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root/OpenMD/trunk/src/utils/MoLocator.cpp
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Comparing trunk/src/utils/MoLocator.cpp (file contents):
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

# Line 96 | Line 96 | namespace OpenMD {
96    void MoLocator::calcRef( void ){
97      AtomStamp* currAtomStamp;
98      RigidBodyStamp* rbStamp;
99 –    unsigned int nAtoms;
100 –    int nRigidBodies;
99      std::vector<RealType> mass;
100      Vector3d coor;
101      Vector3d refMolCom;  
104 –    int nAtomsInRb;
102      RealType totMassInRb;
103      RealType currAtomMass;
104      RealType molMass;
105      
106 <    nAtoms= myStamp->getNAtoms();
107 <    nRigidBodies = myStamp->getNRigidBodies();
106 >    std::size_t nAtoms= myStamp->getNAtoms();
107 >    std::size_t nRigidBodies = myStamp->getNRigidBodies();
108      
109 <    for(unsigned int i = 0; i < nAtoms; i++){
109 >    for(std::size_t i = 0; i < nAtoms; i++){
110        
111        currAtomStamp = myStamp->getAtomStamp(i);
112        
# Line 140 | Line 137 | namespace OpenMD {
137        }
138      }
139      
140 <    for(int i = 0; i < nRigidBodies; i++){
140 >    for(std::size_t i = 0; i < nRigidBodies; i++){
141        
142        rbStamp = myStamp->getRigidBodyStamp(i);
143 <      nAtomsInRb = rbStamp->getNMembers();
143 >      std::size_t nAtomsInRb = rbStamp->getNMembers();
144        
145        coor.x() = 0.0;
146        coor.y() = 0.0;
147        coor.z() = 0.0;
148        totMassInRb = 0.0;
149        
150 <      for(int j = 0; j < nAtomsInRb; j++){
150 >      for(std::size_t j = 0; j < nAtomsInRb; j++){
151          
152          currAtomStamp = myStamp->getAtomStamp(rbStamp->getMemberAt(j));
153          currAtomMass = getAtomMass(currAtomStamp->getType(), myFF);
# Line 173 | Line 170 | namespace OpenMD {
170      refMolCom.y() = 0;
171      refMolCom.z() = 0;
172      
173 <    for(int i = 0; i < nIntegrableObjects; i++){
173 >    for(std::size_t i = 0; i < nIntegrableObjects; i++){
174        refMolCom += refCoords[i] * mass[i];
175        molMass += mass[i];
176      }
# Line 182 | Line 179 | namespace OpenMD {
179      
180      //move the reference center of mass to (0,0,0) and adjust the
181      //reference coordinate of the integrabel objects
182 <    for(int i = 0; i < nIntegrableObjects; i++)
182 >    for(std::size_t i = 0; i < nIntegrableObjects; i++)
183        refCoords[i] -= refMolCom;
184    }
185    
# Line 190 | Line 187 | namespace OpenMD {
187      RealType mass;
188      AtomType* atomType= myFF->getAtomType(at);
189      if (atomType != NULL) {
190 <      mass =     atomType->getMass();
190 >      mass = atomType->getMass();
191      } else {
192        mass = 0.0;
193        std::cerr << "Can not find AtomType: " << at << std::endl;
# Line 203 | Line 200 | namespace OpenMD {
200      RealType totMass = 0;
201      nAtoms = molStamp->getNAtoms();
202      
203 <    for(unsigned int i = 0; i < nAtoms; i++) {
203 >    for(std::size_t i = 0; i < nAtoms; i++) {
204        AtomStamp *currAtomStamp = molStamp->getAtomStamp(i);
205        totMass += getAtomMass(currAtomStamp->getType(), myFF);        
206      }

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