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root/OpenMD/branches/development/src/restraints/MolecularRestraint.cpp

Comparing:
trunk/src/restraints/MolecularRestraint.cpp (file contents), Revision 1360 by cli2, Mon Sep 7 16:31:51 2009 UTC vs.
branches/development/src/restraints/MolecularRestraint.cpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
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).
40		*/
41
42		#include "restraints/MolecularRestraint.hpp"
#	Line 46 | Line 46
46
47		//using namespace JAMA;
48
49	<	namespace oopse {
49	>	namespace OpenMD {
50
51	+
52		void MolecularRestraint::calcForce(std::vector<Vector3d> struc,
53		Vector3d molCom){
54
#	Line 141 | Line 142 | namespace oopse {
142
143		Quat4d quat = A.toQuaternion();
144
144	–	quat.getTwistSwingAxisAngle(twistAngle, swingAngle, swingAxis);
145	–
145		RealType tw, sx, sy, ttw, swingX, swingY;
146	<	quat.toTwistSwing(tw, sx, sy);
148	<	quat.toSwingTwist(swingX, swingY, ttw);
146	>	quat.toSwingTwist(swingX, swingY, twistAngle);
147
150	–	// std::cerr << eularAngles << "\t[" << twistAngle << "," << swingAngle <<
151	–	// "]\t[" << tw << "," << sx << "," << sy << "]\t[" << ttw <<
152	–	// "," << ssx << "," << ssy << "]" << std::endl;
153	–
148		RealType dVdtwist, dVdswing, dVdswingX, dVdswingY;
149		RealType dTwist, dSwing, dSwingX, dSwingY;
150		RealType p;

Comparing:
trunk/src/restraints/MolecularRestraint.cpp (property svn:keywords), Revision 1360 by cli2, Mon Sep 7 16:31:51 2009 UTC vs.
branches/development/src/restraints/MolecularRestraint.cpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

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