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root/OpenMD/trunk/src/optimization/PotentialEnergyObjectiveFunction.cpp
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Comparing:
branches/development/src/optimization/PotentialEnergyObjectiveFunction.cpp (file contents), Revision 1750 by gezelter, Thu Jun 7 12:53:46 2012 UTC vs.
trunk/src/optimization/PotentialEnergyObjectiveFunction.cpp (file contents), Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

# Line 35 | Line 35
35   *                                                                      
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 < * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# Line 84 | Line 84 | namespace OpenMD{
84      SimInfo::MoleculeIterator i;
85      Molecule::IntegrableObjectIterator  j;
86      Molecule* mol;
87 <    StuntDouble* integrableObject;    
87 >    StuntDouble* sd;    
88      int index = 0;
89      
90      for (mol = info_->beginMolecule(i); mol != NULL;
91           mol = info_->nextMolecule(i)) {
92 <      for (integrableObject = mol->beginIntegrableObject(j);
93 <           integrableObject != NULL;
94 <           integrableObject = mol->nextIntegrableObject(j)) {
92 >
93 >      for (sd = mol->beginIntegrableObject(j);  sd != NULL;
94 >           sd = mol->nextIntegrableObject(j)) {
95          
96          position[0] = x[index++];
97          position[1] = x[index++];
98          position[2] = x[index++];
99          
100 <        integrableObject->setPos(position);
100 >        sd->setPos(position);
101          
102 <        if (integrableObject->isDirectional()) {
102 >        if (sd->isDirectional()) {
103            eulerAngle[0] = x[index++];
104            eulerAngle[1] = x[index++];
105            eulerAngle[2] = x[index++];
106            
107 <          integrableObject->setEuler(eulerAngle);
107 >          sd->setEuler(eulerAngle);
108  
109 <          if (integrableObject->isRigidBody()) {
110 <            RigidBody* rb = static_cast<RigidBody*>(integrableObject);
109 >          if (sd->isRigidBody()) {
110 >            RigidBody* rb = static_cast<RigidBody*>(sd);
111              rb->updateAtoms();
112            }        
113 +
114          }
115        }
116      }    
# Line 119 | Line 120 | namespace OpenMD{
120      SimInfo::MoleculeIterator i;
121      Molecule::IntegrableObjectIterator  j;
122      Molecule* mol;
123 <    StuntDouble* integrableObject;    
123 >    StuntDouble* sd;    
124      std::vector<RealType> myGrad;
125      
126      int index = 0;
127      
128      for (mol = info_->beginMolecule(i); mol != NULL;
129           mol = info_->nextMolecule(i)) {
129 –      for (integrableObject = mol->beginIntegrableObject(j);
130 –           integrableObject != NULL;
131 –           integrableObject = mol->nextIntegrableObject(j)) {        
132 –        myGrad = integrableObject->getGrad();
130  
131 +      for (sd = mol->beginIntegrableObject(j); sd != NULL;
132 +           sd = mol->nextIntegrableObject(j)) {        
133 +
134 +        myGrad = sd->getGrad();
135 +
136          for (size_t k = 0; k < myGrad.size(); ++k) {  
137            grad[index++] = myGrad[k];
138          }
139 +
140        }            
141      }        
142    }
# Line 142 | Line 145 | namespace OpenMD{
145      SimInfo::MoleculeIterator i;
146      Molecule::IntegrableObjectIterator  j;
147      Molecule* mol;
148 <    StuntDouble* integrableObject;    
148 >    StuntDouble* sd;    
149  
150      Vector3d pos;
151      Vector3d eulerAngle;
# Line 153 | Line 156 | namespace OpenMD{
156      
157      for (mol = info_->beginMolecule(i); mol != NULL;
158           mol = info_->nextMolecule(i)) {
156 –      for (integrableObject = mol->beginIntegrableObject(j);
157 –           integrableObject != NULL;
158 –           integrableObject = mol->nextIntegrableObject(j)) {        
159  
160 <        pos = integrableObject->getPos();
160 >      for (sd = mol->beginIntegrableObject(j);  sd != NULL;
161 >           sd = mol->nextIntegrableObject(j)) {        
162  
163 +        pos = sd->getPos();
164 +
165          xinit[index++] = pos[0];
166          xinit[index++] = pos[1];
167          xinit[index++] = pos[2];
168                  
169 <        if (integrableObject->isDirectional()) {
170 <          eulerAngle = integrableObject->getEuler();
169 >        if (sd->isDirectional()) {
170 >          eulerAngle = sd->getEuler();
171            xinit[index++] = eulerAngle[0];
172            xinit[index++] = eulerAngle[1];
173            xinit[index++] = eulerAngle[2];          
174          }
175 +
176        }
177      }
178      return xinit;

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