src/perturbations/UniformField.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, 24107 (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, moment;
    RealType chrgToKcal = 23.0609;
    RealType debyeToKcal = 4.8018969509;
    bool isCharge;

    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)) {
          isCharge = false;
          chrg = 0.0;

          FixedChargeAdapter fca = FixedChargeAdapter(atom->getAtomType());
          if ( fca.isFixedCharge() ) {
            isCharge = true;
            chrg = fca.getCharge();
          }
          
          FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atom->getAtomType());
          if ( fqa.isFluctuatingCharge() ) {
            isCharge = true;
            chrg += atom->getFlucQPos();
          }
          
          if (isCharge) {
            EFfrc = EF*chrg;
            EFfrc *= chrgToKcal;
            atom->addFrc(EFfrc);
            // totally 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(atom->getAtomType());
          if (ma.isDipole() ) {
            Vector3d u_i = atom->getElectroFrame().getColumn(2);
            moment = ma.getDipoleMoment();
            moment *= debyeToKcal;
            dip = u_i * moment;
            trq = cross(dip, EF);
            //cerr << "dip = " << dip << "\n";
            // cerr << "trq = " << trq << "\n";
            atom->addTrq(trq);
            pot = -dot(dip, EF);
            //cerr << "pot = " << pot << "\n";
            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 = " << longRangePotential << "\n";
      longRangePotential[ELECTROSTATIC_FAMILY] += fieldPot;
      //cerr << "longRangePotential[ELECTROSTATIC_FAMILY] = " << longRangePotential[ELECTROSTATIC_FAMILY] << "\n";
      snap->setLongRangePotential(longRangePotential);
    }
  }

}
Revision:	1782
Committed:	Wed Aug 22 02:28:28 2012 UTC (12 years, 8 months ago) by gezelter
Original Path:	*trunk/src/perturbations/ElectricField.cpp*
File size:	5512 byte(s)
Log Message:	MERGE OpenMD development branch 1465:1781 into trunk
#	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			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (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			#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			RealType pot, fieldPot, moment;
82			RealType chrgToKcal = 23.0609;
83			RealType debyeToKcal = 4.8018969509;
84			bool isCharge;
85
86			if (doElectricField) {
87			fieldPot = 0.0;
88
89			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
90			for (atom = mol->beginAtom(j); atom != NULL;
91			atom = mol->nextAtom(j)) {
92			isCharge = false;
93			chrg = 0.0;
94
95			FixedChargeAdapter fca = FixedChargeAdapter(atom->getAtomType());
96			if ( fca.isFixedCharge() ) {
97			isCharge = true;
98			chrg = fca.getCharge();
99			}
100
101			FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atom->getAtomType());
102			if ( fqa.isFluctuatingCharge() ) {
103			isCharge = true;
104			chrg += atom->getFlucQPos();
105			}
106
107			if (isCharge) {
108			EFfrc = EF*chrg;
109			EFfrc *= chrgToKcal;
110			atom->addFrc(EFfrc);
111			// totally ad-hoc choice of the origin for potential calculation
112			pos = atom->getPos();
113			pot = -dot(pos, EFfrc);
114			if (doParticlePot) {
115			atom->addParticlePot(pot);
116			}
117			fieldPot += pot;
118			}
119
120			MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType());
121			if (ma.isDipole() ) {
122			Vector3d u_i = atom->getElectroFrame().getColumn(2);
123			moment = ma.getDipoleMoment();
124			moment *= debyeToKcal;
125			dip = u_i * moment;
126			trq = cross(dip, EF);
127			//cerr << "dip = " << dip << "\n";
128			// cerr << "trq = " << trq << "\n";
129			atom->addTrq(trq);
130			pot = -dot(dip, EF);
131			//cerr << "pot = " << pot << "\n";
132			if (doParticlePot) {
133			atom->addParticlePot(pot);
134			}
135			fieldPot += pot;
136			}
137			}
138			}
139			#ifdef IS_MPI
140			MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &fieldPot, 1, MPI::REALTYPE,
141			MPI::SUM);
142			#endif
143			Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
144			longRangePotential = snap->getLongRangePotentials();
145			// << "longRangePotential = " << longRangePotential << "\n";
146			longRangePotential[ELECTROSTATIC_FAMILY] += fieldPot;
147			//cerr << "longRangePotential[ELECTROSTATIC_FAMILY] = " << longRangePotential[ELECTROSTATIC_FAMILY] << "\n";
148			snap->setLongRangePotential(longRangePotential);
149			}
150			}
151
152			}