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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 1842 by gezelter, Tue Jan 29 19:10:04 2013 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 226 | Line 226 | namespace OpenMD {
226		Vector3d apos;
227		Vector3d rpos;
228		Vector3d frc(0.0);
229	<	Vector3d trq(0.0);
229	>	Vector3d trq(0.0);
230	>	Vector3d ef(0.0);
231		Vector3d pos = this->getPos();
231	–	for (int i = 0; i < atoms_.size(); i++) {
232
233	+	int sl = ((snapshotMan_->getCurrentSnapshot())->*storage_).getStorageLayout();
234	+
235	+	for (unsigned int i = 0; i < atoms_.size(); i++) {
236	+
237		afrc = atoms_[i]->getFrc();
238		apos = atoms_[i]->getPos();
239		rpos = apos - pos;
#	Line 246 | Line 250 | namespace OpenMD {
250		if (atoms_[i]->isDirectional()) {
251		atrq = atoms_[i]->getTrq();
252		trq += atrq;
253	<	}
253	>	}
254	>
255	>	if (sl & DataStorage::dslElectricField) {
256	>	ef += atoms_[i]->getElectricField();
257	>	}
258		}
259		addFrc(frc);
260		addTrq(trq);
261	+
262	+	if (sl & DataStorage::dslElectricField) {
263	+	ef /= atoms_.size();
264	+	setElectricField(ef);
265	+	}
266	+
267		}
268
269		Mat3x3d RigidBody::calcForcesAndTorquesAndVirial() {
#	Line 259 | Line 273 | namespace OpenMD {
273		Vector3d rpos;
274		Vector3d dfrc;
275		Vector3d frc(0.0);
276	<	Vector3d trq(0.0);
276	>	Vector3d trq(0.0);
277	>	Vector3d ef(0.0);
278	>
279		Vector3d pos = this->getPos();
280		Mat3x3d tau_(0.0);
281
282	<	for (int i = 0; i < atoms_.size(); i++) {
282	>	int sl = ((snapshotMan_->getCurrentSnapshot())->*storage_).getStorageLayout();
283	>
284	>	for (unsigned int i = 0; i < atoms_.size(); i++) {
285
286		afrc = atoms_[i]->getFrc();
287		apos = atoms_[i]->getPos();
#	Line 282 | Line 300 | namespace OpenMD {
300		atrq = atoms_[i]->getTrq();
301		trq += atrq;
302		}
303	+	if (sl & DataStorage::dslElectricField) {
304	+	ef += atoms_[i]->getElectricField();
305	+	}
306
307		tau_(0,0) -= rpos[0]*afrc[0];
308		tau_(0,1) -= rpos[0]*afrc[1];
#	Line 296 | Line 317 | namespace OpenMD {
317		}
318		addFrc(frc);
319		addTrq(trq);
320	+
321	+	if (sl & DataStorage::dslElectricField) {
322	+	ef /= atoms_.size();
323	+	setElectricField(ef);
324	+	}
325	+
326		return tau_;
327		}
328
#	Line 375 | Line 402 | namespace OpenMD {
402
403
404		Vector3d velRot;
405	<	for (int i =0 ; i < refCoords_.size(); ++i) {
405	>	for (unsigned int i = 0 ; i < refCoords_.size(); ++i) {
406		atoms_[i]->setVel(rbVel + mat * refCoords_[i]);
407		}
408
#	Line 404 | Line 431 | namespace OpenMD {
431
432
433		Vector3d velRot;
434	<	for (int i =0 ; i < refCoords_.size(); ++i) {
434	>	for (unsigned int i = 0 ; i < refCoords_.size(); ++i) {
435		atoms_[i]->setVel(rbVel + mat * refCoords_[i], frame);
436		}
437

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 1842 by gezelter, Tue Jan 29 19:10:04 2013 UTC

#	Line 0 | Line 1
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