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() {

    bool haveA = false;
    bool haveB = false;
    bool haveG = false;
    
    if (simParams->haveUniformGradientDirection1()) {
      std::vector<RealType> d1 = simParams->getUniformGradientDirection1();
      if (d1.size() != 3) {
        sprintf(painCave.errMsg,
                "uniformGradientDirection1: Incorrect number of parameters\n"
                "\tspecified. There should be 3 parameters, but %lu were\n"
                "\tspecified.\n", d1.size());
        painCave.isFatal = 1;
        simError();      
      }
      a_.x() = d1[0];
      a_.y() = d1[1];
      a_.z() = d1[2];

      a_.normalize();
      haveA = true;      
    }
    
    if (simParams->haveUniformGradientDirection2()) {
      std::vector<RealType> d2 = simParams->getUniformGradientDirection2();
      if (d2.size() != 3) {
        sprintf(painCave.errMsg,
                "uniformGradientDirection2: Incorrect number of parameters\n"
                "\tspecified. There should be 3 parameters, but %lu were\n"
                "\tspecified.\n", d2.size());
        painCave.isFatal = 1;
        simError();      
      }
      b_.x() = d2[0];
      b_.y() = d2[1];
      b_.z() = d2[2];

      b_.normalize();
      haveB = true;      
    }

    if (simParams->haveUniformGradientStrength()) {
      g_ = simParams->getUniformGradientStrength();
      haveG = true;
    }

    if (haveA && haveB && haveG) {
      doUniformGradient = true;
      cpsi_ = dot(a_, b_);
      
      Grad_(0,0) = 2.0 * (a_.x()*b_.x() - cpsi_ / 3.0);
      Grad_(0,1) = a_.x()*b_.y() + a_.y()*b_.x();
      Grad_(0,2) = a_.x()*b_.z() + a_.z()*b_.x();
      Grad_(1,0) = Grad_(0,1);
      Grad_(1,1) = 2.0 * (a_.y()*b_.y() - cpsi_ / 3.0);
      Grad_(1,2) = a_.y()*b_.z() + a_.z()*b_.y();
      Grad_(2,0) = Grad_(0,2);
      Grad_(2,1) = Grad_(1,2);
      Grad_(2,2) = 2.0 * (a_.z()*b_.z() - cpsi_ / 3.0);

      Grad_ *= g_ / 2.0;
    } else {
      if (!haveA) {
        sprintf(painCave.errMsg,
                "UniformGradient: uniformGradientDirection1 not specified.\n");
        painCave.isFatal = 1;
        simError();
      }
      if (!haveB) {
        sprintf(painCave.errMsg,
                "UniformGradient: uniformGradientDirection2 not specified.\n");
        painCave.isFatal = 1;
        simError();
      }
      if (!haveG) {
        sprintf(painCave.errMsg,
                "UniformGradient: uniformGradientStrength not specified.\n");
        painCave.isFatal = 1;
        simError();
      }
    }    
    
    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:	2034
Committed:	Mon Nov 3 16:49:03 2014 UTC (11 years ago) by gezelter
File size:	8289 byte(s)
Log Message:	Updating UniformGradient to the new parameter structure (two unit vectors and a gradient strength).
#	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	gezelter	2034
62			bool haveA = false;
63			bool haveB = false;
64			bool haveG = false;
65
66			if (simParams->haveUniformGradientDirection1()) {
67			std::vector<RealType> d1 = simParams->getUniformGradientDirection1();
68			if (d1.size() != 3) {
69	gezelter	2026	sprintf(painCave.errMsg,
70	gezelter	2034	"uniformGradientDirection1: Incorrect number of parameters\n"
71			"\tspecified. There should be 3 parameters, but %lu were\n"
72			"\tspecified.\n", d1.size());
73	gezelter	2026	painCave.isFatal = 1;
74			simError();
75			}
76	gezelter	2034	a_.x() = d1[0];
77			a_.y() = d1[1];
78			a_.z() = d1[2];
79	gezelter	2026
80	gezelter	2034	a_.normalize();
81			haveA = true;
82			}
83
84			if (simParams->haveUniformGradientDirection2()) {
85			std::vector<RealType> d2 = simParams->getUniformGradientDirection2();
86			if (d2.size() != 3) {
87			sprintf(painCave.errMsg,
88			"uniformGradientDirection2: Incorrect number of parameters\n"
89			"\tspecified. There should be 3 parameters, but %lu were\n"
90			"\tspecified.\n", d2.size());
91			painCave.isFatal = 1;
92			simError();
93			}
94			b_.x() = d2[0];
95			b_.y() = d2[1];
96			b_.z() = d2[2];
97
98			b_.normalize();
99			haveB = true;
100			}
101
102			if (simParams->haveUniformGradientStrength()) {
103			g_ = simParams->getUniformGradientStrength();
104			haveG = true;
105			}
106
107			if (haveA && haveB && haveG) {
108			doUniformGradient = true;
109			cpsi_ = dot(a_, b_);
110
111			Grad_(0,0) = 2.0 * (a_.x()*b_.x() - cpsi_ / 3.0);
112			Grad_(0,1) = a_.x()b_.y() + a_.y()b_.x();
113			Grad_(0,2) = a_.x()b_.z() + a_.z()b_.x();
114	gezelter	2026	Grad_(1,0) = Grad_(0,1);
115	gezelter	2034	Grad_(1,1) = 2.0 * (a_.y()*b_.y() - cpsi_ / 3.0);
116			Grad_(1,2) = a_.y()b_.z() + a_.z()b_.y();
117	gezelter	2026	Grad_(2,0) = Grad_(0,2);
118			Grad_(2,1) = Grad_(1,2);
119	gezelter	2034	Grad_(2,2) = 2.0 * (a_.z()*b_.z() - cpsi_ / 3.0);
120
121			Grad_ *= g_ / 2.0;
122			} else {
123			if (!haveA) {
124			sprintf(painCave.errMsg,
125			"UniformGradient: uniformGradientDirection1 not specified.\n");
126			painCave.isFatal = 1;
127			simError();
128			}
129			if (!haveB) {
130			sprintf(painCave.errMsg,
131			"UniformGradient: uniformGradientDirection2 not specified.\n");
132			painCave.isFatal = 1;
133			simError();
134			}
135			if (!haveG) {
136			sprintf(painCave.errMsg,
137			"UniformGradient: uniformGradientStrength not specified.\n");
138			painCave.isFatal = 1;
139			simError();
140			}
141			}
142
143	gezelter	2026	int storageLayout_ = info_->getSnapshotManager()->getStorageLayout();
144			if (storageLayout_ & DataStorage::dslParticlePot) doParticlePot = true;
145			initialized = true;
146			}
147
148			void UniformGradient::applyPerturbation() {
149
150			if (!initialized) initialize();
151
152			SimInfo::MoleculeIterator i;
153			Molecule::AtomIterator j;
154			Molecule* mol;
155			Atom* atom;
156			AtomType* atype;
157			potVec longRangePotential(0.0);
158
159			RealType C;
160			Vector3d D;
161			Mat3x3d Q;
162
163			RealType U;
164			RealType fPot;
165			Vector3d t;
166			Vector3d f;
167
168			Vector3d r;
169			Vector3d EF;
170
171			bool isCharge;
172
173			if (doUniformGradient) {
174
175			U = 0.0;
176			fPot = 0.0;
177
178			for (mol = info_->beginMolecule(i); mol != NULL;
179			mol = info_->nextMolecule(i)) {
180
181			for (atom = mol->beginAtom(j); atom != NULL;
182			atom = mol->nextAtom(j)) {
183
184			isCharge = false;
185			C = 0.0;
186
187			atype = atom->getAtomType();
188
189			r = atom->getPos();
190			EF = Grad_ * r;
191
192			if (atype->isElectrostatic()) {
193			atom->addElectricField(EF * PhysicalConstants::chargeFieldConvert);
194			}
195
196			FixedChargeAdapter fca = FixedChargeAdapter(atype);
197			if ( fca.isFixedCharge() ) {
198			isCharge = true;
199			C = fca.getCharge();
200			}
201
202			FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype);
203			if ( fqa.isFluctuatingCharge() ) {
204			isCharge = true;
205			C += atom->getFlucQPos();
206			atom->addFlucQFrc( dot(r, EF)
207			* PhysicalConstants::chargeFieldConvert );
208			}
209
210			if (isCharge) {
211			f = EF * C * PhysicalConstants::chargeFieldConvert;
212			atom->addFrc(f);
213
214			U = -dot(r, f);
215			if (doParticlePot) {
216			atom->addParticlePot(U);
217			}
218			fPot += U;
219			}
220
221			MultipoleAdapter ma = MultipoleAdapter(atype);
222			if (ma.isDipole() ) {
223			D = atom->getDipole() * PhysicalConstants::dipoleFieldConvert;
224
225			f = D * Grad_;
226			atom->addFrc(f);
227
228			t = cross(D, EF);
229			atom->addTrq(t);
230
231			U = -dot(D, EF);
232			if (doParticlePot) {
233			atom->addParticlePot(U);
234			}
235			fPot += U;
236			}
237
238			if (ma.isQuadrupole() ) {
239			Q = atom->getQuadrupole() * PhysicalConstants::dipoleFieldConvert;
240
241			t = 2.0 * mCross(Q, Grad_);
242			atom->addTrq(t);
243
244			U = -doubleDot(Q, Grad_);
245			if (doParticlePot) {
246			atom->addParticlePot(U);
247			}
248			fPot += U;
249			}
250			}
251			}
252
253			#ifdef IS_MPI
254			MPI_Allreduce(MPI_IN_PLACE, &fPot, 1, MPI_REALTYPE,
255			MPI_SUM, MPI_COMM_WORLD);
256			#endif
257
258			Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
259			longRangePotential = snap->getLongRangePotentials();
260			longRangePotential[ELECTROSTATIC_FAMILY] += fPot;
261			snap->setLongRangePotential(longRangePotential);
262			}
263			}
264			}