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, 234107 (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), initialized_(false) {
    
    Globals* simParams = info_->getSimParams();
    fqParams_ = simParams->getFluctuatingChargeParameters();    
  }

  FluctuatingChargePropagator::~FluctuatingChargePropagator() {
  }

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

  void FluctuatingChargePropagator::initialize() {
    if (info_->usesFluctuatingCharges()) {
      if (info_->getNFluctuatingCharges() > 0) {
        hasFlucQ_ = true;
        fqConstraints_ = new FluctuatingChargeConstraints(info_);
        fqConstraints_->setConstrainRegions(fqParams_->getConstrainRegions());
      }
    }
    
    if (!hasFlucQ_) {
      initialized_ = true;
      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)) {
        cerr << " starts with = " << atom->getFlucQPos() << "\n";
        //atom->setFlucQPos(0.0);
        //atom->setFlucQVel(0.0);
      }
    }
    
    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);
    cerr << "back from minim\n";
    initialized_ = true;
  }

  void FluctuatingChargePropagator::applyConstraints() {
    if (!initialized_) initialize();
    if (!hasFlucQ_) return;
    fqConstraints_->applyConstraints();
  }
}
Revision:	1969
Committed:	Wed Feb 26 14:14:50 2014 UTC (11 years, 2 months ago) by gezelter
File size:	4780 byte(s)
Log Message:	Fixes to deal with deprecation of MPI C++ bindings. We've reverted back to the C calls.
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1718	* [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	jmichalk	1913	info_(info), hasFlucQ_(false), forceMan_(NULL), initialized_(false) {
60	gezelter	1739
61	gezelter	1760	Globals* simParams = info_->getSimParams();
62	gezelter	1908	fqParams_ = simParams->getFluctuatingChargeParameters();
63	gezelter	1760	}
64
65	gezelter	1879	FluctuatingChargePropagator::~FluctuatingChargePropagator() {
66			}
67
68	gezelter	1760	void FluctuatingChargePropagator::setForceManager(ForceManager* forceMan) {
69			forceMan_ = forceMan;
70			}
71
72			void FluctuatingChargePropagator::initialize() {
73	gezelter	1739	if (info_->usesFluctuatingCharges()) {
74			if (info_->getNFluctuatingCharges() > 0) {
75			hasFlucQ_ = true;
76	jmichalk	1920	fqConstraints_ = new FluctuatingChargeConstraints(info_);
77			fqConstraints_->setConstrainRegions(fqParams_->getConstrainRegions());
78	gezelter	1739	}
79			}
80	jmichalk	1913
81			if (!hasFlucQ_) {
82			initialized_ = true;
83			return;
84			}
85	gezelter	1739
86	gezelter	1718	SimInfo::MoleculeIterator i;
87			Molecule::FluctuatingChargeIterator j;
88			Molecule* mol;
89			Atom* atom;
90
91			for (mol = info_->beginMolecule(i); mol != NULL;
92			mol = info_->nextMolecule(i)) {
93			for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
94			atom = mol->nextFluctuatingCharge(j)) {
95	gezelter	1969	cerr << " starts with = " << atom->getFlucQPos() << "\n";
96			//atom->setFlucQPos(0.0);
97			//atom->setFlucQVel(0.0);
98	gezelter	1718	}
99			}
100	gezelter	1739
101	gezelter	1879	FluctuatingChargeObjectiveFunction flucQobjf(info_, forceMan_,
102			fqConstraints_);
103
104	gezelter	1739	DynamicVector<RealType> initCoords = flucQobjf.setInitialCoords();
105	gezelter	1879	Problem problem(flucQobjf, (new NoConstraint()), (new NoStatus()),
106			initCoords);
107
108	gezelter	1739	EndCriteria endCriteria(1000, 100, 1e-5, 1e-5, 1e-5);
109	gezelter	1879
110	gezelter	1739	OptimizationMethod* minim = OptimizationFactory::getInstance()->createOptimization("SD", info_);
111	gezelter	1718
112	gezelter	1879	DumpStatusFunction dsf(info_); // we want a dump file written
113			// every iteration
114	gezelter	1739	minim->minimize(problem, endCriteria);
115	gezelter	1969	cerr << "back from minim\n";
116	jmichalk	1913	initialized_ = true;
117	gezelter	1739	}
118	gezelter	1718
119	gezelter	1739	void FluctuatingChargePropagator::applyConstraints() {
120	jmichalk	1913	if (!initialized_) initialize();
121	gezelter	1739	if (!hasFlucQ_) return;
122			fqConstraints_->applyConstraints();
123	gezelter	1718	}
124			}