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Commit 821e988e authored by Carlo Camilloni's avatar Carlo Camilloni
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Merge branch 'master' of github.com:plumed/plumed2

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user-doc/Installation.txt
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View file @ 821e988e
......@@ -20,8 +20,18 @@ existing trajectories or to play with the included Lennard-Jones code.
Since PLUMED is mostly used to bias on the fly simulations
performed with serious molecular dynamics packages,
below you can find instructions about how to
\link Patching link PLUMED \endlink
to your favorite MD code.
\link Patching patch \endlink
your favorite MD code so that it can be combined with PLUMED.
Again, for the impatients, something like this could do the job:
\verbatim
> source /plumed/root/dir/sourceme.sh
> cd /md/root/dir
> plumed patch -p
\endverbatim
Then compile your MD code.
For some MD software these instructions are not sufficient,
and you are invited to read well the instructions
at the end of this page.
Notice that MD codes could in principle be "PLUMED ready"
in their official distribution. In this case, probably
you have to compile PLUMED first as a library then check their manual to
......@@ -257,7 +267,7 @@ You can force plumed to run anyway using the option --standalone-executable:
Anyway, many features will not be available in this way.
This is currently the only way to use a PLUMED static executable on Windows.
\section Installing Installing PLUMED
\section InstallingPlumed Installing PLUMED
It might be convenient to install PLUMED in a predefined location.
This will allow you to remove the original compilation directory,
......
user-doc/extract
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View file @ 821e988e
#! /bin/bash
if ! plumed ; then
echo "plumed executable not found, I try to source ../sourceme.sh"
source ../sourceme.sh
if ! plumed ; then
echo "Compile plumed first!"
# Making sure that plumed executable is available
echo -n "Searching for plumed ..."
if plumed 2>/dev/null 1>/dev/null ; then
echo " found"
else
echo " not found"
echo -n "Sourcing sourceme.sh and searching again ..."
if source ../sourceme.sh && plumed 2>/dev/null 1>/dev/null ; then
echo " found"
else
echo "ERROR: you should compile plumed first!"
exit 1
fi
fi
# initial cleanup
rm -f errors
rm -rf automatic
mkdir automatic
# Check for files that register actions with no documentation
rm errors
for file in ../src/*/*.cpp
do
nreg=`grep "PLUMED_REGISTER_ACTION" $file | wc -l | awk '{print $1}'`
......@@ -37,18 +44,9 @@ do
echo "*/" >> automatic/$myengine.txt
done
## Check for utilities that register actions with no documentation
#for file in ../utilities/*.cpp
#do
# ndoc=`grep PLUMEDOC $file | grep TOOL | wc -l | awk '{print $1}'`
# if [ $ndoc -eq 0 ] ; then
# echo The following utility has been provided without documentation: $file >> errors
# fi
#done
# Generate all the documentation pages from comments
cat ../*/*/*cpp |
awk 'BEGIN{gfile="automatic/GLOSSARY1.list"; dfile="automatic/DICTIONARY1.list"; }{
awk 'BEGIN{gfile="automatic/GLOSSARY.list"; dfile="automatic/DICTIONARY.list"; }{
if($1=="//+ENDPLUMEDOC"){
inside=0;
print "*/" >output
......@@ -96,8 +94,11 @@ awk 'BEGIN{gfile="automatic/GLOSSARY1.list"; dfile="automatic/DICTIONARY1.list";
}'
# Now put the glossary in alphabetical order
sort automatic/GLOSSARY1.list > automatic/GLOSSARY.list
sort automatic/DICTIONARY1.list > automatic/DICTIONARY.list
sort automatic/GLOSSARY.list > automatic/GLOSSARY1.list
mv automatic/GLOSSARY1.list automatic/GLOSSARY.list
sort automatic/DICTIONARY.list > automatic/DICTIONARY1.list
mv automatic/DICTIONARY1.list automatic/DICTIONARY.list
# Generate links to tutorial pages
for file in ./tutorials/*.txt ; do
......@@ -151,156 +152,82 @@ do
# echo >> automatic/mymodules.list
# Find src files in module and add a link to the module description
for srcfile in `ls ../src/"$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 "\\page $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/"$docfile".tmp
done
done
docfiles=$(cat ../src/"$file"/*cpp | grep PLUMEDOC | grep -v END | awk '{print $3;}')
for docfile in $docfiles ; do
cat automatic/"$docfile".tmp |
awk '{ print }
/\\page '$docfile'/{
print "<table align=center frame=void width=95%% celpadding=5%%>"
print "<tr> <td width=70%%> </td> <td>"
print "<b> This is part of the '$file' \\ref mymodules </b>"
print "</td> </tr> </table>"
}' > automatic/"$docfile"1.tmp
mv automatic/"$docfile"1.tmp automatic/"$docfile".tmp
done
fi
done
echo "</table>" >> automatic/modules.list
# fi
# Generate all the documentation from keywords
source ../sourceme.sh
for file in automatic/*.tmp
do
foundinternal=`grep '//+PLUMEDOC INTERNAL' $file | wc -l | awk '{print $1}'`
flag=`echo $file | sed -e 's/.tmp//g' | sed -e 's/automatic\///g'`
if [ $foundinternal -eq 0 ] ; then
foundexample=`grep "\par Examples" $file | wc -l | awk '{print $1}'`
../src/lib/plumed manual --action=$flag > automatic/$flag.man 2> shit
rm shit
check=`wc -l automatic/$flag.man | awk '{print $1}'`
if [ $check -eq 0 ] ; then
flag=${file#automatic/}
flag=${flag/.tmp}
if grep -q '//+PLUMEDOC INTERNAL' $file 1>/dev/null 2>/dev/null ; then
cp $file automatic/$flag.txt
else
if ! plumed manual --action=$flag > automatic/$flag.man 2> /dev/null ; then
echo Full manual for action $flag will not be generated as you are building the manual from a code where this action was not compiled >> errors
elif [ $foundexample -eq 0 ]
elif ! grep -q "\par Examples" $file 1>/dev/null 2>/dev/null
then
echo There are no examples inside documentation for action: $flag >> errors
fi
cat automatic/$flag.tmp |
{
while read -r LINE ;
do
if [ "$LINE" = "\par Examples" ]
then
cat automatic/$flag.man
echo -E "$LINE"
else
echo -E "$LINE"
fi
done
awk '/\\par Examples/{xx=1}{if(xx==0) printf("%s\n",$0)}' automatic/$flag.tmp
cat automatic/$flag.man
awk '/\\par Examples/{xx=1}{if(xx==1) printf("%s\n",$0)}' automatic/$flag.tmp
} > automatic/$flag.txt
else
cp $file automatic/$flag.txt
fi
done
for file in COLVAR MCOLVAR DCOLVAR MCOLVARF ANALYSIS BIAS GLOSSARY \
DICTIONARY TUTORIALS WEBSITES FUNCTION TOPOLOGY VATOM \
TOOLS
do
mv automatic/$file.list automatic/$file.1.list
{
echo "<table align=center frame=void width=95%% cellpadding=5%%>"
cat automatic/$file.1.list
echo "</table>"
} > automatic/$file.list
rm automatic/$file.1.list
done
for file in Bias Syntax Colvar Functions Group Installation Intro Analysis Glossary Tutorials Modules Regex Misc Tools
do
# first replace with the content of the files
# then grep out the special strings
cat $file.txt |
{
while read -r LINE ;
do
if [ "$LINE" = "@COLVAR@" ]
then
echo "<table align=center frame=void width=95%% cellpadding=5%%>"
cat automatic/COLVAR.list
echo "</table>"
elif [ "$LINE" = "@MCOLVAR@" ]
then
echo "<table align=center frame=void width=95%% cellpadding=5%%>"
cat automatic/MCOLVAR.list
echo "</table>"
elif [ "$LINE" = "@DCOLVAR@" ]
then
echo "<table align=center frame=void width=95%% cellpadding=5%%>"
cat automatic/DCOLVAR.list
echo "</table>"
elif [ "$LINE" = "@MCOLVARF@" ]
then
echo "<table align=center frame=void width=95%% cellpadding=5%%>"
cat automatic/MCOLVARF.list
echo "</table>"
elif [ "$LINE" = "@ANALYSIS@" ]
then
echo "<table align=center frame=void width=95%% cellpadding=5%%>"
cat automatic/ANALYSIS.list
echo "</table>"
elif [ "$LINE" = "@BIAS@" ]
then
echo "<table align=center frame=void width=95%% cellpadding=5%%>"
cat automatic/BIAS.list
echo "</table>"
elif [ "$LINE" = "@GLOSSARY@" ]
then
echo "<table align=center frame=void width=95%% cellpadding=5%%>"
cat automatic/GLOSSARY.list
echo "</table>"
elif [ "$LINE" = "@DICTIONARY@" ]
then
echo "<table align=center frame=void width=95%% cellpadding=5%%>"
cat automatic/DICTIONARY.list
echo "</table>"
elif [ "$LINE" = "@TUTORIALS@" ]
then
echo "<table align=center frame=void width=95%% cellpadding=5%%>"
cat automatic/TUTORIALS.list
echo "</table>"
elif [ "$LINE" = "@WEBSITES@" ]
then
echo "<table align=center frame=void width=95%% cellpadding=5%%>"
cat automatic/WEBSITES.list
echo "</table>"
elif [ "$LINE" = "@MODULES@" ]
then
cat automatic/modules.list
elif [ "$LINE" = "@FUNCTION@" ]
then
echo "<table align=center frame=void width=95%% cellpadding=5%%>"
cat automatic/FUNCTION.list
echo "</table>"
elif [ "$LINE" = "@TOPOLOGY@" ]
then
echo "<table align=center frame=void width=95%% cellpadding=5%%>"
cat automatic/TOPOLOGY.list
echo "</table>"
elif [ "$LINE" = "@VATOM@" ]
then
echo "<table align=center frame=void width=95%% cellpadding=5%%>"
cat automatic/VATOM.list
echo "</table>"
elif [ "$LINE" = "@TOOLS@" ]
then
echo "<table align=center frame=void width=95%% cellpadding=5%%>"
cat automatic/TOOLS.list
echo "</table>"
elif [ "$LINE" = "@CODES@" ]
then
# echo "<table align=center frame=void width=95%% cellpadding=5%%>"
cat automatic/codes.list
# echo "</table>"
else
echo -E "$LINE"
fi
done
} > ${file}PP.txt
sed "
/^ *@COLVAR@ *$/r automatic/COLVAR.list
/^ *@MCOLVAR@ *$/r automatic/MCOLVAR.list
/^ *@DCOLVAR@ *$/r automatic/DCOLVAR.list
/^ *@MCOLVARF@ *$/r automatic/MCOLVARF.list
/^ *@ANALYSIS@ *$/r automatic/ANALYSIS.list
/^ *@BIAS@ *$/r automatic/BIAS.list
/^ *@GLOSSARY@ *$/r automatic/GLOSSARY.list
/^ *@DICTIONARY@ *$/r automatic/DICTIONARY.list
/^ *@TUTORIALS@ *$/r automatic/TUTORIALS.list
/^ *@WEBSITES@ *$/r automatic/WEBSITES.list
/^ *@FUNCTION@ *$/r automatic/FUNCTION.list
/^ *@TOPOLOGY@ *$/r automatic/TOPOLOGY.list
/^ *@VATOM@ *$/r automatic/VATOM.list
/^ *@TOOLS@ *$/r automatic/TOOLS.list
/^ *@MODULES@ *$/r automatic/modules.list
/^ *@CODES@ *$/r automatic/codes.list
" | grep -Ev '^ *"@[A-Z]*@" *$' > ${file}PP.txt
done
user-doc/go-doxygen
+ 15
− 0
View file @ 821e988e
#! /bin/bash
# Making sure that plumed executable is available
echo -n "Searching for plumed ..."
if plumed 2>/dev/null 1>/dev/null ; then
echo " found"
else
echo " not found"
echo -n "Sourcing sourceme.sh and searching again ..."
if source ../sourceme.sh && plumed 2>/dev/null 1>/dev/null ; then
echo " found"
else
echo "ERROR: you should compile plumed first!"
exit 1
fi
fi
{
cat Doxyfile
echo "PROJECT_NUMBER = \"$(plumed info --version)\""
......
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