Fixed warnings

src/ActionWithDistribution.cpp

@@ -129,6 +129,7 @@ Vessel* ActionWithDistribution::getVessel( const std::string& name ){
      }
   }
   error("there is no vessel with name " + name);
+  return NULL;
 }
 
 void ActionWithDistribution::calculateAllVessels( const int& stepn ){

src/BiasMetaD.cpp

@@ -122,14 +122,14 @@ private:
   PlumedOFile hillsOfile_;
   Grid* BiasGrid_;
   FILE* gridfile_;
+  int wgridstride_; 
+  bool grid_;
   double height0_;
   double biasf_;
   double temp_;
-  double* dp_;
   int stride_;
-  int wgridstride_; 
   bool welltemp_;
-  bool grid_;
+  double* dp_;
   int adaptive_;
   FlexibleBin *flexbin;
   int mw_n_;

src/CLToolMain.cpp

@@ -178,7 +178,7 @@ int CLToolMain::run(int argc, char **argv,FILE*in,FILE*out,PlumedCommunicator& p
         "  [help|-h|--help]          : to print this help\n"
         "  [--has-mpi]               : fails if plumed is running with MPI\n"
         "  [--load LIB]              : loads a shared object (typically a plugin library)\n"
-        "  [--standalone-executable] : tells plumed not to look for commands implemented as scripts\n";
+        "  [--standalone-executable] : tells plumed not to look for commands implemented as scripts\n"
         "Commands:\n";
     fprintf(out,"%s",msg.c_str());
     for(unsigned j=0;j<availableCxx.size();++j){

src/ColvarAntibetaRMSD.cpp

@@ -112,7 +112,7 @@ s_cutoff(0)
   backnames[0]="N"; backnames[1]="CA"; backnames[2]="CB"; backnames[3]="C"; backnames[4]="O";
   readBackboneAtoms( backnames, chains );
 
-  bool intra_chain, inter_chain; 
+  bool intra_chain(false), inter_chain(false); 
   std::string style; parse("STYLE",style);
   if( style=="all" ){ 
       intra_chain=true; inter_chain=true;

src/FlexibleBin.cpp

@@ -128,7 +128,6 @@ vector<double> FlexibleBin::getMatrix() const{
 ///
 vector<double> FlexibleBin::getInverseMatrix() const{
 	unsigned ncv=paction->getNumberOfArguments();
-	unsigned dimension=ncv*(ncv+1)/2;	
 	Matrix<double> matrix(ncv,ncv); 
 	unsigned i,j,k;	
 	k=0;

src/FlexibleBin.h

@@ -31,10 +31,10 @@ class ActionWithArguments;
 
 class FlexibleBin{
 	private:
-		double sigma;	
 		const int type;
 		// this contains all the infos about the CVs including periodicity
 		ActionWithArguments *paction;
+		double sigma;	
 		// variance is the matrix that really matters
 		vector<double> variance;	
 		// this is only there

src/Grid.cpp

@@ -456,7 +456,7 @@ Grid* Grid::create(FILE* file, bool dosparse, bool dospline, bool doder)
  vector<double> dx=grid->getDx();
  double f,x;
  while(1){
-  int nread;
+  int nread=0;
   for(unsigned i=0;i<nvar;++i){nread=fscanf(file,"%1000lf",&x);xx[i]=x+dx[i]/2.0;}
   if(nread<1){break;}
   fscanf(file,"%1000lf",&f);

src/NeighborList.cpp

@@ -151,7 +151,7 @@ void NeighborList::setRequestList() {
 vector<AtomNumber>& NeighborList::getReducedAtomList() {
  std::vector< pair<unsigned,unsigned> > newneighbors;
  for(unsigned int i=0;i<size();++i){
-  unsigned newindex0,newindex1;
+  unsigned newindex0=0,newindex1=0;
   AtomNumber index0=fullatomlist_[neighbors_[i].first];
   AtomNumber index1=fullatomlist_[neighbors_[i].second];
   for(unsigned j=0;j<requestlist_.size();++j){

src/PlumedMain.cpp

@@ -61,10 +61,10 @@ PlumedMain::PlumedMain():
   actionSet(*new ActionSet(*this)),
   bias(0.0),
   exchangePatterns(*new(ExchangePatterns)),
-  novirial(false),
   restart(false),
   stopFlag(NULL),
-  stopNow(false)
+  stopNow(false),
+  novirial(false)
 {
   log.link(comm);
   log.setLinePrefix("PLUMED: ");

src/RMSD.cpp

@@ -30,8 +30,14 @@
 using namespace std;
 using namespace PLMD;
 
-RMSD::RMSD(const RMSD & oldrmsd): log(oldrmsd.log),alignmentMethod(oldrmsd.alignmentMethod),reference(oldrmsd.reference),align(oldrmsd.align),displace(oldrmsd.align),myoptimalalignment(oldrmsd.myoptimalalignment){
-}
+RMSD::RMSD(const RMSD & oldrmsd):
+  alignmentMethod(oldrmsd.alignmentMethod),
+  reference(oldrmsd.reference),
+  align(oldrmsd.align),
+  displace(oldrmsd.align),
+  myoptimalalignment(oldrmsd.myoptimalalignment),
+  log(oldrmsd.log)
+  {}
 
 void RMSD::set(const PDB&pdb, string mytype ){
 

src/Tools.cpp

@@ -141,7 +141,7 @@ bool Tools::getParsedLine(PlumedIFile& ifile,vector<string> & words){
   bool inside=false;
   int parlevel=0;
   bool mergenext=false;
-  while(stat=ifile.getline(line)){
+  while((stat=ifile.getline(line))){
     trimComments(line);
     trim(line);
     if(line.length()==0) continue;