Merge branch 'master' of github.com:plumed/plumed2

scripts/vim2html.sh

@@ -18,7 +18,10 @@ Usage:
 Options can be:
 --annotate-syntax Reports annotated syntax on output.
                   Also reports non-annotated regions on stderr
-
+--pdf             To produce a pdf file with syntax highlighting.
+--crop            Crop the pdf file to the only written part. Usefull to insert the pdf in a LaTex file as image.
+--fs              Specify the fontsize of the pdf output.
+--colors          Specify the color palette. Allowed values are: default/ac
 EOF
   exit 0
 fi
@@ -31,12 +34,30 @@ fi
 annotate_syntax=no
 inputfile=""
 outputfile=""
-
+pdf=no
+crop=no
+fontsize=7.5
+prefix=""
+colors=""
 for opt
 do
-  case "$opt" in
+  prefixopt="$prefix$opt"
+  prefix=""
+  case "$prefixopt" in
     (--annotate-syntax)
       annotate_syntax=yes ;;
+    (--pdf)
+      pdf=yes;;
+    (--crop)
+      crop=yes;;
+    (--fs)
+      prefix="--fs=";;
+    (--fs=*)
+      fontsize="${prefixopt#--fs=}";;
+    (--colors)
+      prefix="--colors=";;
+    (--colors=*)
+      colors="${prefixopt#--colors=}";;
     (-*)
       echo "ERROR: Unknown option $opt. Use -h for help."
       exit 1 ;;
@@ -51,7 +72,6 @@ do
       fi
   esac
 done
-
 temp="$( mktemp -dt plumed.XXXXX)"
 
 {
@@ -64,45 +84,95 @@ fi | tr '\r' ' '
 } | {
 cd $temp
 {
-if [ "$annotate_syntax" = "yes" ]; then
 
-vim - -c ":syntax off" \
+case "$colors" in
+(ac)
+  cat > $temp/colors.vim << EOF
+: set bg=dark
+: hi Statement  ctermfg=5 cterm=bold guifg=#ffff60 gui=none
+: highlight Type ctermfg=2 cterm=bold
+: hi Comment  guifg=#80a0ff ctermfg=darkblue
+: hi Constant ctermfg=red guifg=#ffa0a0 cterm=bold
+EOF
+;;
+(*)
+  echo > $temp/colors.vim
+;;
+esac
+
+if [ "$pdf" = "yes" ]; then
+
+# this is a workaround for a bug in TOhtml
+# that does not color properly when there are empty lines
+  sed "s/^$/ /" |
+  vim - -c ":syntax off" \
+        -c ":source $VIMFILE" \
+        -c ":source $temp/colors.vim" \
+        -c ":set printoptions=header:0" \
+        -c ":set printfont=courier:h$fontsize" \
+        -c ":hardcopy > out.ps" \
+        -c ":q!" 1> /dev/null 2> /dev/null
+else
+  if [ "$annotate_syntax" = "yes" ]; then
+
+    vim - -c ":syntax off" \
       -c ":source $VIMFILE" \
       -c ":call PlumedAnnotateSyntax()" \
       -c ":wq! syntax.log" -c ":q!" 1> /dev/null 2> /dev/null
 
-else
-# this is a workaround for a bug in TOhtml
-# that does not color properly when there are empty lines
-sed "s/^$/ /" |
-vim - -c ":syntax off" \
+  else
+    # this is a workaround for a bug in TOhtml
+    # that does not color properly when there are empty lines
+    sed "s/^$/ /" |
+    vim - -c ":syntax off" \
       -c ":source $VIMFILE" \
+      -c ":source $temp/colors.vim" \
       -c ":let g:html_use_css = 0" \
       -c ":let g:html_no_progress" \
       -c ":let g:html_number_lines = 1" \
       -c ":TOhtml" \
       -c ":wq! out.html" -c ":q!" 1> /dev/null 2> /dev/null
+  fi 
 fi
+
+
 }
 }
 
-if [ "$annotate_syntax" = "yes" ] ; then
+if [ "$pdf" = "yes" ]; then
+  ps2pdf $temp/out.ps $temp/out.pdf
+  output="$temp/out.pdf"
+  if [ "$crop" = "yes" ]; then
+    pdfcrop $output $temp/outcrop.pdf
+    output="$temp/outcrop.pdf"
+  fi
+else
+  if [ "$annotate_syntax" = "yes" ] ; then
+    output="$(awk '{if($1=="ANNOTATION") print}' $temp/syntax.log 2>/dev/null)"
+    error="$(awk '{if($1=="ERROR") print}' $temp/syntax.log >&2 2>/dev/null)"
+  else
+    output="$(cat $temp/out.html | sed 's|^<title>.*</title>$||' | sed 's|^<meta.*$||')"
+  fi
+fi
 
-output="$(awk '{if($1=="ANNOTATION") print}' $temp/syntax.log 2>/dev/null)"
-error="$(awk '{if($1=="ERROR") print}' $temp/syntax.log >&2 2>/dev/null)"
 
+if [ "$pdf" = "yes" ]; then
+  if [ -n "$outputfile" ] ; then
+    cp $output $outputfile
+  else
+    echo "You should specify an output file if using pdf opton!"
+    exit 1;
+  fi
 else
 
-output="$(cat $temp/out.html | sed 's|^<title>.*</title>$||' | sed 's|^<meta.*$||')"
+  if [ -n "$outputfile" ] ; then
+    echo "$output" > "$outputfile"
+  else
+    echo "$output"
+  fi
 
 fi
 
-if [ -n "$outputfile" ] ; then
-  echo "$output" > "$outputfile"
-else
-  echo "$output"
-fi
-
 echo "$error" >&2
 
 if [ -n "$error" ] ; then

src/reference/DRMSD.h

@@ -31,18 +31,19 @@ namespace PLMD {
 
 class DRMSD : public SingleDomainRMSD {
 private:
-  bool bounds_were_set;
   bool nopbc;
+protected:
+  bool bounds_were_set;
   double lower, upper;
   std::map< std::pair <unsigned,unsigned> , double> targets;
-  void setup_targets();
 public:
   explicit DRMSD( const ReferenceConfigurationOptions& ro );
 /// This sets upper and lower bounds on distances to be used in DRMSD 
   void setBoundsOnDistances( bool dopbc, double lbound=0.0, double ubound=std::numeric_limits<double>::max( ) );
 /// Check that similar comparisons are being performed - perhaps this is needed ask Davide? GAT
 //  void check( ReferenceConfiguration* , ReferenceConfiguration* );
-  void read( const PDB& );
+  virtual void read( const PDB& );
+  virtual void setup_targets();
   void setReferenceAtoms( const std::vector<Vector>& conf, const std::vector<double>& align_in, const std::vector<double>& displace_in );
   double calc( const std::vector<Vector>& pos, const Pbc& pbc, ReferenceValuePack& myder, const bool& squared ) const ;
 };

user-doc/Installation.txt

@@ -504,6 +504,62 @@ Once ALMOST is installed, PLUMED 2 can then be configured with ALMOST enabled:
 \endverbatim
 with ALMOST_INSTALL_PATH set to the full path to the ALMOST installation folder.
 
+\section installingonacluster Installing PLUMED on a cluster
+
+If you are installing PLUMED on a cluster and you want several users to take advantage of it
+consider the following suggestions.
+
+First of all, we highly recommend using the module file that PLUMED provides to set up the environment.
+Just edit it as necessary to make it suitable for your environment.
+
+Notice that PLUMED can take advantage of many additionaly features if specific libraries are available upon
+compiling it. Install libmatheval first and check if PLUMED `./configure` is detecting it. Libmatheval is a must have with PLUMED.
+If someone uses gromacs, install libxdrfile first and check if PLUMED `./configure` is detecting it.
+PLUMED will be able to write trr/xtc file, simplifying analysis.
+
+Try to patch all MD codes with the `--runtime` option. This will allow independent update of PLUMED and MD codes.
+  Users will be able to combine any of the installed gromacs/amber/etc versions with any of the installed PLUMED versions.
+Notice that it is sometime claimed that statically linked codes are faster. In our experience, this is not true.
+In case you absolutely need a static executable, be ready to face non trivial linking issues. PLUMED is written in C++,
+thus required the appropriate C++ library to be linked, and might require additional libraries (e.g. libmatheval).
+
+Sometime we make small fixes on the patches. For this reason, keep track of which version of PLUMED you used
+to patch each of the MD code. Perhaps you can call the MD code modules with names such as `gromacs/4.6.7p1`,
+`gromacs/4.6.7p2` and write somewhere in the module file which version of PLUMED you used. Alternatively, call them
+something like `gromacs/4.6.7p2.2.0`. In this way, when we report a bug on the mailing list, users will know if the version
+they are using is affected by it.
+
+Usually it is not necessary to install both a MPI and a non-MPI PLUMED version. PLUMED library only calls MPI functions
+when the MD code is compiled with MPI. PLUMED executable calls MPI functions only when it is invoked without `--no-mpi`.
+In many machines it is thus sufficient to run the plumed executable on the login node as
+\verbatim
+> plumed --no-mpi
+\endverbatim
+even though PLUMED was compiled with MPI and the login node does not support MPI.
+The only case where you might need two different PLUMED installation for compute
+and login node is when you are cross compiling.
+
+PLUMED needs to be well optimized to run efficiently.
+If you need a single PLUMED binary to run efficiency on machines with different levels of hardware (e.g.: some
+of your workstations support AVX and some do not), with intel compiler you can use something like
+\verbatim
+./configure CXX=mpicxx CXXFLAGS="-O3 -axSSE2,AVX"
+\endverbatim
+It will take more time to compile but it will allow you to use a single module. Otherwise, you should install two
+PLUMED version with different optimization levels.
+
+Using modules, it is not necessary to make the PLUMED module explicitly dependent on the used library. Imagine a
+scenario where you first installed a module `libmatheval`, then load it while you compile PLUMED. If you
+provide the following option to configure `LDFLAGS="-Wl,-rpath,$LD_LIBRARY_PATH"`, the PLUMED executable and
+library will remember where libmatheval is, without the need to load libmatheval module at runtime.
+Notice that this trick often does not work for fundamental libraries such as C++ and MPI library. As a consequence,
+usually the PLUMED module should load the compiler and MPI modules.
+
+\attention
+In case you found out how to compile PLUMED on some fancy architecture please share your tricks! You can
+either post it in your blog, send it to the mailing list, or ask as to update this paragraph in the manual, we will
+be happy to do so.
+
 \section installinghints Other hints
 
 We here collect a list of suggestions that might be useful on particular

vim/vimsyntax.sh

@@ -26,8 +26,8 @@ endif
 let b:current_syntax="plumedf"
 
 if exists("g:plumed_shortcuts")
-  map <F3> :PMinus<CR>
-  map <F4> :PPlus<CR>
+  noremap <buffer> <F3> :PMinus<CR>
+  noremap <buffer> <F4> :PPlus<CR>
 endif
 
 command! -nargs=0 -count=1 PPlus call PlumedMove(<count>)
@@ -145,15 +145,15 @@ endif
 let b:current_syntax="plumed"
 
 if exists("g:plumed_shortcuts")
-  noremap  <F2> <Esc>:PHelp<CR>
-  inoremap <F2> <C-o>:PHelp<CR>
+  noremap  <buffer> <F2> :PHelp<CR>
+  inoremap <buffer> <F2> <Esc>:PHelp<CR>
 endif
 
 " path for plumed plugin
 let s:path=expand('<sfile>:p:h:h')
 
 " All except space and hash are in word
-set iskeyword=33,34,36-126
+setlocal iskeyword=33,34,36-126
 
 " Matching dots, possibly followed by a comment
 " Only dots are part of the match
@@ -329,6 +329,10 @@ fun! PlumedContextManual()
       execute 'rightbelow split | view ' name
     endif
     let b:plumed_helpfile=1
+" this is to allow closing the window with F2
+    if exists("g:plumed_shortcuts")
+      noremap  <buffer> <F2> :PHelp<CR>
+    endif
   endif
 endfunction