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

Comparing trunk/src/restraints/ObjectRestraint.cpp (file contents):
Revision 1360 by cli2, Mon Sep 7 16:31:51 2009 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 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, 234107 (2008).
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/ObjectRestraint.hpp"
44
45	<	namespace oopse {
45	>	namespace OpenMD {
46
47		void ObjectRestraint::calcForce(Vector3d struc) {
48
49		pot_ = 0.0;
49	–
50		if (restType_ & rtDisplacement) {
51	<	Vector3d del = struc - refPos_;
51	>	Vector3d del = struc - refPos_;
52	>	RealType r = del.length();
53		Vector3d frc = -kDisp_ * del;
54	<	pot_ += 0.5 * kDisp_ * del.lengthSquare();
54	>	RealType p = 0.5 * kDisp_ * del.lengthSquare();
55	>	pot_ = p;
56		force_ = frc * scaleFactor_;
57	+	restInfo_[rtDisplacement] = std::make_pair(r,p);
58		}
59		}
60
#	Line 68 | Line 71 | namespace oopse {
71
72		Quat4d quat = temp.toQuaternion();
73
74	<	RealType twistAngle, swingAngle;
74	>	RealType twistAngle;
75		Vector3d swingAxis;
76	<	RealType tw, swingX, swingY;
76	>	RealType swingX, swingY;
77
78	<	quat.getTwistSwingAxisAngle(twistAngle, swingAngle, swingAxis);
79	<	quat.toSwingTwist(tw, swingX, swingY);
77	<
78	<	RealType dVdtwist, dVdswingX, dVdswingY;
79	<	RealType dTwist, dSwingX, dSwingY;
78	>	quat.toSwingTwist(swingX, swingY, twistAngle);
79	>
80		RealType p;
81		Vector3d tTwist, tSwing;
82
83		if (restType_ & rtTwist){
84	<	dTwist = twistAngle - twist0_;
85	<	dVdtwist = kTwist_ * sin(dTwist);
84	>	RealType dTwist = twistAngle - twist0_;
85	>	RealType dVdtwist = kTwist_ * sin(dTwist);
86		p = kTwist_ * (1.0 - cos(dTwist) );
87		pot_ += p;
88		tBody -= dVdtwist * V3Z;
#	Line 90 | Line 90 | namespace oopse {
90		}
91
92		if (restType_ & rtSwingX){
93	<	dSwingX = swingX - swingX0_;
94	<	dVdswingX = kSwingX_ * 0.5 * sin(2.0 * dSwingX);
93	>	RealType dSwingX = swingX - swingX0_;
94	>	RealType dVdswingX = kSwingX_ * 0.5 * sin(2.0 * dSwingX);
95		p = 0.25 * kSwingX_ * (1.0 - cos(2.0 * dSwingX));
96		pot_ += p;
97		tBody -= dVdswingX * V3X;
#	Line 99 | Line 99 | namespace oopse {
99		}
100
101		if (restType_ & rtSwingY){
102	<	dSwingY = swingY - swingY0_;
103	<	dVdswingY = kSwingY_ * 0.5 * sin(2.0 * dSwingY);
102	>	RealType dSwingY = swingY - swingY0_;
103	>	RealType dVdswingY = kSwingY_ * 0.5 * sin(2.0 * dSwingY);
104		p = 0.25 * kSwingY_ * (1.0 - cos(2.0 * dSwingY));
105		pot_ += p;
106		tBody -= dVdswingY * V3Y;
107		restInfo_[rtSwingY] = std::make_pair(swingY, p);
108		}
109
110	–	std::cerr << "sw = " << swingAngle << " tw = " << twistAngle << "\n";
111	–	std::cerr << "tbod = " << tBody << "\n";
110		Vector3d tLab = A.transpose() * tBody;
111		torque_ = tLab * scaleFactor_;
112		}

Comparing trunk/src/restraints/ObjectRestraint.cpp (property svn:keywords):
Revision 1360 by cli2, Mon Sep 7 16:31:51 2009 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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