--- trunk/src/utils/MoLocator.cpp	2006/05/17 21:51:42	963
+++ trunk/src/utils/MoLocator.cpp	2012/08/22 02:28:28	1782
@@ -6,19 +6,10 @@
  * redistribute this software in source and binary code form, provided
  * that the following conditions are met:
  *
- * 1. Acknowledgement of the program authors must be made in any
- *    publication of scientific results based in part on use of the
- *    program.  An acceptable form of acknowledgement is citation of
- *    the article in which the program was described (Matthew
- *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
- *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
- *    Parallel Simulation Engine for Molecular Dynamics,"
- *    J. Comput. Chem. 26, pp. 252-271 (2005))
- *
- * 2. Redistributions of source code must retain the above copyright
+ * 1. Redistributions of source code must retain the above copyright
  *    notice, this list of conditions and the following disclaimer.
  *
- * 3. Redistributions in binary form must reproduce the above copyright
+ * 2. Redistributions in binary form must reproduce the above copyright
  *    notice, this list of conditions and the following disclaimer in the
  *    documentation and/or other materials provided with the
  *    distribution.
@@ -37,6 +28,16 @@
  * arising out of the use of or inability to use software, even if the
  * University of Notre Dame has been advised of the possibility of
  * such damages.
+ *
+ * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
+ * research, please cite the appropriate papers when you publish your
+ * work.  Good starting points are:
+ *                                                                      
+ * [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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
  
 #include <iostream>
@@ -48,7 +49,7 @@
 #include "utils/MoLocator.hpp"
 #include "types/AtomType.hpp"
 
-namespace oopse {
+namespace OpenMD {
   MoLocator::MoLocator( MoleculeStamp* theStamp, ForceField* theFF){
     
     myStamp = theStamp;
@@ -58,6 +59,7 @@ namespace oopse {
   }
   
   void MoLocator::placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol){
+
     Vector3d newCoor;
     Vector3d curRefCoor;  
     RotMat3x3d rotMat = latVec2RotMat(ort);
@@ -71,20 +73,20 @@ namespace oopse {
     }
     
     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;
+     
+      sd->setPos(newCoor);
+      sd->setVel(V3Zero);
       
-      integrableObject->setPos( newCoor);
-      integrableObject->setVel(V3Zero);
-      
-      if(integrableObject->isDirectional()){
-        integrableObject->setA(rotMat * integrableObject->getA());
-        integrableObject->setJ(V3Zero);  
+      if(sd->isDirectional()){
+        sd->setA(rotMat * sd->getA());
+        sd->setJ(V3Zero);  
       }        
     }
   }
@@ -92,7 +94,7 @@ namespace oopse {
   void MoLocator::calcRef( void ){
     AtomStamp* currAtomStamp;
     RigidBodyStamp* rbStamp;
-    int nAtoms; 
+    unsigned int nAtoms; 
     int nRigidBodies;
     std::vector<RealType> mass;
     Vector3d coor;
@@ -105,7 +107,7 @@ namespace oopse {
     nAtoms= myStamp->getNAtoms();
     nRigidBodies = myStamp->getNRigidBodies();
     
-    for(size_t i=0; i<nAtoms; i++){
+    for(unsigned int i = 0; i < nAtoms; i++){
       
       currAtomStamp = myStamp->getAtomStamp(i);
       
@@ -195,11 +197,11 @@ namespace oopse {
   }
   
   RealType getMolMass(MoleculeStamp *molStamp, ForceField *myFF) {
-    int nAtoms;
+    unsigned int nAtoms;
     RealType totMass = 0;
     nAtoms = molStamp->getNAtoms();
     
-    for(size_t i = 0; i < nAtoms; i++) {
+    for(unsigned int i = 0; i < nAtoms; i++) {
       AtomStamp *currAtomStamp = molStamp->getAtomStamp(i);
       totMass += getAtomMass(currAtomStamp->getType(), myFF);         
     }