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root/OpenMD/trunk/src/restraints/MolecularRestraint.cpp

Comparing trunk/src/restraints/MolecularRestraint.cpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 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
43		#include "restraints/MolecularRestraint.hpp"
#	Line 48 | Line 49 | namespace OpenMD {
49
50		namespace OpenMD {
51
52	+
53		void MolecularRestraint::calcForce(std::vector<Vector3d> struc,
54		Vector3d molCom){
55
#	Line 84 | Line 86 | namespace OpenMD {
86
87		Mat3x3d R(0.0);
88
89	<	for (int n = 0; n < struc.size(); n++){
89	>	for (unsigned int n = 0; n < struc.size(); n++){
90
91		/*
92		* correlation matrix R:
#	Line 136 | Line 138 | namespace OpenMD {
138		Vector3d eularAngles = A.toEulerAngles();
139
140
141	<	RealType twistAngle, swingAngle;
141	>	RealType twistAngle;
142		Vector3d swingAxis;
143
144		Quat4d quat = A.toQuaternion();
145
146	<	quat.getTwistSwingAxisAngle(twistAngle, swingAngle, swingAxis);
146	>	RealType swingX, swingY;
147	>	quat.toSwingTwist(swingX, swingY, twistAngle);
148
149	<	RealType tw, sx, sy, ttw, swingX, swingY;
150	<	quat.toTwistSwing(tw, sx, sy);
148	<	quat.toSwingTwist(swingX, swingY, ttw);
149	<
150	<	// std::cerr << eularAngles << "\t[" << twistAngle << "," << swingAngle <<
151	<	// "]\t[" << tw << "," << sx << "," << sy << "]\t[" << ttw <<
152	<	// "," << ssx << "," << ssy << "]" << std::endl;
153	<
154	<	RealType dVdtwist, dVdswing, dVdswingX, dVdswingY;
155	<	RealType dTwist, dSwing, dSwingX, dSwingY;
149	>	RealType dVdtwist, dVdswingX, dVdswingY;
150	>	RealType dTwist, dSwingX, dSwingY;
151		RealType p;
152
153		if (restType_ & rtTwist){
#	Line 195 | Line 190 | namespace OpenMD {
190
191		Vector3d rLab, rBody, txr, fBody, fLab;
192
193	<	for (int i = 0; i < struc.size(); i++) {
193	>	for (unsigned int i = 0; i < struc.size(); i++) {
194
195		rLab = struc[i];
196		rBody = A * rLab;

Comparing trunk/src/restraints/MolecularRestraint.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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