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root/OpenMD/trunk/src/utils/MoLocator.cpp
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Comparing trunk/src/utils/MoLocator.cpp (file contents):
Revision 1878 by gezelter, Wed Aug 22 02:28:28 2012 UTC vs.
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 58 | Line 58 | namespace OpenMD {
58      calcRef();
59    }
60    
61 <  void MoLocator::placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol){
61 >  void MoLocator::placeMol( const Vector3d& offset, const Vector3d& ort,
62 >                            Molecule* mol) {
63  
64      Vector3d newCoor;
65      Vector3d curRefCoor;  
# Line 66 | Line 67 | namespace OpenMD {
67      
68      if(mol->getNIntegrableObjects() != nIntegrableObjects){
69        sprintf( painCave.errMsg,
70 <               "MoLocator error.\n"
71 <               "  The number of integrable objects of MoleculeStamp is not the same as  that of Molecule\n");
70 >               "MoLocator::placeMol error.\n"
71 >               "\tThe number of integrable objects of MoleculeStamp is not\n"
72 >               "\tthe same as that of Molecule\n");
73        painCave.isFatal = 1;
74        simError();
75      }
# Line 113 | Line 115 | namespace OpenMD {
115        
116        if( !currAtomStamp->havePosition() ){
117          sprintf( painCave.errMsg,
118 <                 "MoLocator error.\n"
119 <                 "  Component %s, atom %s does not have a position specified.\n"
120 <                 "  This means MoLocator cannot initalize it's position.\n",
118 >                 "MoLocator::calcRef error.\n"
119 >                 "\tComponent %s, atom %s does not have a position specified.\n"
120 >                 "\tThis means MoLocator cannot initalize it's position.\n",
121                   myStamp->getName().c_str(),
122                   currAtomStamp->getType().c_str());
123          
# Line 178 | Line 180 | namespace OpenMD {
180      
181      refMolCom /= molMass;
182      
183 <    //move the reference center of mass to (0,0,0) and adjust the reference coordinate
184 <    //of the integrabel objects
183 >    //move the reference center of mass to (0,0,0) and adjust the
184 >    //reference coordinate of the integrabel objects
185      for(int i = 0; i < nIntegrableObjects; i++)
186        refCoords[i] -= refMolCom;
187    }
188    
189 <  RealType getAtomMass(const std::string& at, ForceField* myFF) {
189 >  RealType MoLocator::getAtomMass(const std::string& at, ForceField* myFF) {
190      RealType mass;
191      AtomType* atomType= myFF->getAtomType(at);
192      if (atomType != NULL) {
# Line 196 | Line 198 | namespace OpenMD {
198      return mass;
199    }
200    
201 <  RealType getMolMass(MoleculeStamp *molStamp, ForceField *myFF) {
201 >  RealType MoLocator::getMolMass(MoleculeStamp *molStamp, ForceField *myFF) {
202      unsigned int nAtoms;
203      RealType totMass = 0;
204      nAtoms = molStamp->getNAtoms();
# Line 207 | Line 209 | namespace OpenMD {
209      }
210      return totMass;
211    }
212 <  RotMat3x3d latVec2RotMat(const Vector3d& lv){
212 >
213 >  RotMat3x3d MoLocator::latVec2RotMat(const Vector3d& lv){
214      
215      RealType theta =acos(lv[2]);
216      RealType phi = atan2(lv[1], lv[0]);
217      RealType psi = 0;
218      
219 <    return RotMat3x3d(phi, theta, psi);
217 <    
219 >    return RotMat3x3d(phi, theta, psi);    
220    }
221   }
222  

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