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).
 */
 
#ifdef IS_MPI
#include <mpi.h>
#endif

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

namespace OpenMD {

  FluctuatingChargeConstraints::FluctuatingChargeConstraints(SimInfo* info) : 
    info_(info), initialized_(false), hasFlucQ_(false),
    constrainRegions_(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_Allreduce(MPI_IN_PLACE, &totalFrc, 1, MPI_REALTYPE, 
                  MPI_SUM, MPI_COMM_WORLD);

    if (constrainRegions_) {
      MPI_Allreduce(MPI_IN_PLACE, &regionForce_[0], 
                    regionForce_.size(), MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
      MPI_Allreduce(MPI_IN_PLACE, &regionCharges_[0], 
                    regionCharges_.size(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
    }

#endif

    // divide by the total number of fluctuating charges:
    totalFrc /= info_->getNFluctuatingCharges();
    
    // do the same in the regions:
    if (constrainRegions_) {
      for (unsigned 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:	2070
Committed:	Sat Mar 7 16:59:57 2015 UTC (10 years, 1 month ago) by gezelter
File size:	6588 byte(s)
Log Message:	More edits for gcc warnings
#	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	#ifdef IS_MPI
44	#include <mpi.h>
45	#endif
46
47	#include "FluctuatingChargeConstraints.hpp"
48	#include "primitives/Molecule.hpp"
49
50	namespace OpenMD {
51
52	FluctuatingChargeConstraints::FluctuatingChargeConstraints(SimInfo* info) :
53	info_(info), initialized_(false), hasFlucQ_(false),
54	constrainRegions_(false) {
55	}
56
57	void FluctuatingChargeConstraints::initialize(){
58	if(info_->usesFluctuatingCharges()){
59	if(info_->getNFluctuatingCharges() > 0){
60	hasFlucQ_ = true;
61	}
62	}
63	initialized_ = true;
64	}
65
66
67	void FluctuatingChargeConstraints::setConstrainRegions(bool cr) {
68	constrainRegions_ = cr;
69
70	if (!initialized_) initialize();
71
72	regionKeys_.clear();
73	regionForce_.clear();
74	regionCharges_.clear();
75
76	if (constrainRegions_) {
77	SimInfo::MoleculeIterator i;
78	Molecule* mol;
79	int reg;
80	std::set<int> regions;
81
82	for (mol = info_->beginMolecule(i); mol != NULL;
83	mol = info_->nextMolecule(i)) {
84	reg = mol->getRegion();
85	if (reg >= 0) regions.insert(reg);
86	}
87	// resize the keys vector to the largest found value for regions.
88	regionKeys_.resize( *(regions.end()) );
89	int which = 0;
90	for (std::set<int>::iterator r=regions.begin(); r!=regions.end(); ++r) {
91	regionKeys_[ (*r) ] = which;
92	which++;
93	}
94	regionForce_.resize( regionKeys_.size() );
95	regionCharges_.resize( regionKeys_.size() );
96	}
97	}
98
99
100	void FluctuatingChargeConstraints::applyConstraints() {
101	if (!initialized_) initialize();
102	if (!hasFlucQ_) return;
103
104	SimInfo::MoleculeIterator i;
105	Molecule::FluctuatingChargeIterator j;
106	Molecule* mol;
107	Atom* atom;
108
109	RealType totalFrc, totalMolFrc, regionFrc, constrainedFrc;
110	// accumulate the total system fluctuating charge forces
111	totalFrc = 0.0;
112	if (constrainRegions_) {
113	std::fill(regionForce_.begin(), regionForce_.end(), 0.0);
114	std::fill(regionCharges_.begin(), regionCharges_.end(), 0);
115	}
116
117	for (mol = info_->beginMolecule(i); mol != NULL;
118	mol = info_->nextMolecule(i)) {
119
120	int region = mol->getRegion();
121
122	for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
123	atom = mol->nextFluctuatingCharge(j)) {
124
125	RealType frc = atom->getFlucQFrc();
126	totalFrc += frc;
127	if (constrainRegions_) {
128	if (region >= 0) {
129	regionForce_[regionKeys_[region]] += frc;
130	regionCharges_[regionKeys_[region]] += 1;
131	}
132	}
133	}
134	}
135
136	#ifdef IS_MPI
137	// in parallel, we need to add up the contributions from all
138	// processors:
139	MPI_Allreduce(MPI_IN_PLACE, &totalFrc, 1, MPI_REALTYPE,
140	MPI_SUM, MPI_COMM_WORLD);
141
142	if (constrainRegions_) {
143	MPI_Allreduce(MPI_IN_PLACE, &regionForce_[0],
144	regionForce_.size(), MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
145	MPI_Allreduce(MPI_IN_PLACE, &regionCharges_[0],
146	regionCharges_.size(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
147	}
148
149	#endif
150
151	// divide by the total number of fluctuating charges:
152	totalFrc /= info_->getNFluctuatingCharges();
153
154	// do the same in the regions:
155	if (constrainRegions_) {
156	for (unsigned int i = 0; i < regionForce_.size(); ++i) {
157	regionForce_[ i ] /= regionCharges_[ i ];
158	}
159	}
160
161	for (mol = info_->beginMolecule(i); mol != NULL;
162	mol = info_->nextMolecule(i)) {
163
164	if (constrainRegions_) {
165	int region = mol->getRegion();
166	if (region >= 0)
167	regionFrc = regionForce_[regionKeys_[region]];
168	else
169	regionFrc = 0.0;
170	} else {
171	regionFrc = 0.0;
172	}
173
174	totalMolFrc = 0.0;
175
176	// molecular constraints can be done with a second loop.
177	if (mol->constrainTotalCharge()) {
178	for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
179	atom = mol->nextFluctuatingCharge(j)) {
180	totalMolFrc += atom->getFlucQFrc();
181	}
182	totalMolFrc /= mol->getNFluctuatingCharges();
183	}
184
185	for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
186	atom = mol->nextFluctuatingCharge(j)) {
187	constrainedFrc = atom->getFlucQFrc() - totalFrc - totalMolFrc;
188
189	//constrainedFrc = atom->getFlucQFrc() - totalMolFrc;
190
191	if (constrainRegions_)
192	constrainedFrc -= regionFrc;
193
194	atom->setFlucQFrc(constrainedFrc);
195	}
196	}
197	}
198	}