diff --git a/patches/gromacs-4.5.5.config b/patches/gromacs-4.5.5.config
index c4c96cc70c23ae5ce30c003563e8c5e5a23acc93..8529732bb2d56c68645d017d87ec94464e22f7e3 100644
--- a/patches/gromacs-4.5.5.config
+++ b/patches/gromacs-4.5.5.config
@@ -18,3 +18,10 @@ function plumed_after_revert(){
mv src/kernel/Makefile.plumedbck src/kernel/Makefile
}
+function plumed_patch_info(){
+ echo ""
+ echo "PLUMED can be incorporated into gromacs using a simple patching procedure."
+ echo "Patching must be done _after_ gromacs has been configured but _before_ gromacs is compiled"
+ echo
+ echo "For more information on gromacs you should visit http://www.gromacs.org"
+}
diff --git a/patches/gromacs-4.6.3.config b/patches/gromacs-4.6.3.config
index a5d00fcea22295d52544fcd345e60947ff7553ef..b5d89332bfd90c7da73c33769c3f5ff3e8529642 100644
--- a/patches/gromacs-4.6.3.config
+++ b/patches/gromacs-4.6.3.config
@@ -4,3 +4,11 @@ function plumed_preliminary_test(){
# check if the README contains the word GROMACS and if gromacs has been already configured
grep -q GROMACS README 1>/dev/null 2>/dev/null
}
+
+function plumed_patch_info(){
+ echo ""
+ echo "PLUMED can be incorporated into gromacs using a simple patching procedure."
+ echo "Patching must be done _before_ the cmake command is invoked"
+ echo
+ echo "For more information on gromacs you should visit http://www.gromacs.org"
+}
diff --git a/patches/lammps-6Apr13.config b/patches/lammps-6Apr13.config
index 7aa1e453acc89b3e771728925a4620caa2836edd..a83ff65c1a8e63d7f15d7d5aae0e6bdcafcc0f35 100644
--- a/patches/lammps-6Apr13.config
+++ b/patches/lammps-6Apr13.config
@@ -14,3 +14,14 @@ function plumed_after_revert(){
rm -fr src/USER-PLUMED/
}
+function plumed_patch_info(){
+ echo ""
+ echo "PLUMED can be incorporated into LAMMPS using a simple patching procedure."
+ echo "Patching must be done _before_ LAMMPS is configured."
+ echo "After patching, one should enable PLUMED using the command"
+ echo "make yes-user-plumed"
+ echo "In the same way, before reverting one should disable PLUMED using the command"
+ echo "make no-user-plumed"
+ echo
+ echo "For more information on LAMMPS you should visit http://lammps.sandia.gov/"
+}
diff --git a/patches/namd-2.8.config b/patches/namd-2.8.config
index 3eff738a2fc6ae97add7a847e49352c15fcbe335..3bef46c3c5a3bd83f44e12caf867f063f2b40df4 100644
--- a/patches/namd-2.8.config
+++ b/patches/namd-2.8.config
@@ -4,3 +4,9 @@ function plumed_preliminary_test(){
# check if the README.txt contains the word NAMD
grep -q NAMD README.txt 1>/dev/null 2>/dev/null && test -f */Make.config
}
+
+function plumed_patch_info(){
+ echo ""
+ echo ""
+ echo "For more information on NAMD you should visit http://www.ks.uiuc.edu/Research/namd/"
+}
diff --git a/patches/patch.sh b/patches/patch.sh
index fc77435c8b6ca6db9b5eff1b8972fcafa9b3c6a4..6ee52c5af150b5a0fa557119189d4d6203d9b605 100755
--- a/patches/patch.sh
+++ b/patches/patch.sh
@@ -17,6 +17,8 @@ Actions (choose one):
same as save, but save also original files
-n NEWENGINE, --new NEWENGINE
create a new patch named NEWENGINE (*)
+ -i, --info
+ output information on the patching procedure for a particular code
Options:
-e ENGINE, --engine ENGINE
set MD engine to ENGINE (default: choose interactively)
@@ -30,6 +32,9 @@ Options:
same as --mode runtime
-d FILE, --diff FILE
set the path to diff file (default: ROOT/patches/ENGINE.diff) (*)
+ -q, --quiet
+ do not write loggin information; useful with -i to print just
+ the patching information
-f, --force
force patching (*)
@@ -49,7 +54,7 @@ multiple_actions=
otherfiles=
save_originals=
-
+quiet=
for option
do
@@ -64,6 +69,7 @@ do
(--save-originals) test -n "$action" && multiple_actions=yes ; action=save ; save_originals=yes ;;
(--revert|-R|-r) test -n "$action" && multiple_actions=yes ; action=revert ;;
(--list-engines|-l) test -n "$action" && multiple_actions=yes ; action=list ;;
+ (--info|-i) test -n "$action" && multiple_actions=yes ; action=info ;;
(--new=*) test -n "$action" && multiple_actions=yes ; action=new ; newpatch="${prefix_option#--new=}" ;;
(--description) echo "patch an MD engine" ; exit ;;
(--engine=*) engine="${prefix_option#--engine=}" ;;
@@ -78,6 +84,7 @@ do
(--shared) mode=shared ;;
(--runtime) mode=runtime ;;
(--force|-f) force=yes ;;
+ (--quiet|-q) quiet=yes ;;
(*)
echo "ERROR: Unknown option $prefix_option. Use -h for help."
exit
@@ -94,8 +101,8 @@ if [ -z "$action" ] ; then
exit
fi
-echo "PLUMED patching tool"
-echo
+test -n "$quiet" || echo "PLUMED patching tool"
+test -n "$quiet" || echo
if [ -z "$PLUMED_ROOT" ]
then
echo "ERROR: I cannot find PLUMED"
@@ -133,14 +140,14 @@ fi
if [ "$action" == new ]
then
- echo "Creating a new patch"
+ test -n "$quiet" || echo "Creating a new patch"
if [[ -e "$PLUMED_ROOT"/patches/"$newpatch".diff ]] ; then
echo "ERROR: patch $newpatch is already defined"
exit
fi
touch "$PLUMED_ROOT"/patches/"$newpatch".diff
- echo "Created file $PLUMED_ROOT/patches/$newpatch.diff"
- echo "Also consider the possibility of adding a $PLUMED_ROOT/patches/$newpatch.config file"
+ test -n "$quiet" || echo "Created file $PLUMED_ROOT/patches/$newpatch.diff"
+ test -n "$quiet" || echo "Also consider the possibility of adding a $PLUMED_ROOT/patches/$newpatch.config file"
exit
fi
@@ -169,19 +176,19 @@ then
test -d "$PLUMED_ROOT/patches/${engine}" && otherfiles="$PLUMED_ROOT/patches/${engine}/"
fi
-echo "MD engine: $engine"
-echo "PLUMED location: $PLUMED_ROOT"
-echo "diff file: $diff"
+test -n "$quiet" || echo "MD engine: $engine"
+test -n "$quiet" || echo "PLUMED location: $PLUMED_ROOT"
+test -n "$quiet" || echo "diff file: $diff"
if [ -f "$config" ]
then
- echo "sourcing config file: $config"
+ test -n "$quiet" || echo "sourcing config file: $config"
source "$config"
fi
if [ -d "$otherfiles" ]
then
- echo "extra files located in: $otherfiles"
+ test -n "$quiet" || echo "extra files located in: $otherfiles"
fi
case "$mode" in
@@ -220,16 +227,16 @@ case "$action" in
exit
fi
if type -t plumed_before_patch 1>/dev/null ; then
- echo "Executing plumed_before_patch function"
+ test -n "$quiet" || echo "Executing plumed_before_patch function"
plumed_before_patch
fi
- echo "Linking Plumed.h and Plumed.inc ($mode mode)"
+ test -n "$quiet" || echo "Linking Plumed.h and Plumed.inc ($mode mode)"
ln -s "$PLUMED_ROOT/src/wrapper/Plumed.h"
ln -s "$PLUMED_ROOT/src/lib/Plumed.inc.$mode" Plumed.inc
ln -s "$PLUMED_ROOT/src/lib/Plumed.cmake.$mode" Plumed.cmake
if [ -d "$diff" ]; then
- echo "Patching with on-the-fly diff from stored originals"
+ test -n "$quiet" || echo "Patching with on-the-fly diff from stored originals"
PREPLUMED=$(cd $diff ; find . -name "*.preplumed" | sort)
for bckfile in $PREPLUMED ; do
file="${bckfile%.preplumed}"
@@ -241,15 +248,23 @@ case "$action" in
fi
done
else
- echo "Patching with stored diff"
+ test -n "$quiet" || echo "Patching with stored diff"
bash "$diff"
fi
if type -t plumed_after_patch 1>/dev/null ; then
- echo "Executing plumed_after_patch function"
+ test -n "$quiet" || echo "Executing plumed_after_patch function"
plumed_after_patch
fi
;;
+ (info)
+ if type -t plumed_patch_info 1>/dev/null ; then
+ test -n "$quiet" || echo "Executing plumed_patch_info function"
+ plumed_patch_info
+ else
+ echo "No special info for this MD engine"
+ fi
+ ;;
(save)
if [ ! -L Plumed.h -o ! -L Plumed.inc ]
then
@@ -271,9 +286,9 @@ case "$action" in
exit
fi
fi
- echo "Saving your changes to $diff"
- echo "Preplumed files:"
- echo "$PREPLUMED"
+ test -n "$quiet" || echo "Saving your changes to $diff"
+ test -n "$quiet" || echo "Preplumed files:"
+ test -n "$quiet" || echo "$PREPLUMED"
if [ -d "$diff" ] && [ -z "$save_originals" ]; then
echo "This patch uses the dir format (originals are saved)"
echo "Are you sure you want to save the single diff?"
@@ -290,10 +305,10 @@ case "$action" in
fi
done
if [ "$answer" = originals ] ; then
- echo "saving originals"
+ test -n "$quiet" || echo "saving originals"
save_originals=yes
else
- echo "saving single diff file"
+ test -n "$quiet" || echo "saving single diff file"
fi
fi
test -e "$diff" && rm -r "$diff"
@@ -328,21 +343,21 @@ EOF
exit
fi
if type -t plumed_before_revert 1>/dev/null ; then
- echo "Executing plumed_before_revert function"
+ test -n "$quiet" || echo "Executing plumed_before_revert function"
plumed_before_revert
fi
if [ ! -L Plumed.h -o ! -L Plumed.inc ]
then
echo "WARNING: I cannot find Plumed.h and Plumed.inc files. You have likely not patched yet."
else
- echo "Removing Plumed.h and Plumed.inc"
+ test -n "$quiet" || echo "Removing Plumed.h and Plumed.inc"
rm Plumed.h Plumed.inc Plumed.cmake
fi
PREPLUMED=$(find . -name "*.preplumed")
if ! test "$PREPLUMED" ; then
echo "No .preplumed file found, nothing to restore."
else
- echo "Reverting changes and touching reverted files"
+ test -n "$quiet" || echo "Reverting changes and touching reverted files"
for bckfile in $PREPLUMED ; do
file="${bckfile%.preplumed}"
mv "$bckfile" "$file"
@@ -350,7 +365,7 @@ EOF
done
fi
if type -t plumed_after_revert 1>/dev/null ; then
- echo "Executing plumed_after_revert function"
+ test -n "$quiet" || echo "Executing plumed_after_revert function"
plumed_after_revert
fi
esac
diff --git a/patches/qespresso-5.0.2.config b/patches/qespresso-5.0.2.config
index 84c8e48453a9c74b3998ecf58c1ef6fe42d95a5d..f7c7b6ff5255426bf2178facfc72cc428d32e120 100644
--- a/patches/qespresso-5.0.2.config
+++ b/patches/qespresso-5.0.2.config
@@ -15,3 +15,9 @@ awk '{if($1=="LIBS" && $2=="="){print $0" $(PLUMED_LOAD) "}else{print }}' make.s
function plumed_after_revert(){
mv make.sys.old make.sys
}
+
+function plumed_patch_info(){
+ echo ""
+ echo "For more information on Quantum Espresso you should visit http://www.quantum-espresso.org"
+}
+
diff --git a/user-doc/Modules.txt b/user-doc/Modules.txt
index 0b6d9c5604a1e772babd27a07b29b4f82e2e4228..f4996b6cb2abaff1d5d21614bfa80172ccea5afd 100644
--- a/user-doc/Modules.txt
+++ b/user-doc/Modules.txt
@@ -1,47 +1,23 @@
/**
-@page mymodules Modules
+@page mymodules module
-PLUMED 2 is written and maintained by five core developers none of whom work full
-time on the maintanence and upkeep of the code. From our point of view it is thus
-desirable to keep the core of the code small. In addition, we are very keen that
-users who contribute functionality to PLUMED get the plaudits that they deserve.
-For these reasons many of PLUMED's more advanced functionalities are provided in
-modules that users can download. To download a module you simply change to the
-<c> plumed2/mymodules </c> directory and issue the following command:
+The functionality in PLUMED 2 is divided into a small number of modules. Some
+users may only wish to use a subset of the functionality available within the
+code while others may wish to use some of PLUMED's more complicated features.
+For this reason the plumed source code is divided into modules, which users can
+activate or deactivate to their hearts content.
-\verbatim
-./plumed-get-module.sh <name of module>
-\endverbatim
+- To activate a module add a file called modulename.on to the plumed2/src directory
+- To deactivate a module add a file called modulename.off to the plumed2/src directory
-The following optional modules can be added to PLUMED 2:
+Obviously, in the above instructions modulename should be replaced by the name of the
+module that you would like to activate or deactivate.
-@MODULES@
-
-\section addmodule Adding a module
-
-If you have a PLUMED module that you would like us to advertise on the website
-you should copy the directory structure from <c> plumed2/template-module </c>
-as well as all the files inside that directory and place your source and regtest
-files in appropriate directories. You are responsible for finding a suitable
-web repository to host the code that you have developed (we use http://www.assembla.com
-for PLUMED). You do not need to give us write access to your repository as ensuring that
-your code keeps working with any new release of PLUMED is YOUR responsibility.
-
-Once you are ready to release your code simply send any email to one of the developers
-with a txt file that contains the following information in the following format:
-
-\verbatim
-NAME: <the name of your module>
+Some modules are active by default in the version of PLUMED 2 that you download from
+the website while others are inactive. The following lists all of the modules that
+are available in plumed and tells you whether or not they are active by default.
-AUTHOR: <the list of people involved in the development of the module>
-
-REPOSITORY: <the command that retreives the code e.g. git clone git@git.assembla.com:plumed2.git>
-
-DESCRIPTION:
-
-<a short description of what it is your module calculates>
-<citations and equations can be included using the usual doxygen commands>
-\endverbatim
+@MODULES@
*/
diff --git a/user-doc/extract b/user-doc/extract
index 6443e5d4d2bece46f110c1f24342f08c5086079d..d361a36779f675d14d53204cdbd247ffd939b5d9 100755
--- a/user-doc/extract
+++ b/user-doc/extract
@@ -18,7 +18,13 @@ done
# Create the list of codes that plumed works with from the set of available patches
for file in ../patches/*.diff
do
- echo "- $file" | sed -e 's/.diff//' | sed -e 's/..\/patches\///' >> automatic/codes.list
+ myengine=`echo "$file" | sed -e 's/.diff//' | sed -e 's/..\/patches\///'`
+ mytag=`echo "$myengine" | sed -e 's/\./\_/g'`
+ echo "- \subpage $mytag" >> automatic/codes.list
+ echo "/**" >> automatic/$myengine.txt
+ echo "\page $mytag $myengine" >> automatic/$myengine.txt
+ plumed patch -e $myengine -i -q >> automatic/$myengine.txt
+ echo "*/" >> automatic/$myengine.txt
done
## Check for utilities that register actions with no documentation
@@ -105,53 +111,62 @@ done
# Find what modules the user has installed
# Find the list of modules
-if [ -d ../mymodules ] ; then
- sed -i '' -e 's/type="user" visible="no" url="mymodules.html"/type="user" visible="yes" url="mymodules.html"/' PlumedLayout.xml
- for file in `ls ../mymodules/available-modules/`
- do
- #Â Check if module has been installed
- if [ -d "../mymodules/$file" ] ; then
- # Generate documentation and accreditation on modules page
- echo "\section $file" >> automatic/mymodules.list
- echo >> automatic/mymodules.list
- echo "<table align=center frame=void width=95%% celpadding=5%%>" >> automatic/mymodules.list
- echo "<tr> <td width=70%%> </td> </tr> <td>" >> automatic/mymodules.list
- author=`grep AUTHOR: ../mymodules/available-modules/"$file" | sed -e 's/AUTHOR://'`
- echo "<b> author: $author </b>" >> automatic/mymodules.list
- echo "</td> </tr>" >> automatic/mymodules.list
- echo "<tr> <td colspan="2">" >> automatic/mymodules.list
- dline=`grep -n DESCRIPTION: ../mymodules/available-modules/"$file" | sed -n 's/^\([0-9]*\)[:].*/\1/p'` >> automatic/mymodules.list
- tail -n +$(($dline+1)) ../mymodules/available-modules/"$file" >> automatic/mymodules.list
- echo "</td> </tr> </table>" >> automatic/mymodules.list
- echo >> automatic/mymodules.list
- echo >> automatic/mymodules.list
-
- # Find src files in module and add a link to the module description
- for srcfile in `ls ../mymodules/"$file"/src/*cpp` ; do
- ndocs=`grep PLUMEDOC "$srcfile" | wc -l | awk '{print $1}'`
- for ((line=1;line<$ndocs;++line)) ; do
- docfile=`grep PLUMEDOC "$srcfile" | grep -v END | head -n $line | tail -n 1 | awk '{print $3}'`
- cat automatic/"$docfile".tmp |
- {
- while read -r LINE ; do
- if `echo $LINE | grep "\section $docfile" 1>/dev/null 2>&1`
- then
- echo $LINE
- echo "<table align=center frame=void width=95%% celpadding=5%%>"
- echo "<tr> <td width=70%%> </td> <td>"
- echo "<b> This is part of the \ref $file module </b>"
- echo "</td> </tr> </table>"
- else
- echo "$LINE"
- fi
- done
- } > automatic/"$docfile"1.tmp
- mv automatic/"$docfile"1.tmp automatic/"$docfile".tmp
- done
- done
- fi
- done
-fi
+# if [ -d ../mymodules ] ; then
+# sed -i '' -e 's/type="user" visible="no" url="mymodules.html"/type="user" visible="yes" url="mymodules.html"/' PlumedLayout.xml
+echo "<table align=center frame=void width=65%% cellpadding=5%%>" > automatic/modules.list
+echo "<tr> <td> <b> Module name </b> </td> <td> <b> Default behavior </b> </td> </tr>" >> automatic/modules.list
+for file in `ls ../src/*/module.type | sed -e 's/..\/src\///' | sed -e 's/\/module.type//'`
+do
+ dstr=`head ../src/$file/module.type`
+ if [ "$dstr" != "always" ] ; then
+ echo "<tr> <td> $file </td>" >> automatic/modules.list
+ if [ "$dstr" == "default-on" ] ; then
+ echo "<td> on </td> </tr>" >> automatic/modules.list
+ else
+ echo "<td> off </td> </tr>" >> automatic/modules.list
+ fi
+# # Generate documentation and accreditation on modules page
+# echo "\section $file" >> automatic/mymodules.list
+# echo >> automatic/mymodules.list
+# echo "<table align=center frame=void width=95%% celpadding=5%%>" >> automatic/mymodules.list
+# echo "<tr> <td width=70%%> </td> </tr> <td>" >> automatic/mymodules.list
+# author=`grep AUTHOR: ../mymodules/available-modules/"$file" | sed -e 's/AUTHOR://'`
+# echo "<b> author: $author </b>" >> automatic/mymodules.list
+# echo "</td> </tr>" >> automatic/mymodules.list
+# echo "<tr> <td colspan="2">" >> automatic/mymodules.list
+# dline=`grep -n DESCRIPTION: ../mymodules/available-modules/"$file" | sed -n 's/^\([0-9]*\)[:].*/\1/p'` >> automatic/mymodules.list
+# tail -n +$(($dline+1)) ../mymodules/available-modules/"$file" >> automatic/mymodules.list
+# echo "</td> </tr> </table>" >> automatic/mymodules.list
+# echo >> automatic/mymodules.list
+# echo >> automatic/mymodules.list
+
+ # Find src files in module and add a link to the module description
+ for srcfile in `ls ../src/"$file"/*cpp` ; do
+ ndocs=`grep PLUMEDOC "$srcfile" | grep -v END | wc -l | awk '{print $1}'`
+ for ((line=1;line<=$ndocs;++line)) ; do
+ docfile=`grep PLUMEDOC "$srcfile" | grep -v END | head -n $line | tail -n 1 | awk '{print $3}'`
+ cat automatic/"$docfile".tmp |
+ {
+ while read -r LINE ; do
+ if `echo $LINE | grep "section $docfile" 1>/dev/null 2>&1`
+ then
+ echo $LINE
+ echo "<table align=center frame=void width=95%% celpadding=5%%>"
+ echo "<tr> <td width=70%%> </td> <td>"
+ echo "<b> This is part of the $file \\ref mymodules </b>"
+ echo "</td> </tr> </table>"
+ else
+ echo "$LINE"
+ fi
+ done
+ } > automatic/"$docfile"1.tmp
+ mv automatic/"$docfile"1.tmp automatic/"$docfile".tmp
+ done
+ done
+ fi
+done
+echo "</table>" >> automatic/modules.list
+# fi
# Generate all the documentation from keywords
source ../sourceme.sh
@@ -237,7 +252,7 @@ cat $file.txt |
echo "</table>"
elif [ "$LINE" = "@MODULES@" ]
then
- cat automatic/mymodules.list
+ cat automatic/modules.list
elif [ "$LINE" = "@FUNCTION@" ]
then
echo "<table align=center frame=void width=95%% cellpadding=5%%>"