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:	2047
Committed:	Thu Dec 11 16:16:43 2014 UTC (10 years, 11 months ago) by gezelter
File size:	8290 byte(s)
Log Message:	Added UniformGradient to perturbation list.
#	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	gezelter	2047
123	gezelter	2034	} else {
124			if (!haveA) {
125			sprintf(painCave.errMsg,
126			"UniformGradient: uniformGradientDirection1 not specified.\n");
127			painCave.isFatal = 1;
128			simError();
129			}
130			if (!haveB) {
131			sprintf(painCave.errMsg,
132			"UniformGradient: uniformGradientDirection2 not specified.\n");
133			painCave.isFatal = 1;
134			simError();
135			}
136			if (!haveG) {
137			sprintf(painCave.errMsg,
138			"UniformGradient: uniformGradientStrength not specified.\n");
139			painCave.isFatal = 1;
140			simError();
141			}
142			}
143
144	gezelter	2026	int storageLayout_ = info_->getSnapshotManager()->getStorageLayout();
145			if (storageLayout_ & DataStorage::dslParticlePot) doParticlePot = true;
146			initialized = true;
147			}
148
149			void UniformGradient::applyPerturbation() {
150
151			if (!initialized) initialize();
152
153			SimInfo::MoleculeIterator i;
154			Molecule::AtomIterator j;
155			Molecule* mol;
156			Atom* atom;
157			AtomType* atype;
158			potVec longRangePotential(0.0);
159
160			RealType C;
161			Vector3d D;
162			Mat3x3d Q;
163
164			RealType U;
165			RealType fPot;
166			Vector3d t;
167			Vector3d f;
168
169			Vector3d r;
170			Vector3d EF;
171
172			bool isCharge;
173
174			if (doUniformGradient) {
175
176			U = 0.0;
177			fPot = 0.0;
178
179			for (mol = info_->beginMolecule(i); mol != NULL;
180			mol = info_->nextMolecule(i)) {
181
182			for (atom = mol->beginAtom(j); atom != NULL;
183			atom = mol->nextAtom(j)) {
184
185			isCharge = false;
186			C = 0.0;
187
188			atype = atom->getAtomType();
189
190			r = atom->getPos();
191			EF = Grad_ * r;
192
193			if (atype->isElectrostatic()) {
194			atom->addElectricField(EF * PhysicalConstants::chargeFieldConvert);
195			}
196
197			FixedChargeAdapter fca = FixedChargeAdapter(atype);
198			if ( fca.isFixedCharge() ) {
199			isCharge = true;
200			C = fca.getCharge();
201			}
202
203			FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype);
204			if ( fqa.isFluctuatingCharge() ) {
205			isCharge = true;
206			C += atom->getFlucQPos();
207			atom->addFlucQFrc( dot(r, EF)
208			* PhysicalConstants::chargeFieldConvert );
209			}
210
211			if (isCharge) {
212			f = EF * C * PhysicalConstants::chargeFieldConvert;
213			atom->addFrc(f);
214
215			U = -dot(r, f);
216			if (doParticlePot) {
217			atom->addParticlePot(U);
218			}
219			fPot += U;
220			}
221
222			MultipoleAdapter ma = MultipoleAdapter(atype);
223			if (ma.isDipole() ) {
224			D = atom->getDipole() * PhysicalConstants::dipoleFieldConvert;
225
226			f = D * Grad_;
227			atom->addFrc(f);
228
229			t = cross(D, EF);
230			atom->addTrq(t);
231
232			U = -dot(D, EF);
233			if (doParticlePot) {
234			atom->addParticlePot(U);
235			}
236			fPot += U;
237			}
238
239			if (ma.isQuadrupole() ) {
240			Q = atom->getQuadrupole() * PhysicalConstants::dipoleFieldConvert;
241
242			t = 2.0 * mCross(Q, Grad_);
243			atom->addTrq(t);
244
245			U = -doubleDot(Q, Grad_);
246			if (doParticlePot) {
247			atom->addParticlePot(U);
248			}
249			fPot += U;
250			}
251			}
252			}
253
254			#ifdef IS_MPI
255			MPI_Allreduce(MPI_IN_PLACE, &fPot, 1, MPI_REALTYPE,
256			MPI_SUM, MPI_COMM_WORLD);
257			#endif
258
259			Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
260			longRangePotential = snap->getLongRangePotentials();
261			longRangePotential[ELECTROSTATIC_FAMILY] += fPot;
262			snap->setLongRangePotential(longRangePotential);
263			}
264			}
265			}