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) {
    
    if (info_->usesFluctuatingCharges()) {
      if (info_->getNFluctuatingCharges() > 0) {
        hasFlucQ_ = 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);
        
      }
      for (std::set<int>::iterator r=regions.begin(); r!=regions.end(); ++r) {
        regionKeys_.push_back( (*r) );
      }
      regionForce_.resize( regionKeys_.size() );
      regionCharges_.resize( regionKeys_.size() );
    }
  }


  void FluctuatingChargeConstraints::applyConstraints() {
    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_) {
          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();
        regionFrc = regionForce_[regionKeys_[region]];
      } 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:	1908
Committed:	Fri Jul 19 21:25:45 2013 UTC (11 years, 9 months ago) by gezelter
File size:	6261 byte(s)
Log Message:	Added infrastructure for region-constrained fluctuating charges.
#	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) {
54
55	if (info_->usesFluctuatingCharges()) {
56	if (info_->getNFluctuatingCharges() > 0) {
57	hasFlucQ_ = true;
58	}
59	}
60	}
61
62	void FluctuatingChargeConstraints::setConstrainRegions(bool cr) {
63	constrainRegions_ = cr;
64	regionKeys_.clear();
65	regionForce_.clear();
66	regionCharges_.clear();
67
68	if (constrainRegions_) {
69	SimInfo::MoleculeIterator i;
70	Molecule* mol;
71	int reg;
72	std::set<int> regions;
73
74	for (mol = info_->beginMolecule(i); mol != NULL;
75	mol = info_->nextMolecule(i)) {
76	reg = mol->getRegion();
77	if (reg >= 0) regions.insert(reg);
78
79	}
80	for (std::set<int>::iterator r=regions.begin(); r!=regions.end(); ++r) {
81	regionKeys_.push_back( (*r) );
82	}
83	regionForce_.resize( regionKeys_.size() );
84	regionCharges_.resize( regionKeys_.size() );
85	}
86	}
87
88
89	void FluctuatingChargeConstraints::applyConstraints() {
90	if (!hasFlucQ_) return;
91
92	SimInfo::MoleculeIterator i;
93	Molecule::FluctuatingChargeIterator j;
94	Molecule* mol;
95	Atom* atom;
96
97	RealType totalFrc, totalMolFrc, regionFrc, constrainedFrc;
98
99	// accumulate the total system fluctuating charge forces
100	totalFrc = 0.0;
101	if (constrainRegions_) {
102	std::fill(regionForce_.begin(), regionForce_.end(), 0.0);
103	std::fill(regionCharges_.begin(), regionCharges_.end(), 0);
104	}
105
106	for (mol = info_->beginMolecule(i); mol != NULL;
107	mol = info_->nextMolecule(i)) {
108
109	int region = mol->getRegion();
110
111	for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
112	atom = mol->nextFluctuatingCharge(j)) {
113
114	RealType frc = atom->getFlucQFrc();
115	totalFrc += frc;
116	if (constrainRegions_) {
117	regionForce_[regionKeys_[region]] += frc;
118	regionCharges_[regionKeys_[region]] += 1;
119	}
120	}
121	}
122
123	#ifdef IS_MPI
124	// in parallel, we need to add up the contributions from all
125	// processors:
126	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalFrc, 1, MPI::REALTYPE,
127	MPI::SUM);
128
129	if (constrainRegions_) {
130	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &regionForce_[0],
131	regionForce_.size(), MPI::REALTYPE, MPI::SUM);
132	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &regionCharges_[0],
133	regionCharges_.size(), MPI::INT, MPI::SUM);
134	}
135
136	#endif
137
138	// divide by the total number of fluctuating charges:
139	totalFrc /= info_->getNFluctuatingCharges();
140
141	// do the same in the regions:
142	if (constrainRegions_) {
143	for (int i = 0; i < regionForce_.size(); ++i) {
144	regionForce_[ i ] /= regionCharges_[ i ];
145	}
146	}
147
148	for (mol = info_->beginMolecule(i); mol != NULL;
149	mol = info_->nextMolecule(i)) {
150
151	if (constrainRegions_) {
152	int region = mol->getRegion();
153	regionFrc = regionForce_[regionKeys_[region]];
154	} else {
155	regionFrc = 0.0;
156	}
157
158	totalMolFrc = 0.0;
159
160	// molecular constraints can be done with a second loop.
161	if (mol->constrainTotalCharge()) {
162	for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
163	atom = mol->nextFluctuatingCharge(j)) {
164	totalMolFrc += atom->getFlucQFrc();
165	}
166	totalMolFrc /= mol->getNFluctuatingCharges();
167	}
168
169	for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
170	atom = mol->nextFluctuatingCharge(j)) {
171	//constrainedFrc = atom->getFlucQFrc() - totalFrc - totalMolFrc;
172
173	constrainedFrc = atom->getFlucQFrc() - totalMolFrc;
174
175	if (constrainRegions_)
176	constrainedFrc -= regionFrc;
177
178	atom->setFlucQFrc(constrainedFrc);
179	}
180	}
181	}
182	}