From 9177592a13b7a93ff33fad58ee52fd92a3162221 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Thu, 16 Jun 2011 14:41:13 +0200
Subject: [PATCH] Small cleanup
I removed some unused methods to manipulate atoms
---
src/Atoms.cpp | 2 +-
src/MDAtoms.cpp | 42 +++---------------------------------------
src/MDAtoms.h | 2 +-
3 files changed, 5 insertions(+), 41 deletions(-)
diff --git a/src/Atoms.cpp b/src/Atoms.cpp
index 663906379..cfab5b581 100644
--- a/src/Atoms.cpp
+++ b/src/Atoms.cpp
@@ -162,7 +162,7 @@ void Atoms::updateForces(){
};
if(forceOnEnergy*forceOnEnergy>epsilon){
double alpha=1.0-forceOnEnergy;
- mdatoms->rescaleForces(0,gatindex.size(),alpha);
+ mdatoms->rescaleForces(gatindex.size(),alpha);
}
if(!any)return;
mdatoms->updateForces(gatindex,forces);
diff --git a/src/MDAtoms.cpp b/src/MDAtoms.cpp
index 47a97368f..dc207701c 100644
--- a/src/MDAtoms.cpp
+++ b/src/MDAtoms.cpp
@@ -35,16 +35,12 @@ public:
*(static_cast<T*>(m))=T(d);
}
void getBox(Tensor &)const;
- void getPositions(int first,int last,vector<Vector>&)const;
void getPositions(const vector<int>&index,vector<Vector>&positions)const;
- void getMasses(int first,int last,vector<double>&)const;
void getMasses(const vector<int>&index,vector<double>&)const;
- void getCharges(int first,int last,vector<double>&)const;
void getCharges(const vector<int>&index,vector<double>&)const;
void updateVirial(const Tensor&)const;
- void updateForces(int first,int last,const vector<Vector>&);
void updateForces(const vector<int>&index,const vector<Vector>&);
- void rescaleForces(int first,int last,double factor);
+ void rescaleForces(int n,double factor);
int getRealPrecision()const;
};
@@ -76,28 +72,6 @@ void MDAtomsBase::setUnits(double l,double e){
scalev=e;
}
-template <class T>
-void MDAtomsTyped<T>::getPositions(int first,int last,vector<Vector>&positions)const{
- for(int i=first;i<last;i++){
- positions[i][0]=px[stride*i]*scalep;
- positions[i][1]=py[stride*i]*scalep;
- positions[i][2]=pz[stride*i]*scalep;
- }
-}
-
-template <class T>
-void MDAtomsTyped<T>::getMasses(int first,int last,vector<double>&masses)const{
- if(m) for(int i=first;i<last;i++) masses[i]=m[i];
- else for(int i=first;i<last;i++) masses[i]=0.0;
-}
-
-template <class T>
-void MDAtomsTyped<T>::getCharges(int first,int last,vector<double>&charges)const{
- if(c) for(int i=first;i<last;i++) charges[i]=c[i];
- else for(int i=first;i<last;i++) charges[i]=0.0;
-}
-
-
template <class T>
void MDAtomsTyped<T>::getBox(Tensor&box)const{
if(this->box) for(int i=0;i<3;i++)for(int j=0;j<3;j++) box(i,j)=this->box[3*i+j]*scaleb;
@@ -130,16 +104,6 @@ void MDAtomsTyped<T>::updateVirial(const Tensor&virial)const{
if(this->virial) for(int i=0;i<3;i++)for(int j=0;j<3;j++) this->virial[3*i+j]+=T(virial(i,j)*scalev);
}
-
-template <class T>
-void MDAtomsTyped<T>::updateForces(int first,int last,const vector<Vector>&forces){
- for(int i=first;i<last;i++){
- fx[stride*i]+=T(scalef*forces[i][0]);
- fy[stride*i]+=T(scalef*forces[i][1]);
- fz[stride*i]+=T(scalef*forces[i][2]);
- }
-}
-
template <class T>
void MDAtomsTyped<T>::updateForces(const vector<int>&index,const vector<Vector>&forces){
for(unsigned i=0;i<index.size();++i){
@@ -150,8 +114,8 @@ void MDAtomsTyped<T>::updateForces(const vector<int>&index,const vector<Vector>&
}
template <class T>
-void MDAtomsTyped<T>::rescaleForces(int first,int last,double factor){
- for(int i=first;i<last;++i){
+void MDAtomsTyped<T>::rescaleForces(int n,double factor){
+ for(int i=0;i<n;++i){
fx[stride*i]*=T(factor);
fy[stride*i]*=T(factor);
fz[stride*i]*=T(factor);
diff --git a/src/MDAtoms.h b/src/MDAtoms.h
index f0cfca73b..4f2114c94 100644
--- a/src/MDAtoms.h
+++ b/src/MDAtoms.h
@@ -33,7 +33,7 @@ public:
virtual void getCharges(const std::vector<int>&index,std::vector<double>&)const=0;
virtual void updateVirial(const Tensor&)const=0;
virtual void updateForces(const std::vector<int>&index,const std::vector<Vector>&)=0;
- virtual void rescaleForces(int first,int last,double factor)=0;
+ virtual void rescaleForces(int n,double factor)=0;
virtual int getRealPrecision()const=0;
static MDAtomsBase* create(int);
};
--
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