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) : initialized(false),
                                                    doUniformGradient(false), 
                                                    doParticlePot(false),
                                                    info_(info) {
    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:	2071
Committed:	Sat Mar 7 21:41:51 2015 UTC (10 years, 1 month ago) by gezelter
File size:	8187 byte(s)
Log Message:	Reducing the number of warnings when using g++ to compile.
#	Content
1	/*
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) : initialized(false),
54	doUniformGradient(false),
55	doParticlePot(false),
56	info_(info) {
57	simParams = info_->getSimParams();
58	}
59
60	void UniformGradient::initialize() {
61
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	sprintf(painCave.errMsg,
70	"uniformGradientDirection1: Incorrect number of parameters\n"
71	"\tspecified. There should be 3 parameters, but %lu were\n"
72	"\tspecified.\n", d1.size());
73	painCave.isFatal = 1;
74	simError();
75	}
76	a_.x() = d1[0];
77	a_.y() = d1[1];
78	a_.z() = d1[2];
79
80	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	Grad_(1,0) = Grad_(0,1);
115	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	Grad_(2,0) = Grad_(0,2);
118	Grad_(2,1) = Grad_(1,2);
119	Grad_(2,2) = 2.0 * (a_.z()*b_.z() - cpsi_ / 3.0);
120
121	Grad_ *= g_ / 2.0;
122
123	} 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	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	}