src/perturbations/UniformGradient.cpp

/*
 * Copyright (c) 2014 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/UniformGradient.hpp"
#include "types/FixedChargeAdapter.hpp"
#include "types/FluctuatingChargeAdapter.hpp"
#include "types/MultipoleAdapter.hpp"
#include "primitives/Molecule.hpp"
#include "nonbonded/NonBondedInteraction.hpp"
#include "utils/PhysicalConstants.hpp"

namespace OpenMD {
  
  UniformGradient::UniformGradient(SimInfo* info) : info_(info), 
                                            doUniformGradient(false), 
                                            doParticlePot(false),
                                            initialized(false) {
    simParams = info_->getSimParams();
  }
  
  void UniformGradient::initialize() {
    if (simParams->haveUniformGradient()) {
      doUniformGradient = true;
      std::vector<RealType> pv = simParams->getUniformGradient();            
      if (pv.size() != 5) {
        sprintf(painCave.errMsg,
                "UniformGradient: Incorrect number of parameters specified.\n"
                "\tthere should be 5 parameters, but %lu were specified.\n", pv.size());
        painCave.isFatal = 1;
        simError();      
      }
      pars_.a = pv[0];
      pars_.b = pv[1];
      pars_.c = pv[2];
      pars_.alpha = pv[3];
      pars_.beta = pv[4];

      Grad_(0,0) = pars_.alpha;
      Grad_(0,1) = pars_.a;
      Grad_(0,2) = pars_.b;
      Grad_(1,0) = Grad_(0,1);
      Grad_(1,1) = pars_.beta;
      Grad_(1,2) = pars_.c;
      Grad_(2,0) = Grad_(0,2);
      Grad_(2,1) = Grad_(1,2);
      Grad_(2,2) = - (Grad_(0,0) + Grad_(1,1));
    }   
    int storageLayout_ = info_->getSnapshotManager()->getStorageLayout();
    if (storageLayout_ & DataStorage::dslParticlePot) doParticlePot = true;
    initialized = true;
  }
  
  void UniformGradient::applyPerturbation() {

    if (!initialized) initialize();

    SimInfo::MoleculeIterator i;
    Molecule::AtomIterator  j;
    Molecule* mol;
    Atom* atom;
    AtomType* atype;
    potVec longRangePotential(0.0);

    RealType C;
    Vector3d D;
    Mat3x3d Q;

    RealType U;
    RealType fPot;
    Vector3d t;
    Vector3d f;

    Vector3d r;
    Vector3d EF;

    bool isCharge;

    if (doUniformGradient) {

      U = 0.0;
      fPot = 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;
          C = 0.0;
          
          atype = atom->getAtomType();

          r = atom->getPos();
          EF = Grad_ * r;
          
          if (atype->isElectrostatic()) {
            atom->addElectricField(EF * PhysicalConstants::chargeFieldConvert);
          }
          
          FixedChargeAdapter fca = FixedChargeAdapter(atype);
          if ( fca.isFixedCharge() ) {
            isCharge = true;
            C = fca.getCharge();
          }
          
          FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype);
          if ( fqa.isFluctuatingCharge() ) {
            isCharge = true;
            C += atom->getFlucQPos();
            atom->addFlucQFrc( dot(r, EF) 
                               * PhysicalConstants::chargeFieldConvert );
          }
          
          if (isCharge) {
            f = EF * C * PhysicalConstants::chargeFieldConvert;
            atom->addFrc(f);

            U = -dot(r, f);
            if (doParticlePot) {      
              atom->addParticlePot(U);
            }
            fPot += U;
          }
            
          MultipoleAdapter ma = MultipoleAdapter(atype);
          if (ma.isDipole() ) {
            D = atom->getDipole() * PhysicalConstants::dipoleFieldConvert;
            
            f = D * Grad_;
            atom->addFrc(f);

            t = cross(D, EF);
            atom->addTrq(t);

            U = -dot(D, EF);
            if (doParticlePot) {      
              atom->addParticlePot(U);
            }
            fPot += U;
          }

          if (ma.isQuadrupole() ) {
            Q = atom->getQuadrupole() * PhysicalConstants::dipoleFieldConvert;
            
            t = 2.0 * mCross(Q, Grad_);
            atom->addTrq(t);

            U = -doubleDot(Q, Grad_);
            if (doParticlePot) {      
              atom->addParticlePot(U);
            }
            fPot += U;
          }
        }
      }

#ifdef IS_MPI
      MPI_Allreduce(MPI_IN_PLACE, &fPot, 1, MPI_REALTYPE, 
                    MPI_SUM, MPI_COMM_WORLD);
#endif

      Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
      longRangePotential = snap->getLongRangePotentials();
      longRangePotential[ELECTROSTATIC_FAMILY] += fPot;
      snap->setLongRangePotential(longRangePotential);
    }
  }
}
Revision:	2026
Committed:	Wed Oct 22 12:23:59 2014 UTC (10 years, 6 months ago) by gezelter
File size:	6652 byte(s)
Log Message:	Starting to add support for UniformGradient. Changed Vector3d input type to a more general std::vector<RealType> input. This change alters RNEMD and UniformField inputs.
#	User	Rev	Content
1	gezelter	2026	/*
2			* Copyright (c) 2014 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			#include "perturbations/UniformGradient.hpp"
44			#include "types/FixedChargeAdapter.hpp"
45			#include "types/FluctuatingChargeAdapter.hpp"
46			#include "types/MultipoleAdapter.hpp"
47			#include "primitives/Molecule.hpp"
48			#include "nonbonded/NonBondedInteraction.hpp"
49			#include "utils/PhysicalConstants.hpp"
50
51			namespace OpenMD {
52
53			UniformGradient::UniformGradient(SimInfo* info) : info_(info),
54			doUniformGradient(false),
55			doParticlePot(false),
56			initialized(false) {
57			simParams = info_->getSimParams();
58			}
59
60			void UniformGradient::initialize() {
61			if (simParams->haveUniformGradient()) {
62			doUniformGradient = true;
63			std::vector<RealType> pv = simParams->getUniformGradient();
64			if (pv.size() != 5) {
65			sprintf(painCave.errMsg,
66			"UniformGradient: Incorrect number of parameters specified.\n"
67			"\tthere should be 5 parameters, but %lu were specified.\n", pv.size());
68			painCave.isFatal = 1;
69			simError();
70			}
71			pars_.a = pv[0];
72			pars_.b = pv[1];
73			pars_.c = pv[2];
74			pars_.alpha = pv[3];
75			pars_.beta = pv[4];
76
77			Grad_(0,0) = pars_.alpha;
78			Grad_(0,1) = pars_.a;
79			Grad_(0,2) = pars_.b;
80			Grad_(1,0) = Grad_(0,1);
81			Grad_(1,1) = pars_.beta;
82			Grad_(1,2) = pars_.c;
83			Grad_(2,0) = Grad_(0,2);
84			Grad_(2,1) = Grad_(1,2);
85			Grad_(2,2) = - (Grad_(0,0) + Grad_(1,1));
86			}
87			int storageLayout_ = info_->getSnapshotManager()->getStorageLayout();
88			if (storageLayout_ & DataStorage::dslParticlePot) doParticlePot = true;
89			initialized = true;
90			}
91
92			void UniformGradient::applyPerturbation() {
93
94			if (!initialized) initialize();
95
96			SimInfo::MoleculeIterator i;
97			Molecule::AtomIterator j;
98			Molecule* mol;
99			Atom* atom;
100			AtomType* atype;
101			potVec longRangePotential(0.0);
102
103			RealType C;
104			Vector3d D;
105			Mat3x3d Q;
106
107			RealType U;
108			RealType fPot;
109			Vector3d t;
110			Vector3d f;
111
112			Vector3d r;
113			Vector3d EF;
114
115			bool isCharge;
116
117			if (doUniformGradient) {
118
119			U = 0.0;
120			fPot = 0.0;
121
122			for (mol = info_->beginMolecule(i); mol != NULL;
123			mol = info_->nextMolecule(i)) {
124
125			for (atom = mol->beginAtom(j); atom != NULL;
126			atom = mol->nextAtom(j)) {
127
128			isCharge = false;
129			C = 0.0;
130
131			atype = atom->getAtomType();
132
133			r = atom->getPos();
134			EF = Grad_ * r;
135
136			if (atype->isElectrostatic()) {
137			atom->addElectricField(EF * PhysicalConstants::chargeFieldConvert);
138			}
139
140			FixedChargeAdapter fca = FixedChargeAdapter(atype);
141			if ( fca.isFixedCharge() ) {
142			isCharge = true;
143			C = fca.getCharge();
144			}
145
146			FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype);
147			if ( fqa.isFluctuatingCharge() ) {
148			isCharge = true;
149			C += atom->getFlucQPos();
150			atom->addFlucQFrc( dot(r, EF)
151			* PhysicalConstants::chargeFieldConvert );
152			}
153
154			if (isCharge) {
155			f = EF * C * PhysicalConstants::chargeFieldConvert;
156			atom->addFrc(f);
157
158			U = -dot(r, f);
159			if (doParticlePot) {
160			atom->addParticlePot(U);
161			}
162			fPot += U;
163			}
164
165			MultipoleAdapter ma = MultipoleAdapter(atype);
166			if (ma.isDipole() ) {
167			D = atom->getDipole() * PhysicalConstants::dipoleFieldConvert;
168
169			f = D * Grad_;
170			atom->addFrc(f);
171
172			t = cross(D, EF);
173			atom->addTrq(t);
174
175			U = -dot(D, EF);
176			if (doParticlePot) {
177			atom->addParticlePot(U);
178			}
179			fPot += U;
180			}
181
182			if (ma.isQuadrupole() ) {
183			Q = atom->getQuadrupole() * PhysicalConstants::dipoleFieldConvert;
184
185			t = 2.0 * mCross(Q, Grad_);
186			atom->addTrq(t);
187
188			U = -doubleDot(Q, Grad_);
189			if (doParticlePot) {
190			atom->addParticlePot(U);
191			}
192			fPot += U;
193			}
194			}
195			}
196
197			#ifdef IS_MPI
198			MPI_Allreduce(MPI_IN_PLACE, &fPot, 1, MPI_REALTYPE,
199			MPI_SUM, MPI_COMM_WORLD);
200			#endif
201
202			Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
203			longRangePotential = snap->getLongRangePotentials();
204			longRangePotential[ELECTROSTATIC_FAMILY] += fPot;
205			snap->setLongRangePotential(longRangePotential);
206			}
207			}
208			}