src/perturbations/ElectricField.cpp

/*
 * Copyright (c) 2005 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 "perturbations/ElectricField.hpp"
#include "types/FixedChargeAdapter.hpp"
#include "types/FluctuatingChargeAdapter.hpp"
#include "types/MultipoleAdapter.hpp"
#include "primitives/Molecule.hpp"
#include "nonbonded/NonBondedInteraction.hpp"

namespace OpenMD {

  ElectricField::ElectricField(SimInfo* info) : info_(info), 
                                                doElectricField(false), 
                                                doParticlePot(false),
                                                initialized(false) {
    simParams = info_->getSimParams();
  }

  void ElectricField::initialize() {
    if (simParams->haveElectricField()) {
      doElectricField = true;
      EF = simParams->getElectricField();
    }   
    int storageLayout_ = info_->getSnapshotManager()->getStorageLayout();
    if (storageLayout_ & DataStorage::dslParticlePot) doParticlePot = true;
    initialized = true;
  }

  void ElectricField::applyPerturbation() {
    if (!initialized) initialize();

    SimInfo::MoleculeIterator i;
    Molecule::AtomIterator  j;
    Molecule* mol;
    Atom* atom;
    potVec longRangePotential(0.0);
    Vector3d dip;
    Vector3d trq;
    Vector3d EFfrc;                             
    Vector3d pos;
    RealType chrg;
    RealType pot, fieldPot;
    RealType chrgToKcal = 23.0609;
    RealType debyeToKcal = 4.8018969509;


    if (doElectricField) {
      fieldPot = 0.0;

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

        for (atom = mol->beginAtom(j); atom != NULL;
             atom = mol->nextAtom(j)) {

          bool isCharge = false;
          chrg = 0.0;
          
          AtomType* atype = atom->getAtomType();
          
          if (atype->isElectrostatic()) {
            atom->addElectricField(EF * chrgToKcal);
          }
          
          FixedChargeAdapter fca = FixedChargeAdapter(atype);
          if ( fca.isFixedCharge() ) {
            isCharge = true;
            chrg = fca.getCharge();
          }
          
          FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype);
          if ( fqa.isFluctuatingCharge() ) {
            isCharge = true;
            chrg += atom->getFlucQPos();
          }
          
          if (isCharge) {
            EFfrc = EF*chrg;
            EFfrc *= chrgToKcal;
            atom->addFrc(EFfrc);
            // ad-hoc choice of the origin for potential calculation
            pos = atom->getPos();
            pot = -dot(pos, EFfrc);
            if (doParticlePot) {      
              atom->addParticlePot(pot);
            }
            fieldPot += pot;
          }
            
          MultipoleAdapter ma = MultipoleAdapter(atype);
          if (ma.isDipole() ) {
            Vector3d dipole = atom->getDipole();
            dipole *= debyeToKcal;

            trq = cross(dipole, EF);
            atom->addTrq(trq);

            pot = -dot(dipole, EF);
            if (doParticlePot) {      
              atom->addParticlePot(pot);
            }
            fieldPot += pot;
          }
        }
      }
#ifdef IS_MPI
      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &fieldPot, 1, MPI::REALTYPE, 
                                MPI::SUM);
#endif
      Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
      longRangePotential = snap->getLongRangePotentials();
      longRangePotential[ELECTROSTATIC_FAMILY] += fieldPot;
      snap->setLongRangePotential(longRangePotential);
    }
  }
}
Revision:	1874
Committed:	Wed May 15 15:09:35 2013 UTC (11 years, 11 months ago) by gezelter
File size:	5278 byte(s)
Log Message:	Fixed a bunch of cppcheck warnings.
#	User	Rev	Content
1	jmarr	1780	/*
2			* Copyright (c) 2005 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	jmarr	1780	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41			*/
42			#include "perturbations/ElectricField.hpp"
43			#include "types/FixedChargeAdapter.hpp"
44			#include "types/FluctuatingChargeAdapter.hpp"
45			#include "types/MultipoleAdapter.hpp"
46			#include "primitives/Molecule.hpp"
47			#include "nonbonded/NonBondedInteraction.hpp"
48
49			namespace OpenMD {
50
51			ElectricField::ElectricField(SimInfo* info) : info_(info),
52			doElectricField(false),
53			doParticlePot(false),
54			initialized(false) {
55			simParams = info_->getSimParams();
56			}
57
58			void ElectricField::initialize() {
59			if (simParams->haveElectricField()) {
60			doElectricField = true;
61			EF = simParams->getElectricField();
62			}
63			int storageLayout_ = info_->getSnapshotManager()->getStorageLayout();
64			if (storageLayout_ & DataStorage::dslParticlePot) doParticlePot = true;
65			initialized = true;
66			}
67
68			void ElectricField::applyPerturbation() {
69			if (!initialized) initialize();
70
71			SimInfo::MoleculeIterator i;
72			Molecule::AtomIterator j;
73			Molecule* mol;
74			Atom* atom;
75			potVec longRangePotential(0.0);
76			Vector3d dip;
77			Vector3d trq;
78			Vector3d EFfrc;
79			Vector3d pos;
80			RealType chrg;
81	gezelter	1825	RealType pot, fieldPot;
82	jmarr	1780	RealType chrgToKcal = 23.0609;
83			RealType debyeToKcal = 4.8018969509;
84
85	gezelter	1874
86	jmarr	1780	if (doElectricField) {
87			fieldPot = 0.0;
88
89	gezelter	1844	for (mol = info_->beginMolecule(i); mol != NULL;
90			mol = info_->nextMolecule(i)) {
91
92	jmarr	1780	for (atom = mol->beginAtom(j); atom != NULL;
93			atom = mol->nextAtom(j)) {
94	gezelter	1844
95	gezelter	1874	bool isCharge = false;
96	jmarr	1780	chrg = 0.0;
97	gezelter	1844
98	gezelter	1874	AtomType* atype = atom->getAtomType();
99	gezelter	1844
100			if (atype->isElectrostatic()) {
101			atom->addElectricField(EF * chrgToKcal);
102			}
103
104			FixedChargeAdapter fca = FixedChargeAdapter(atype);
105	jmarr	1780	if ( fca.isFixedCharge() ) {
106			isCharge = true;
107			chrg = fca.getCharge();
108			}
109
110	gezelter	1844	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype);
111	jmarr	1780	if ( fqa.isFluctuatingCharge() ) {
112			isCharge = true;
113			chrg += atom->getFlucQPos();
114			}
115
116			if (isCharge) {
117			EFfrc = EF*chrg;
118			EFfrc *= chrgToKcal;
119			atom->addFrc(EFfrc);
120	gezelter	1787	// ad-hoc choice of the origin for potential calculation
121	jmarr	1780	pos = atom->getPos();
122			pot = -dot(pos, EFfrc);
123			if (doParticlePot) {
124			atom->addParticlePot(pot);
125			}
126			fieldPot += pot;
127			}
128
129	gezelter	1844	MultipoleAdapter ma = MultipoleAdapter(atype);
130	jmarr	1780	if (ma.isDipole() ) {
131	gezelter	1787	Vector3d dipole = atom->getDipole();
132			dipole *= debyeToKcal;
133
134			trq = cross(dipole, EF);
135	jmarr	1780	atom->addTrq(trq);
136	gezelter	1787
137			pot = -dot(dipole, EF);
138	jmarr	1780	if (doParticlePot) {
139			atom->addParticlePot(pot);
140			}
141			fieldPot += pot;
142			}
143			}
144			}
145			#ifdef IS_MPI
146			MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &fieldPot, 1, MPI::REALTYPE,
147			MPI::SUM);
148			#endif
149			Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
150			longRangePotential = snap->getLongRangePotentials();
151			longRangePotential[ELECTROSTATIC_FAMILY] += fieldPot;
152			snap->setLongRangePotential(longRangePotential);
153			}
154			}
155			}