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root/OpenMD/trunk/src/primitives/RigidBody.cpp

Comparing trunk/src/primitives/RigidBody.cpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 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 118 | Line 120 | namespace OpenMD {
120		ephi[1] = 0.0;
121		ephi[2] = 1.0;
122
123	<	etheta[0] = -sphi;
124	<	etheta[1] =  cphi;
123	>	//etheta[0] = -sphi;
124	>	//etheta[1] =  cphi;
125	>	//etheta[2] =  0.0;
126	>
127	>	etheta[0] = cphi;
128	>	etheta[1] = sphi;
129		etheta[2] =  0.0;
130
131		epsi[0] = stheta * cphi;
#	Line 224 | 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 259 | 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 371 | 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 400 | 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

Comparing trunk/src/primitives/RigidBody.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1797 by gezelter, Mon Sep 10 20:58:00 2012 UTC

#	Line 0 | Line 1
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