diff --git a/src/core/ActionWithArguments.cpp b/src/core/ActionWithArguments.cpp
index 2490129bb2ec01c08ff0a3d82d4cf9668461fd71..b492410ca7a7c1252890dc3b9f2930fd3d206fb5 100644
--- a/src/core/ActionWithArguments.cpp
+++ b/src/core/ActionWithArguments.cpp
@@ -98,10 +98,9 @@ void ActionWithArguments::interpretArgumentList(const std::vector<std::string>&
std::vector<std::string> ss=all[j]->getComponentsVector();
for(unsigned k=0;k<ss.size();++k){
unsigned ll=strlen(ss[k].c_str())+1;
- char*str;
- str=new char [ll];
- strcpy(str,ss[k].c_str());
- char *ppstr=str;
+ std::vector<char> str(ll);
+ strcpy(&str[0],ss[k].c_str());
+ const char *ppstr=&str[0];
if(!regexec(preg, ppstr , preg->re_nsub, pmatch, 0)) {
log.printf(" Something matched with \"%s\" : ",ss[k].c_str());
do {
@@ -123,7 +122,6 @@ void ActionWithArguments::interpretArgumentList(const std::vector<std::string>&
ppstr += pmatch[0].rm_eo; /* Restart from last match */
} while(!regexec(preg,ppstr,preg->re_nsub,pmatch,0));
}
- delete [] str;
}
};
regfree(preg);
diff --git a/src/core/Atoms.cpp b/src/core/Atoms.cpp
index 70f39aaa76f5fb7d1efb23c3bc46a5979ba31385..2c3a5fbdcf1617ca1878d44dc137d21b1394f383 100644
--- a/src/core/Atoms.cpp
+++ b/src/core/Atoms.cpp
@@ -381,8 +381,9 @@ void Atoms::setAtomsContiguous(int start){
}
void Atoms::setRealPrecision(int p){
+ MDAtomsBase *x=MDAtomsBase::create(p);
delete mdatoms;
- mdatoms=MDAtomsBase::create(p);
+ mdatoms=x;
}
int Atoms::getRealPrecision()const{
diff --git a/src/core/CLToolMain.cpp b/src/core/CLToolMain.cpp
index 09d20edc03de851c01cac43e3d4f5b1f480b03d0..f60bca99d04489358648b0109aee9b55f52546a4 100644
--- a/src/core/CLToolMain.cpp
+++ b/src/core/CLToolMain.cpp
@@ -76,15 +76,18 @@ void CLToolMain::cmd(const std::string& word,void*val){
} else if(word=="run"){
CHECK_NULL(val,word);
argc=argv.size();
- char**v=new char* [argc];
+ int n=0; for(int i=0;i<argc;++i) n+=argv[i].length()+1;
+ std::vector<char> args(n);
+ std::vector<char*> v(argc);
+ char* ptr=&args[0];
for(int i=0;i<argc;++i){
- v[i]=new char [argv[i].length()+1];
- for(unsigned c=0;c<argv[i].length();++c) v[i][c]=argv[i][c];
- v[i][argv[i].length()]=0;
+ v[i]=ptr;
+ for(unsigned c=0;c<argv[i].length();++c){
+ *ptr=argv[i][c]; ptr++;
+ }
+ *ptr=0; ptr++;
}
- int ret=run(argc,v,in,out,comm);
- for(int i=0;i<argc;++i) delete [] v[i];
- delete [] v;
+ int ret=run(argc,&v[0],in,out,comm);
*static_cast<int*>(val)=ret;
} else {
plumed_merror("cannot interpret cmd(\"CLTool " + word + "\"). check plumed developers manual to see the available commands.");
diff --git a/src/core/PlumedMain.cpp b/src/core/PlumedMain.cpp
index d28039dbf6297a264d799f2be6f13c79ad9807f6..8e92c93a62d99b710561827b97606bbfd0b7dd21 100644
--- a/src/core/PlumedMain.cpp
+++ b/src/core/PlumedMain.cpp
@@ -547,7 +547,8 @@ void PlumedMain::readInputWords(const std::vector<std::string> & words){
log<<"I cannot understand line:";
for(unsigned i=0;i<interpreted.size();++i) log<<" "<<interpreted[i];
log<<"\n";
- exit(1);
+ log.flush();
+ plumed_error();
};
action->checkRead();
actionSet.push_back(action);
diff --git a/src/function/FuncSumHills.cpp b/src/function/FuncSumHills.cpp
index 21843d1813d6990499bd2f038402e8b5e2f2e870..25ed19207d65c136961d338ee9d9c7b5ec26763f 100644
--- a/src/function/FuncSumHills.cpp
+++ b/src/function/FuncSumHills.cpp
@@ -364,11 +364,10 @@ historep(NULL)
}
if(integratehills) {
- FilesHandler *hillsHandler;
- hillsHandler=new FilesHandler(hillsFiles,parallelread,*this, log);
+ FilesHandler hillsHandler(hillsFiles,parallelread,*this, log);
vector<double> vmin,vmax;
vector<unsigned> vbin;
- hillsHandler->getMinMaxBin(tmphillsvalues,comm,vmin,vmax,vbin);
+ hillsHandler.getMinMaxBin(tmphillsvalues,comm,vmin,vmax,vbin);
log<<" found boundaries from hillsfile: \n";
gmin.resize(vmin.size());
gmax.resize(vmax.size());
@@ -382,15 +381,13 @@ historep(NULL)
Tools::convert(vmax[i],gmax[i]);
log<<" variable "<< getPntrToArgument(i)->getName()<<" min: "<<gmin[i]<<" max: "<<gmax[i]<<" nbin: "<<gbin[i]<<"\n";
}
- delete hillsHandler;
}
// if at this stage bins are not there then do it with histo
if(gmin.size()==0){
- FilesHandler *histoHandler;
- histoHandler=new FilesHandler(histoFiles,parallelread,*this, log);
+ FilesHandler histoHandler(histoFiles,parallelread,*this, log);
vector<double> vmin,vmax;
vector<unsigned> vbin;
- histoHandler->getMinMaxBin(tmphistovalues,comm,vmin,vmax,vbin,histoSigma);
+ histoHandler.getMinMaxBin(tmphistovalues,comm,vmin,vmax,vbin,histoSigma);
log<<" found boundaries from histofile: \n";
gmin.resize(vmin.size());
gmax.resize(vmax.size());
@@ -404,7 +401,6 @@ historep(NULL)
Tools::convert(vmax[i],gmax[i]);
log<<" variable "<< proj[i] <<" min: "<<gmin[i]<<" max: "<<gmax[i]<<" nbin: "<<gbin[i]<<"\n";
}
- delete histoHandler;
}
log<<" done!\n";
log<<" \n";
@@ -529,9 +525,9 @@ historep(NULL)
if(integratehills){
log<<" Bias: Projecting on subgrid... \n";
- BiasWeight *Bw=new BiasWeight(beta);
+ BiasWeight Bw(beta);
Grid biasGrid=*(biasrep->getGridPtr());
- Grid smallGrid=biasGrid.project(proj,Bw);
+ Grid smallGrid=biasGrid.project(proj,&Bw);
OFile gridfile; gridfile.link(*this);
std::ostringstream ostr;ostr<<nfiles;
string myout;
@@ -543,7 +539,6 @@ historep(NULL)
smallGrid.writeToFile(gridfile);
gridfile.close();
if(!ibias)integratehills=false;// once you get to the final bunch just give up
- delete Bw;
}
// this should be removed
if(integratehisto){
@@ -616,8 +611,6 @@ historep(NULL)
nfiles++;
}
- if(hillsHandler) delete hillsHandler;
- if(histoHandler) delete histoHandler;
return;
}
diff --git a/src/generic/DumpAtoms.cpp b/src/generic/DumpAtoms.cpp
index 1ec293ccb6e2b37489e343a0973c7a486affb5f7..2358cbe305ad863517b3f64e8aa88101785ba1fc 100644
--- a/src/generic/DumpAtoms.cpp
+++ b/src/generic/DumpAtoms.cpp
@@ -278,17 +278,19 @@ void DumpAtoms::update(){
} else if(type=="xtc" || type=="trr"){
matrix box;
const Tensor & t(getPbc().getBox());
- rvec* pos=new rvec [getNumberOfAtoms()];
- for(int i=0;i<3;i++) for(int j=0;j<3;j++) box[i][j]=lenunit*t(i,j);
- for(int i=0;i<getNumberOfAtoms();i++) for(int j=0;j<3;j++) pos[i][j]=lenunit*getPosition(i)(j);
int natoms=getNumberOfAtoms();
int step=getStep();
float time=getTime()/plumed.getAtoms().getUnits().getTime();
float precision=Tools::fastpow(10.0,iprecision);
+ for(int i=0;i<3;i++) for(int j=0;j<3;j++) box[i][j]=lenunit*t(i,j);
+ rvec* pos=new rvec [natoms];
+// Notice that code below cannot throw any exception.
+// Thus, this pointer is excepton safe
+ for(int i=0;i<natoms;i++) for(int j=0;j<3;j++) pos[i][j]=lenunit*getPosition(i)(j);
if(type=="xtc"){
- write_xtc(xd,natoms,step,time,box,pos,precision);
+ write_xtc(xd,natoms,step,time,box,&pos[0],precision);
} else if(type=="trr"){
- write_trr(xd,natoms,step,time,0.0,box,pos,NULL,NULL);
+ write_trr(xd,natoms,step,time,0.0,box,&pos[0],NULL,NULL);
}
delete [] pos;
#endif