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

README

@@ -20,7 +20,7 @@ INSTALL
 
 Extensive installation instructions are in the user documentation.
 Links to precompiled versions of the documentation can be found here:
-http://www.plumed-code.org/documentation
+http://www.plumed.org/documentation
 
 Needed software:
 * GNU make

developer-doc/PlumedDeveloperHeader.html

@@ -24,7 +24,7 @@ $mathjax
 <tbody>
 <tr style="height: 30px;">
 <td valign="center"> &nbsp; <img src="pigeon.png" width="120"/></td>
-<td style="padding-left: 0.2em;" width="74%"> <a href="http://www.plumed-code.org"> <img src="logo.png" width="400" /> </td>
+<td style="padding-left: 0.2em;" width="74%"> <a href="http://www.plumed.org"> <img src="logo.png" width="400" /> </td>
 <td style="padding-left: 0.2em;" align="right"> <a href="../../user-doc/html/index.html"> <img src="developer-logo.png" width="180" /> </a> </td>
 </tr>
 </tbody>

src/bias/PBMetaD.cpp

@@ -254,8 +254,8 @@ void PBMetaD::registerKeywords(Keywords& keys){
 }
 
 PBMetaD::~PBMetaD(){
-  for(int i=0; i<BiasGrids_.size();   ++i) delete BiasGrids_[i];
-  for(int i=0; i<hillsOfiles_.size(); ++i){
+  for(unsigned i=0; i<BiasGrids_.size();   ++i) delete BiasGrids_[i];
+  for(unsigned i=0; i<hillsOfiles_.size(); ++i){
    hillsOfiles_[i]->close();
    delete hillsOfiles_[i];
   }
@@ -263,8 +263,8 @@ PBMetaD::~PBMetaD(){
 
 PBMetaD::PBMetaD(const ActionOptions& ao):
 PLUMED_BIAS_INIT(ao),
-height0_(std::numeric_limits<double>::max()), biasf_(1.0), kbt_(0.0),
-grid_(false), stride_(0), welltemp_(false),
+grid_(false), height0_(std::numeric_limits<double>::max()),
+biasf_(1.0), kbt_(0.0), stride_(0), welltemp_(false),
 multiple_w(false), doInt_(false), isFirstStep(true)
 {
 
@@ -429,7 +429,7 @@ multiple_w(false), doInt_(false), isFirstStep(true)
   }
 
 // read Gaussians if restarting
-  for(int i=0;i<hillsfname.size();++i){
+  for(unsigned i=0;i<hillsfname.size();++i){
    IFile *ifile = new IFile();
    ifile->link(*this);
    if(ifile->FileExist(hillsfname[i])){
@@ -444,8 +444,19 @@ multiple_w(false), doInt_(false), isFirstStep(true)
    }
   }
 
+  comm.Barrier();
+
+// this barrier is needed when using walkers_mpi
+// to be sure that all files have been read before
+// backing them up
+// it should not be used when walkers_mpi is false otherwise
+// it would introduce troubles when using replicas without METAD
+// (e.g. in bias exchange with a neutral replica)
+// see issue #168 on github
+  if(comm.Get_rank()==0 && multiple_w) multi_sim_comm.Barrier();
+
 // open hills files for writing
- for(int i=0;i<hillsfname.size();++i){
+ for(unsigned i=0;i<hillsfname.size();++i){
   OFile *ofile = new OFile();
   ofile->link(*this);
   string hillsfname_tmp = hillsfname[i];

src/core/PlumedMain.cpp

@@ -489,7 +489,7 @@ void PlumedMain::init(){
   log<<"Please cite this paper when using PLUMED ";
   log<<cite("Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput. Phys. Commun. 185, 604 (2014)");
   log<<"\n";
-  log<<"For further information see the PLUMED web page at http://www.plumed-code.org\n";
+  log<<"For further information see the PLUMED web page at http://www.plumed.org\n";
   log.printf("Molecular dynamics engine: %s\n",MDEngine.c_str());
   log.printf("Precision of reals: %d\n",atoms.getRealPrecision());
   log.printf("Running over %d %s\n",comm.Get_size(),(comm.Get_size()>1?"nodes":"node"));
@@ -525,7 +525,10 @@ void PlumedMain::readInputFile(std::string str){
   std::vector<std::string> words;
   while(Tools::getParsedLine(ifile,words) && words[0]!="ENDPLUMED") readInputWords(words);
   log.printf("END FILE: %s\n",str.c_str());
-  log.flush();	
+  log.flush();
+
+  //comm.Barrier();	
+  //if(comm.Get_rank()==0) multi_sim_comm.Barrier();	
 
   pilots=actionSet.select<ActionPilot*>();
 }

user-doc/PlumedUserHeader.html

@@ -24,7 +24,7 @@ $mathjax
 <tbody>
 <tr style="height: 30px;">
 <td valign="center"> &nbsp; <img src="pigeon.png" width="120"/></td>
-<td style="padding-left: 0.2em;" width="74%"> <a href="http://www.plumed-code.org"> <img src="logo.png" width="400" /> </td>
+<td style="padding-left: 0.2em;" width="74%"> <a href="http://www.plumed.org"> <img src="logo.png" width="400" /> </td>
 <td style="padding-left: 0.2em;" align="right"> <a href="../../developer-doc/html/index.html"> <img src="user-logo.png" width="180" /> </a> </td>
 </tr>
 </tbody>