From 53c606f4a4c32848ca3f00985c33cf1f4546d0c5 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Fri, 1 Sep 2017 10:10:32 +0200
Subject: [PATCH] unique_ptr: generic and cltools
---
src/cltools/Driver.cpp | 20 +++++++++++---------
src/cltools/SimpleMD.cpp | 7 +++----
src/cltools/pesmd.cpp | 5 +++--
src/generic/DumpAtoms.cpp | 6 ++----
src/generic/FitToTemplate.cpp | 13 ++++---------
src/generic/Read.cpp | 29 ++++++++++++++++-------------
6 files changed, 39 insertions(+), 41 deletions(-)
diff --git a/src/cltools/Driver.cpp b/src/cltools/Driver.cpp
index aa8a9deaf..e4a150740 100644
--- a/src/cltools/Driver.cpp
+++ b/src/cltools/Driver.cpp
@@ -30,6 +30,7 @@
#include <cstring>
#include <vector>
#include <map>
+#include <memory>
#include "tools/Units.h"
#include "tools/PDB.h"
#include "tools/FileBase.h"
@@ -287,10 +288,9 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc) {
std::string fakein;
bool debugfloat=parse("--debug-float",fakein);
if(debugfloat && sizeof(real)!=sizeof(float)) {
- CLTool* cl=cltoolRegister().create(CLToolOptions("driver-float")); //new Driver<float>(*this);
+ std::unique_ptr<CLTool> cl(cltoolRegister().create(CLToolOptions("driver-float")));
cl->setInputData(this->getInputData());
int ret=cl->main(in,out,pc);
- delete cl;
return ret;
}
@@ -358,7 +358,10 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc) {
molfile_plugin_t *api=NULL;
void *h_in=NULL;
molfile_timestep_t ts_in; // this is the structure that has the timestep
- ts_in.coords=NULL;
+// a std::unique_ptr<float> with the same scope as ts_in
+// it is necessary in order to store the pointer to ts_in.coords
+ std::unique_ptr<float[]> ts_in_coords;
+ ts_in.coords=ts_in_coords.get();
ts_in.A=-1; // we use this to check whether cell is provided or not
#endif
@@ -511,7 +514,8 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc) {
if(command_line_natoms>=0) natoms=command_line_natoms;
else error("this file format does not provide number of atoms; use --natoms on the command line");
}
- ts_in.coords = new float [3*natoms];
+ ts_in_coords.reset(new float [3*natoms]);
+ ts_in.coords = ts_in_coords.get();
#endif
} else if(trajectory_fmt=="xdr-xtc" || trajectory_fmt=="xdr-trr") {
#ifdef __PLUMED_HAS_XDRFILE
@@ -739,18 +743,17 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc) {
int localstep;
float time;
matrix box;
- rvec* pos=new rvec[natoms];
+ std::unique_ptr<rvec[]> pos(new rvec[natoms]);
float prec,lambda;
int ret;
- if(trajectory_fmt=="xdr-xtc") ret=read_xtc(xd,natoms,&localstep,&time,box,pos,&prec);
- if(trajectory_fmt=="xdr-trr") ret=read_trr(xd,natoms,&localstep,&time,&lambda,box,pos,NULL,NULL);
+ if(trajectory_fmt=="xdr-xtc") ret=read_xtc(xd,natoms,&localstep,&time,box,pos.get(),&prec);
+ if(trajectory_fmt=="xdr-trr") ret=read_trr(xd,natoms,&localstep,&time,&lambda,box,pos.get(),NULL,NULL);
if(stride==0) step=localstep;
if(ret==exdrENDOFFILE) break;
if(ret!=exdrOK) break;
for(unsigned i=0; i<3; i++) for(unsigned j=0; j<3; j++) cell[3*i+j]=box[i][j];
for(unsigned i=0; i<natoms; i++) for(unsigned j=0; j<3; j++)
coordinates[3*i+j]=real(pos[i][j]);
- delete [] pos;
#endif
} else {
if(trajectory_fmt=="xyz") {
@@ -944,7 +947,6 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc) {
#endif
#ifdef __PLUMED_HAS_MOLFILE_PLUGINS
if(h_in) api->close_file_read(h_in);
- if(ts_in.coords) delete [] ts_in.coords;
#endif
if(grex_log) fclose(grex_log);
diff --git a/src/cltools/SimpleMD.cpp b/src/cltools/SimpleMD.cpp
index 78a938fa5..b8272f20c 100644
--- a/src/cltools/SimpleMD.cpp
+++ b/src/cltools/SimpleMD.cpp
@@ -28,6 +28,7 @@
#include <cstdio>
#include <cmath>
#include <vector>
+#include <memory>
using namespace std;
@@ -443,10 +444,10 @@ private:
Random random; // random numbers stream
- PLMD::Plumed* plumed=NULL;
+ std::unique_ptr<Plumed> plumed;
// Commenting the next line it is possible to switch-off plumed
- plumed=new PLMD::Plumed;
+ plumed.reset(new PLMD::Plumed);
if(plumed) {
int s=sizeof(double);
@@ -608,8 +609,6 @@ private:
// close the statistic file if it was open:
if(write_statistics_fp) fclose(write_statistics_fp);
- if(plumed) delete plumed;
-
return 0;
}
diff --git a/src/cltools/pesmd.cpp b/src/cltools/pesmd.cpp
index 8479c73c7..210796b95 100755
--- a/src/cltools/pesmd.cpp
+++ b/src/cltools/pesmd.cpp
@@ -29,6 +29,7 @@
#include <cstdio>
#include <cmath>
#include <vector>
+#include <memory>
//+PLUMEDOC TOOLS pesmd
/*
@@ -183,7 +184,8 @@ public:
else if( lperiod ) error("invalid dimension for periodic potential must be 1, 2 or 3");
// Create plumed object and initialize
- PLMD::Plumed* plumed=new PLMD::Plumed; int s=sizeof(double);
+ std::unique_ptr<PLMD::Plumed> plumed(new PLMD::Plumed);
+ int s=sizeof(double);
plumed->cmd("setRealPrecision",&s);
if(Communicator::initialized()) plumed->cmd("setMPIComm",&pc.Get_comm());
plumed->cmd("setNoVirial");
@@ -309,7 +311,6 @@ public:
if( pc.Get_rank()==0 ) fprintf(fp,"%u %f %f %f \n", istep, istep*tstep, tke, therm_eng );
}
- delete plumed;
fclose(fp);
return 0;
diff --git a/src/generic/DumpAtoms.cpp b/src/generic/DumpAtoms.cpp
index bc98a58d2..f914d9bec 100644
--- a/src/generic/DumpAtoms.cpp
+++ b/src/generic/DumpAtoms.cpp
@@ -28,6 +28,7 @@
#include "core/Atoms.h"
#include "tools/Units.h"
#include <cstdio>
+#include <memory>
#include "core/SetupMolInfo.h"
#include "core/ActionSet.h"
@@ -308,16 +309,13 @@ void DumpAtoms::update() {
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
+ std::unique_ptr<rvec[]> pos(new rvec [natoms]);
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[0],precision);
} else if(type=="trr") {
write_trr(xd,natoms,step,time,0.0,box,&pos[0],NULL,NULL);
}
- delete [] pos;
#endif
} else plumed_merror("unknown file type "+type);
}
diff --git a/src/generic/FitToTemplate.cpp b/src/generic/FitToTemplate.cpp
index b227be8a1..2e45956b7 100644
--- a/src/generic/FitToTemplate.cpp
+++ b/src/generic/FitToTemplate.cpp
@@ -37,6 +37,7 @@
#include <vector>
#include <string>
+#include <memory>
using namespace std;
@@ -155,7 +156,7 @@ class FitToTemplate:
Vector center;
Vector shift;
// optimal alignment related stuff
- PLMD::RMSD* rmsd;
+ std::unique_ptr<PLMD::RMSD> rmsd;
Tensor rotation;
Matrix< std::vector<Vector> > drotdpos;
std::vector<Vector> positions;
@@ -167,7 +168,6 @@ class FitToTemplate:
public:
explicit FitToTemplate(const ActionOptions&ao);
- ~FitToTemplate();
static void registerKeywords( Keywords& keys );
void calculate();
void apply();
@@ -188,8 +188,7 @@ FitToTemplate::FitToTemplate(const ActionOptions&ao):
Action(ao),
ActionPilot(ao),
ActionAtomistic(ao),
- ActionWithValue(ao),
- rmsd(NULL)
+ ActionWithValue(ao)
{
string reference;
parse("REFERENCE",reference);
@@ -231,7 +230,7 @@ FitToTemplate::FitToTemplate(const ActionOptions&ao):
for(unsigned i=0; i<weights.size(); ++i) positions[i]-=center;
if(type=="OPTIMAL" or type=="OPTIMAL-FAST" ) {
- rmsd=new RMSD();
+ rmsd.reset(new RMSD());
rmsd->set(weights,weights_measure,positions,type,false,false);// note: the reference is shifted now with center in the origin
log<<" Method chosen for fitting: "<<rmsd->getMethod()<<" \n";
}
@@ -331,9 +330,5 @@ void FitToTemplate::apply() {
}
}
-FitToTemplate::~FitToTemplate() {
- if(rmsd) delete rmsd;
-}
-
}
}
diff --git a/src/generic/Read.cpp b/src/generic/Read.cpp
index bb81b915e..e6dee365e 100644
--- a/src/generic/Read.cpp
+++ b/src/generic/Read.cpp
@@ -26,6 +26,7 @@
#include "core/ActionSet.h"
#include "core/Atoms.h"
#include "tools/IFile.h"
+#include <memory>
namespace PLMD {
namespace generic {
@@ -71,12 +72,16 @@ private:
bool cloned_file;
unsigned nlinesPerStep;
std::string filename;
+/// Unique pointer with the same scope as ifile.
+ std::unique_ptr<IFile> ifile_ptr;
+/// Pointer to input file.
+/// It is either pointing to the content of ifile_ptr
+/// or to the file it is cloned from.
IFile* ifile;
- std::vector<Value*> readvals;
+ std::vector<std::unique_ptr<Value>> readvals;
public:
static void registerKeywords( Keywords& keys );
explicit Read(const ActionOptions&);
- ~Read();
void prepare();
void apply() {}
void calculate();
@@ -131,7 +136,8 @@ Read::Read(const ActionOptions&ao):
}
}
if( !cloned_file ) {
- ifile=new IFile();
+ ifile_ptr.reset(new IFile());
+ ifile=ifile_ptr.get();
if( !ifile->FileExist(filename) ) error("could not find file named " + filename);
ifile->link(*this);
ifile->open(filename);
@@ -153,25 +159,25 @@ Read::Read(const ActionOptions&ao):
ifile->scanFieldList( fieldnames );
for(unsigned i=0; i<fieldnames.size(); ++i) {
if( fieldnames[i].substr(0,dot)==label ) {
- readvals.push_back(new Value(this, fieldnames[i], false) ); addComponentWithDerivatives( fieldnames[i].substr(dot+1) );
+ readvals.emplace_back(new Value(this, fieldnames[i], false) ); addComponentWithDerivatives( fieldnames[i].substr(dot+1) );
if( ifile->FieldExist("min_" + fieldnames[i]) ) componentIsPeriodic( fieldnames[i].substr(dot+1), "-pi","pi" );
else componentIsNotPeriodic( fieldnames[i].substr(dot+1) );
}
}
} else {
- readvals.push_back(new Value(this, valread[0], false) ); addComponentWithDerivatives( name );
+ readvals.emplace_back(new Value(this, valread[0], false) ); addComponentWithDerivatives( name );
if( ifile->FieldExist("min_" + valread[0]) ) componentIsPeriodic( valread[0].substr(dot+1), "-pi", "pi" );
else componentIsNotPeriodic( valread[0].substr(dot+1) );
for(unsigned i=1; i<valread.size(); ++i) {
if( valread[i].substr(0,dot)!=label ) error("all values must be from the same Action when using READ");;
- readvals.push_back(new Value(this, valread[i], false) ); addComponentWithDerivatives( valread[i].substr(dot+1) );
+ readvals.emplace_back(new Value(this, valread[i], false) ); addComponentWithDerivatives( valread[i].substr(dot+1) );
if( ifile->FieldExist("min_" + valread[i]) ) componentIsPeriodic( valread[i].substr(dot+1), "-pi", "pi" );
else componentIsNotPeriodic( valread[i].substr(dot+1) );
}
}
} else {
if( valread.size()!=1 ) error("all values must be from the same Action when using READ");
- readvals.push_back(new Value(this, valread[0], false) ); addValueWithDerivatives();
+ readvals.emplace_back(new Value(this, valread[0], false) ); addValueWithDerivatives();
if( ifile->FieldExist("min_" + valread[0]) ) setPeriodic( "-pi", "pi" );
else setNotPeriodic();
log.printf(" reading value %s and storing as %s\n",valread[0].c_str(),getLabel().c_str() );
@@ -179,11 +185,6 @@ Read::Read(const ActionOptions&ao):
checkRead();
}
-Read::~Read() {
- if( !cloned_file ) { ifile->close(); delete ifile; }
- for(unsigned i=0; i<readvals.size(); ++i) delete readvals[i];
-}
-
std::string Read::getFilename() const {
return filename;
}
@@ -216,7 +217,9 @@ void Read::prepare() {
void Read::calculate() {
std::string smin, smax;
for(unsigned i=0; i<readvals.size(); ++i) {
- ifile->scanField( readvals[i] );
+// .get returns the raw pointer
+// ->get calls the Value::get() method
+ ifile->scanField( readvals[i].get() );
getPntrToComponent(i)->set( readvals[i]->get() );
if( readvals[i]->isPeriodic() ) {
readvals[i]->getDomain( smin, smax );
--
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