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root/OpenMD/branches/development/src/primitives/RigidBody.cpp
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trunk/src/primitives/RigidBody.cpp (file contents), Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC vs.
branches/development/src/primitives/RigidBody.cpp (file contents), Revision 1798 by gezelter, Thu Sep 13 14:10:11 2012 UTC

# Line 36 | Line 36
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).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42   #include <algorithm>
43   #include <math.h>
# Line 52 | Line 53 | namespace OpenMD {
53    void RigidBody::setPrevA(const RotMat3x3d& a) {
54      ((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a;
55      
56 <    for (int i =0 ; i < atoms_.size(); ++i){
56 >    for (unsigned int i = 0 ; i < atoms_.size(); ++i){
57        if (atoms_[i]->isDirectional()) {
58          atoms_[i]->setPrevA(refOrients_[i].transpose() * a);
59        }
# Line 64 | Line 65 | namespace OpenMD {
65    void RigidBody::setA(const RotMat3x3d& a) {
66      ((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;
67  
68 <    for (int i =0 ; i < atoms_.size(); ++i){
68 >    for (unsigned int i = 0 ; i < atoms_.size(); ++i){
69        if (atoms_[i]->isDirectional()) {
70          atoms_[i]->setA(refOrients_[i].transpose() * a);
71        }
# Line 73 | Line 74 | namespace OpenMD {
74    
75    void RigidBody::setA(const RotMat3x3d& a, int snapshotNo) {
76      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a;
77 <    
78 <    //((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_] = a.transpose() * sU_;    
78 <    
79 <    for (int i =0 ; i < atoms_.size(); ++i){
77 >        
78 >    for (unsigned int i = 0 ; i < atoms_.size(); ++i){
79        if (atoms_[i]->isDirectional()) {
80          atoms_[i]->setA(refOrients_[i].transpose() * a, snapshotNo);
81        }
# Line 93 | Line 92 | namespace OpenMD {
92      Vector3d force;
93      Vector3d torque;
94      Vector3d myEuler;
95 <    RealType phi, theta, psi;
95 >    RealType phi, theta;
96 >    // RealType psi;
97      RealType cphi, sphi, ctheta, stheta;
98      Vector3d ephi;
99      Vector3d etheta;
# Line 105 | Line 105 | namespace OpenMD {
105      
106      phi = myEuler[0];
107      theta = myEuler[1];
108 <    psi = myEuler[2];
108 >    // psi = myEuler[2];
109      
110      cphi = cos(phi);
111      sphi = sin(phi);
# Line 228 | Line 228 | namespace OpenMD {
228      Vector3d frc(0.0);
229      Vector3d trq(0.0);    
230      Vector3d pos = this->getPos();
231 <    for (int i = 0; i < atoms_.size(); i++) {
231 >    for (unsigned int i = 0; i < atoms_.size(); i++) {
232  
233        afrc = atoms_[i]->getFrc();
234        apos = atoms_[i]->getPos();
# Line 263 | Line 263 | namespace OpenMD {
263      Vector3d pos = this->getPos();
264      Mat3x3d tau_(0.0);
265  
266 <    for (int i = 0; i < atoms_.size(); i++) {
266 >    for (unsigned int i = 0; i < atoms_.size(); i++) {
267        
268        afrc = atoms_[i]->getFrc();
269        apos = atoms_[i]->getPos();
# Line 375 | Line 375 | namespace OpenMD {
375  
376  
377      Vector3d velRot;        
378 <    for (int i =0 ; i < refCoords_.size(); ++i) {
378 >    for (unsigned int i = 0 ; i < refCoords_.size(); ++i) {
379        atoms_[i]->setVel(rbVel + mat * refCoords_[i]);
380      }
381  
# Line 404 | Line 404 | namespace OpenMD {
404  
405  
406      Vector3d velRot;        
407 <    for (int i =0 ; i < refCoords_.size(); ++i) {
407 >    for (unsigned int i = 0 ; i < refCoords_.size(); ++i) {
408        atoms_[i]->setVel(rbVel + mat * refCoords_[i], frame);
409      }
410  

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