src/flucq/FluctuatingChargeObjectiveFunction.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 "flucq/FluctuatingChargeObjectiveFunction.hpp"

namespace OpenMD{
  
  FluctuatingChargeObjectiveFunction::FluctuatingChargeObjectiveFunction(SimInfo* info, ForceManager* forceMan, FluctuatingChargeConstraints* fqConstraints)
    : info_(info), forceMan_(forceMan), fqConstraints_(fqConstraints), 
      thermo(info) {       
  }
  
  RealType FluctuatingChargeObjectiveFunction::value(const DynamicVector<RealType>& x) {
    setCoor(x);
    forceMan_->calcForces();

    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    potVec pot = curSnapshot->getLongRangePotentials();
    potVec exPot = curSnapshot->getExcludedPotentials();  
  
    return pot[ELECTROSTATIC_FAMILY] + exPot[ELECTROSTATIC_FAMILY];
  }
  
  void FluctuatingChargeObjectiveFunction::gradient(DynamicVector<RealType>& grad, const DynamicVector<RealType>& x) {
    int shakeStatus;
    
    setCoor(x);     
    
    forceMan_->calcForces(); 
    fqConstraints_->applyConstraints();

    getGrad(grad);      
  }
  
  RealType FluctuatingChargeObjectiveFunction::valueAndGradient(DynamicVector<RealType>& grad,
                                                              const DynamicVector<RealType>& x) {

    setCoor(x);     

    forceMan_->calcForces();
    fqConstraints_->applyConstraints();
    
    getGrad(grad); 

    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    potVec pot = curSnapshot->getLongRangePotentials();
    potVec exPot = curSnapshot->getExcludedPotentials();    

    return pot[ELECTROSTATIC_FAMILY] + exPot[ELECTROSTATIC_FAMILY];
  }
  
  void FluctuatingChargeObjectiveFunction::setCoor(const DynamicVector<RealType> &x) const {
    SimInfo::MoleculeIterator i;
    Molecule::FluctuatingChargeIterator  j;
    Molecule* mol;
    Atom* atom;
    int index = 0;
    
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {
      
      for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
           atom = mol->nextFluctuatingCharge(j)) {
       
        atom->setFlucQPos(x[index++]);
      }
    }    
  }
  
  void FluctuatingChargeObjectiveFunction::getGrad(DynamicVector<RealType> &grad) {
    SimInfo::MoleculeIterator i;
    Molecule::FluctuatingChargeIterator  j;
    Molecule* mol;
    Atom* atom;
    
    int index = 0;
    
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {

      for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
           atom = mol->nextFluctuatingCharge(j)) {

        grad[index++] = -atom->getFlucQFrc();
      }
    }
  }

  DynamicVector<RealType> FluctuatingChargeObjectiveFunction::setInitialCoords() {
    SimInfo::MoleculeIterator i;
    Molecule::FluctuatingChargeIterator  j;
    Molecule* mol;
    Atom* atom;
    
    int index = 0;    
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {

      for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
           atom = mol->nextFluctuatingCharge(j)) {
        
        index++;
      }
    }

    DynamicVector<RealType> initCoords(index);
    index = 0;
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {

      for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
           atom = mol->nextFluctuatingCharge(j)) {
        
        initCoords[index++] = atom->getFlucQPos();
      }
    }   
    return initCoords;
  }
}
Revision:	1761
Committed:	Fri Jun 22 20:01:37 2012 UTC (12 years, 10 months ago) by gezelter
File size:	5662 byte(s)
Log Message:	fixes for fluctuating charges
#	User	Rev	Content
1	gezelter	1740	/*
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 "flucq/FluctuatingChargeObjectiveFunction.hpp"
44
45			namespace OpenMD{
46
47			FluctuatingChargeObjectiveFunction::FluctuatingChargeObjectiveFunction(SimInfo* info, ForceManager* forceMan, FluctuatingChargeConstraints* fqConstraints)
48			: info_(info), forceMan_(forceMan), fqConstraints_(fqConstraints),
49			thermo(info) {
50			}
51
52			RealType FluctuatingChargeObjectiveFunction::value(const DynamicVector<RealType>& x) {
53			setCoor(x);
54			forceMan_->calcForces();
55	gezelter	1760
56	gezelter	1740	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
57	gezelter	1760	potVec pot = curSnapshot->getLongRangePotentials();
58			potVec exPot = curSnapshot->getExcludedPotentials();
59
60			return pot[ELECTROSTATIC_FAMILY] + exPot[ELECTROSTATIC_FAMILY];
61	gezelter	1740	}
62
63			void FluctuatingChargeObjectiveFunction::gradient(DynamicVector<RealType>& grad, const DynamicVector<RealType>& x) {
64			int shakeStatus;
65
66			setCoor(x);
67
68			forceMan_->calcForces();
69			fqConstraints_->applyConstraints();
70	gezelter	1761
71	gezelter	1740	getGrad(grad);
72			}
73
74			RealType FluctuatingChargeObjectiveFunction::valueAndGradient(DynamicVector<RealType>& grad,
75			const DynamicVector<RealType>& x) {
76
77			setCoor(x);
78
79			forceMan_->calcForces();
80			fqConstraints_->applyConstraints();
81
82			getGrad(grad);
83
84			Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
85	gezelter	1760	potVec pot = curSnapshot->getLongRangePotentials();
86			potVec exPot = curSnapshot->getExcludedPotentials();
87
88			return pot[ELECTROSTATIC_FAMILY] + exPot[ELECTROSTATIC_FAMILY];
89	gezelter	1740	}
90
91			void FluctuatingChargeObjectiveFunction::setCoor(const DynamicVector<RealType> &x) const {
92			SimInfo::MoleculeIterator i;
93			Molecule::FluctuatingChargeIterator j;
94			Molecule* mol;
95			Atom* atom;
96			int index = 0;
97
98			for (mol = info_->beginMolecule(i); mol != NULL;
99			mol = info_->nextMolecule(i)) {
100
101			for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
102			atom = mol->nextFluctuatingCharge(j)) {
103	gezelter	1756
104	gezelter	1740	atom->setFlucQPos(x[index++]);
105			}
106			}
107			}
108
109			void FluctuatingChargeObjectiveFunction::getGrad(DynamicVector<RealType> &grad) {
110			SimInfo::MoleculeIterator i;
111			Molecule::FluctuatingChargeIterator j;
112			Molecule* mol;
113			Atom* atom;
114
115			int index = 0;
116
117			for (mol = info_->beginMolecule(i); mol != NULL;
118			mol = info_->nextMolecule(i)) {
119
120			for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
121			atom = mol->nextFluctuatingCharge(j)) {
122	gezelter	1756
123	gezelter	1761	grad[index++] = -atom->getFlucQFrc();
124	gezelter	1740	}
125			}
126			}
127
128			DynamicVector<RealType> FluctuatingChargeObjectiveFunction::setInitialCoords() {
129			SimInfo::MoleculeIterator i;
130			Molecule::FluctuatingChargeIterator j;
131			Molecule* mol;
132			Atom* atom;
133
134			int index = 0;
135			for (mol = info_->beginMolecule(i); mol != NULL;
136			mol = info_->nextMolecule(i)) {
137
138			for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
139			atom = mol->nextFluctuatingCharge(j)) {
140
141			index++;
142			}
143			}
144
145			DynamicVector<RealType> initCoords(index);
146			index = 0;
147			for (mol = info_->beginMolecule(i); mol != NULL;
148			mol = info_->nextMolecule(i)) {
149
150			for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
151			atom = mol->nextFluctuatingCharge(j)) {
152
153			initCoords[index++] = atom->getFlucQPos();
154			}
155			}
156			return initCoords;
157			}
158			}