Commit: 24c26ce8c0c54c30933f649a535491602360d896 - MolDS (git)

Commit MetaInfo

• Révision: 24c26ce8c0c54c30933f649a535491602360d896 (tree)
• l'heure: 2012-07-03 01:04:06
• Auteur: Mikiya Fujii <mikiya.fujii@gmai...>
• Commiter: Mikiya Fujii

Message de Log

Cndo2::GetDiatomVdWCorrectionEnergy is refactored. #28554

git-svn-id: https://svn.sourceforge.jp/svnroot/molds/trunk@858 1136aad2-a195-0410-b898-f5ea1d11b9d8

Change Summary

• modified: src/cndo/Cndo2.cpp
• modified: src/cndo/Cndo2.h

Modification

--- a/src/cndo/Cndo2.cpp
+++ b/src/cndo/Cndo2.cpp
@@ -306,6 +306,19 @@ double Cndo2::GetDiatomCoreRepulsionEnergy(int indexAtomA, int indexAtomB) const
    return atomA.GetCoreCharge()*atomB.GetCoreCharge()/distance; 
 }
 
+// First derivative of the core repulsion related to the coordinate of atom A.
+double Cndo2::GetDiatomCoreRepulsionFirstDerivative(int indexAtomA, int indexAtomB, 
+                                                    CartesianType axisA) const{
+   double value=0.0;
+   const Atom& atomA = *this->molecule->GetAtom(indexAtomA);
+   const Atom& atomB = *this->molecule->GetAtom(indexAtomB);
+   double distance = this->molecule->GetDistanceAtoms(indexAtomA, indexAtomB);
+   value = atomA.GetCoreCharge()*atomB.GetCoreCharge();
+   value *= (atomA.GetXyz()[axisA] - atomB.GetXyz()[axisA])/distance;
+   value *= -1.0/pow(distance,2.0);
+   return value;
+}
+
 // See (2) in [G_2004] ((11) in [G_2006])
 void Cndo2::CalcVdWCorrectionEnergy(){
    double value = 0.0;
@@ -317,6 +330,11 @@ void Cndo2::CalcVdWCorrectionEnergy(){
    this->vdWCorrectionEnergy = value;
 }
 
+// See damping function in (2) in [G_2004] ((11) in [G_2006])
+double Cndo2::GetVdwDampingValue(double vdWDistance, double distance) const{
+   double dampingFactor = Parameters::GetInstance()->GetVdWDampingFactorSCF();
+   return 1.0/(1.0+exp(-1.0*dampingFactor*(distance/vdWDistance - 1.0)));
+}
 // See (2) in [G_2004] ((11) in [G_2006])
 double Cndo2::GetDiatomVdWCorrectionEnergy(int indexAtomA, int indexAtomB) const{
    const Atom& atomA = *this->molecule->GetAtom(indexAtomA);
@@ -325,25 +343,11 @@ double Cndo2::GetDiatomVdWCorrectionEnergy(int indexAtomA, int indexAtomB) const
    double vdWDistance = atomA.GetVdWRadii() + atomB.GetVdWRadii();
    double vdWCoefficients = 2.0*atomA.GetVdWCoefficient()*atomB.GetVdWCoefficient()
                            /(atomA.GetVdWCoefficient()+atomB.GetVdWCoefficient());
-   double dampingFactor = Parameters::GetInstance()->GetVdWDampingFactorSCF();
-   double damping = 1.0/(1.0+exp(-1.0*dampingFactor*(distance/vdWDistance - 1.0)));
+   double damping = this->GetVdwDampingValue(vdWDistance, distance);
    double scalingFactor = Parameters::GetInstance()->GetVdWScalingFactorSCF();
    return -1.0*scalingFactor*vdWCoefficients*pow(distance,-6.0)*damping;
 }
 
-// First derivative of the core repulsion related to the coordinate of atom A.
-double Cndo2::GetDiatomCoreRepulsionFirstDerivative(int indexAtomA, int indexAtomB, 
-                                                    CartesianType axisA) const{
-   double value=0.0;
-   const Atom& atomA = *this->molecule->GetAtom(indexAtomA);
-   const Atom& atomB = *this->molecule->GetAtom(indexAtomB);
-   double distance = this->molecule->GetDistanceAtoms(indexAtomA, indexAtomB);
-   value = atomA.GetCoreCharge()*atomB.GetCoreCharge();
-   value *= (atomA.GetXyz()[axisA] - atomB.GetXyz()[axisA])/distance;
-   value *= -1.0/pow(distance,2.0);
-   return value;
-}
-
 // First derivative of the vdW correction related to the coordinate of atom A.
 // See (2) in [G_2004] ((11) in [G_2006]).
 double Cndo2::GetDiatomVdWCorrectionFirstDerivative(int indexAtomA, int indexAtomB, 

--- a/src/cndo/Cndo2.h
+++ b/src/cndo/Cndo2.h
@@ -259,6 +259,7 @@ private:
    void OutputSCFMulliken() const;
    void CalcCoreRepulsionEnergy();
    void CalcVdWCorrectionEnergy();
+   double GetVdwDampingValue(double vdWDistance, double distance) const;
    void CalcElectronicDipoleMomentGroundState(double*** electronicTransitionDipoleMoments,
                                               double const* const* const* cartesianMatrix,
                                               const MolDS_base::Molecule& molecule,