diff --git a/src/ActionWithDistribution.cpp b/src/ActionWithDistribution.cpp
index 2fedc367aec2c98898cbcf1ca9ac1b2941dcf2c7..e158da78cabf165ce12bdc425e2015778d4c1bd4 100644
--- a/src/ActionWithDistribution.cpp
+++ b/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 ){
diff --git a/src/BiasMetaD.cpp b/src/BiasMetaD.cpp
index 06c0e28d63aaf72118f414efcafaf96fa31410dd..f864d61af526498ec125a3e33923041176a1f6eb 100644
--- a/src/BiasMetaD.cpp
+++ b/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_;
diff --git a/src/CLToolMain.cpp b/src/CLToolMain.cpp
index 7c9040022c87a643f4202ef31acfac1058d5ece2..fff30417aa941ddee5814c4a5256bd5537344d71 100644
--- a/src/CLToolMain.cpp
+++ b/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){
diff --git a/src/ColvarAntibetaRMSD.cpp b/src/ColvarAntibetaRMSD.cpp
index 8198b1c1e70375b0b8523fc26f594b5b9c08e629..8a10de10e78a7699bd58b24c3464d9951e343c70 100644
--- a/src/ColvarAntibetaRMSD.cpp
+++ b/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;
diff --git a/src/FlexibleBin.cpp b/src/FlexibleBin.cpp
index 0ad7e3ce3921993820c194af426f4f9a05f861db..064f49b91e2421256ef46aec8844aec016d82457 100644
--- a/src/FlexibleBin.cpp
+++ b/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;
diff --git a/src/FlexibleBin.h b/src/FlexibleBin.h
index b80a6ea91cf182b881bfdcb99e13e9dffe92733b..da5ef6c146a17dfbdfbdbf5fd94bcb22acd64411 100644
--- a/src/FlexibleBin.h
+++ b/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
diff --git a/src/Grid.cpp b/src/Grid.cpp
index b842a473b0c7a7eca734a6ade7069812f644a644..0a19659f264876925f3f1f284f07a39efc661edb 100644
--- a/src/Grid.cpp
+++ b/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);
diff --git a/src/NeighborList.cpp b/src/NeighborList.cpp
index 40f1f57994d439640bb27ddb5ad5828e8db429d3..ebfc18a020905f01c3a3a2195b2e58e5b872d977 100644
--- a/src/NeighborList.cpp
+++ b/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){
diff --git a/src/PlumedMain.cpp b/src/PlumedMain.cpp
index 8facfdf86afb5b2f8387bf25beee1f9d919bd4f9..9317d490927837303d47baab4cc238f157072b03 100644
--- a/src/PlumedMain.cpp
+++ b/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: ");
diff --git a/src/RMSD.cpp b/src/RMSD.cpp
index 2922fa8bb29e16386f596438f4375314f4343ddc..108ac893e90c14fa78d4287dacfc8ddee8c993a1 100644
--- a/src/RMSD.cpp
+++ b/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 ){
diff --git a/src/Tools.cpp b/src/Tools.cpp
index 11190a9e5c2eac16eb92ca1ab2b060faa3968fac..1393b49b5cdde8a11bb54db8f271c67ecb3c453c 100644
--- a/src/Tools.cpp
+++ b/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;