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), hasFlucQ_(false) {
    
    if (info_->usesFluctuatingCharges()) {
      if (info_->getNFluctuatingCharges() > 0) {
        hasFlucQ_ = true;
      }
    }
  }

  void FluctuatingChargeConstraints::applyConstraints() {
    if (!hasFlucQ_) return;
    
    SimInfo::MoleculeIterator i;
    Molecule::FluctuatingChargeIterator  j;
    Molecule* mol;
    Atom* atom;
    
    RealType totalFrc, totalMolFrc, constrainedFrc;
    
    // accumulate the total system fluctuating charge forces
    totalFrc = 0.0;

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

      for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
           atom = mol->nextFluctuatingCharge(j)) {
        totalFrc += atom->getFlucQFrc();
      }

    }

#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);
#endif
 
    // divide by the total number of fluctuating charges:
    totalFrc /= info_->getNFluctuatingCharges();

    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {     
      
      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;
        atom->setFlucQFrc(constrainedFrc);
      }      
    }
  }
}
Revision:	1850
Committed:	Wed Feb 20 15:39:39 2013 UTC (12 years, 2 months ago) by gezelter
File size:	4256 byte(s)
Log Message:	Fixed a widespread typo in the license
#	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	1850	* [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			info_(info), hasFlucQ_(false) {
54
55			if (info_->usesFluctuatingCharges()) {
56			if (info_->getNFluctuatingCharges() > 0) {
57			hasFlucQ_ = true;
58			}
59			}
60			}
61
62			void FluctuatingChargeConstraints::applyConstraints() {
63			if (!hasFlucQ_) return;
64
65			SimInfo::MoleculeIterator i;
66			Molecule::FluctuatingChargeIterator j;
67			Molecule* mol;
68			Atom* atom;
69
70			RealType totalFrc, totalMolFrc, constrainedFrc;
71
72			// accumulate the total system fluctuating charge forces
73			totalFrc = 0.0;
74
75			for (mol = info_->beginMolecule(i); mol != NULL;
76			mol = info_->nextMolecule(i)) {
77
78			for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
79			atom = mol->nextFluctuatingCharge(j)) {
80			totalFrc += atom->getFlucQFrc();
81			}
82
83			}
84
85			#ifdef IS_MPI
86			// in parallel, we need to add up the contributions from all
87			// processors:
88			MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalFrc, 1, MPI::REALTYPE,
89			MPI::SUM);
90			#endif
91
92			// divide by the total number of fluctuating charges:
93			totalFrc /= info_->getNFluctuatingCharges();
94
95			for (mol = info_->beginMolecule(i); mol != NULL;
96			mol = info_->nextMolecule(i)) {
97
98			totalMolFrc = 0.0;
99
100			// molecular constraints can be done with a second loop.
101			if (mol->constrainTotalCharge()) {
102			for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
103			atom = mol->nextFluctuatingCharge(j)) {
104			totalMolFrc += atom->getFlucQFrc();
105			}
106			totalMolFrc /= mol->getNFluctuatingCharges();
107			}
108
109			for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
110			atom = mol->nextFluctuatingCharge(j)) {
111			constrainedFrc = atom->getFlucQFrc() - totalFrc - totalMolFrc;
112			atom->setFlucQFrc(constrainedFrc);
113			}
114			}
115			}
116			}