src/flucq/FluctuatingChargeConstraints.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 "FluctuatingChargeConstraints.hpp"
#include "primitives/Molecule.hpp"

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

namespace OpenMD {

  FluctuatingChargeConstraints::FluctuatingChargeConstraints(SimInfo* info) : 
    info_(info), constrainRegions_(false), hasFlucQ_(false), initialized_(false) {
    
  }

  void FluctuatingChargeConstraints::initialize(){
    if(info_->usesFluctuatingCharges()){
      if(info_->getNFluctuatingCharges() > 0){
        hasFlucQ_ = true;
      }
    }
    initialized_ = true;
  }

  void FluctuatingChargeConstraints::setConstrainRegions(bool cr) {
    constrainRegions_ = cr;
    regionKeys_.clear();
    regionForce_.clear();
    regionCharges_.clear();

    if (constrainRegions_) {
      SimInfo::MoleculeIterator i;
      Molecule* mol;
      int reg;
      std::set<int> regions;      

      for (mol = info_->beginMolecule(i); mol != NULL; 
           mol = info_->nextMolecule(i)) {
        reg = mol->getRegion();
        if (reg >= 0) regions.insert(reg);
      }
      // resize the keys vector to the largest found value for regions.
      regionKeys_.resize( *(regions.end()) );
      int which = 0;
      for (std::set<int>::iterator r=regions.begin(); r!=regions.end(); ++r) {
        regionKeys_[ (*r) ] = which;
        which++;
      }
      regionForce_.resize( regionKeys_.size() );
      regionCharges_.resize( regionKeys_.size() );
    }
  }


  void FluctuatingChargeConstraints::applyConstraints() {
    if (!initialized_) initialize();
    if (!hasFlucQ_) return;
    SimInfo::MoleculeIterator i;
    Molecule::FluctuatingChargeIterator  j;
    Molecule* mol;
    Atom* atom;
    
    RealType totalFrc, totalMolFrc, regionFrc, constrainedFrc;
    // accumulate the total system fluctuating charge forces
    totalFrc = 0.0;
    if (constrainRegions_) {
      std::fill(regionForce_.begin(), regionForce_.end(), 0.0); 
      std::fill(regionCharges_.begin(), regionCharges_.end(), 0); 
    }

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

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

        RealType frc = atom->getFlucQFrc();
        totalFrc += frc;
        if (constrainRegions_) {
          if (region >= 0) {        
            regionForce_[regionKeys_[region]] += frc;
            regionCharges_[regionKeys_[region]] += 1;
          }
        }
      }
    }

#ifdef IS_MPI
    // in parallel, we need to add up the contributions from all
    // processors:
    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalFrc, 1, MPI::REALTYPE, 
                              MPI::SUM);

    if (constrainRegions_) {
      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &regionForce_[0], 
                                regionForce_.size(), MPI::REALTYPE, MPI::SUM);
      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &regionCharges_[0], 
                                regionCharges_.size(), MPI::INT, MPI::SUM);
    }

#endif

    // divide by the total number of fluctuating charges:
    totalFrc /= info_->getNFluctuatingCharges();
    
    // do the same in the regions:
    if (constrainRegions_) {
      for (int i = 0; i < regionForce_.size(); ++i)  {
        regionForce_[ i ] /= regionCharges_[ i ];
      }
    }

    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {     
      
      if (constrainRegions_) {
        int region = mol->getRegion();
        if (region >= 0) 
          regionFrc = regionForce_[regionKeys_[region]];
        else
          regionFrc = 0.0;
      } else {
        regionFrc = 0.0;
      }

      totalMolFrc = 0.0;
      
      // molecular constraints can be done with a second loop.
      if (mol->constrainTotalCharge()) {
        for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
             atom = mol->nextFluctuatingCharge(j)) {
          totalMolFrc += atom->getFlucQFrc();
        }
        totalMolFrc /= mol->getNFluctuatingCharges();
      }

      for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
           atom = mol->nextFluctuatingCharge(j)) {
        //constrainedFrc = atom->getFlucQFrc() - totalFrc - totalMolFrc;

        constrainedFrc = atom->getFlucQFrc() - totalMolFrc;

        if (constrainRegions_) 
          constrainedFrc -= regionFrc;
        
        atom->setFlucQFrc(constrainedFrc);
      }      
    }
  }
}
Revision:	1913
Committed:	Wed Jul 24 20:00:51 2013 UTC (11 years, 9 months ago) by jmichalk
File size:	6572 byte(s)
Log Message:	Fixed some bugs in the flucQ constraints.
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1740	* [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 "FluctuatingChargeConstraints.hpp"
44			#include "primitives/Molecule.hpp"
45
46			#ifdef IS_MPI
47			#include <mpi.h>
48			#endif
49
50			namespace OpenMD {
51
52			FluctuatingChargeConstraints::FluctuatingChargeConstraints(SimInfo* info) :
53	jmichalk	1913	info_(info), constrainRegions_(false), hasFlucQ_(false), initialized_(false) {
54	gezelter	1740
55	jmichalk	1913	}
56
57			void FluctuatingChargeConstraints::initialize(){
58			if(info_->usesFluctuatingCharges()){
59			if(info_->getNFluctuatingCharges() > 0){
60			hasFlucQ_ = true;
61	gezelter	1740	}
62			}
63	jmichalk	1913	initialized_ = true;
64	gezelter	1740	}
65
66	gezelter	1908	void FluctuatingChargeConstraints::setConstrainRegions(bool cr) {
67			constrainRegions_ = cr;
68			regionKeys_.clear();
69			regionForce_.clear();
70			regionCharges_.clear();
71
72			if (constrainRegions_) {
73			SimInfo::MoleculeIterator i;
74			Molecule* mol;
75			int reg;
76			std::set<int> regions;
77
78			for (mol = info_->beginMolecule(i); mol != NULL;
79			mol = info_->nextMolecule(i)) {
80			reg = mol->getRegion();
81			if (reg >= 0) regions.insert(reg);
82			}
83	jmichalk	1913	// resize the keys vector to the largest found value for regions.
84			regionKeys_.resize( *(regions.end()) );
85			int which = 0;
86	gezelter	1908	for (std::set<int>::iterator r=regions.begin(); r!=regions.end(); ++r) {
87	jmichalk	1913	regionKeys_[ (*r) ] = which;
88			which++;
89	gezelter	1908	}
90			regionForce_.resize( regionKeys_.size() );
91			regionCharges_.resize( regionKeys_.size() );
92			}
93			}
94
95
96	gezelter	1740	void FluctuatingChargeConstraints::applyConstraints() {
97	jmichalk	1913	if (!initialized_) initialize();
98	gezelter	1740	if (!hasFlucQ_) return;
99			SimInfo::MoleculeIterator i;
100			Molecule::FluctuatingChargeIterator j;
101			Molecule* mol;
102			Atom* atom;
103
104	gezelter	1908	RealType totalFrc, totalMolFrc, regionFrc, constrainedFrc;
105	gezelter	1740	// accumulate the total system fluctuating charge forces
106			totalFrc = 0.0;
107	gezelter	1908	if (constrainRegions_) {
108			std::fill(regionForce_.begin(), regionForce_.end(), 0.0);
109			std::fill(regionCharges_.begin(), regionCharges_.end(), 0);
110			}
111	gezelter	1740
112			for (mol = info_->beginMolecule(i); mol != NULL;
113			mol = info_->nextMolecule(i)) {
114
115	gezelter	1908	int region = mol->getRegion();
116
117	gezelter	1740	for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
118			atom = mol->nextFluctuatingCharge(j)) {
119	gezelter	1908
120			RealType frc = atom->getFlucQFrc();
121			totalFrc += frc;
122			if (constrainRegions_) {
123	jmichalk	1913	if (region >= 0) {
124			regionForce_[regionKeys_[region]] += frc;
125			regionCharges_[regionKeys_[region]] += 1;
126			}
127	gezelter	1908	}
128	gezelter	1740	}
129			}
130
131			#ifdef IS_MPI
132			// in parallel, we need to add up the contributions from all
133			// processors:
134			MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalFrc, 1, MPI::REALTYPE,
135			MPI::SUM);
136	gezelter	1908
137			if (constrainRegions_) {
138			MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &regionForce_[0],
139			regionForce_.size(), MPI::REALTYPE, MPI::SUM);
140			MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &regionCharges_[0],
141			regionCharges_.size(), MPI::INT, MPI::SUM);
142			}
143
144	gezelter	1740	#endif
145	gezelter	1908
146	gezelter	1740	// divide by the total number of fluctuating charges:
147			totalFrc /= info_->getNFluctuatingCharges();
148	gezelter	1908
149			// do the same in the regions:
150			if (constrainRegions_) {
151			for (int i = 0; i < regionForce_.size(); ++i) {
152			regionForce_[ i ] /= regionCharges_[ i ];
153			}
154			}
155	gezelter	1740
156			for (mol = info_->beginMolecule(i); mol != NULL;
157			mol = info_->nextMolecule(i)) {
158
159	gezelter	1908	if (constrainRegions_) {
160			int region = mol->getRegion();
161	jmichalk	1913	if (region >= 0)
162			regionFrc = regionForce_[regionKeys_[region]];
163			else
164			regionFrc = 0.0;
165	gezelter	1908	} else {
166			regionFrc = 0.0;
167			}
168
169	gezelter	1740	totalMolFrc = 0.0;
170	gezelter	1908
171	gezelter	1740	// molecular constraints can be done with a second loop.
172			if (mol->constrainTotalCharge()) {
173			for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
174			atom = mol->nextFluctuatingCharge(j)) {
175			totalMolFrc += atom->getFlucQFrc();
176			}
177			totalMolFrc /= mol->getNFluctuatingCharges();
178			}
179
180			for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
181			atom = mol->nextFluctuatingCharge(j)) {
182	gezelter	1879	//constrainedFrc = atom->getFlucQFrc() - totalFrc - totalMolFrc;
183	gezelter	1908
184	gezelter	1879	constrainedFrc = atom->getFlucQFrc() - totalMolFrc;
185	gezelter	1908
186			if (constrainRegions_)
187			constrainedFrc -= regionFrc;
188
189	gezelter	1740	atom->setFlucQFrc(constrainedFrc);
190			}
191			}
192			}
193			}