src/flucq/FluctuatingChargePropagator.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/FluctuatingChargePropagator.hpp"
#include "flucq/FluctuatingChargeObjectiveFunction.hpp"
#include "optimization/Constraint.hpp"
#include "optimization/Problem.hpp"
#include "optimization/EndCriteria.hpp"
#include "optimization/StatusFunction.hpp"
#include "optimization/OptimizationFactory.hpp"

#ifdef IS_MPI
#include <mpi.h>
#endif

using namespace QuantLib;
namespace OpenMD {

  FluctuatingChargePropagator::FluctuatingChargePropagator(SimInfo* info) : 
    info_(info), hasFlucQ_(false), forceMan_(NULL) {
    
    Globals* simParams = info_->getSimParams();
    fqParams_ = simParams->getFluctuatingChargeParameters();
  }

  void FluctuatingChargePropagator::setForceManager(ForceManager* forceMan) {
    forceMan_ = forceMan;
  }

  void FluctuatingChargePropagator::initialize() {

    if (info_->usesFluctuatingCharges()) {
      if (info_->getNFluctuatingCharges() > 0) {
        hasFlucQ_ = true;
        fqConstraints_ = new FluctuatingChargeConstraints(info_);        
      }
    }

    if (!hasFlucQ_) return;

    SimInfo::MoleculeIterator i;
    Molecule::FluctuatingChargeIterator  j;
    Molecule* mol;
    Atom* atom;
    
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {
      for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
           atom = mol->nextFluctuatingCharge(j)) {
        atom->setFlucQPos(0.0);
        atom->setFlucQVel(0.0);
      }
    }
    
    fqConstraints_ = new FluctuatingChargeConstraints(info_);
    FluctuatingChargeObjectiveFunction flucQobjf(info_, forceMan_, fqConstraints_);    
    DynamicVector<RealType> initCoords = flucQobjf.setInitialCoords();
    Problem problem(flucQobjf, *(new NoConstraint()), *(new NoStatus()), initCoords);
    EndCriteria endCriteria(1000, 100, 1e-5, 1e-5, 1e-5);       
    OptimizationMethod* minim = OptimizationFactory::getInstance()->createOptimization("SD", info_);

    DumpStatusFunction dsf(info_);  // we want a dump file written every iteration

    minim->minimize(problem, endCriteria);
  }

  void FluctuatingChargePropagator::applyConstraints() {
    if (!hasFlucQ_) return;
    fqConstraints_->applyConstraints();
  }
}
Revision:	1768
Committed:	Sat Jul 7 03:59:27 2012 UTC (12 years, 10 months ago) by gezelter
File size:	4366 byte(s)
Log Message:	Fixed a bug in the FluctuatingChargeLangevin propagator, updated some samples.
#	User	Rev	Content
1	gezelter	1718	/*
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	gezelter	1739	#include "flucq/FluctuatingChargePropagator.hpp"
44			#include "flucq/FluctuatingChargeObjectiveFunction.hpp"
45			#include "optimization/Constraint.hpp"
46			#include "optimization/Problem.hpp"
47			#include "optimization/EndCriteria.hpp"
48			#include "optimization/StatusFunction.hpp"
49			#include "optimization/OptimizationFactory.hpp"
50
51	gezelter	1718	#ifdef IS_MPI
52			#include <mpi.h>
53			#endif
54
55	gezelter	1739	using namespace QuantLib;
56	gezelter	1718	namespace OpenMD {
57
58	gezelter	1760	FluctuatingChargePropagator::FluctuatingChargePropagator(SimInfo* info) :
59			info_(info), hasFlucQ_(false), forceMan_(NULL) {
60	gezelter	1739
61	gezelter	1760	Globals* simParams = info_->getSimParams();
62			fqParams_ = simParams->getFluctuatingChargeParameters();
63			}
64
65			void FluctuatingChargePropagator::setForceManager(ForceManager* forceMan) {
66			forceMan_ = forceMan;
67			}
68
69			void FluctuatingChargePropagator::initialize() {
70
71	gezelter	1739	if (info_->usesFluctuatingCharges()) {
72			if (info_->getNFluctuatingCharges() > 0) {
73			hasFlucQ_ = true;
74	gezelter	1760	fqConstraints_ = new FluctuatingChargeConstraints(info_);
75	gezelter	1739	}
76			}
77
78	gezelter	1718	if (!hasFlucQ_) return;
79
80			SimInfo::MoleculeIterator i;
81			Molecule::FluctuatingChargeIterator j;
82			Molecule* mol;
83			Atom* atom;
84
85			for (mol = info_->beginMolecule(i); mol != NULL;
86			mol = info_->nextMolecule(i)) {
87			for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
88			atom = mol->nextFluctuatingCharge(j)) {
89	gezelter	1739	atom->setFlucQPos(0.0);
90			atom->setFlucQVel(0.0);
91	gezelter	1718	}
92			}
93	gezelter	1739
94	gezelter	1748	fqConstraints_ = new FluctuatingChargeConstraints(info_);
95	gezelter	1739	FluctuatingChargeObjectiveFunction flucQobjf(info_, forceMan_, fqConstraints_);
96			DynamicVector<RealType> initCoords = flucQobjf.setInitialCoords();
97			Problem problem(flucQobjf, (new NoConstraint()), (new NoStatus()), initCoords);
98			EndCriteria endCriteria(1000, 100, 1e-5, 1e-5, 1e-5);
99			OptimizationMethod* minim = OptimizationFactory::getInstance()->createOptimization("SD", info_);
100	gezelter	1718
101	gezelter	1760	DumpStatusFunction dsf(info_); // we want a dump file written every iteration
102	jmichalk	1754
103	gezelter	1739	minim->minimize(problem, endCriteria);
104			}
105	gezelter	1718
106	gezelter	1739	void FluctuatingChargePropagator::applyConstraints() {
107			if (!hasFlucQ_) return;
108			fqConstraints_->applyConstraints();
109	gezelter	1718	}
110			}