src/optimization/PotentialEnergyObjectiveFunction.cpp

/*
 * Copyright (c) 2012 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#include "optimization/PotentialEnergyObjectiveFunction.hpp"

namespace OpenMD{

  PotentialEnergyObjectiveFunction::PotentialEnergyObjectiveFunction(SimInfo* info, ForceManager* forceMan)
    : info_(info), forceMan_(forceMan), thermo(info) {   
    shake_ = new Shake(info_);    
  }
  

  
  RealType PotentialEnergyObjectiveFunction::value(const DynamicVector<RealType>& x) {
    setCoor(x);
    shake_->constraintR();
    forceMan_->calcForces();
    shake_->constraintF();
    return thermo.getPotential();
  }
  
  void PotentialEnergyObjectiveFunction::gradient(DynamicVector<RealType>& grad, const DynamicVector<RealType>& x) {
    
    setCoor(x);       
    shake_->constraintR();
    forceMan_->calcForces();
    shake_->constraintF();
    getGrad(grad);
  }
  
  RealType PotentialEnergyObjectiveFunction::valueAndGradient(DynamicVector<RealType>& grad,
                                                              const DynamicVector<RealType>& x) {
    setCoor(x);
    shake_->constraintR();
    forceMan_->calcForces();
    shake_->constraintF();
    getGrad(grad); 
    return thermo.getPotential();
  }
  
  void PotentialEnergyObjectiveFunction::setCoor(const DynamicVector<RealType> &x) const {
    Vector3d position;
    Vector3d eulerAngle;
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* sd;    
    int index = 0;
    
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {

      for (sd = mol->beginIntegrableObject(j);  sd != NULL;
           sd = mol->nextIntegrableObject(j)) {
        
        position[0] = x[index++];
        position[1] = x[index++];
        position[2] = x[index++];
        
        sd->setPos(position);
        
        if (sd->isDirectional()) {
          eulerAngle[0] = x[index++];
          eulerAngle[1] = x[index++];
          eulerAngle[2] = x[index++];
          
          sd->setEuler(eulerAngle);

          if (sd->isRigidBody()) {
            RigidBody* rb = static_cast<RigidBody*>(sd);
            rb->updateAtoms();
          }        

        }
      }
    }    
  }
  
  void PotentialEnergyObjectiveFunction::getGrad(DynamicVector<RealType> &grad) {
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* sd;    
    std::vector<RealType> myGrad;
    
    int index = 0;
    
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {

      for (sd = mol->beginIntegrableObject(j); sd != NULL;
           sd = mol->nextIntegrableObject(j)) {        

        myGrad = sd->getGrad();

        for (size_t k = 0; k < myGrad.size(); ++k) {   
          grad[index++] = myGrad[k];
        }

      }            
    }         
  }

  DynamicVector<RealType> PotentialEnergyObjectiveFunction::setInitialCoords() {
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* sd;    

    Vector3d pos;
    Vector3d eulerAngle;
    
    DynamicVector<RealType> xinit(info_->getNdfLocal(), 0.0);

    int index = 0;
    
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {

      for (sd = mol->beginIntegrableObject(j);  sd != NULL;
           sd = mol->nextIntegrableObject(j)) {        

        pos = sd->getPos();

        xinit[index++] = pos[0];
        xinit[index++] = pos[1];
        xinit[index++] = pos[2];
                
        if (sd->isDirectional()) {
          eulerAngle = sd->getEuler();
          xinit[index++] = eulerAngle[0];
          xinit[index++] = eulerAngle[1];
          xinit[index++] = eulerAngle[2];          
        }

      }
    }
    return xinit;
  }
}
Revision:	1769
Committed:	Mon Jul 9 14:15:52 2012 UTC (12 years, 9 months ago) by gezelter
File size:	5937 byte(s)
Log Message:	Code readability updates.
#	User	Rev	Content
1	gezelter	1741	/*
2			* Copyright (c) 2012 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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41			*/
42
43			#include "optimization/PotentialEnergyObjectiveFunction.hpp"
44
45			namespace OpenMD{
46
47			PotentialEnergyObjectiveFunction::PotentialEnergyObjectiveFunction(SimInfo* info, ForceManager* forceMan)
48	gezelter	1748	: info_(info), forceMan_(forceMan), thermo(info) {
49			shake_ = new Shake(info_);
50	gezelter	1741	}
51
52
53
54			RealType PotentialEnergyObjectiveFunction::value(const DynamicVector<RealType>& x) {
55			setCoor(x);
56	gezelter	1748	shake_->constraintR();
57	gezelter	1741	forceMan_->calcForces();
58	gezelter	1748	shake_->constraintF();
59	gezelter	1741	return thermo.getPotential();
60			}
61
62			void PotentialEnergyObjectiveFunction::gradient(DynamicVector<RealType>& grad, const DynamicVector<RealType>& x) {
63
64	gezelter	1748	setCoor(x);
65			shake_->constraintR();
66			forceMan_->calcForces();
67			shake_->constraintF();
68			getGrad(grad);
69	gezelter	1741	}
70
71			RealType PotentialEnergyObjectiveFunction::valueAndGradient(DynamicVector<RealType>& grad,
72			const DynamicVector<RealType>& x) {
73	gezelter	1748	setCoor(x);
74			shake_->constraintR();
75			forceMan_->calcForces();
76			shake_->constraintF();
77	gezelter	1741	getGrad(grad);
78			return thermo.getPotential();
79			}
80
81			void PotentialEnergyObjectiveFunction::setCoor(const DynamicVector<RealType> &x) const {
82			Vector3d position;
83			Vector3d eulerAngle;
84			SimInfo::MoleculeIterator i;
85			Molecule::IntegrableObjectIterator j;
86			Molecule* mol;
87	gezelter	1769	StuntDouble* sd;
88	gezelter	1741	int index = 0;
89
90			for (mol = info_->beginMolecule(i); mol != NULL;
91			mol = info_->nextMolecule(i)) {
92	gezelter	1769
93			for (sd = mol->beginIntegrableObject(j); sd != NULL;
94			sd = mol->nextIntegrableObject(j)) {
95	gezelter	1741
96			position[0] = x[index++];
97			position[1] = x[index++];
98			position[2] = x[index++];
99
100	gezelter	1769	sd->setPos(position);
101	gezelter	1741
102	gezelter	1769	if (sd->isDirectional()) {
103	gezelter	1741	eulerAngle[0] = x[index++];
104			eulerAngle[1] = x[index++];
105			eulerAngle[2] = x[index++];
106
107	gezelter	1769	sd->setEuler(eulerAngle);
108	gezelter	1748
109	gezelter	1769	if (sd->isRigidBody()) {
110			RigidBody* rb = static_cast<RigidBody*>(sd);
111	gezelter	1748	rb->updateAtoms();
112			}
113	gezelter	1769
114	gezelter	1748	}
115	gezelter	1741	}
116			}
117			}
118
119			void PotentialEnergyObjectiveFunction::getGrad(DynamicVector<RealType> &grad) {
120			SimInfo::MoleculeIterator i;
121			Molecule::IntegrableObjectIterator j;
122			Molecule* mol;
123	gezelter	1769	StuntDouble* sd;
124	gezelter	1741	std::vector<RealType> myGrad;
125
126			int index = 0;
127
128			for (mol = info_->beginMolecule(i); mol != NULL;
129			mol = info_->nextMolecule(i)) {
130	gezelter	1750
131	gezelter	1769	for (sd = mol->beginIntegrableObject(j); sd != NULL;
132			sd = mol->nextIntegrableObject(j)) {
133
134			myGrad = sd->getGrad();
135
136	gezelter	1750	for (size_t k = 0; k < myGrad.size(); ++k) {
137	gezelter	1741	grad[index++] = myGrad[k];
138			}
139	gezelter	1769
140	gezelter	1741	}
141			}
142			}
143
144			DynamicVector<RealType> PotentialEnergyObjectiveFunction::setInitialCoords() {
145			SimInfo::MoleculeIterator i;
146			Molecule::IntegrableObjectIterator j;
147			Molecule* mol;
148	gezelter	1769	StuntDouble* sd;
149	gezelter	1741
150			Vector3d pos;
151			Vector3d eulerAngle;
152
153			DynamicVector<RealType> xinit(info_->getNdfLocal(), 0.0);
154
155			int index = 0;
156
157			for (mol = info_->beginMolecule(i); mol != NULL;
158			mol = info_->nextMolecule(i)) {
159
160	gezelter	1769	for (sd = mol->beginIntegrableObject(j); sd != NULL;
161			sd = mol->nextIntegrableObject(j)) {
162	gezelter	1741
163	gezelter	1769	pos = sd->getPos();
164
165	gezelter	1741	xinit[index++] = pos[0];
166			xinit[index++] = pos[1];
167			xinit[index++] = pos[2];
168
169	gezelter	1769	if (sd->isDirectional()) {
170			eulerAngle = sd->getEuler();
171	gezelter	1741	xinit[index++] = eulerAngle[0];
172			xinit[index++] = eulerAngle[1];
173			xinit[index++] = eulerAngle[2];
174			}
175	gezelter	1769
176	gezelter	1741	}
177			}
178			return xinit;
179			}
180			}