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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#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_;
      if (printRest_) 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();

      Vector3d euler = temp.toEulerAngles();

      Quat4d quat = temp.toQuaternion();

      RealType twistAngle;
      Vector3d swingAxis;
      RealType swingX, swingY;
      
      quat.toSwingTwist(swingX, swingY, twistAngle);


      RealType p;
      Vector3d tTwist, tSwing;

      if (restType_ & rtTwist){
        RealType dTwist = twistAngle - twist0_;      
        /// RealType dVdtwist = kTwist_ * sin(dTwist);
        /// p = kTwist_ * (1.0 - cos(dTwist) );
        RealType dVdtwist = kTwist_ * dTwist;
        p = 0.5 * kTwist_ * dTwist * dTwist;
        pot_ += p;
        tBody -= dVdtwist * V3Z;
        if (printRest_) restInfo_[rtTwist] = std::make_pair(twistAngle, p);
      }

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

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

      Vector3d tLab = A.transpose() * tBody;      
      torque_ = tLab * scaleFactor_;      
    }
  }
}
Revision:	2024
Committed:	Thu Oct 16 19:13:51 2014 UTC (10 years, 6 months ago) by gezelter
File size:	4645 byte(s)
Log Message:	Added Radial and Z-projected velocity autocorrelation functions Started to add SequentialProps program Mucking about with angular restraint potentials
#	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, 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 OpenMD {
46
47	void ObjectRestraint::calcForce(Vector3d struc) {
48
49	pot_ = 0.0;
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
56	pot_ = p;
57	force_ = frc * scaleFactor_;
58	if (printRest_) restInfo_[rtDisplacement] = std::make_pair(r,p);
59	}
60	}
61
62	void ObjectRestraint::calcForce(Vector3d struc, RotMat3x3d A) {
63
64	calcForce(struc);
65
66	// rtDisplacement is 1, so anything higher than that requires orientations:
67	if (restType_ > 1) {
68
69	Vector3d tBody(0.0);
70
71	RotMat3x3d temp = A * refA_.transpose();
72
73	Vector3d euler = temp.toEulerAngles();
74
75	Quat4d quat = temp.toQuaternion();
76
77	RealType twistAngle;
78	Vector3d swingAxis;
79	RealType swingX, swingY;
80
81	quat.toSwingTwist(swingX, swingY, twistAngle);
82
83
84	RealType p;
85	Vector3d tTwist, tSwing;
86
87	if (restType_ & rtTwist){
88	RealType dTwist = twistAngle - twist0_;
89	/// RealType dVdtwist = kTwist_ * sin(dTwist);
90	/// p = kTwist_ * (1.0 - cos(dTwist) );
91	RealType dVdtwist = kTwist_ * dTwist;
92	p = 0.5 * kTwist_ * dTwist * dTwist;
93	pot_ += p;
94	tBody -= dVdtwist * V3Z;
95	if (printRest_) restInfo_[rtTwist] = std::make_pair(twistAngle, p);
96	}
97
98	if (restType_ & rtSwingX){
99	RealType dSwingX = swingX - swingX0_;
100	/// RealType dVdswingX = kSwingX_ * 0.5 * sin(2.0 * dSwingX);
101	/// p = 0.25 * kSwingX_ * (1.0 - cos(2.0 * dSwingX));
102	RealType dVdswingX = kSwingX_ * dSwingX;
103	p = 0.5 * kSwingX_ * dSwingX * dSwingX;
104	pot_ += p;
105	tBody -= dVdswingX * V3X;
106	if (printRest_) restInfo_[rtSwingX] = std::make_pair(swingX, p);
107	}
108
109	if (restType_ & rtSwingY){
110	RealType dSwingY = swingY - swingY0_;
111	/// RealType dVdswingY = kSwingY_ * 0.5 * sin(2.0 * dSwingY);
112	/// p = 0.25 * kSwingY_ * (1.0 - cos(2.0 * dSwingY));
113	RealType dVdswingY = kSwingY_ * dSwingY;
114	p = 0.5 * kSwingX_ * dSwingY * dSwingY;
115	pot_ += p;
116	tBody -= dVdswingY * V3Y;
117	if (printRest_) restInfo_[rtSwingY] = std::make_pair(swingY, p);
118	}
119
120	Vector3d tLab = A.transpose() * tBody;
121	torque_ = tLab * scaleFactor_;
122	}
123	}
124	}