Commit: 9660892e0aea1d75ff76355c00b404c6687611ed - MolDS (git)

Commit MetaInfo

• Revisión: 9660892e0aea1d75ff76355c00b404c6687611ed (tree)
• Tiempo: 2012-11-20 02:07:23
• Autor: Mikiya Fujii <mikiya.fujii@gmai...>
• Commiter: Mikiya Fujii

Log Message

Sync methods for molecular configuration and momenuta are added to Molecule-class. #30153

git-svn-id: https://svn.sourceforge.jp/svnroot/molds/trunk@1121 1136aad2-a195-0410-b898-f5ea1d11b9d8

Cambiar Resumen

• modified: src/base/Molecule.cpp
• modified: src/base/Molecule.h
• modified: src/mc/MC.cpp
• modified: src/mc/MC.h
• modified: src/nasco/NASCO.cpp
• modified: src/nasco/NASCO.h

Diferencia incremental

--- a/src/base/Molecule.cpp
+++ b/src/base/Molecule.cpp
@@ -625,7 +625,6 @@ void Molecule::OutputRotatingConditions(RotatingType rotatingType,
    }
 }
 
-
 void Molecule::Translate(){
    this->OutputLog(this->messageStartTranslate);
    double x = Parameters::GetInstance()->GetTranslatingDifference()[0];
@@ -681,6 +680,41 @@ double Molecule::GetDistanceAtoms(const Atom& atomA, const Atom& atomB) const{
 
 }
 
+void Molecule::SynchronizeConfigurationTo(const Molecule& ref){
+   for(int a=0; a<this->GetNumberAtoms(); a++){
+      Atom& atom = *this->GetAtom(a);
+      const Atom& refAtom = *ref.GetAtom(a);
+      for(int i=0; i<CartesianType_end; i++){
+         atom.GetXyz()[i] = refAtom.GetXyz()[i];
+      }
+   }
+   this->CalcXyzCOC();
+   this->CalcXyzCOM();
+}
+
+void Molecule::SynchronizeMomentaTo(const Molecule& ref){
+   for(int a=0; a<this->GetNumberAtoms(); a++){
+      Atom& atom = *this->GetAtom(a);
+      const Atom& refAtom = *ref.GetAtom(a);
+      for(int i=0; i<CartesianType_end; i++){
+         atom.GetPxyz()[i] = refAtom.GetPxyz()[i];
+      }
+   }
+}
+
+void Molecule::SynchronizePhaseSpacePointTo(const Molecule& ref){
+   for(int a=0; a<this->GetNumberAtoms(); a++){
+      Atom& atom = *this->GetAtom(a);
+      const Atom& refAtom = *ref.GetAtom(a);
+      for(int i=0; i<CartesianType_end; i++){
+         atom.GetXyz() [i] = refAtom.GetXyz() [i];
+         atom.GetPxyz()[i] = refAtom.GetPxyz()[i];
+      }
+   }
+   this->CalcXyzCOC();
+   this->CalcXyzCOM();
+}
+
 }
 
 

--- a/src/base/Molecule.h
+++ b/src/base/Molecule.h
@@ -50,6 +50,9 @@ public:
    double GetDistanceAtoms(int indexAtomA, int indexAtomB) const;
    double GetDistanceAtoms(const MolDS_base_atoms::Atom& atomA, 
                            const MolDS_base_atoms::Atom& atomB) const;
+   void SynchronizeConfigurationTo  (const Molecule& ref);
+   void SynchronizeMomentaTo        (const Molecule& ref);
+   void SynchronizePhaseSpacePointTo(const Molecule& ref);
 private:
    std::vector<MolDS_base_atoms::Atom*>* atomVect;
    double* xyzCOM; // x, y, z coordinates of Center of Mass;

--- a/src/mc/MC.cpp
+++ b/src/mc/MC.cpp
@@ -126,14 +126,14 @@ void MC::DoMC(int totalSteps, int elecState, double temperature, double stepWidt
 
       // which Electronic Structure is used?
       if(UsesTrial(*currentES, *trialES, elecState, &realRand, temperature)){
-         this->SynchronousMolecularConfiguration(this->molecule, trialMolecule);
+         this->molecule->SynchronizeConfigurationTo(trialMolecule);
          swap(currentES, trialES);
          currentES->SetMolecule(this->molecule);
          trialES->SetMolecule(&trialMolecule);
          transitionRate += 1.0;
       }
       else{
-         this->SynchronousMolecularConfiguration(&trialMolecule, *this->molecule);
+         trialMolecule.SynchronizeConfigurationTo(*this->molecule);
       }
       
       // output molecular states
@@ -205,19 +205,6 @@ bool MC::UsesTrial(const ElectronicStructure& currentES,
    }
 }
 
-void MC::SynchronousMolecularConfiguration(Molecule* target, 
-                                           const Molecule& refference) const{
-   for(int a=0; a<target->GetNumberAtoms(); a++){
-      Atom* targetAtom = target->GetAtom(a);
-      const Atom& refferenceAtom = *refference.GetAtom(a);
-      for(int i=0; i<CartesianType_end; i++){
-         targetAtom->GetXyz()[i] = refferenceAtom.GetXyz()[i];
-      }
-   }
-   target->CalcXyzCOC();
-   target->CalcXyzCOM();
-}
-
 void MC::OutputMolecule(const ElectronicStructure& electronicStructure,
                         const Molecule& molecule,
                         int elecState) const{

--- a/src/mc/MC.h
+++ b/src/mc/MC.h
@@ -55,8 +55,6 @@ private:
                                     boost::uniform_real<>
                                  > (*realRand),
                                  double dr) const;
-   void SynchronousMolecularConfiguration(MolDS_base::Molecule* target, 
-                                          const MolDS_base::Molecule& refference) const;
    bool UsesTrial(const MolDS_base::ElectronicStructure& currentES, 
                   const MolDS_base::ElectronicStructure& trialES,
                   int elecState,

--- a/src/nasco/NASCO.cpp
+++ b/src/nasco/NASCO.cpp
@@ -145,8 +145,8 @@ void NASCO::DoNASCO(Molecule& molecule){
          // decide next eigenstates
          this->DecideNextElecState(&elecState, &nonAdiabaticPhaseIndex, numElecStates, overlapESs, &realRand);
 
-         // Synchronous molecular configuration and electronic states
-         this->SynchronousMolecularConfiguration(molecule, tmpMolecule);
+         // Synchronize molecular configuration and electronic states
+         molecule.SynchronizeConfigurationTo(tmpMolecule);
          swap(currentES, tmpES);
          currentES->SetMolecule(&molecule);
          tmpES->SetMolecule(&tmpMolecule);
@@ -197,19 +197,6 @@ void NASCO::UpdateCoordinates(Molecule& tmpMolecule,
    tmpMolecule.CalcXyzCOC();
 }
 
-void NASCO::SynchronousMolecularConfiguration(Molecule& target, 
-                                              const Molecule& refference) const{
-   for(int a=0; a<target.GetNumberAtoms(); a++){
-      Atom& targetAtom = *target.GetAtom(a);
-      const Atom& refferenceAtom = *refference.GetAtom(a);
-      for(int i=0; i<CartesianType_end; i++){
-         targetAtom.GetXyz()[i] = refferenceAtom.GetXyz()[i];
-      }
-   }
-   target.CalcXyzCOC();
-   target.CalcXyzCOM();
-}
-
 void NASCO::DecideNextElecState(int* elecState, 
                                 int* nonAdiabaticPhaseIndex,
                                 int numElecStates,

--- a/src/nasco/NASCO.h
+++ b/src/nasco/NASCO.h
@@ -58,8 +58,6 @@ private:
    void UpdateCoordinates(MolDS_base::Molecule& tmpMolecule, 
                           const MolDS_base::Molecule& molecule,
                           const double dt) const;
-   void SynchronousMolecularConfiguration(MolDS_base::Molecule& target, 
-                                          const MolDS_base::Molecule& refference) const;
    void DecideNextElecState(int* elecState, 
                             int* nonAdiabaticPhaseIndex,
                             int numElecStates,