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root/OpenMD/branches/development/src/primitives/RigidBody.cpp

Comparing:
trunk/src/primitives/RigidBody.cpp (file contents), Revision 1424 by gezelter, Tue Mar 30 15:05:38 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

Comparing:
trunk/src/primitives/RigidBody.cpp (property svn:keywords), Revision 1424 by gezelter, Tue Mar 30 15:05:38 2010 UTC vs.
branches/development/src/primitives/RigidBody.cpp (property svn:keywords), Revision 1798 by gezelter, Thu Sep 13 14:10:11 2012 UTC

#	Line 0 | Line 1
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