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root/OpenMD/trunk/src/primitives/RigidBody.cpp
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Comparing trunk/src/primitives/RigidBody.cpp (file contents):
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC vs.
Revision 1797 by gezelter, Mon Sep 10 20:58:00 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 76 | Line 77 | namespace OpenMD {
77      
78      //((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_] = a.transpose() * sU_;    
79      
80 <    for (int i =0 ; i < atoms_.size(); ++i){
80 >    for (unsigned int i = 0 ; i < atoms_.size(); ++i){
81        if (atoms_[i]->isDirectional()) {
82          atoms_[i]->setA(refOrients_[i].transpose() * a, snapshotNo);
83        }
# Line 93 | Line 94 | namespace OpenMD {
94      Vector3d force;
95      Vector3d torque;
96      Vector3d myEuler;
97 <    RealType phi, theta, psi;
97 >    RealType phi, theta;
98 >    // RealType psi;
99      RealType cphi, sphi, ctheta, stheta;
100      Vector3d ephi;
101      Vector3d etheta;
# Line 105 | Line 107 | namespace OpenMD {
107      
108      phi = myEuler[0];
109      theta = myEuler[1];
110 <    psi = myEuler[2];
110 >    // psi = myEuler[2];
111      
112      cphi = cos(phi);
113      sphi = sin(phi);
# Line 228 | Line 230 | namespace OpenMD {
230      Vector3d frc(0.0);
231      Vector3d trq(0.0);    
232      Vector3d pos = this->getPos();
233 <    for (int i = 0; i < atoms_.size(); i++) {
233 >    for (unsigned int i = 0; i < atoms_.size(); i++) {
234  
235        afrc = atoms_[i]->getFrc();
236        apos = atoms_[i]->getPos();
# Line 263 | Line 265 | namespace OpenMD {
265      Vector3d pos = this->getPos();
266      Mat3x3d tau_(0.0);
267  
268 <    for (int i = 0; i < atoms_.size(); i++) {
268 >    for (unsigned int i = 0; i < atoms_.size(); i++) {
269        
270        afrc = atoms_[i]->getFrc();
271        apos = atoms_[i]->getPos();
# Line 375 | Line 377 | namespace OpenMD {
377  
378  
379      Vector3d velRot;        
380 <    for (int i =0 ; i < refCoords_.size(); ++i) {
380 >    for (unsigned int i = 0 ; i < refCoords_.size(); ++i) {
381        atoms_[i]->setVel(rbVel + mat * refCoords_[i]);
382      }
383  
# Line 404 | Line 406 | namespace OpenMD {
406  
407  
408      Vector3d velRot;        
409 <    for (int i =0 ; i < refCoords_.size(); ++i) {
409 >    for (unsigned int i = 0 ; i < refCoords_.size(); ++i) {
410        atoms_[i]->setVel(rbVel + mat * refCoords_[i], frame);
411      }
412  

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