--- trunk/src/utils/MoLocator.cpp	2010/05/10 17:28:26	1442
+++ trunk/src/utils/MoLocator.cpp	2015/03/07 21:41:51	2071
@@ -35,8 +35,9 @@
  *                                                                      
  * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
  * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
- * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
- * [4]  Vardeman & Gezelter, in progress (2009).                        
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
  
 #include <iostream>
@@ -57,7 +58,8 @@ namespace OpenMD {
     calcRef();
   }
   
-  void MoLocator::placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol){
+  void MoLocator::placeMol( const Vector3d& offset, const Vector3d& ort, 
+                            Molecule* mol) {
 
     Vector3d newCoor;
     Vector3d curRefCoor;  
@@ -65,27 +67,28 @@ namespace OpenMD {
     
     if(mol->getNIntegrableObjects() != nIntegrableObjects){
       sprintf( painCave.errMsg,
-               "MoLocator error.\n"
-               "  The number of integrable objects of MoleculeStamp is not the same as  that of Molecule\n");
+               "MoLocator::placeMol error.\n"
+               "\tThe number of integrable objects of MoleculeStamp is not\n"
+               "\tthe same as that of Molecule\n");
       painCave.isFatal = 1;
       simError();
     }
     
     Molecule::IntegrableObjectIterator ii;
-    StuntDouble* integrableObject;
+    StuntDouble* sd;
     int i;
-    for (integrableObject = mol->beginIntegrableObject(ii), i = 0; integrableObject != NULL; 
-         integrableObject = mol->nextIntegrableObject(ii), ++i) { 
+    for (sd = mol->beginIntegrableObject(ii), i = 0; sd != NULL; 
+         sd = mol->nextIntegrableObject(ii), ++i) { 
       
       newCoor = rotMat * refCoords[i];
       newCoor += offset;
      
-      integrableObject->setPos(newCoor);
-      integrableObject->setVel(V3Zero);
+      sd->setPos(newCoor);
+      sd->setVel(V3Zero);
       
-      if(integrableObject->isDirectional()){
-        integrableObject->setA(rotMat * integrableObject->getA());
-        integrableObject->setJ(V3Zero);  
+      if(sd->isDirectional()){
+        sd->setA(rotMat * sd->getA());
+        sd->setJ(V3Zero);  
       }        
     }
   }
@@ -93,28 +96,25 @@ namespace OpenMD {
   void MoLocator::calcRef( void ){
     AtomStamp* currAtomStamp;
     RigidBodyStamp* rbStamp;
-    int nAtoms; 
-    int nRigidBodies;
     std::vector<RealType> mass;
     Vector3d coor;
     Vector3d refMolCom;  
-    int nAtomsInRb;
     RealType totMassInRb;
     RealType currAtomMass;
     RealType molMass;
     
-    nAtoms= myStamp->getNAtoms();
-    nRigidBodies = myStamp->getNRigidBodies();
+    std::size_t nAtoms= myStamp->getNAtoms();
+    std::size_t nRigidBodies = myStamp->getNRigidBodies();
     
-    for(size_t i=0; i<nAtoms; i++){
+    for(std::size_t i = 0; i < nAtoms; i++){
       
       currAtomStamp = myStamp->getAtomStamp(i);
       
       if( !currAtomStamp->havePosition() ){
         sprintf( painCave.errMsg,
-                 "MoLocator error.\n"
-                 "  Component %s, atom %s does not have a position specified.\n"
-                 "  This means MoLocator cannot initalize it's position.\n",
+                 "MoLocator::calcRef error.\n"
+                 "\tComponent %s, atom %s does not have a position specified.\n"
+                 "\tThis means MoLocator cannot initalize it's position.\n",
                  myStamp->getName().c_str(),
                  currAtomStamp->getType().c_str());
         
@@ -137,17 +137,17 @@ namespace OpenMD {
       }
     }
     
-    for(int i = 0; i < nRigidBodies; i++){
+    for(std::size_t i = 0; i < nRigidBodies; i++){
       
       rbStamp = myStamp->getRigidBodyStamp(i);
-      nAtomsInRb = rbStamp->getNMembers();
+      std::size_t nAtomsInRb = rbStamp->getNMembers();
       
       coor.x() = 0.0;
       coor.y() = 0.0;
       coor.z() = 0.0;
       totMassInRb = 0.0;
       
-      for(int j = 0; j < nAtomsInRb; j++){
+      for(std::size_t j = 0; j < nAtomsInRb; j++){
         
         currAtomStamp = myStamp->getAtomStamp(rbStamp->getMemberAt(j));
         currAtomMass = getAtomMass(currAtomStamp->getType(), myFF);
@@ -170,24 +170,24 @@ namespace OpenMD {
     refMolCom.y() = 0;
     refMolCom.z() = 0;
     
-    for(int i = 0; i < nIntegrableObjects; i++){
+    for(std::size_t i = 0; i < nIntegrableObjects; i++){
       refMolCom += refCoords[i] * mass[i];
       molMass += mass[i];
     }
     
     refMolCom /= molMass;
     
-    //move the reference center of mass to (0,0,0) and adjust the reference coordinate 
-    //of the integrabel objects
-    for(int i = 0; i < nIntegrableObjects; i++)
+    //move the reference center of mass to (0,0,0) and adjust the
+    //reference coordinate of the integrabel objects
+    for(std::size_t i = 0; i < nIntegrableObjects; i++)
       refCoords[i] -= refMolCom;
   }
   
-  RealType getAtomMass(const std::string& at, ForceField* myFF) {
+  RealType MoLocator::getAtomMass(const std::string& at, ForceField* myFF) {
     RealType mass;
     AtomType* atomType= myFF->getAtomType(at);
     if (atomType != NULL) {
-      mass =     atomType->getMass();
+      mass = atomType->getMass();
     } else {
       mass = 0.0;
       std::cerr << "Can not find AtomType: " << at << std::endl;
@@ -195,25 +195,25 @@ namespace OpenMD {
     return mass;
   }
   
-  RealType getMolMass(MoleculeStamp *molStamp, ForceField *myFF) {
-    int nAtoms;
+  RealType MoLocator::getMolMass(MoleculeStamp *molStamp, ForceField *myFF) {
+    unsigned int nAtoms;
     RealType totMass = 0;
     nAtoms = molStamp->getNAtoms();
     
-    for(size_t i = 0; i < nAtoms; i++) {
+    for(std::size_t i = 0; i < nAtoms; i++) {
       AtomStamp *currAtomStamp = molStamp->getAtomStamp(i);
       totMass += getAtomMass(currAtomStamp->getType(), myFF);         
     }
     return totMass;
   }
-  RotMat3x3d latVec2RotMat(const Vector3d& lv){
+
+  RotMat3x3d MoLocator::latVec2RotMat(const Vector3d& lv){
     
     RealType theta =acos(lv[2]);
     RealType phi = atan2(lv[1], lv[0]);
     RealType psi = 0;
     
-    return RotMat3x3d(phi, theta, psi);
-    
+    return RotMat3x3d(phi, theta, psi);    
   }
 }