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;

    if (!initialized_) initialize();

    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:	1920
Committed:	Wed Jul 31 19:30:46 2013 UTC (11 years, 9 months ago) by jmichalk
File size:	6608 byte(s)
Log Message:	Had to move initialization of FluctuatingChargeConstraints into FluctuatingChargePropagator::initialize, I think I did this before, but must not have committed it and then an svn up killed it... The change was made because systems weren't undergoing charge constraints JRM
#	Content
1	/*
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, 234107 (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 "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	info_(info), constrainRegions_(false), hasFlucQ_(false), initialized_(false) {
54	}
55
56	void FluctuatingChargeConstraints::initialize(){
57	if(info_->usesFluctuatingCharges()){
58	if(info_->getNFluctuatingCharges() > 0){
59	hasFlucQ_ = true;
60	}
61	}
62	initialized_ = true;
63	}
64
65
66	void FluctuatingChargeConstraints::setConstrainRegions(bool cr) {
67	constrainRegions_ = cr;
68
69	if (!initialized_) initialize();
70
71	regionKeys_.clear();
72	regionForce_.clear();
73	regionCharges_.clear();
74
75	if (constrainRegions_) {
76	SimInfo::MoleculeIterator i;
77	Molecule* mol;
78	int reg;
79	std::set<int> regions;
80
81	for (mol = info_->beginMolecule(i); mol != NULL;
82	mol = info_->nextMolecule(i)) {
83	reg = mol->getRegion();
84	if (reg >= 0) regions.insert(reg);
85	}
86	// resize the keys vector to the largest found value for regions.
87	regionKeys_.resize( *(regions.end()) );
88	int which = 0;
89	for (std::set<int>::iterator r=regions.begin(); r!=regions.end(); ++r) {
90	regionKeys_[ (*r) ] = which;
91	which++;
92	}
93	regionForce_.resize( regionKeys_.size() );
94	regionCharges_.resize( regionKeys_.size() );
95	}
96	}
97
98
99	void FluctuatingChargeConstraints::applyConstraints() {
100	if (!initialized_) initialize();
101	if (!hasFlucQ_) return;
102
103	SimInfo::MoleculeIterator i;
104	Molecule::FluctuatingChargeIterator j;
105	Molecule* mol;
106	Atom* atom;
107
108	RealType totalFrc, totalMolFrc, regionFrc, constrainedFrc;
109	// accumulate the total system fluctuating charge forces
110	totalFrc = 0.0;
111	if (constrainRegions_) {
112	std::fill(regionForce_.begin(), regionForce_.end(), 0.0);
113	std::fill(regionCharges_.begin(), regionCharges_.end(), 0);
114	}
115
116	for (mol = info_->beginMolecule(i); mol != NULL;
117	mol = info_->nextMolecule(i)) {
118
119	int region = mol->getRegion();
120
121	for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
122	atom = mol->nextFluctuatingCharge(j)) {
123
124	RealType frc = atom->getFlucQFrc();
125	totalFrc += frc;
126	if (constrainRegions_) {
127	if (region >= 0) {
128	regionForce_[regionKeys_[region]] += frc;
129	regionCharges_[regionKeys_[region]] += 1;
130	}
131	}
132	}
133	}
134
135	#ifdef IS_MPI
136	// in parallel, we need to add up the contributions from all
137	// processors:
138	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalFrc, 1, MPI::REALTYPE,
139	MPI::SUM);
140
141	if (constrainRegions_) {
142	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &regionForce_[0],
143	regionForce_.size(), MPI::REALTYPE, MPI::SUM);
144	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &regionCharges_[0],
145	regionCharges_.size(), MPI::INT, MPI::SUM);
146	}
147
148	#endif
149
150	// divide by the total number of fluctuating charges:
151	totalFrc /= info_->getNFluctuatingCharges();
152
153	// do the same in the regions:
154	if (constrainRegions_) {
155	for (int i = 0; i < regionForce_.size(); ++i) {
156	regionForce_[ i ] /= regionCharges_[ i ];
157	}
158	}
159
160	for (mol = info_->beginMolecule(i); mol != NULL;
161	mol = info_->nextMolecule(i)) {
162
163	if (constrainRegions_) {
164	int region = mol->getRegion();
165	if (region >= 0)
166	regionFrc = regionForce_[regionKeys_[region]];
167	else
168	regionFrc = 0.0;
169	} else {
170	regionFrc = 0.0;
171	}
172
173	totalMolFrc = 0.0;
174
175	// molecular constraints can be done with a second loop.
176	if (mol->constrainTotalCharge()) {
177	for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
178	atom = mol->nextFluctuatingCharge(j)) {
179	totalMolFrc += atom->getFlucQFrc();
180	}
181	totalMolFrc /= mol->getNFluctuatingCharges();
182	}
183
184	for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
185	atom = mol->nextFluctuatingCharge(j)) {
186	//constrainedFrc = atom->getFlucQFrc() - totalFrc - totalMolFrc;
187
188	constrainedFrc = atom->getFlucQFrc() - totalMolFrc;
189
190	if (constrainRegions_)
191	constrainedFrc -= regionFrc;
192
193	atom->setFlucQFrc(constrainedFrc);
194	}
195	}
196	}
197	}