src/restraints/MolecularRestraint.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/MolecularRestraint.hpp"
#include "math/SquareMatrix3.hpp"
#include "math/SVD.hpp"
#include <utility>

//using namespace JAMA;

namespace OpenMD {


  void MolecularRestraint::calcForce(std::vector<Vector3d> struc, 
                                     Vector3d molCom){

    assert(struc.size() == ref_.size());

    std::vector<Vector3d>::iterator it;

    // clear out initial values:
    pot_ = 0.0;
    for(it = forces_.begin(); it != forces_.end(); ++it)
      (*it) = 0.0;

   
    if (restType_ & rtDisplacement) {
      Vector3d del = molCom - refCom_;     
      
      RealType r = del.length();
      RealType p = 0.5 * kDisp_ * r * r;

      pot_ += p;

      if (printRest_) restInfo_[rtDisplacement] = std::make_pair(r, p);

      for(it = forces_.begin(); it != forces_.end(); ++it)
        (*it) = -kDisp_ * del * scaleFactor_;
    }

    for(it = struc.begin(); it != struc.end(); ++it)
      (*it) -= molCom;

    // rtDisplacement = 1, so anything higher than that requires orientations:
    if (restType_ > 1) {
      Vector3d tBody(0.0);
      
      Mat3x3d R(0.0);
      
      for (unsigned int n = 0; n < struc.size(); n++){

        /*
         * correlation matrix R:   
         *   R(i,j) = sum(over n): y(n,i) * x(n,j)  
         *   where x(n) and y(n) are two vector sets   
         */
        
        R += outProduct(struc[n], ref_[n]);
      }    

      // SVD class uses dynamic matrices, so we must wrap the correlation
      // matrix before calling SVD and then unwrap the results into Mat3x3d 
      // and Vector3d before we use them.
      
      DynamicRectMatrix<RealType> Rtmp(3, 3, 0.0);
      DynamicRectMatrix<RealType> vtmp(3, 3);
      DynamicVector<RealType>     stmp(3);
      DynamicRectMatrix<RealType> wtmp(3, 3);

      Rtmp.setSubMatrix(0, 0, R);
    
      // Heavy lifting goes here:
      
      JAMA::SVD<RealType> svd(Rtmp);

      svd.getU(vtmp);
      svd.getSingularValues(stmp);
      svd.getV(wtmp);

      Mat3x3d v;
      Vector3d s;
      Mat3x3d w_tr;
      
      vtmp.getSubMatrix(0, 0, v);
      stmp.getSubVector(0, s);
      wtmp.getSubMatrix(0, 0, w_tr);

      bool is_reflection = (v.determinant() * w_tr.determinant()) < 0.0;
      
      if (is_reflection){        
        v(2, 0) = -v(2, 0);
        v(2, 1) = -v(2, 1);
        v(2, 2) = -v(2, 2);
      }
      
      RotMat3x3d Atrans = v * w_tr.transpose();
      RotMat3x3d A = Atrans.transpose();

      Vector3d eularAngles = A.toEulerAngles();


      RealType twistAngle;
      Vector3d swingAxis;

      Quat4d quat = A.toQuaternion();  

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

      RealType dVdtwist, dVdswingX, dVdswingY;
      RealType dTwist, dSwingX, dSwingY;
      RealType p;

      if (restType_ & rtTwist){
        dTwist = twistAngle - twist0_;
        /// dVdtwist = kTwist_ * sin(dTwist) ;
        /// p = kTwist_ * (1.0 - cos(dTwist) ) ;
        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){
        dSwingX = swingX - swingX0_;
        /// dVdswingX = kSwingX_ * 2.0 * sin(2.0 * dSwingX);
        /// p = kSwingX_ * (1.0 - cos(2.0 * dSwingX));
        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){
        dSwingY = swingY - swingY0_;
        /// dVdswingY = kSwingY_ * 2.0 * sin(2.0 * dSwingY);
        /// p = kSwingY_ * (1.0 - cos(2.0 * dSwingY));
        dVdswingY = kSwingY_ * dSwingY;        
        p = 0.5 * kSwingX_ * dSwingY * dSwingY;
        pot_ += p;
        tBody -= dVdswingY * V3Y;
        if (printRest_) restInfo_[rtSwingY] = std::make_pair(swingY, p);
      }

            
      RealType t2 = dot(tBody, tBody);     
      
      Vector3d rLab, rBody, txr, fBody, fLab;

      for (unsigned int i = 0; i < struc.size(); i++) {
                   
        rLab = struc[i];        
        rBody = A * rLab;
        
        txr = cross(tBody, rBody);
        fBody = txr * t2;
        fLab = Atrans * fBody;        
        fLab *= scaleFactor_;
          
        forces_[i] += fLab;
      }

      // test the force vectors and see if it is the right orientation
//       std::cout << struc.size() << std::endl << std::endl;
//       for (int i = 0; i != struc.size(); ++i){
//         std::cout << "H\t" << struc[i].x() << "\t" << struc[i].y() << "\t" << struc[i].z() << "\t";
//         std::cout << forces_[i].x() << "\t" << forces_[i].y() << "\t" << forces_[i].z() << std::endl;
//       }
    }
  }
}
Revision:	2024
Committed:	Thu Oct 16 19:13:51 2014 UTC (10 years, 6 months ago) by gezelter
File size:	7047 byte(s)
Log Message:	Added Radial and Z-projected velocity autocorrelation functions Started to add SequentialProps program Mucking about with angular restraint potentials
#	User	Rev	Content
1	cli2	1360	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	cli2	1360	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	cli2	1360	* 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	gezelter	1390	*
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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	cli2	1360	*/
42
43			#include "restraints/MolecularRestraint.hpp"
44			#include "math/SquareMatrix3.hpp"
45			#include "math/SVD.hpp"
46			#include <utility>
47
48			//using namespace JAMA;
49
50	gezelter	1390	namespace OpenMD {
51	cli2	1360
52	cli2	1407
53	cli2	1360	void MolecularRestraint::calcForce(std::vector<Vector3d> struc,
54			Vector3d molCom){
55
56			assert(struc.size() == ref_.size());
57
58			std::vector<Vector3d>::iterator it;
59
60			// clear out initial values:
61			pot_ = 0.0;
62			for(it = forces_.begin(); it != forces_.end(); ++it)
63			(*it) = 0.0;
64
65
66			if (restType_ & rtDisplacement) {
67			Vector3d del = molCom - refCom_;
68
69			RealType r = del.length();
70			RealType p = 0.5 * kDisp_ * r * r;
71
72			pot_ += p;
73
74	gezelter	2020	if (printRest_) restInfo_[rtDisplacement] = std::make_pair(r, p);
75	cli2	1360
76			for(it = forces_.begin(); it != forces_.end(); ++it)
77			(it) = -kDisp_ del * scaleFactor_;
78			}
79
80			for(it = struc.begin(); it != struc.end(); ++it)
81			(*it) -= molCom;
82
83			// rtDisplacement = 1, so anything higher than that requires orientations:
84			if (restType_ > 1) {
85			Vector3d tBody(0.0);
86
87			Mat3x3d R(0.0);
88
89	gezelter	1782	for (unsigned int n = 0; n < struc.size(); n++){
90	cli2	1360
91			/*
92			* correlation matrix R:
93			* R(i,j) = sum(over n): y(n,i) * x(n,j)
94			* where x(n) and y(n) are two vector sets
95			*/
96
97			R += outProduct(struc[n], ref_[n]);
98			}
99
100			// SVD class uses dynamic matrices, so we must wrap the correlation
101			// matrix before calling SVD and then unwrap the results into Mat3x3d
102			// and Vector3d before we use them.
103
104			DynamicRectMatrix<RealType> Rtmp(3, 3, 0.0);
105			DynamicRectMatrix<RealType> vtmp(3, 3);
106			DynamicVector<RealType> stmp(3);
107			DynamicRectMatrix<RealType> wtmp(3, 3);
108
109			Rtmp.setSubMatrix(0, 0, R);
110
111			// Heavy lifting goes here:
112
113			JAMA::SVD<RealType> svd(Rtmp);
114
115			svd.getU(vtmp);
116			svd.getSingularValues(stmp);
117			svd.getV(wtmp);
118
119			Mat3x3d v;
120			Vector3d s;
121			Mat3x3d w_tr;
122
123			vtmp.getSubMatrix(0, 0, v);
124			stmp.getSubVector(0, s);
125			wtmp.getSubMatrix(0, 0, w_tr);
126
127			bool is_reflection = (v.determinant() * w_tr.determinant()) < 0.0;
128
129			if (is_reflection){
130			v(2, 0) = -v(2, 0);
131			v(2, 1) = -v(2, 1);
132			v(2, 2) = -v(2, 2);
133			}
134
135			RotMat3x3d Atrans = v * w_tr.transpose();
136			RotMat3x3d A = Atrans.transpose();
137
138			Vector3d eularAngles = A.toEulerAngles();
139
140
141	gezelter	1782	RealType twistAngle;
142	cli2	1360	Vector3d swingAxis;
143
144			Quat4d quat = A.toQuaternion();
145
146	gezelter	1782	RealType swingX, swingY;
147	cli2	1407	quat.toSwingTwist(swingX, swingY, twistAngle);
148	cli2	1360
149	gezelter	1782	RealType dVdtwist, dVdswingX, dVdswingY;
150			RealType dTwist, dSwingX, dSwingY;
151	cli2	1360	RealType p;
152
153			if (restType_ & rtTwist){
154			dTwist = twistAngle - twist0_;
155	gezelter	2024	/// dVdtwist = kTwist_ * sin(dTwist) ;
156			/// p = kTwist_ * (1.0 - cos(dTwist) ) ;
157			dVdtwist = kTwist_ * dTwist;
158			p = 0.5 * kTwist_ * dTwist * dTwist;
159	cli2	1360	pot_ += p;
160			tBody -= dVdtwist * V3Z;
161	gezelter	2020	if (printRest_) restInfo_[rtTwist] = std::make_pair(twistAngle, p);
162	cli2	1360	}
163
164			if (restType_ & rtSwingX){
165			dSwingX = swingX - swingX0_;
166	gezelter	2024	/// dVdswingX = kSwingX_ * 2.0 * sin(2.0 * dSwingX);
167			/// p = kSwingX_ * (1.0 - cos(2.0 * dSwingX));
168			dVdswingX = kSwingX_ * dSwingX;
169			p = 0.5 * kSwingX_ * dSwingX * dSwingX;
170	cli2	1360	pot_ += p;
171			tBody -= dVdswingX * V3X;
172	gezelter	2020	if (printRest_) restInfo_[rtSwingX] = std::make_pair(swingX, p);
173	cli2	1360	}
174			if (restType_ & rtSwingY){
175			dSwingY = swingY - swingY0_;
176	gezelter	2024	/// dVdswingY = kSwingY_ * 2.0 * sin(2.0 * dSwingY);
177			/// p = kSwingY_ * (1.0 - cos(2.0 * dSwingY));
178			dVdswingY = kSwingY_ * dSwingY;
179			p = 0.5 * kSwingX_ * dSwingY * dSwingY;
180	cli2	1360	pot_ += p;
181			tBody -= dVdswingY * V3Y;
182	gezelter	2020	if (printRest_) restInfo_[rtSwingY] = std::make_pair(swingY, p);
183	cli2	1360	}
184
185
186			RealType t2 = dot(tBody, tBody);
187
188			Vector3d rLab, rBody, txr, fBody, fLab;
189
190	gezelter	1782	for (unsigned int i = 0; i < struc.size(); i++) {
191	cli2	1360
192			rLab = struc[i];
193			rBody = A * rLab;
194
195			txr = cross(tBody, rBody);
196			fBody = txr * t2;
197			fLab = Atrans * fBody;
198			fLab *= scaleFactor_;
199
200			forces_[i] += fLab;
201			}
202
203			// test the force vectors and see if it is the right orientation
204			// std::cout << struc.size() << std::endl << std::endl;
205			// for (int i = 0; i != struc.size(); ++i){
206			// std::cout << "H\t" << struc[i].x() << "\t" << struc[i].y() << "\t" << struc[i].z() << "\t";
207			// std::cout << forces_[i].x() << "\t" << forces_[i].y() << "\t" << forces_[i].z() << std::endl;
208			// }
209			}
210			}
211			}