--- trunk/src/primitives/RigidBody.cpp	2008/01/23 16:38:22	1211
+++ trunk/src/primitives/RigidBody.cpp	2012/09/10 20:58:00	1797
@@ -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.
@@ -37,13 +28,23 @@
  * 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 <algorithm>
 #include <math.h>
 #include "primitives/RigidBody.hpp"
 #include "utils/simError.h"
 #include "utils/NumericConstant.hpp"
-namespace oopse {
+namespace OpenMD {
   
   RigidBody::RigidBody() : StuntDouble(otRigidBody, &Snapshot::rigidbodyData),
                            inertiaTensor_(0.0){    
@@ -52,7 +53,7 @@ namespace oopse {
   void RigidBody::setPrevA(const RotMat3x3d& a) {
     ((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a;
     
-    for (int i =0 ; i < atoms_.size(); ++i){
+    for (unsigned int i = 0 ; i < atoms_.size(); ++i){
       if (atoms_[i]->isDirectional()) {
 	atoms_[i]->setPrevA(refOrients_[i].transpose() * a);
       }
@@ -64,7 +65,7 @@ namespace oopse {
   void RigidBody::setA(const RotMat3x3d& a) {
     ((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;
 
-    for (int i =0 ; i < atoms_.size(); ++i){
+    for (unsigned int i = 0 ; i < atoms_.size(); ++i){
       if (atoms_[i]->isDirectional()) {
 	atoms_[i]->setA(refOrients_[i].transpose() * a);
       }
@@ -76,7 +77,7 @@ namespace oopse {
     
     //((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_] = a.transpose() * sU_;    
     
-    for (int i =0 ; i < atoms_.size(); ++i){
+    for (unsigned int i = 0 ; i < atoms_.size(); ++i){
       if (atoms_[i]->isDirectional()) {
 	atoms_[i]->setA(refOrients_[i].transpose() * a, snapshotNo);
       }
@@ -93,7 +94,8 @@ namespace oopse {
     Vector3d force;
     Vector3d torque;
     Vector3d myEuler;
-    RealType phi, theta, psi;
+    RealType phi, theta;
+    // RealType psi;
     RealType cphi, sphi, ctheta, stheta;
     Vector3d ephi;
     Vector3d etheta;
@@ -105,7 +107,7 @@ namespace oopse {
     
     phi = myEuler[0];
     theta = myEuler[1];
-    psi = myEuler[2];
+    // psi = myEuler[2];
     
     cphi = cos(phi);
     sphi = sin(phi);
@@ -118,9 +120,13 @@ namespace oopse {
     ephi[1] = 0.0;
     ephi[2] = 1.0;
     
+    //etheta[0] = -sphi;
+    //etheta[1] =  cphi;
+    //etheta[2] =  0.0;
+    
     etheta[0] = cphi;
     etheta[1] = sphi;
-    etheta[2] = 0.0;
+    etheta[2] =  0.0;
     
     epsi[0] = stheta * cphi;
     epsi[1] = stheta * sphi;
@@ -193,7 +199,7 @@ namespace oopse {
         
     int nLinearAxis = 0;
     for (int i = 0; i < 3; i++) {    
-      if (fabs(evals[i]) < oopse::epsilon) {
+      if (fabs(evals[i]) < OpenMD::epsilon) {
 	linear_ = true;
 	linearAxis_ = i;
 	++ nLinearAxis;
@@ -203,7 +209,7 @@ namespace oopse {
     if (nLinearAxis > 1) {
       sprintf( painCave.errMsg,
 	       "RigidBody error.\n"
-	       "\tOOPSE found more than one axis in this rigid body with a vanishing \n"
+	       "\tOpenMD found more than one axis in this rigid body with a vanishing \n"
 	       "\tmoment of inertia.  This can happen in one of three ways:\n"
 	       "\t 1) Only one atom was specified, or \n"
 	       "\t 2) All atoms were specified at the same location, or\n"
@@ -224,7 +230,7 @@ namespace oopse {
     Vector3d frc(0.0);
     Vector3d trq(0.0);    
     Vector3d pos = this->getPos();
-    for (int i = 0; i < atoms_.size(); i++) {
+    for (unsigned int i = 0; i < atoms_.size(); i++) {
 
       afrc = atoms_[i]->getFrc();
       apos = atoms_[i]->getPos();
@@ -259,7 +265,7 @@ namespace oopse {
     Vector3d pos = this->getPos();
     Mat3x3d tau_(0.0);
 
-    for (int i = 0; i < atoms_.size(); i++) {
+    for (unsigned int i = 0; i < atoms_.size(); i++) {
       
       afrc = atoms_[i]->getFrc();
       apos = atoms_[i]->getPos();
@@ -371,7 +377,7 @@ namespace oopse {
 
 
     Vector3d velRot;        
-    for (int i =0 ; i < refCoords_.size(); ++i) {
+    for (unsigned int i = 0 ; i < refCoords_.size(); ++i) {
       atoms_[i]->setVel(rbVel + mat * refCoords_[i]);
     }
 
@@ -400,7 +406,7 @@ namespace oopse {
 
 
     Vector3d velRot;        
-    for (int i =0 ; i < refCoords_.size(); ++i) {
+    for (unsigned int i = 0 ; i < refCoords_.size(); ++i) {
       atoms_[i]->setVel(rbVel + mat * refCoords_[i], frame);
     }