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Comparing branches/development/src/optimization/PotentialEnergyObjectiveFunction.cpp (file contents):
Revision 1741 by gezelter, Tue Jun 5 18:02:44 2012 UTC vs.
Revision 1750 by gezelter, Thu Jun 7 12:53:46 2012 UTC

# Line 45 | Line 45 | namespace OpenMD{
45   namespace OpenMD{
46  
47    PotentialEnergyObjectiveFunction::PotentialEnergyObjectiveFunction(SimInfo* info, ForceManager* forceMan)
48 <    : info_(info), forceMan_(forceMan), thermo(info) {      
48 >    : info_(info), forceMan_(forceMan), thermo(info) {  
49 >    shake_ = new Shake(info_);    
50    }
51    
52  
53    
54    RealType PotentialEnergyObjectiveFunction::value(const DynamicVector<RealType>& x) {
55      setCoor(x);
56 +    shake_->constraintR();
57      forceMan_->calcForces();
58 +    shake_->constraintF();
59      return thermo.getPotential();
60    }
61    
62    void PotentialEnergyObjectiveFunction::gradient(DynamicVector<RealType>& grad, const DynamicVector<RealType>& x) {
63      
64 <    setCoor(x);        
65 <    forceMan_->calcForces();
66 <    getGrad(grad);      
64 >    setCoor(x);      
65 >    shake_->constraintR();
66 >    forceMan_->calcForces();
67 >    shake_->constraintF();
68 >    getGrad(grad);
69    }
70    
71    RealType PotentialEnergyObjectiveFunction::valueAndGradient(DynamicVector<RealType>& grad,
72                                                                const DynamicVector<RealType>& x) {
73 <  
74 <    setCoor(x);    
75 <    forceMan_->calcForces();  
73 >    setCoor(x);
74 >    shake_->constraintR();
75 >    forceMan_->calcForces();
76 >    shake_->constraintF();
77      getGrad(grad);
78      return thermo.getPotential();
79    }
# Line 99 | Line 105 | namespace OpenMD{
105            eulerAngle[2] = x[index++];
106            
107            integrableObject->setEuler(eulerAngle);
108 <          }
108 >
109 >          if (integrableObject->isRigidBody()) {
110 >            RigidBody* rb = static_cast<RigidBody*>(integrableObject);
111 >            rb->updateAtoms();
112 >          }        
113 >        }
114        }
115      }    
116    }
# Line 119 | Line 130 | namespace OpenMD{
130             integrableObject != NULL;
131             integrableObject = mol->nextIntegrableObject(j)) {        
132          myGrad = integrableObject->getGrad();
133 <        for (size_t k = 0; k < myGrad.size(); ++k) {
133 >
134 >        for (size_t k = 0; k < myGrad.size(); ++k) {  
135            grad[index++] = myGrad[k];
136          }
137        }            

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