Merge branch 'release-4-5-patches'

diff --git a/acinclude.m4 b/acinclude.m4
index 8c5fb69f768be0e4daab6401240bafbd1e1e8bb5..f54eb9726c8da338601d26a306b3b91721a4da9d 100644 (file)
--- a/acinclude.m4
+++ b/acinclude.m4
@@ -483,6 +483,10 @@ case "${host_cpu}-${host_os}" in
     # use 8 segments (max 2Gb) instead of 1 (max 256Meg) by default.
     xLDFLAGS="$xLDFLAGS -bmaxdata:0x80000000"
     case "${gmxcpu}" in
+      power6*)
+        xCFLAGS="-O3 -qarch=pwr6 -qtune=pwr6 -qmaxmem=-1 -qstrict -qaltivec -qenablevmx -qvecnvol"
+        xFFLAGS="-O3 -qarch=pwr6 -qtune=pwr6 -qmaxmem=-1 -qhot -qstrict -qaltivec -qenablevmx -qvecnvol"
+        ;;
       power5*)
         xCFLAGS="-O3 -qarch=pwr5 -qtune=pwr5 -qmaxmem=16384"
         xFFLAGS="-O3 -Q -qarch=pwr5 -qtune=pwr5 -qmaxmem=16384 -qhot -qnoipa"

diff --git a/scripts/GMXRC.bash.cmakein b/scripts/GMXRC.bash.cmakein
index 52717cc5fb4c2175b159cc81c4d313445c966eca..45e44c5a049f7e3db4e3775bc31a479fb4504255 100644 (file)
--- a/scripts/GMXRC.bash.cmakein
+++ b/scripts/GMXRC.bash.cmakein
@@ -1,4 +1,4 @@
-# zsh configuration file for Gromacs
+# bash configuration file for Gromacs
 # First we remove old gromacs stuff from the paths
 # by selecting everything else.
 # This is not 100% necessary, but very useful when we
@@ -8,11 +8,7 @@
 tmppath=""
 for i in `echo $LD_LIBRARY_PATH | sed "s/:/ /g"`; do
   if test "$i" != "$GMXLDLIB"; then
-    if test "${tmppath}" == ""; then
-      tmppath=$i
-    else
-    tmppath=${tmppath}:$i
-  fi
+    tmppath="${i}${tmppath:+:}${tmppath}"
   fi
 done
 LD_LIBRARY_PATH=$tmppath
@@ -21,7 +17,7 @@ LD_LIBRARY_PATH=$tmppath
 tmppath=""
 for i in `echo $PKG_CONFIG_PATH | sed "s/:/ /g"`; do
   if test "$i" != "$GMXLDLIB/pkgconfig"; then
-    tmppath=${tmppath}:$i
+    tmppath="${i}${tmppath:+:}${tmppath}"
   fi
 done
 PKG_CONFIG_PATH=$tmppath
@@ -30,7 +26,7 @@ PKG_CONFIG_PATH=$tmppath
 tmppath=""
 for i in `echo $PATH | sed "s/:/ /g"`; do
   if test "$i" != "$GMXBIN"; then
-    tmppath=${tmppath}:$i
+    tmppath="${i}${tmppath:+:}${tmppath}"
   fi
 done
 PATH=$tmppath
@@ -39,12 +35,9 @@ PATH=$tmppath
 tmppath=""
 for i in `echo $MANPATH | sed "s/:/ /g"`; do
   if test "$i" != "$GMXMAN"; then
-    tmppath=${tmppath}:$i
+    tmppath="${i}${tmppath:+:}${tmppath}"
   fi
 done
-if test "$tmppath" == ""; then
-    tmppath=":"
-fi
 MANPATH=$tmppath
 
 ##########################################################
@@ -57,11 +50,11 @@ GMXLDLIB=@LIB_INSTALL_DIR@
 GMXMAN=@MAN_INSTALL_DIR@
 GMXDATA=@DATA_INSTALL_DIR@
        
-# NB: The variables already begin with ':' now, or are empty
-LD_LIBRARY_PATH=${GMXLDLIB}${LD_LIBRARY_PATH}
-PKG_CONFIG_PATH=${GMXLDLIB}/pkgconfig${PKG_CONFIG_PATH}
-PATH=${GMXBIN}${PATH}
-MANPATH=${GMXMAN}${MANPATH}
+LD_LIBRARY_PATH=${GMXLDLIB}${LD_LIBRARY_PATH:+:}${LD_LIBRARY_PATH}
+PKG_CONFIG_PATH=${GMXLDLIB}/pkgconfig${PKG_CONFIG_PATH:+:}${PKG_CONFIG_PATH}
+PATH=${GMXBIN}${PATH:+:}${PATH}
+#debian/ubuntu needs a : at the end
+MANPATH=${GMXMAN}:${MANPATH}
 
 # export should be separate, so /bin/sh understands it
 export GMXBIN GMXLDLIB GMXMAN GMXDATA LD_LIBRARY_PATH PATH MANPATH PKG_CONFIG_PATH

diff --git a/scripts/GMXRC.bash.in b/scripts/GMXRC.bash.in
index e0b69b472df1de5a6d34aac207f4f69bf11922f8..a4e8aa361e399702e8c10b8e35d0edf475d83db2 100644 (file)
--- a/scripts/GMXRC.bash.in
+++ b/scripts/GMXRC.bash.in
@@ -1,4 +1,4 @@
-# zsh configuration file for Gromacs
+# bash configuration file for Gromacs
 # First we remove old gromacs stuff from the paths
 # by selecting everything else.
 # This is not 100% necessary, but very useful when we
@@ -8,11 +8,7 @@
 tmppath=""
 for i in `echo $LD_LIBRARY_PATH | sed "s/:/ /g"`; do
   if test "$i" != "$GMXLDLIB"; then
-    if test "${tmppath}" == ""; then
-      tmppath=$i
-    else
-    tmppath=${tmppath}:$i
-  fi
+    tmppath="${i}${tmppath:+:}${tmppath}"
   fi
 done
 LD_LIBRARY_PATH=$tmppath
@@ -21,7 +17,7 @@ LD_LIBRARY_PATH=$tmppath
 tmppath=""
 for i in `echo $PKG_CONFIG_PATH | sed "s/:/ /g"`; do
   if test "$i" != "$GMXLDLIB/pkgconfig"; then
-    tmppath=${tmppath}:$i
+    tmppath="${i}${tmppath:+:}${tmppath}"
   fi
 done
 PKG_CONFIG_PATH=$tmppath
@@ -30,7 +26,7 @@ PKG_CONFIG_PATH=$tmppath
 tmppath=""
 for i in `echo $PATH | sed "s/:/ /g"`; do
   if test "$i" != "$GMXBIN"; then
-    tmppath=${tmppath}:$i
+    tmppath="${i}${tmppath:+:}${tmppath}"
   fi
 done
 PATH=$tmppath
@@ -39,12 +35,9 @@ PATH=$tmppath
 tmppath=""
 for i in `echo $MANPATH | sed "s/:/ /g"`; do
   if test "$i" != "$GMXMAN"; then
-    tmppath=${tmppath}:$i
+    tmppath="${i}${tmppath:+:}${tmppath}"
   fi
 done
-if test "$tmppath" == ""; then
-    tmppath=":"
-fi
 MANPATH=$tmppath
 
 ##########################################################
@@ -57,11 +50,11 @@ GMXLDLIB=@libdir@
 GMXMAN=@mandir@
 GMXDATA=@datadir@
        
-# NB: The variables already begin with ':' now, or are empty
-LD_LIBRARY_PATH=${GMXLDLIB}${LD_LIBRARY_PATH}
-PKG_CONFIG_PATH=${GMXLDLIB}/pkgconfig${PKG_CONFIG_PATH}
-PATH=${GMXBIN}${PATH}
-MANPATH=${GMXMAN}${MANPATH}
+LD_LIBRARY_PATH=${GMXLDLIB}${LD_LIBRARY_PATH:+:}${LD_LIBRARY_PATH}
+PKG_CONFIG_PATH=${GMXLDLIB}/pkgconfig${PKG_CONFIG_PATH:+:}${PKG_CONFIG_PATH}
+PATH=${GMXBIN}${PATH:+:}${PATH}
+#debian/ubuntu needs a : at the end
+MANPATH=${GMXMAN}:${MANPATH}
 
 # export should be separate, so /bin/sh understands it
 export GMXBIN GMXLDLIB GMXMAN GMXDATA LD_LIBRARY_PATH PATH MANPATH PKG_CONFIG_PATH

diff --git a/scripts/GMXRC.csh.cmakein b/scripts/GMXRC.csh.cmakein
index 0e18ba3dbe516b025bb8de4802daa7382c8e4744..328e0976b0967eb3bbdae4cda01d7152f54208eb 100644 (file)
--- a/scripts/GMXRC.csh.cmakein
+++ b/scripts/GMXRC.csh.cmakein
@@ -29,25 +29,40 @@ setenv LD_LIBRARY_PATH $tmppath
 # remove previous gromacs part from PKG_CONFIG_PATH
 set tmppath = ""
 foreach i ( `echo $PKG_CONFIG_PATH | sed "s/:/ /g"` )
-  if ( "$i" != "$GMXLDLIB/pkgconfig" ) set tmppath = "${tmppath}:$i"
+  if ( "$i" != "$GMXLDLIB/pkgconfig" ) then
+    if ("${tmppath}" == "") then
+      set tmppath = "$i"
+    else
+      set tmppath = "${tmppath}:$i"
+    endif
+  endif
 end
 setenv PKG_CONFIG_PATH $tmppath
 
 # remove gromacs stuff from binary path
 set tmppath = ""
 foreach i ( `echo $PATH | sed "s/:/ /g"` )
-  if ( "$i" != "$GMXBIN" ) set tmppath = "${tmppath}:$i"
+  if ( "$i" != "$GMXBIN" ) then
+    if ("${tmppath}" == "") then
+      set tmppath = "$i"
+    else
+      set tmppath = "${tmppath}:$i"
+    endif
+  endif
 end
 setenv PATH $tmppath
 
 # and remove stuff from manual path
 set tmppath = ""
 foreach i ( `echo $MANPATH | sed "s/:/ /g"` )
-  if ( "$i" != "$GMXMAN" ) set tmppath = "${tmppath}:$i"
+  if ( "$i" != "$GMXMAN" ) then 
+    if ("${tmppath}" == "") then
+      set tmppath = "$i"
+    else
+      set tmppath = "${tmppath}:$i"
+    endif
+  endif
 end
-if ("$tmppath" == "") then
-    set tmppath = ":"
-endif
 setenv MANPATH $tmppath
 
 ##########################################################
@@ -60,11 +75,16 @@ setenv GMXLDLIB @LIB_INSTALL_DIR@
 setenv GMXMAN @MAN_INSTALL_DIR@
 setenv GMXDATA @DATA_INSTALL_DIR@
 
-# old variables begin with ':' now, or are empty.
-setenv PATH ${GMXBIN}${PATH}
+#make them begin with :
+if ($?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ":${LD_LIBRARY_PATH}"
+if ($?PKG_CONFIG_PATH) setenv PKG_CONFIG_PATH ":${PKG_CONFIG_PATH}"
+
+#path is never empty
+setenv PATH ${GMXBIN}:${PATH}
 setenv LD_LIBRARY_PATH ${GMXLDLIB}${LD_LIBRARY_PATH}
 setenv PKG_CONFIG_PATH ${GMXLDLIB}/pkgconfig${PKG_CONFIG_PATH}
-setenv MANPATH ${GMXMAN}${MANPATH}
+#debian/ubuntu needs a : at the end
+setenv MANPATH ${GMXMAN}:${MANPATH}
 
 setenv GMXFONT 10x20
 

diff --git a/scripts/GMXRC.csh.in b/scripts/GMXRC.csh.in
index 766446010275e7be80aa9ab133d17b6caa4bde14..d05d255e0fbdce4b64f70177fb84a5a5466440d4 100644 (file)
--- a/scripts/GMXRC.csh.in
+++ b/scripts/GMXRC.csh.in
@@ -29,25 +29,40 @@ setenv LD_LIBRARY_PATH $tmppath
 # remove previous gromacs part from PKG_CONFIG_PATH
 set tmppath = ""
 foreach i ( `echo $PKG_CONFIG_PATH | sed "s/:/ /g"` )
-  if ( "$i" != "$GMXLDLIB/pkgconfig" ) set tmppath = "${tmppath}:$i"
+  if ( "$i" != "$GMXLDLIB/pkgconfig" ) then
+    if ("${tmppath}" == "") then
+      set tmppath = "$i"
+    else
+      set tmppath = "${tmppath}:$i"
+    endif
+  endif
 end
 setenv PKG_CONFIG_PATH $tmppath
 
 # remove gromacs stuff from binary path
 set tmppath = ""
 foreach i ( `echo $PATH | sed "s/:/ /g"` )
-  if ( "$i" != "$GMXBIN" ) set tmppath = "${tmppath}:$i"
+  if ( "$i" != "$GMXBIN" ) then
+    if ("${tmppath}" == "") then
+      set tmppath = "$i"
+    else
+      set tmppath = "${tmppath}:$i"
+    endif
+  endif
 end
 setenv PATH $tmppath
 
 # and remove stuff from manual path
 set tmppath = ""
 foreach i ( `echo $MANPATH | sed "s/:/ /g"` )
-  if ( "$i" != "$GMXMAN" ) set tmppath = "${tmppath}:$i"
+  if ( "$i" != "$GMXMAN" ) then 
+    if ("${tmppath}" == "") then
+      set tmppath = "$i"
+    else
+      set tmppath = "${tmppath}:$i"
+    endif
+  endif
 end
-if ("$tmppath" == "") then
-    set tmppath = ":"
-endif
 setenv MANPATH $tmppath
 
 ##########################################################
@@ -60,11 +75,16 @@ setenv GMXLDLIB @libdir@
 setenv GMXMAN @mandir@
 setenv GMXDATA @datadir@
 
-# old variables begin with ':' now, or are empty.
-setenv PATH ${GMXBIN}${PATH}
+#make them begin with :
+if ($?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ":${LD_LIBRARY_PATH}"
+if ($?PKG_CONFIG_PATH) setenv PKG_CONFIG_PATH ":${PKG_CONFIG_PATH}"
+
+#path is never empty
+setenv PATH ${GMXBIN}:${PATH}
 setenv LD_LIBRARY_PATH ${GMXLDLIB}${LD_LIBRARY_PATH}
 setenv PKG_CONFIG_PATH ${GMXLDLIB}/pkgconfig${PKG_CONFIG_PATH}
-setenv MANPATH ${GMXMAN}${MANPATH}
+#debian/ubuntu needs a : at the end
+setenv MANPATH ${GMXMAN}:${MANPATH}
 
 setenv GMXFONT 10x20
 

diff --git a/scripts/GMXRC.zsh.cmakein b/scripts/GMXRC.zsh.cmakein
index 0a29da2418cc26a67967057f3f036f0aad8b204d..750c0501119db8acd93bfcd36b02b785fe4f8bf9 100644 (file)
--- a/scripts/GMXRC.zsh.cmakein
+++ b/scripts/GMXRC.zsh.cmakein
@@ -4,24 +4,24 @@
 # This is not 100% necessary, but very useful when we
 # repeatedly switch between gmx versions in a shell.
 
+# ATTENTION
+# zsh understands sh syntax - so this is just a copy from GMXRC.bash.in
+# BEGIN COPY
+
 # First remove gromacs part of ld_library_path
 tmppath=""
 for i in `echo $LD_LIBRARY_PATH | sed "s/:/ /g"`; do
   if test "$i" != "$GMXLDLIB"; then
-    if test "${tmppath}" = ""; then
-      tmppath=$i
-    else
-    tmppath=${tmppath}:$i
-  fi
+    tmppath="${i}${tmppath:+:}${tmppath}"
   fi
 done
 LD_LIBRARY_PATH=$tmppath
 
-# First remove gromacs part of PKG_CONFIG_PATH
+# remove gromacs part of PKG_CONFIG_PATH
 tmppath=""
 for i in `echo $PKG_CONFIG_PATH | sed "s/:/ /g"`; do
   if test "$i" != "$GMXLDLIB/pkgconfig"; then
-    tmppath=${tmppath}:$i
+    tmppath="${i}${tmppath:+:}${tmppath}"
   fi
 done
 PKG_CONFIG_PATH=$tmppath
@@ -30,7 +30,7 @@ PKG_CONFIG_PATH=$tmppath
 tmppath=""
 for i in `echo $PATH | sed "s/:/ /g"`; do
   if test "$i" != "$GMXBIN"; then
-    tmppath=${tmppath}:$i
+    tmppath="${i}${tmppath:+:}${tmppath}"
   fi
 done
 PATH=$tmppath
@@ -39,12 +39,9 @@ PATH=$tmppath
 tmppath=""
 for i in `echo $MANPATH | sed "s/:/ /g"`; do
   if test "$i" != "$GMXMAN"; then
-    tmppath=${tmppath}:$i
+    tmppath="${i}${tmppath:+:}${tmppath}"
   fi
 done
-if test "$tmppath" = ""; then
-    tmppath=":"
-fi
 MANPATH=$tmppath
 
 ##########################################################
@@ -52,16 +49,21 @@ MANPATH=$tmppath
 # things in separate vars, so we can remove them later.
 # If you move gromacs, change the next four line.
 ##########################################################
-export GMXBIN=@BIN_INSTALL_DIR@
-export GMXLDLIB=@LIB_INSTALL_DIR@
-export GMXMAN=@MAN_INSTALL_DIR@
-export GMXDATA=@DATA_INSTALL_DIR@
+GMXBIN=@BIN_INSTALL_DIR@
+GMXLDLIB=@LIB_INSTALL_DIR@
+GMXMAN=@MAN_INSTALL_DIR@
+GMXDATA=@DATA_INSTALL_DIR@
        
-# NB: The variables already begin with ':' now, or are empty
-export LD_LIBRARY_PATH=${GMXLDLIB}${LD_LIBRARY_PATH}
-export PKG_CONFIG_PATH=${GMXLDLIB}/pkgconfig${PKG_CONFIG_PATH}
-export PATH=${GMXBIN}${PATH}
-export MANPATH=${GMXMAN}${MANPATH}
+LD_LIBRARY_PATH=${GMXLDLIB}${LD_LIBRARY_PATH:+:}${LD_LIBRARY_PATH}
+PKG_CONFIG_PATH=${GMXLDLIB}/pkgconfig${PKG_CONFIG_PATH:+:}${PKG_CONFIG_PATH}
+PATH=${GMXBIN}${PATH:+:}${PATH}
+#debian/ubuntu needs a : at the end
+MANPATH=${GMXMAN}:${MANPATH}
+
+# export should be separate, so /bin/sh understands it
+export GMXBIN GMXLDLIB GMXMAN GMXDATA LD_LIBRARY_PATH PATH MANPATH PKG_CONFIG_PATH
+
+# END COPY
 
 # read zsh completions if understand how to use them
 if compctl >& /dev/null; then

diff --git a/scripts/GMXRC.zsh.in b/scripts/GMXRC.zsh.in
index 45522bbdfcdba76cd423c8fedbd1d356a9bf24c5..030238465b7b7100755fb71a0fffaa13e71f1e5b 100644 (file)
--- a/scripts/GMXRC.zsh.in
+++ b/scripts/GMXRC.zsh.in
@@ -4,24 +4,24 @@
 # This is not 100% necessary, but very useful when we
 # repeatedly switch between gmx versions in a shell.
 
+# ATTENTION
+# zsh understands sh syntax - so this is just a copy from GMXRC.bash.in
+# BEGIN COPY
+
 # First remove gromacs part of ld_library_path
 tmppath=""
 for i in `echo $LD_LIBRARY_PATH | sed "s/:/ /g"`; do
   if test "$i" != "$GMXLDLIB"; then
-    if test "${tmppath}" = ""; then
-      tmppath=$i
-    else
-    tmppath=${tmppath}:$i
-  fi
+    tmppath="${i}${tmppath:+:}${tmppath}"
   fi
 done
 LD_LIBRARY_PATH=$tmppath
 
-# First remove gromacs part of PKG_CONFIG_PATH
+# remove gromacs part of PKG_CONFIG_PATH
 tmppath=""
 for i in `echo $PKG_CONFIG_PATH | sed "s/:/ /g"`; do
   if test "$i" != "$GMXLDLIB/pkgconfig"; then
-    tmppath=${tmppath}:$i
+    tmppath="${i}${tmppath:+:}${tmppath}"
   fi
 done
 PKG_CONFIG_PATH=$tmppath
@@ -30,7 +30,7 @@ PKG_CONFIG_PATH=$tmppath
 tmppath=""
 for i in `echo $PATH | sed "s/:/ /g"`; do
   if test "$i" != "$GMXBIN"; then
-    tmppath=${tmppath}:$i
+    tmppath="${i}${tmppath:+:}${tmppath}"
   fi
 done
 PATH=$tmppath
@@ -39,12 +39,9 @@ PATH=$tmppath
 tmppath=""
 for i in `echo $MANPATH | sed "s/:/ /g"`; do
   if test "$i" != "$GMXMAN"; then
-    tmppath=${tmppath}:$i
+    tmppath="${i}${tmppath:+:}${tmppath}"
   fi
 done
-if test "$tmppath" = ""; then
-    tmppath=":"
-fi
 MANPATH=$tmppath
 
 ##########################################################
@@ -52,16 +49,21 @@ MANPATH=$tmppath
 # things in separate vars, so we can remove them later.
 # If you move gromacs, change the next four line.
 ##########################################################
-export GMXBIN=@bindir@
-export GMXLDLIB=@libdir@
-export GMXMAN=@mandir@
-export GMXDATA=@datadir@
+GMXBIN=@bindir@
+GMXLDLIB=@libdir@
+GMXMAN=@mandir@
+GMXDATA=@datadir@
        
-# NB: The variables already begin with ':' now, or are empty
-export LD_LIBRARY_PATH=${GMXLDLIB}${LD_LIBRARY_PATH}
-export PKG_CONFIG_PATH=${GMXLDLIB}/pkgconfig${PKG_CONFIG_PATH}
-export PATH=${GMXBIN}${PATH}
-export MANPATH=${GMXMAN}${MANPATH}
+LD_LIBRARY_PATH=${GMXLDLIB}${LD_LIBRARY_PATH:+:}${LD_LIBRARY_PATH}
+PKG_CONFIG_PATH=${GMXLDLIB}/pkgconfig${PKG_CONFIG_PATH:+:}${PKG_CONFIG_PATH}
+PATH=${GMXBIN}${PATH:+:}${PATH}
+#debian/ubuntu needs a : at the end
+MANPATH=${GMXMAN}:${MANPATH}
+
+# export should be separate, so /bin/sh understands it
+export GMXBIN GMXLDLIB GMXMAN GMXDATA LD_LIBRARY_PATH PATH MANPATH PKG_CONFIG_PATH
+
+# END COPY
 
 # read zsh completions if understand how to use them
 if compctl >& /dev/null; then

diff --git a/share/html/online/mdp_opt.html b/share/html/online/mdp_opt.html
index a510d3e84bf6c3d04bd4f63c96d50cd0567c2916..1f6f16de4a2f59289d217bcb32d94e37d66f383d 100644 (file)
--- a/share/html/online/mdp_opt.html
+++ b/share/html/online/mdp_opt.html
@@ -874,7 +874,7 @@ steps of the gromacs implementation for the current time step pressure.</dd>
 </dl></dd>
 <dt><b>MTTK</b></dt>
 <dd>Martyna-Tuckerman-Tobias-Klein implementation, only useable with <b>md-vv</b>
-or <b>md-vv-avek</b>, very similar to Parinello-Raphman.  
+or <b>md-vv-avek</b>, very similar to Parrinello-Rahman.  
 As for Nose-Hoover temperature coupling the time constant <b>tau_p</b>
 [ps] is the period of pressure fluctuations at equilibrium. This is
 probably a better method when you want to apply pressure scaling