC = 'gcc'
++     set gentoo-CC = 'gcc'
+      set CFLAGS = "-DLINUX $ARCH -O3 -fstrict-aliasing -I./"
+      set CLIBS  = "-lpthread"
+ 
+diff -urN gamess.orig/ddi/kickoff/ddikick.c gamess/ddi/kickoff/ddikick.c
+--- gamess.orig/ddi/kickoff/ddikick.c	2008-05-06 12:16:12.000000000 +0200
++++ gamess/ddi/kickoff/ddikick.c	2011-10-11 12:25:11.862714681 +0200
+@@ -105,7 +105,7 @@
+           remoteshell = argv[++i];
+        } else {
+           if((remoteshell = getenv("DDI_RSH")) == NULL) {
+-              remoteshell = (char *) strdup("rsh");
++              remoteshell = (char *) strdup("ssh");
+           }
+        }
+ 
+diff -urN gamess.orig/lked gamess/lked
+--- gamess.orig/lked	2011-08-11 17:41:02.000000000 +0200
++++ gamess/lked	2011-10-11 12:26:38.564634821 +0200
+@@ -53,7 +53,7 @@
+ #
+ #   3. optional Nuclear-Electronic Orbital method, using NEO code
+ #
+-set NEO=false
++set NEO=true
+ #
+ #   4. optional Nvidia/CUDA code, for closed shell SCF Fock construction 
+ #         see ~/gamess/libcchem/aaa.readme.1st for more information
+@@ -356,17 +356,17 @@
+    switch ($GMS_FORTRAN)
+      case g77:
+         set LDR='g77'
+-        set LDOPTS=' '  # add '-Wl,-M' to see load map
++        set gentoo-LDOPTS=' '  # add '-Wl,-M' to see load map
+         set FORTLIBS=' '
+         breaksw
+      case gfortran:
+         set LDR='gfortran'
+-        set LDOPTS=' '
++        set gentoo-LDOPTS=' '
+         set FORTLIBS=' '
+         breaksw
+      case ifort:
+         set LDR='ifort'
+-        set LDOPTS=' '  # add '-Wl,-M' to see load map
++        set gentoo-LDOPTS=' '  # add '-Wl,-M' to see load map
+         set FORTLIBS='-Vaxlib'
+         breaksw
+      case pgf77:
+@@ -376,7 +376,7 @@
+         breaksw
+      case f2c:
+         set LDR='gcc'
+-        set LDOPTS=' '
++        set gentoo-LDOPTS=' '
+         set FORTLIBS='-lf2c -lm'
+         breaksw
+      default:
+@@ -427,12 +427,7 @@
+       #     Otherwise, attempt a link against shared object libs.
+       #     See the 64 bit Atlas below for a way to fix the linker's
+       #     not being able to locate -lf77blas, if that happens.
+-      if (-e $GMS_MATHLIB_PATH/libf77blas.a) then
+-         set MATHLIBS="$GMS_MATHLIB_PATH/libf77blas.a"
+-         set MATHLIBS="$MATHLIBS $GMS_MATHLIB_PATH/libatlas.a"
+-      else
+-         set MATHLIBS="-L$GMS_MATHLIB_PATH -lf77blas -latlas"
+-      endif
++      set MATHLIBS=`${PKG_CONFIG} --libs blas`
+       set BLAS=' '
+       breaksw
+ 
+@@ -466,12 +461,12 @@
+    switch ($GMS_FORTRAN)
+       case gfortran:
+          set LDR='gfortran'
+-         set LDOPTS=' '
++         set gentoo-LDOPTS=' '
+          set FORTLIBS=' '
+          breaksw
+       case ifort:
+          set LDR='ifort'
+-         set LDOPTS='-i8'  # -Wl,-M generates a load map
++         set gentoo-LDOPTS=' '  # -Wl,-M generates a load map
+ #            this auxiliary library seems to have disappeared in ifort 10
+          set FORTLIBS=' '
+          if($GMS_IFORT_VERNO < 10) set FORTLIBS='-Vaxlib'
+@@ -556,12 +551,7 @@
+       #          ln -s liblapack_atlas.so.3.0 liblapack.so
+       #          ln -s liblapack.so.3.0       liblapack.so
+       #     It is strange the RPM's don't do these soft links for us.
+-      if (-e $GMS_MATHLIB_PATH/libf77blas.a) then
+-         set MATHLIBS="$GMS_MATHLIB_PATH/libf77blas.a"
+-         set MATHLIBS="$MATHLIBS $GMS_MATHLIB_PATH/libatlas.a"
+-      else
+-         set MATHLIBS="-L$GMS_MATHLIB_PATH -lf77blas -latlas"
+-      endif
++      set MATHLIBS=`${PKG_CONFIG} --libs blas`
+       set BLAS=' '
+       breaksw
+ 
+diff -urN gamess.orig/runall gamess/runall
+--- gamess.orig/runall	2009-02-28 00:57:18.000000000 +0100
++++ gamess/runall	2011-10-11 12:27:32.195586568 +0200
+@@ -10,7 +10,6 @@
+ #
+ #  Only the following two lines need to be customized:
+ #
+-chdir /u1/mike/gamess
+ set VERNO=00
+ #
+ #  Loop over all Ntest jobs supplied with GAMESS
+@@ -27,7 +26,7 @@
+      gms -v $VERNO -q ti -l exam$NUM.log exam$NUM
+      sleep 5
+   else
+-     ./rungms exam$NUM $VERNO 1  >&  exam$NUM.log
++     rungms exam$NUM $VERNO 1  >&  exam$NUM.log
+   endif
+   @ i++
+ end
+diff -urN gamess.orig/rungms gamess/rungms
+--- gamess.orig/rungms	2011-08-04 21:03:11.000000000 +0200
++++ gamess/rungms	2011-10-11 12:30:05.244448126 +0200
+@@ -55,7 +55,7 @@
+ #       one for LoadLeveler "ll-gms" on the IBM SP line.
+ #
+ set TARGET=sockets
+-set SCR=/scr/$USER
++set SCR=`pwd`
+ #
+ set JOB=$1      # name of the input file xxx.inp, give only the xxx part
+ set VERNO=$2    # revision number of the executable created by 'lked' step
+@@ -144,7 +144,7 @@
+ #     used by the NEO method.  See NEO's documentation for more details.
+ #
+ set echo
+-setenv AUXDATA ~mike/gamess/auxdata
++setenv AUXDATA /usr/share/gamess
+ setenv  EXTBAS /dev/null
+ setenv  NUCBAS /dev/null
+ setenv  POSBAS /dev/null
+@@ -153,12 +153,12 @@
+ setenv MCPPATH $AUXDATA/MCP
+ setenv BASPATH $AUXDATA/BASES
+ setenv QUANPOL $AUXDATA/QUANPOL
+-setenv  MAKEFP ~$USER/scr/$JOB.efp
+-setenv   GAMMA ~$USER/scr/$JOB.gamma
+-setenv TRAJECT ~$USER/scr/$JOB.trj
+-setenv RESTART ~$USER/scr/$JOB.rst
++setenv  MAKEFP $SCR/$JOB.efp
++setenv   GAMMA $SCR/$JOB.gamma
++setenv TRAJECT $SCR/$JOB.trj
++setenv RESTART $SCR/$JOB.rst
+ setenv   INPUT $SCR/$JOB.F05
+-setenv   PUNCH ~$USER/scr/$JOB.dat
++setenv   PUNCH $SCR/$JOB.dat
+ setenv  AOINTS $SCR/$JOB.F08
+ setenv  MOINTS $SCR/$JOB.F09
+ setenv DICTNRY $SCR/$JOB.F10
+@@ -347,7 +347,7 @@
+     if (null$4 == null) set ELGNAME=ELGFILE
+     set echo
+     setenv AOINTS   $SCR/$ELGNAME.F08
+-    setenv ELGDOS   ~$USER/scr/$JOB.ldos
++    setenv ELGDOS   $SCR/$JOB.ldos
+     setenv ELGDAT   $SCR/$ELGNAME.F71
+     setenv ELGPAR   $SCR/$ELGNAME.F72
+     setenv ELGCUT   $SCR/$ELGNAME.F74
+@@ -500,7 +500,7 @@
+    if ($os == AIX)     set GMSPATH=/u1/mike/gamess
+    if ($os == Darwin)  set GMSPATH=/Users/mike/desktop/gamess
+    if ($os == HP-UX)   set GMSPATH=/zr/mike/gamess
+-   if ($os == Linux)   set GMSPATH=/cu/mike/gamess
++   if ($os == Linux)   set GMSPATH=/usr/bin
+    if ($os == OSF1)    set GMSPATH=/in/mike/gamess
+    if ($os == SunOS)   set GMSPATH=/hf/mike/gamess
+ #       special compilation for Sun E450 uSPARC       (uname also= SunOS)
diff --git a/sci-chemistry/gamess/files/gamess-checktst.patch b/sci-chemistry/gamess/files/gamess-checktst.patch
new file mode 100644
index 000000000000..9fc1547e4540
--- /dev/null
+++ b/sci-chemistry/gamess/files/gamess-checktst.patch
@@ -0,0 +1,21 @@
+--- gamess.orig/tools/checktst/checktst	2008-12-30 16:33:09.000000000 +0100
++++ gamess/tools/checktst/checktst	2011-10-11 22:06:26.019798622 +0200
+@@ -6,7 +6,6 @@
+ #
+ # Only the path name in the very next line needs to be customized.
+ #
+-set GMSPATH=~/gamess
+ 
+ # The Ntest outputs are assumed to be named exam01.log, exam02.log, ...
+ # but the user will be allowed to specify the directory containing them.
+@@ -66,8 +65,8 @@
+ setenv tolW 0.1
+ setenv tolX 0.00001
+ 
+-set script=$GMSPATH/tools/checktst/exam
+-setenv chkabs $GMSPATH/tools/checktst/chkabs
++set script=./exam
++setenv chkabs ./chkabs
+ 
+ #   If we don't see the message about GAMESS exiting normally,
+ #   then there is surely a mistake, and we want to focus the
diff --git a/sci-chemistry/gamess/files/gamess-qmmm-tinker-fix-idate.patch b/sci-chemistry/gamess/files/gamess-qmmm-tinker-fix-idate.patch
new file mode 100644
index 000000000000..34f291382d41
--- /dev/null
+++ b/sci-chemistry/gamess/files/gamess-qmmm-tinker-fix-idate.patch
@@ -0,0 +1,20 @@
+diff -urN gamess/tinker.orig/Libtad.f gamess/tinker/Libtad.f
+--- gamess/tinker.orig/Libtad.f	2010-05-12 21:41:56.000000000 +0400
++++ gamess/tinker/Libtad.f	2010-12-08 01:05:31.000000000 +0300
+@@ -1332,11 +1332,15 @@
+ c     and for Macintosh under Absoft Pro Fortran 5.0
+ c
+       integer hms(3)
++      integer tarray(3)
+       call itime (hms)
+       hour = hms(1)
+       minute = hms(2)
+       second = hms(3)
+-      call idate (month,day,year)
++      call idate (tarray)
++      month = tarray(1)
++      day = tarray(2)
++      year = tarray(3)
+ c
+ c     code for IBM RS/6000 under AIX appends an underscore
+ c