diff --git a/src/analysis/Analysis.cpp b/src/analysis/Analysis.cpp
index cedef3453d271668f34ca9199ff0da95cf0c226d..272ed5f1f77676a5d02c626436134c12f1c43ca5 100644
--- a/src/analysis/Analysis.cpp
+++ b/src/analysis/Analysis.cpp
@@ -222,8 +222,9 @@ argument_names(getNumberOfArguments())
}
void Analysis::readDataFromFile( const std::string& filename ){
- FILE* fp=fopen(filename.c_str(),"r"); double tstep, oldtstep;
+ FILE* fp=fopen(filename.c_str(),"r");
if(fp!=NULL){
+ double tstep, oldtstep;
bool do_read=true, first=true;
while (do_read) {
PDB mypdb;
diff --git a/src/bias/MetaD.cpp b/src/bias/MetaD.cpp
index d6e06289a9fdc661f8bc5e7b50912ba0d70ec5c3..b9e92fa8153875356375ecac7d130a1533cab943 100644
--- a/src/bias/MetaD.cpp
+++ b/src/bias/MetaD.cpp
@@ -1056,10 +1056,10 @@ double MetaD::evaluateGaussian
if(cv.size()>0) pcv=&cv[0];
if(doInt_){
plumed_dbg_assert(cv.size()==1);
- pcv=&(tmpcv[0]);
tmpcv[0]=cv[0];
if(cv[0]<lowI_) tmpcv[0]=lowI_;
if(cv[0]>uppI_) tmpcv[0]=uppI_;
+ pcv=&(tmpcv[0]);
}
if(hill.multivariate){
unsigned k=0;
diff --git a/src/bias/PBMetaD.cpp b/src/bias/PBMetaD.cpp
index 66ae2e20a4830a0cc7261f4ec65cb485fc2fb0f9..9606572ca797c4239cfc6ced3e4d882b24490b0f 100644
--- a/src/bias/PBMetaD.cpp
+++ b/src/bias/PBMetaD.cpp
@@ -219,7 +219,7 @@ private:
std::string fmt;
public:
- PBMetaD(const ActionOptions&);
+ explicit PBMetaD(const ActionOptions&);
~PBMetaD();
void calculate();
void update();
@@ -633,10 +633,10 @@ double PBMetaD::evaluateGaussian
if(cv.size()>0) pcv=&cv[0];
if(doInt_){
plumed_assert(cv.size()==1);
- pcv=&(tmpcv[0]);
tmpcv[0]=cv[0];
if(cv[0]<lowI_[iarg]) tmpcv[0]=lowI_[iarg];
if(cv[0]>uppI_[iarg]) tmpcv[0]=uppI_[iarg];
+ pcv=&(tmpcv[0]);
}
double dp = difference(0,hill.center[0],pcv[0]) / hill.sigma[0];
double dp2 = 0.5 * dp * dp;
diff --git a/src/core/ActionWithArguments.cpp b/src/core/ActionWithArguments.cpp
index ed99a28a25f5366409376c2e89039b8a712da904..6010bf054317c12a22f3ed74ef90cb8eb26d566b 100644
--- a/src/core/ActionWithArguments.cpp
+++ b/src/core/ActionWithArguments.cpp
@@ -55,9 +55,8 @@ void ActionWithArguments::interpretArgumentList(const std::vector<std::string>&
for(unsigned i=0;i<c.size();i++){
// is a regex? then just interpret it. The signal is ()
std::size_t found1 = c[i].find("(");
- std::size_t found2 ;
if(found1!=std::string::npos){
- found2=c[i].find(")",found1+1,1); // find it again
+ std::size_t found2=c[i].find(")",found1+1,1); // find it again
if(found2!=std::string::npos){
// start regex parsing
#ifdef __PLUMED_HAS_CREGEX
@@ -84,10 +83,8 @@ void ActionWithArguments::interpretArgumentList(const std::vector<std::string>&
std::vector<ActionWithValue*> all=plumed.getActionSet().select<ActionWithValue*>();
if( all.empty() ) error("your input file is not telling plumed to calculate anything");
for(unsigned j=0;j<all.size();j++){
- std::string thisargument=all[j]->getLabel();
std::vector<std::string> ss=all[j]->getComponentsVector();
for(unsigned k=0;k<ss.size();++k){
- thisargument=ss[k];
unsigned ll=strlen(ss[k].c_str())+1;
char*str;
str=new char [ll];
diff --git a/src/core/MDAtoms.cpp b/src/core/MDAtoms.cpp
index c9f564e2b8a910bce88cf91eb78bf843d576b8e0..e4cff7366adeae42b920d05a3f79fc70527e9215 100644
--- a/src/core/MDAtoms.cpp
+++ b/src/core/MDAtoms.cpp
@@ -144,8 +144,7 @@ void MDAtomsTyped<T>::updateVirial(const Tensor&virial)const{
template <class T>
void MDAtomsTyped<T>::updateForces(const vector<int>&index,const vector<Vector>&forces){
- unsigned nt=OpenMP::getGoodNumThreads(fx,stride*index.size());
-#pragma omp parallel for num_threads(nt)
+#pragma omp parallel for num_threads(OpenMP::getGoodNumThreads(fx,stride*index.size()))
for(unsigned i=0;i<index.size();++i){
fx[stride*i]+=scalef*T(forces[index[i]][0]);
fy[stride*i]+=scalef*T(forces[index[i]][1]);
@@ -156,8 +155,7 @@ void MDAtomsTyped<T>::updateForces(const vector<int>&index,const vector<Vector>&
template <class T>
void MDAtomsTyped<T>::rescaleForces(const vector<int>&index,double factor){
if(virial) for(unsigned i=0;i<3;i++)for(unsigned j=0;j<3;j++) virial[3*i+j]*=T(factor);
- unsigned nt=OpenMP::getGoodNumThreads(fx,stride*index.size());
-#pragma omp parallel for num_threads(nt)
+#pragma omp parallel for num_threads(OpenMP::getGoodNumThreads(fx,stride*index.size()))
for(unsigned i=0;i<index.size();++i){
fx[stride*i]*=T(factor);
fy[stride*i]*=T(factor);
diff --git a/src/core/SetupMolInfo.cpp b/src/core/SetupMolInfo.cpp
index 13b33234a63b4e4daff1f14a1bc52c7de1800c90..af6a4d51383d92301b7695e3ad7768c601946e30 100644
--- a/src/core/SetupMolInfo.cpp
+++ b/src/core/SetupMolInfo.cpp
@@ -97,7 +97,6 @@ pdb(*new(PDB))
void SetupMolInfo::getBackbone( std::vector<std::string>& restrings, const std::string& fortype, std::vector< std::vector<AtomNumber> >& backbone ){
if( fortype!=mytype ) error("cannot calculate a variable designed for " + fortype + " molecules for molecule type " + mytype );
if( MolDataClass::numberOfAtomsPerResidueInBackbone( mytype )==0 ) error("backbone is not defined for molecule type " + mytype );
- bool useter=false; // This is used to deal with terminal groups in WHOLEMOLECULES
if( read_backbone.size()!=0 ){
if( restrings.size()!=1 ) error("cannot interpret anything other than all for residues when using CHAIN keywords");
@@ -108,6 +107,7 @@ void SetupMolInfo::getBackbone( std::vector<std::string>& restrings, const std::
for(unsigned j=0;j<read_backbone[i].size();++j) backbone[i][j]=read_backbone[i][j];
}
} else {
+ bool useter=false; // This is used to deal with terminal groups in WHOLEMOLECULES
if( restrings.size()==1 ){
useter=( restrings[0].find("ter")!=std::string::npos );
if( restrings[0].find("all")!=std::string::npos ){
diff --git a/src/function/FuncPathMSD.cpp b/src/function/FuncPathMSD.cpp
index ec1392aedbaab9bd1d97c12d74be29a8dc537ec5..193fb149cd7f8c9273295e4020728d5dc64153c8 100644
--- a/src/function/FuncPathMSD.cpp
+++ b/src/function/FuncPathMSD.cpp
@@ -208,7 +208,6 @@ void FuncPathMSD::calculate(){
// log.printf("NOW CALCULATE! \n");
double s_path=0.;
double partition=0.;
- double tmp;
if(neighpair.empty()){ // at first step, resize it
neighpair.resize(allArguments.size());
for(unsigned i=0;i<allArguments.size();i++)neighpair[i].first=allArguments[i];
@@ -229,7 +228,7 @@ void FuncPathMSD::calculate(){
int n=0;
for(pairiter it=neighpair.begin();it!=neighpair.end();++it){
double expval=(*it).second;
- tmp=lambda*expval*(s_path-(indexmap[(*it).first]))/partition;
+ double tmp=lambda*expval*(s_path-(indexmap[(*it).first]))/partition;
setDerivative(val_s_path,n,tmp);
setDerivative(val_z_path,n,expval/partition);
n++;
diff --git a/src/generic/DumpAtoms.cpp b/src/generic/DumpAtoms.cpp
index e70daee115907e507497cfd7e6a216bf45de420d..a7c87a184a7f038c4ac7c2dacec00493db14d6a8 100644
--- a/src/generic/DumpAtoms.cpp
+++ b/src/generic/DumpAtoms.cpp
@@ -208,9 +208,9 @@ DumpAtoms::DumpAtoms(const ActionOptions&ao):
of.link(*this);
of.open(file);
std::string path=of.getPath();
- std::string mode=of.getMode();
log<<" Writing on file "<<path<<"\n";
#ifdef __PLUMED_HAS_XDRFILE
+ std::string mode=of.getMode();
if(type=="xtc"){
of.close();
xd=xdrfile_open(path.c_str(),mode.c_str());
diff --git a/src/tools/Grid.cpp b/src/tools/Grid.cpp
index 1fe6d0e6219dc3d8546b28ac49cf13e183d56d9e..52b97fe9b4e4e672c51056917edfc7e9c03388a4 100644
--- a/src/tools/Grid.cpp
+++ b/src/tools/Grid.cpp
@@ -338,12 +338,12 @@ void Grid::addKernel( const KernelFunctions& kernel ){
}
}
- double newval; std::vector<double> der( dimension_ );
+ std::vector<double> der( dimension_ );
for(unsigned i=0;i<neighbors.size();++i){
index_t ineigh=neighbors[i];
getPoint( ineigh, xx );
for(unsigned j=0;j<dimension_;++j) vv[j]->set(xx[j]);
- newval = kernel.evaluate( vv, der, usederiv_ );
+ double newval = kernel.evaluate( vv, der, usederiv_ );
if( usederiv_ ) addValueAndDerivatives( ineigh, newval, der );
else addValue( ineigh, newval );
}
diff --git a/src/tools/RMSD.cpp b/src/tools/RMSD.cpp
index 5cd3197c8fcc58fd363204c5c494920f58add3a3..b5cad41683682314630c4f67b4fc81d35a674d55 100644
--- a/src/tools/RMSD.cpp
+++ b/src/tools/RMSD.cpp
@@ -970,7 +970,6 @@ std::vector<Vector> RMSDCoreData::getDDistanceDPositions(){
plumed_massert(!retrieve_only_rotation,"You used only_rotation=true in doCoreCalc therefore you cannot retrieve this information now");
if(!hasDistance)plumed_merror("getDPositionsDerivatives needs to calculate the distance via getDistance first !");
if(!isInitialized)plumed_merror("getDPositionsDerivatives needs to initialize the coreData first!");
- vector<Vector> ddist_tmp(n);
Vector csum;
Vector tmp1,tmp2;
for(unsigned iat=0;iat<n;iat++){
@@ -1003,7 +1002,6 @@ std::vector<Vector> RMSDCoreData::getDDistanceDReference(){
derivatives.resize(n);
double prefactor=1.0;
if(!distanceIsMSD) prefactor*=0.5/dist;
- vector<Vector> ddist_tmp(n);
Vector csum,tmp1,tmp2;
plumed_massert(!retrieve_only_rotation,"You used only_rotation=true in doCoreCalc therefore you cannot retrieve this information now");
@@ -1046,7 +1044,6 @@ std::vector<Vector> RMSDCoreData::getDDistanceDReferenceSOMA(){
derivatives.resize(n);
double prefactor=1.0;
if(!distanceIsMSD) prefactor*=0.5/dist;
- vector<Vector> ddist_tmp(n);
Vector csum,tmp1,tmp2;
plumed_massert(!retrieve_only_rotation,"You used only_rotation=true in doCoreCalc therefore you cannot retrieve this information now");