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root/OpenMD/trunk/src/utils/MoLocator.cpp
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Comparing trunk/src/utils/MoLocator.cpp (file contents):
Revision 501 by gezelter, Thu Apr 14 21:20:36 2005 UTC vs.
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# Line 107 | Line 107 | namespace oopse {
107      
108      for(size_t i=0; i<nAtoms; i++){
109        
110 <      currAtomStamp = myStamp->getAtom(i);
110 >      currAtomStamp = myStamp->getAtomStamp(i);
111        
112        if( !currAtomStamp->havePosition() ){
113          sprintf( painCave.errMsg,
114                   "MoLocator error.\n"
115                   "  Component %s, atom %s does not have a position specified.\n"
116                   "  This means MoLocator cannot initalize it's position.\n",
117 <                 myStamp->getID(),
118 <                 currAtomStamp->getType() );
117 >                 myStamp->getName().c_str(),
118 >                 currAtomStamp->getType().c_str());
119          
120          painCave.isFatal = 1;
121          simError();
# Line 138 | Line 138 | namespace oopse {
138      
139      for(int i = 0; i < nRigidBodies; i++){
140        
141 <      rbStamp = myStamp->getRigidBody(i);
141 >      rbStamp = myStamp->getRigidBodyStamp(i);
142        nAtomsInRb = rbStamp->getNMembers();
143        
144        coor.x() = 0.0;
# Line 148 | Line 148 | namespace oopse {
148        
149        for(int j = 0; j < nAtomsInRb; j++){
150          
151 <        currAtomStamp = myStamp->getAtom(rbStamp->getMember(j));
151 >        currAtomStamp = myStamp->getAtomStamp(rbStamp->getMemberAt(j));
152          currAtomMass = getAtomMass(currAtomStamp->getType(), myFF);
153          totMassInRb +=  currAtomMass;
154          
# Line 178 | Line 178 | namespace oopse {
178      
179      //move the reference center of mass to (0,0,0) and adjust the reference coordinate
180      //of the integrabel objects
181 <  for(int i = 0; i < nIntegrableObjects; i++)
182 <    refCoords[i] -= refMolCom;
181 >    for(int i = 0; i < nIntegrableObjects; i++)
182 >      refCoords[i] -= refMolCom;
183    }
184    
185    double getAtomMass(const std::string& at, ForceField* myFF) {
# Line 200 | Line 200 | namespace oopse {
200      nAtoms = molStamp->getNAtoms();
201      
202      for(size_t i = 0; i < nAtoms; i++) {
203 <      AtomStamp *currAtomStamp = molStamp->getAtom(i);
203 >      AtomStamp *currAtomStamp = molStamp->getAtomStamp(i);
204        totMass += getAtomMass(currAtomStamp->getType(), myFF);        
205      }
206      return totMass;

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