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, 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;

    if (doElectricField) {
      const RealType chrgToKcal = 23.0609;
      const RealType debyeToKcal = 4.8018969509;
      RealType pot;
      RealType 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;
          RealType chrg = 0.0;
          
          AtomType* atype = atom->getAtomType();

          // ad-hoc choice of the origin for potential calculation and
          // fluctuating charge force:
          pos = atom->getPos();
          
          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();
            atom->addFlucQFrc( dot(pos,EF) * chrgToKcal );
          }
          
          if (isCharge) {
            EFfrc = EF*chrg;
            EFfrc *= chrgToKcal;
            atom->addFrc(EFfrc);
            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_Allreduce(MPI_IN_PLACE, &fieldPot, 1, MPI_REALTYPE, 
                    MPI_SUM, MPI_COMM_WORLD);
#endif
      Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
      longRangePotential = snap->getLongRangePotentials();
      longRangePotential[ELECTROSTATIC_FAMILY] += fieldPot;
      snap->setLongRangePotential(longRangePotential);
    }
  }
}
Revision:	1987
Committed:	Thu Apr 17 19:07:31 2014 UTC (11 years ago) by gezelter
Original Path:	*trunk/src/perturbations/ElectricField.cpp*
File size:	5386 byte(s)
Log Message:	Removing vestiges of deprecated MPI:: namespace C++ MPI bindings
#	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	1879	* [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
81			if (doElectricField) {
82	gezelter	1879	const RealType chrgToKcal = 23.0609;
83			const RealType debyeToKcal = 4.8018969509;
84			RealType pot;
85			RealType fieldPot = 0.0;
86	jmarr	1780
87	gezelter	1879	for (mol = info_->beginMolecule(i); mol != NULL;
88			mol = info_->nextMolecule(i)) {
89
90	jmarr	1780	for (atom = mol->beginAtom(j); atom != NULL;
91			atom = mol->nextAtom(j)) {
92
93	gezelter	1879	bool isCharge = false;
94			RealType chrg = 0.0;
95
96			AtomType* atype = atom->getAtomType();
97	gezelter	1908
98			// ad-hoc choice of the origin for potential calculation and
99			// fluctuating charge force:
100			pos = atom->getPos();
101	gezelter	1879
102			if (atype->isElectrostatic()) {
103			atom->addElectricField(EF * chrgToKcal);
104			}
105
106			FixedChargeAdapter fca = FixedChargeAdapter(atype);
107	jmarr	1780	if ( fca.isFixedCharge() ) {
108			isCharge = true;
109			chrg = fca.getCharge();
110			}
111
112	gezelter	1879	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype);
113	jmarr	1780	if ( fqa.isFluctuatingCharge() ) {
114			isCharge = true;
115			chrg += atom->getFlucQPos();
116	gezelter	1908	atom->addFlucQFrc( dot(pos,EF) * chrgToKcal );
117	jmarr	1780	}
118
119			if (isCharge) {
120			EFfrc = EF*chrg;
121			EFfrc *= chrgToKcal;
122			atom->addFrc(EFfrc);
123			pot = -dot(pos, EFfrc);
124			if (doParticlePot) {
125			atom->addParticlePot(pot);
126			}
127			fieldPot += pot;
128			}
129
130	gezelter	1879	MultipoleAdapter ma = MultipoleAdapter(atype);
131	jmarr	1780	if (ma.isDipole() ) {
132	gezelter	1879	Vector3d dipole = atom->getDipole();
133			dipole *= debyeToKcal;
134
135			trq = cross(dipole, EF);
136	jmarr	1780	atom->addTrq(trq);
137	gezelter	1879
138			pot = -dot(dipole, EF);
139	jmarr	1780	if (doParticlePot) {
140			atom->addParticlePot(pot);
141			}
142			fieldPot += pot;
143			}
144			}
145			}
146			#ifdef IS_MPI
147	gezelter	1987	MPI_Allreduce(MPI_IN_PLACE, &fieldPot, 1, MPI_REALTYPE,
148			MPI_SUM, MPI_COMM_WORLD);
149	jmarr	1780	#endif
150			Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
151			longRangePotential = snap->getLongRangePotentials();
152			longRangePotential[ELECTROSTATIC_FAMILY] += fieldPot;
153			snap->setLongRangePotential(longRangePotential);
154			}
155			}
156			}