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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */

#include "restraints/ObjectRestraint.hpp"

namespace oopse {

  void ObjectRestraint::calcForce(Vector3d struc) {

    pot_ = 0.0;
    
    if (restType_ & rtDisplacement) {
      Vector3d del = struc - refPos_;  
      Vector3d frc = -kDisp_ * del;
      pot_ += 0.5 * kDisp_ * del.lengthSquare();
      force_ = frc * scaleFactor_;
    }
  }
    
  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);
      }

      std::cerr << "sw = " << swingAngle << " tw = " << twistAngle << "\n";
      std::cerr << "tbod = " << tBody << "\n";
      Vector3d tLab = A.transpose() * tBody;      
      torque_ = tLab * scaleFactor_;      
    }
  }
}
Revision:	1360
Committed:	Mon Sep 7 16:31:51 2009 UTC (15 years, 7 months ago) by cli2
File size:	4232 byte(s)
Log Message:	Added new restraint infrastructure Added MolecularRestraints Added ObjectRestraints Added RestraintStamp Updated thermodynamic integration to use ObjectRestraints Added Quaternion mathematics for twist swing decompositions Significantly updated RestWriter and RestReader to use dump-like files Added selections for x, y, and z coordinates of atoms Removed monolithic Restraints class Fixed a few bugs in gradients of Euler angles in DirectionalAtom and RigidBody Added some rotational capabilities to prinicpalAxisCalculator
#	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. 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
19	* notice, this list of conditions and the following disclaimer.
20	*
21	* 3. Redistributions in binary form must reproduce the above copyright
22	* notice, this list of conditions and the following disclaimer in the
23	* documentation and/or other materials provided with the
24	* distribution.
25	*
26	* This software is provided "AS IS," without a warranty of any
27	* kind. All express or implied conditions, representations and
28	* warranties, including any implied warranty of merchantability,
29	* fitness for a particular purpose or non-infringement, are hereby
30	* excluded. The University of Notre Dame and its licensors shall not
31	* be liable for any damages suffered by licensee as a result of
32	* using, modifying or distributing the software or its
33	* derivatives. In no event will the University of Notre Dame or its
34	* licensors be liable for any lost revenue, profit or data, or for
35	* direct, indirect, special, consequential, incidental or punitive
36	* damages, however caused and regardless of the theory of liability,
37	* arising out of the use of or inability to use software, even if the
38	* University of Notre Dame has been advised of the possibility of
39	* such damages.
40	*/
41
42	#include "restraints/ObjectRestraint.hpp"
43
44	namespace oopse {
45
46	void ObjectRestraint::calcForce(Vector3d struc) {
47
48	pot_ = 0.0;
49
50	if (restType_ & rtDisplacement) {
51	Vector3d del = struc - refPos_;
52	Vector3d frc = -kDisp_ * del;
53	pot_ += 0.5 * kDisp_ * del.lengthSquare();
54	force_ = frc * scaleFactor_;
55	}
56	}
57
58	void ObjectRestraint::calcForce(Vector3d struc, RotMat3x3d A) {
59
60	calcForce(struc);
61
62	// rtDisplacement is 1, so anything higher than that requires orientations:
63	if (restType_ > 1) {
64
65	Vector3d tBody(0.0);
66
67	RotMat3x3d temp = A * refA_.transpose();
68
69	Quat4d quat = temp.toQuaternion();
70
71	RealType twistAngle, swingAngle;
72	Vector3d swingAxis;
73	RealType tw, swingX, swingY;
74
75	quat.getTwistSwingAxisAngle(twistAngle, swingAngle, swingAxis);
76	quat.toSwingTwist(tw, swingX, swingY);
77
78	RealType dVdtwist, dVdswingX, dVdswingY;
79	RealType dTwist, dSwingX, dSwingY;
80	RealType p;
81	Vector3d tTwist, tSwing;
82
83	if (restType_ & rtTwist){
84	dTwist = twistAngle - twist0_;
85	dVdtwist = kTwist_ * sin(dTwist);
86	p = kTwist_ * (1.0 - cos(dTwist) );
87	pot_ += p;
88	tBody -= dVdtwist * V3Z;
89	restInfo_[rtTwist] = std::make_pair(twistAngle, p);
90	}
91
92	if (restType_ & rtSwingX){
93	dSwingX = swingX - swingX0_;
94	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;
98	restInfo_[rtSwingX] = std::make_pair(swingX, p);
99	}
100
101	if (restType_ & rtSwingY){
102	dSwingY = swingY - swingY0_;
103	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";
112	Vector3d tLab = A.transpose() * tBody;
113	torque_ = tLab * scaleFactor_;
114	}
115	}
116	}