Commit: 5fffb26b6616ac88b69ee5388ed07db66420f873 - MolDS (git)

Commit MetaInfo

• Revisión: 5fffb26b6616ac88b69ee5388ed07db66420f873 (tree)
• Tiempo: 2013-05-23 19:23:28
• Autor: Mikiya Fujii <mikiya.fujii@gmai...>
• Commiter: Mikiya Fujii

Log Message

Cache of distance of each atom is implemented to be used. #31421

git-svn-id: https://svn.sourceforge.jp/svnroot/molds/trunk@1354 1136aad2-a195-0410-b898-f5ea1d11b9d8

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• modified: src/base/InputParser.cpp
• modified: src/base/Molecule.cpp
• modified: src/base/atoms/Atom.cpp
• modified: src/base/atoms/Atom.h
• modified: src/base/atoms/Catom.cpp
• modified: src/base/atoms/Catom.h
• modified: src/base/atoms/Hatom.cpp
• modified: src/base/atoms/Hatom.h
• modified: src/base/atoms/Liatom.cpp
• modified: src/base/atoms/Liatom.h
• modified: src/base/atoms/Natom.cpp
• modified: src/base/atoms/Natom.h
• modified: src/base/atoms/Oatom.cpp
• modified: src/base/atoms/Oatom.h
• modified: src/base/atoms/Satom.cpp
• modified: src/base/atoms/Satom.h
• modified: src/base/factories/AtomFactory.cpp
• modified: src/base/factories/AtomFactory.h

Diferencia incremental

--- a/src/base/InputParser.cpp
+++ b/src/base/InputParser.cpp
@@ -475,7 +475,8 @@ int InputParser::ParseMolecularGeometry(Molecule* molecule, vector<string>* inpu
       else if((*inputTerms)[parseIndex] == "s"){
          atomType = S;
       }
-      Atom* atom = AtomFactory::Create(atomType, x, y, z);
+      int index = molecule->GetNumberAtoms();
+      Atom* atom = AtomFactory::Create(atomType, index, x, y, z);
       molecule->AddAtom(atom);
       parseIndex += 4;
    }

--- a/src/base/Molecule.cpp
+++ b/src/base/Molecule.cpp
@@ -77,6 +77,7 @@ void Molecule::CopyInitialize(const Molecule& rhs){
    for(int i=0; i<rhs.atomVect->size(); i++){
       Atom* atom = (*rhs.atomVect)[i];
       this->atomVect->push_back(AtomFactory::Create(atom->GetAtomType(),
+                                                    atom->GetIndex(),
                                                     atom->GetXyz()[XAxis],
                                                     atom->GetXyz()[YAxis],
                                                     atom->GetXyz()[ZAxis],
@@ -252,13 +253,14 @@ void Molecule::CalcDistanceMatrix(){
    }
    for(int a=0; a<this->atomVect->size(); a++){
       const Atom& atomA = *(*this->atomVect)[a];
-      for(int b=0; b<this->atomVect->size(); b++){
+      for(int b=a; b<this->atomVect->size(); b++){
          const Atom& atomB = *(*this->atomVect)[b];
          double distance=0.0;
          distance = sqrt( pow(atomA.GetXyz()[0] - atomB.GetXyz()[0], 2.0)
                          +pow(atomA.GetXyz()[1] - atomB.GetXyz()[1], 2.0)
                          +pow(atomA.GetXyz()[2] - atomB.GetXyz()[2], 2.0) );
          this->distanceMatrix[a][b] = distance;
+         this->distanceMatrix[b][a] = distance;
       }
    }
 }
@@ -680,17 +682,11 @@ void Molecule::OutputTranslatingConditions(double const* translatingDifference)
 }
 
 double Molecule::GetDistanceAtoms(int indexAtomA, int indexAtomB) const{
-   const Atom& atomA = *(*this->atomVect)[indexAtomA];
-   const Atom& atomB = *(*this->atomVect)[indexAtomB];
-   return this->GetDistanceAtoms(atomA, atomB);
+   return this->distanceMatrix[indexAtomA][indexAtomB];
 }
 
 double Molecule::GetDistanceAtoms(const Atom& atomA, const Atom& atomB) const{
-   double distance=0.0;
-   distance = sqrt( pow(atomA.GetXyz()[0] - atomB.GetXyz()[0], 2.0)
-                   +pow(atomA.GetXyz()[1] - atomB.GetXyz()[1], 2.0)
-                   +pow(atomA.GetXyz()[2] - atomB.GetXyz()[2], 2.0) );
-   return distance;
+   return this->GetDistanceAtoms(atomA.GetIndex(), atomB.GetIndex());
 }
 
 void Molecule::SynchronizeConfigurationTo(const Molecule& ref){

--- a/src/base/atoms/Atom.cpp
+++ b/src/base/atoms/Atom.cpp
@@ -38,7 +38,7 @@ using namespace std;
 using namespace MolDS_base;
 
 namespace MolDS_base_atoms{
-Atom::Atom(){
+Atom::Atom(int index){
    this->SetMessages();
    this->xyz = NULL;
    this->pxyz = NULL;
@@ -51,6 +51,7 @@ Atom::Atom(){
       MallocerFreer::GetInstance()->Free<double>(&this->pxyz, CartesianType_end);
       throw MolDSException(ex.what());
    }
+   this->index = index;
 }
 
 Atom::~Atom(){

--- a/src/base/atoms/Atom.h
+++ b/src/base/atoms/Atom.h
@@ -22,8 +22,9 @@ namespace MolDS_base_atoms{
 
 class Atom : public MolDS_base::PrintController{
 public:
-   Atom();
+   Atom(int index);
    virtual ~Atom();
+   inline int GetIndex() const{return this->index;}
    double* GetXyz() const;
    void    SetXyz(double x, double y, double z) const;
    double* GetPxyz() const;
@@ -224,6 +225,7 @@ protected:
    double pm3DBondingParameterP; // Table II in ref. [MH_2007] for H, C, N, O, and Table IV in re. [MMHBV_2007] for S.
    double pm3DAlpha; // Table II in ref. [MH_2007] for H, C, N, O, and Table IV in re. [MMHBV_2007] for S.
 private:
+   Atom();
    std::string errorMessageIonPot;
    std::string errorMessageAtomType;
    std::string errorMessageNumberValences;
@@ -276,6 +278,7 @@ private:
    std::string errorMessageSetXyzCoordinatesNull;
    std::string errorMessageGetPxyzMomentaNull;
    std::string errorMessageSetPxyzMomentaNull;
+   int index;
    void SetMessages();
    double GetRealAngularPartAO(double theta, 
                                double phi, 

--- a/src/base/atoms/Catom.cpp
+++ b/src/base/atoms/Catom.cpp
@@ -33,7 +33,7 @@
 using namespace std;
 using namespace MolDS_base;
 namespace MolDS_base_atoms{
-Catom::Catom() : Atom(){
+Catom::Catom(int index) : Atom(index){
    this->SetAtomicParameters();
 }
 

--- a/src/base/atoms/Catom.h
+++ b/src/base/atoms/Catom.h
@@ -21,8 +21,9 @@
 namespace MolDS_base_atoms{
 class Catom : public Atom {
 public:
-   Catom();
+   Catom(int index);
 private:
+   Catom();
    void SetAtomicParameters();
 };
 }

--- a/src/base/atoms/Hatom.cpp
+++ b/src/base/atoms/Hatom.cpp
@@ -35,7 +35,7 @@ using namespace MolDS_base;
 
 namespace MolDS_base_atoms{
 
-Hatom::Hatom() : Atom(){
+Hatom::Hatom(int index) : Atom(index){
    this->SetAtomicParameters();
 }
 

--- a/src/base/atoms/Hatom.h
+++ b/src/base/atoms/Hatom.h
@@ -22,8 +22,9 @@ namespace MolDS_base_atoms{
 
 class Hatom : public Atom {
 public:
-   Hatom();
+   Hatom(int index);
 private:
+   Hatom();
    void SetAtomicParameters();
 };
 

--- a/src/base/atoms/Liatom.cpp
+++ b/src/base/atoms/Liatom.cpp
@@ -34,7 +34,7 @@ using namespace std;
 using namespace MolDS_base;
 
 namespace MolDS_base_atoms{
-Liatom::Liatom() : Atom(){
+Liatom::Liatom(int index) : Atom(index){
    this->SetAtomicParameters();
 }
 

--- a/src/base/atoms/Liatom.h
+++ b/src/base/atoms/Liatom.h
@@ -21,8 +21,9 @@
 namespace MolDS_base_atoms{
 class Liatom : public Atom {
 public:
-   Liatom();
+   Liatom(int index);
 private:
+   Liatom();
    void SetAtomicParameters();
 };
 }

--- a/src/base/atoms/Natom.cpp
+++ b/src/base/atoms/Natom.cpp
@@ -33,7 +33,7 @@
 using namespace std;
 using namespace MolDS_base;
 namespace MolDS_base_atoms{
-Natom::Natom() : Atom(){
+Natom::Natom(int index) : Atom(index){
    this->SetAtomicParameters();
 }
 

--- a/src/base/atoms/Natom.h
+++ b/src/base/atoms/Natom.h
@@ -21,8 +21,9 @@
 namespace MolDS_base_atoms{
 class Natom : public Atom {
 public:
-   Natom();
+   Natom(int index);
 private:
+   Natom();
    void SetAtomicParameters();
 };
 }

--- a/src/base/atoms/Oatom.cpp
+++ b/src/base/atoms/Oatom.cpp
@@ -33,7 +33,7 @@
 using namespace std;
 using namespace MolDS_base;
 namespace MolDS_base_atoms{
-Oatom::Oatom() : Atom(){
+Oatom::Oatom(int index) : Atom(index){
    this->SetAtomicParameters();
 }
 

--- a/src/base/atoms/Oatom.h
+++ b/src/base/atoms/Oatom.h
@@ -21,8 +21,9 @@
 namespace MolDS_base_atoms{
 class Oatom : public Atom {
 public:
-   Oatom();
+   Oatom(int index);
 private:
+   Oatom();
    void SetAtomicParameters();
 };
 }

--- a/src/base/atoms/Satom.cpp
+++ b/src/base/atoms/Satom.cpp
@@ -33,7 +33,7 @@
 using namespace std;
 using namespace MolDS_base;
 namespace MolDS_base_atoms{
-Satom::Satom() : Atom(){
+Satom::Satom(int index) : Atom(index){
    this->SetAtomicParameters();
 }
 

--- a/src/base/atoms/Satom.h
+++ b/src/base/atoms/Satom.h
@@ -21,8 +21,9 @@
 namespace MolDS_base_atoms{
 class Satom : public Atom {
 public:
-   Satom();
+   Satom(int index);
 private:
+   Satom();
    void SetAtomicParameters();
 };
 }

--- a/src/base/factories/AtomFactory.cpp
+++ b/src/base/factories/AtomFactory.cpp
@@ -43,25 +43,25 @@ namespace MolDS_base_factories{
 string AtomFactory::errorMessageNotEnableAtom = "Error in base::AtomFactory::Create: Not Enable AtomType is set.";
 string AtomFactory::errorMessageAtomType = "\tatom type = ";
 
-Atom* AtomFactory::Create(AtomType atomType, double x, double y, double z, double px, double py, double pz){
+Atom* AtomFactory::Create(AtomType atomType, int index, double x, double y, double z, double px, double py, double pz){
    Atom* atom=NULL;
    if(atomType == H){
-      atom = new Hatom();
+      atom = new Hatom(index);
    }
    else if(atomType == Li){
-      atom = new Liatom();
+      atom = new Liatom(index);
    }
    else if(atomType == C){
-      atom = new Catom();
+      atom = new Catom(index);
    }
    else if(atomType == N){
-      atom = new Natom();
+      atom = new Natom(index);
    }
    else if(atomType == O){
-      atom = new Oatom();
+      atom = new Oatom(index);
    }
    else if(atomType == S){
-      atom = new Satom();
+      atom = new Satom(index);
    }
    else{
       stringstream ss;
@@ -74,11 +74,11 @@ Atom* AtomFactory::Create(AtomType atomType, double x, double y, double z, doubl
    return atom;
 }
 
-Atom* AtomFactory::Create(AtomType atomType, double x, double y, double z){
+Atom* AtomFactory::Create(AtomType atomType, int index, double x, double y, double z){
    double px=0.0;
    double py=0.0;
    double pz=0.0;
-   return AtomFactory::Create(atomType, x, y, z, px, py, pz);
+   return AtomFactory::Create(atomType, index, x, y, z, px, py, pz);
 }
 }
 

--- a/src/base/factories/AtomFactory.h
+++ b/src/base/factories/AtomFactory.h
@@ -24,6 +24,7 @@ namespace MolDS_base_factories{
 class AtomFactory{
 public:
    static MolDS_base_atoms::Atom* Create(MolDS_base::AtomType atomType,
+                                         int index,
                                          double x,
                                          double y,
                                          double z,
@@ -31,6 +32,7 @@ public:
                                          double py,
                                          double pz);
    static MolDS_base_atoms::Atom* Create(MolDS_base::AtomType atomType,
+                                         int index,
                                          double x,
                                          double y,
                                          double z);