Commit: f0be6da1644b96ca8a27fb4b10f857ceec6d96f1 - MolDS (git)

Commit MetaInfo

• Révision: f0be6da1644b96ca8a27fb4b10f857ceec6d96f1 (tree)
• l'heure: 2014-01-05 02:28:30
• Auteur: Mikiya Fujii <mikiya.fujii@gmai...>
• Commiter: Mikiya Fujii

Message de Log

Bugs in the constructor and destructor of ghost atoms are fixed. #32750

git-svn-id: https://svn.sourceforge.jp/svnroot/molds/trunk@1613 1136aad2-a195-0410-b898-f5ea1d11b9d8

Change Summary

• 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/atoms/ghost/Ghost.cpp
• modified: src/base/atoms/ghost/Ghost.h
• modified: src/base/atoms/ghost/GhostCatom.cpp
• modified: src/base/atoms/ghost/GhostCatom.h
• modified: src/base/atoms/ghost/GhostHatom.cpp
• modified: src/base/atoms/ghost/GhostHatom.h
• modified: src/base/atoms/ghost/GhostLiatom.cpp
• modified: src/base/atoms/ghost/GhostLiatom.h
• modified: src/base/atoms/ghost/GhostNatom.cpp
• modified: src/base/atoms/ghost/GhostNatom.h
• modified: src/base/atoms/ghost/GhostOatom.cpp
• modified: src/base/atoms/ghost/GhostOatom.h
• modified: src/base/atoms/ghost/GhostSatom.cpp
• modified: src/base/atoms/ghost/GhostSatom.h

Modification

--- a/src/base/atoms/Atom.cpp
+++ b/src/base/atoms/Atom.cpp
@@ -58,8 +58,6 @@ Atom::Atom(int index){
    this->index = index;
 }
 
-Atom::Atom(){}
-
 Atom::~Atom(){
    MallocerFreer::GetInstance()->Free<double>(&this->xyz, CartesianType_end);
    MallocerFreer::GetInstance()->Free<double>(&this->pxyz, CartesianType_end);
@@ -163,7 +161,11 @@ double* Atom::GetPxyz() const{
 
 void Atom::SetXyz(double x, double y, double z) const{
 #ifdef MOLDS_DBG
-   if(this->xyz==NULL) throw MolDSException(this->errorMessageSetXyzCoordinatesNull);
+   if(this->xyz==NULL){
+      printf("xyz\n\n");
+      throw MolDSException("aaa");
+      //throw MolDSException(this->errorMessageSetXyzCoordinatesNull);
+   }
 #endif
    xyz[0]= x; xyz[1]= y; xyz[2]= z;
 }

--- a/src/base/atoms/Atom.h
+++ b/src/base/atoms/Atom.h
@@ -107,7 +107,6 @@ public:
    double GetPm3PddgParameterPa(int paIndex) const;
    double GetPm3PddgParameterDa(int daIndex) const;
 protected:
-   Atom();
    double* xyz; // coordinates
    double* pxyz; // momentum. Note that this is not velocity!! 
    MolDS_base::AtomType atomType;
@@ -231,6 +230,7 @@ protected:
    double pm3DAlpha; // Table II in ref. [MH_2007] for H, C, N, O, and Table IV in re. [MMHBV_2007] for S.
    virtual void SetAtomicParameters() = 0;
 private:
+   Atom();
    std::string errorMessageIonPot;
    std::string errorMessageAtomType;
    std::string errorMessageNumberValences;

--- a/src/base/atoms/Catom.cpp
+++ b/src/base/atoms/Catom.cpp
@@ -42,6 +42,8 @@ Catom::Catom(int index) : Atom(index){
    this->SetAtomicParameters();
 }
 
+Catom::~Catom(){}
+
 void Catom::SetAtomicParameters(){
    this->atomType = C;
    this->atomicMass = 12.0107*Parameters::GetInstance()->GetGMolin2AU();

--- a/src/base/atoms/Catom.h
+++ b/src/base/atoms/Catom.h
@@ -22,6 +22,7 @@ namespace MolDS_base_atoms{
 class Catom : virtual public Atom {
 public:
    Catom(int index);
+   virtual ~Catom();
 protected:
    void virtual SetAtomicParameters();
 private:

--- a/src/base/atoms/Hatom.cpp
+++ b/src/base/atoms/Hatom.cpp
@@ -45,6 +45,8 @@ Hatom::Hatom(int index) : Atom(index){
    this->SetAtomicParameters();
 }
 
+Hatom::~Hatom(){}
+
 void Hatom::SetAtomicParameters(){
    this->atomType = H;
    this->atomicMass = 1.00794*Parameters::GetInstance()->GetGMolin2AU();

--- a/src/base/atoms/Hatom.h
+++ b/src/base/atoms/Hatom.h
@@ -23,6 +23,7 @@ namespace MolDS_base_atoms{
 class Hatom : virtual public Atom {
 public:
    Hatom(int index);
+   virtual ~Hatom();
 protected:
    void virtual SetAtomicParameters();
 private:

--- a/src/base/atoms/Liatom.cpp
+++ b/src/base/atoms/Liatom.cpp
@@ -43,6 +43,8 @@ Liatom::Liatom(int index) : Atom(index){
    this->SetAtomicParameters();
 }
 
+Liatom::~Liatom(){}
+
 void Liatom::SetAtomicParameters(){
    this->atomType = Li;
    this->atomicMass = 6.941*Parameters::GetInstance()->GetGMolin2AU();

--- a/src/base/atoms/Liatom.h
+++ b/src/base/atoms/Liatom.h
@@ -22,6 +22,7 @@ namespace MolDS_base_atoms{
 class Liatom : virtual public Atom {
 public:
    Liatom(int index);
+   virtual ~Liatom();
 protected:
    void virtual SetAtomicParameters();
 private:

--- a/src/base/atoms/Natom.cpp
+++ b/src/base/atoms/Natom.cpp
@@ -42,6 +42,8 @@ Natom::Natom(int index) : Atom(index){
    this->SetAtomicParameters();
 }
 
+Natom::~Natom(){}
+
 void Natom::SetAtomicParameters(){
    this->atomType = N;
    this->atomicMass = 14.00674*Parameters::GetInstance()->GetGMolin2AU();

--- a/src/base/atoms/Natom.h
+++ b/src/base/atoms/Natom.h
@@ -22,6 +22,7 @@ namespace MolDS_base_atoms{
 class Natom : virtual public Atom {
 public:
    Natom(int index);
+   virtual ~Natom();
 protected:
    void virtual SetAtomicParameters();
 private:

--- a/src/base/atoms/Oatom.cpp
+++ b/src/base/atoms/Oatom.cpp
@@ -42,6 +42,8 @@ Oatom::Oatom(int index) : Atom(index){
    this->SetAtomicParameters();
 }
 
+Oatom::~Oatom(){}
+
 void Oatom::SetAtomicParameters(){
    this->atomType = O;
    this->atomicMass = 15.9994*Parameters::GetInstance()->GetGMolin2AU();

--- a/src/base/atoms/Oatom.h
+++ b/src/base/atoms/Oatom.h
@@ -22,6 +22,7 @@ namespace MolDS_base_atoms{
 class Oatom : virtual public Atom {
 public:
    Oatom(int index);
+   virtual ~Oatom();
 protected:
    void virtual SetAtomicParameters();
 private:

--- a/src/base/atoms/Satom.cpp
+++ b/src/base/atoms/Satom.cpp
@@ -42,6 +42,8 @@ Satom::Satom(int index) : Atom(index){
    this->SetAtomicParameters();
 }
 
+Satom::~Satom(){}
+
 void Satom::SetAtomicParameters(){
    this->atomType = S;
    this->atomicMass = 32.066*Parameters::GetInstance()->GetGMolin2AU();

--- a/src/base/atoms/Satom.h
+++ b/src/base/atoms/Satom.h
@@ -22,6 +22,7 @@ namespace MolDS_base_atoms{
 class Satom : virtual public Atom {
 public:
    Satom(int index);
+   virtual ~Satom();
 protected:
    void virtual SetAtomicParameters();
 private:

--- a/src/base/atoms/ghost/Ghost.cpp
+++ b/src/base/atoms/ghost/Ghost.cpp
@@ -39,9 +39,12 @@ using namespace std;
 using namespace MolDS_base;
 using namespace MolDS_base_atoms;
 namespace MolDS_base_atoms_ghost{
-Ghost::Ghost() : Atom(){
+Ghost::Ghost(int index) : Atom(index){
+   this->SetAtomicParameters();
 }
 
+Ghost::~Ghost(){}
+
 void Ghost::SetAtomicParameters(){
    this->atomicMass = 0.0;
    this->coreCharge = 0.0;

--- a/src/base/atoms/ghost/Ghost.h
+++ b/src/base/atoms/ghost/Ghost.h
@@ -21,10 +21,12 @@
 namespace MolDS_base_atoms_ghost{
 class Ghost : virtual public MolDS_base_atoms::Atom {
 public:
-   Ghost();
+   Ghost(int index);
+   virtual ~Ghost();
 protected:
    void virtual SetAtomicParameters();
 private:
+   Ghost();
 };
 }
 #endif

--- a/src/base/atoms/ghost/GhostCatom.cpp
+++ b/src/base/atoms/ghost/GhostCatom.cpp
@@ -41,12 +41,13 @@ using namespace std;
 using namespace MolDS_base;
 using namespace MolDS_base_atoms;
 namespace MolDS_base_atoms_ghost{
-GhostCatom::GhostCatom(int index) : Catom(index),Ghost(){
+GhostCatom::GhostCatom(int index) : Atom(index),Catom(index),Ghost(index){
+   this->SetAtomicParameters();
 }
 
+GhostCatom::~GhostCatom(){}
+
 void GhostCatom::SetAtomicParameters(){
-   Catom::SetAtomicParameters();
-   Ghost::SetAtomicParameters();
    this->atomType = ghostC;
 }
 }

--- a/src/base/atoms/ghost/GhostCatom.h
+++ b/src/base/atoms/ghost/GhostCatom.h
@@ -22,6 +22,7 @@ namespace MolDS_base_atoms_ghost{
 class GhostCatom : public MolDS_base_atoms::Catom, public Ghost {
 public:
    GhostCatom(int index);
+   ~GhostCatom();
 protected:
    void virtual SetAtomicParameters();
 private:

--- a/src/base/atoms/ghost/GhostHatom.cpp
+++ b/src/base/atoms/ghost/GhostHatom.cpp
@@ -41,12 +41,13 @@ using namespace std;
 using namespace MolDS_base;
 using namespace MolDS_base_atoms;
 namespace MolDS_base_atoms_ghost{
-GhostHatom::GhostHatom(int index) : Hatom(index),Ghost(){
+GhostHatom::GhostHatom(int index) : Atom(index),Hatom(index),Ghost(index){
+   this->SetAtomicParameters();
 }
 
+GhostHatom::~GhostHatom(){}
+
 void GhostHatom::SetAtomicParameters(){
-   Hatom::SetAtomicParameters();
-   Ghost::SetAtomicParameters();
    this->atomType = ghostH;
 }
 }

--- a/src/base/atoms/ghost/GhostHatom.h
+++ b/src/base/atoms/ghost/GhostHatom.h
@@ -22,6 +22,7 @@ namespace MolDS_base_atoms_ghost{
 class GhostHatom : public MolDS_base_atoms::Hatom, public Ghost {
 public:
    GhostHatom(int index);
+   ~GhostHatom();
 protected:
    void virtual SetAtomicParameters();
 private:

--- a/src/base/atoms/ghost/GhostLiatom.cpp
+++ b/src/base/atoms/ghost/GhostLiatom.cpp
@@ -41,9 +41,12 @@ using namespace std;
 using namespace MolDS_base;
 using namespace MolDS_base_atoms;
 namespace MolDS_base_atoms_ghost{
-GhostLiatom::GhostLiatom(int index) : Liatom(index),Ghost(){
+GhostLiatom::GhostLiatom(int index) : Atom(index),Liatom(index),Ghost(index){
+   this->SetAtomicParameters();
 }
 
+GhostLiatom::~GhostLiatom(){}
+
 void GhostLiatom::SetAtomicParameters(){
    Liatom::SetAtomicParameters();
    Ghost::SetAtomicParameters();

--- a/src/base/atoms/ghost/GhostLiatom.h
+++ b/src/base/atoms/ghost/GhostLiatom.h
@@ -22,6 +22,7 @@ namespace MolDS_base_atoms_ghost{
 class GhostLiatom : public MolDS_base_atoms::Liatom, public Ghost {
 public:
    GhostLiatom(int index);
+   ~GhostLiatom();
 protected:
    void virtual SetAtomicParameters();
 private:

--- a/src/base/atoms/ghost/GhostNatom.cpp
+++ b/src/base/atoms/ghost/GhostNatom.cpp
@@ -41,12 +41,13 @@ using namespace std;
 using namespace MolDS_base;
 using namespace MolDS_base_atoms;
 namespace MolDS_base_atoms_ghost{
-GhostNatom::GhostNatom(int index) : Natom(index),Ghost(){
+GhostNatom::GhostNatom(int index) : Atom(index),Natom(index),Ghost(index){
+   this->SetAtomicParameters();
 }
 
+GhostNatom::~GhostNatom(){}
+
 void GhostNatom::SetAtomicParameters(){
-   Natom::SetAtomicParameters();
-   Ghost::SetAtomicParameters();
    this->atomType = ghostN;
 }
 }

--- a/src/base/atoms/ghost/GhostNatom.h
+++ b/src/base/atoms/ghost/GhostNatom.h
@@ -22,6 +22,7 @@ namespace MolDS_base_atoms_ghost{
 class GhostNatom : public MolDS_base_atoms::Natom, public Ghost {
 public:
    GhostNatom(int index);
+   ~GhostNatom();
 protected:
    void virtual SetAtomicParameters();
 private:

--- a/src/base/atoms/ghost/GhostOatom.cpp
+++ b/src/base/atoms/ghost/GhostOatom.cpp
@@ -41,12 +41,13 @@ using namespace std;
 using namespace MolDS_base;
 using namespace MolDS_base_atoms;
 namespace MolDS_base_atoms_ghost{
-GhostOatom::GhostOatom(int index) : Oatom(index),Ghost(){
+GhostOatom::GhostOatom(int index) : Atom(index),Oatom(index),Ghost(index){
+   this->SetAtomicParameters();
 }
 
+GhostOatom::~GhostOatom(){}
+
 void GhostOatom::SetAtomicParameters(){
-   Oatom::SetAtomicParameters();
-   Ghost::SetAtomicParameters();
    this->atomType = ghostO;
 }
 }

--- a/src/base/atoms/ghost/GhostOatom.h
+++ b/src/base/atoms/ghost/GhostOatom.h
@@ -22,6 +22,7 @@ namespace MolDS_base_atoms_ghost{
 class GhostOatom : public MolDS_base_atoms::Oatom, public Ghost {
 public:
    GhostOatom(int index);
+   ~GhostOatom();
 protected:
    void virtual SetAtomicParameters();
 private:

--- a/src/base/atoms/ghost/GhostSatom.cpp
+++ b/src/base/atoms/ghost/GhostSatom.cpp
@@ -41,12 +41,13 @@ using namespace std;
 using namespace MolDS_base;
 using namespace MolDS_base_atoms;
 namespace MolDS_base_atoms_ghost{
-GhostSatom::GhostSatom(int index) : Satom(index),Ghost(){
+GhostSatom::GhostSatom(int index) : Atom(index),Satom(index),Ghost(index){
+   this->SetAtomicParameters();
 }
 
+GhostSatom::~GhostSatom(){}
+
 void GhostSatom::SetAtomicParameters(){
-   Satom::SetAtomicParameters();
-   Ghost::SetAtomicParameters();
    this->atomType = ghostS;
 }
 }

--- a/src/base/atoms/ghost/GhostSatom.h
+++ b/src/base/atoms/ghost/GhostSatom.h
@@ -22,6 +22,7 @@ namespace MolDS_base_atoms_ghost{
 class GhostSatom : public MolDS_base_atoms::Satom, public Ghost {
 public:
    GhostSatom(int index);
+   ~GhostSatom();
 protected:
    void virtual SetAtomicParameters();
 private: