src/restraints/ObjectRestraint.cpp

/*
 * Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */

#include "restraints/ObjectRestraint.hpp"

namespace OpenMD {

  void ObjectRestraint::calcForce(Vector3d struc) {

    pot_ = 0.0;
    
    if (restType_ & rtDisplacement) {
      Vector3d del = struc - refPos_;
      RealType r = del.length();  
      Vector3d frc = -kDisp_ * del;
      RealType p = 0.5 * kDisp_ * del.lengthSquare();
      pot_ += p;
      force_ = frc * scaleFactor_;
      restInfo_[rtDisplacement] = std::make_pair(r,p);
    }
  }
    
  void ObjectRestraint::calcForce(Vector3d struc, RotMat3x3d A) {

    calcForce(struc);

    // rtDisplacement is 1, so anything higher than that requires orientations:
    if (restType_ > 1) {
      
      Vector3d tBody(0.0);
      
      RotMat3x3d temp = A * refA_.transpose();

      Quat4d quat = temp.toQuaternion();

      RealType twistAngle, swingAngle;
      Vector3d swingAxis;
      RealType tw, swingX, swingY;
      
      quat.getTwistSwingAxisAngle(twistAngle, swingAngle, swingAxis);
      quat.toSwingTwist(tw, swingX, swingY);
      
      RealType dVdtwist, dVdswingX, dVdswingY;
      RealType dTwist, dSwingX, dSwingY;
      RealType p;
      Vector3d tTwist, tSwing;

      if (restType_ & rtTwist){
        dTwist = twistAngle - twist0_;
        dVdtwist = kTwist_ * sin(dTwist);
        p = kTwist_ * (1.0 - cos(dTwist) );
        pot_ += p;
        tBody -= dVdtwist * V3Z;
        restInfo_[rtTwist] = std::make_pair(twistAngle, p);
      }

      if (restType_ & rtSwingX){
        dSwingX = swingX - swingX0_;
        dVdswingX = kSwingX_ * 0.5 * sin(2.0 * dSwingX);
        p = 0.25 * kSwingX_ * (1.0 - cos(2.0 * dSwingX));
        pot_ += p;
        tBody -= dVdswingX * V3X;
        restInfo_[rtSwingX] = std::make_pair(swingX, p);
      }

      if (restType_ & rtSwingY){
        dSwingY = swingY - swingY0_;
        dVdswingY = kSwingY_ * 0.5 * sin(2.0 * dSwingY);
        p = 0.25 * kSwingY_ * (1.0 - cos(2.0 * dSwingY));
        pot_ += p;
        tBody -= dVdswingY * V3Y;
        restInfo_[rtSwingY] = std::make_pair(swingY, p);
      }

      Vector3d tLab = A.transpose() * tBody;      
      torque_ = tLab * scaleFactor_;      
    }
  }
}
Revision:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
Original Path:	*trunk/src/restraints/ObjectRestraint.cpp*
File size:	4261 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	Content
1	/*
2	* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
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.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
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/ObjectRestraint.hpp"
43
44	namespace OpenMD {
45
46	void ObjectRestraint::calcForce(Vector3d struc) {
47
48	pot_ = 0.0;
49
50	if (restType_ & rtDisplacement) {
51	Vector3d del = struc - refPos_;
52	RealType r = del.length();
53	Vector3d frc = -kDisp_ * del;
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
61	void ObjectRestraint::calcForce(Vector3d struc, RotMat3x3d A) {
62
63	calcForce(struc);
64
65	// rtDisplacement is 1, so anything higher than that requires orientations:
66	if (restType_ > 1) {
67
68	Vector3d tBody(0.0);
69
70	RotMat3x3d temp = A * refA_.transpose();
71
72	Quat4d quat = temp.toQuaternion();
73
74	RealType twistAngle, swingAngle;
75	Vector3d swingAxis;
76	RealType tw, swingX, swingY;
77
78	quat.getTwistSwingAxisAngle(twistAngle, swingAngle, swingAxis);
79	quat.toSwingTwist(tw, swingX, swingY);
80
81	RealType dVdtwist, dVdswingX, dVdswingY;
82	RealType dTwist, dSwingX, dSwingY;
83	RealType p;
84	Vector3d tTwist, tSwing;
85
86	if (restType_ & rtTwist){
87	dTwist = twistAngle - twist0_;
88	dVdtwist = kTwist_ * sin(dTwist);
89	p = kTwist_ * (1.0 - cos(dTwist) );
90	pot_ += p;
91	tBody -= dVdtwist * V3Z;
92	restInfo_[rtTwist] = std::make_pair(twistAngle, p);
93	}
94
95	if (restType_ & rtSwingX){
96	dSwingX = swingX - swingX0_;
97	dVdswingX = kSwingX_ * 0.5 * sin(2.0 * dSwingX);
98	p = 0.25 * kSwingX_ * (1.0 - cos(2.0 * dSwingX));
99	pot_ += p;
100	tBody -= dVdswingX * V3X;
101	restInfo_[rtSwingX] = std::make_pair(swingX, p);
102	}
103
104	if (restType_ & rtSwingY){
105	dSwingY = swingY - swingY0_;
106	dVdswingY = kSwingY_ * 0.5 * sin(2.0 * dSwingY);
107	p = 0.25 * kSwingY_ * (1.0 - cos(2.0 * dSwingY));
108	pot_ += p;
109	tBody -= dVdswingY * V3Y;
110	restInfo_[rtSwingY] = std::make_pair(swingY, p);
111	}
112
113	Vector3d tLab = A.transpose() * tBody;
114	torque_ = tLab * scaleFactor_;
115	}
116	}
117	}