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/UniformField.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 {
  
  UniformField::UniformField(SimInfo* info) : info_(info), 
                                            doUniformField(false), 
                                            doParticlePot(false),
                                            initialized(false) {
    simParams = info_->getSimParams();
  }
  
  void UniformField::initialize() {

    std::vector<RealType> ef;

    if (simParams->haveElectricField()) {
      doUniformField = true;
      ef = simParams->getElectricField();            
    }   
    if (simParams->haveUniformField()) {
      doUniformField = true;
      ef = simParams->getUniformField();
    }   
    if (ef.size() != 3) {
      sprintf(painCave.errMsg,
              "UniformField: Incorrect number of parameters specified.\n"
              "\tthere should be 3 parameters, but %lu were specified.\n", ef.size());
      painCave.isFatal = 1;
      simError();      
    }
    EF.x() = ef[0];
    EF.y() = ef[1];
    EF.z() = ef[2];

    int storageLayout_ = info_->getSnapshotManager()->getStorageLayout();
    if (storageLayout_ & DataStorage::dslParticlePot) doParticlePot = true;
    initialized = true;
  }
  
  void UniformField::applyPerturbation() {

    if (!initialized) initialize();

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

    RealType C;
    Vector3d D;
    RealType U;
    RealType fPot;
    Vector3d t;
    Vector3d f;
    Vector3d r;

    bool isCharge;

    if (doUniformField) {

      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();

          // ad-hoc choice of the origin for potential calculation and
          // fluctuating charge force:

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

            U = -dot(D, EF);

            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 (11 years ago) by gezelter
File size:	6047 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	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	gezelter	2020
43			#include "perturbations/UniformField.hpp"
44	jmarr	1780	#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	gezelter	2020	#include "utils/PhysicalConstants.hpp"
50	jmarr	1780
51			namespace OpenMD {
52	gezelter	2020
53			UniformField::UniformField(SimInfo* info) : info_(info),
54			doUniformField(false),
55			doParticlePot(false),
56			initialized(false) {
57	jmarr	1780	simParams = info_->getSimParams();
58			}
59	gezelter	2020
60			void UniformField::initialize() {
61	gezelter	2026
62			std::vector<RealType> ef;
63
64	jmarr	1780	if (simParams->haveElectricField()) {
65	gezelter	2020	doUniformField = true;
66	gezelter	2026	ef = simParams->getElectricField();
67	jmarr	1780	}
68	gezelter	2020	if (simParams->haveUniformField()) {
69			doUniformField = true;
70	gezelter	2026	ef = simParams->getUniformField();
71	gezelter	2020	}
72	gezelter	2026	if (ef.size() != 3) {
73			sprintf(painCave.errMsg,
74			"UniformField: Incorrect number of parameters specified.\n"
75			"\tthere should be 3 parameters, but %lu were specified.\n", ef.size());
76			painCave.isFatal = 1;
77			simError();
78			}
79			EF.x() = ef[0];
80			EF.y() = ef[1];
81			EF.z() = ef[2];
82
83	jmarr	1780	int storageLayout_ = info_->getSnapshotManager()->getStorageLayout();
84			if (storageLayout_ & DataStorage::dslParticlePot) doParticlePot = true;
85			initialized = true;
86			}
87	gezelter	2020
88			void UniformField::applyPerturbation() {
89	jmarr	1780
90			if (!initialized) initialize();
91
92			SimInfo::MoleculeIterator i;
93			Molecule::AtomIterator j;
94			Molecule* mol;
95			Atom* atom;
96	gezelter	2020	AtomType* atype;
97	jmarr	1780	potVec longRangePotential(0.0);
98
99	gezelter	2020	RealType C;
100			Vector3d D;
101			RealType U;
102			RealType fPot;
103			Vector3d t;
104			Vector3d f;
105			Vector3d r;
106	jmarr	1780
107	gezelter	2020	bool isCharge;
108
109			if (doUniformField) {
110
111			U = 0.0;
112			fPot = 0.0;
113
114	gezelter	1879	for (mol = info_->beginMolecule(i); mol != NULL;
115			mol = info_->nextMolecule(i)) {
116
117	jmarr	1780	for (atom = mol->beginAtom(j); atom != NULL;
118			atom = mol->nextAtom(j)) {
119
120	gezelter	2020	isCharge = false;
121			C = 0.0;
122	gezelter	1879
123	gezelter	2020	atype = atom->getAtomType();
124	gezelter	1908
125			// ad-hoc choice of the origin for potential calculation and
126			// fluctuating charge force:
127	gezelter	2020
128			r = atom->getPos();
129	gezelter	1879
130			if (atype->isElectrostatic()) {
131	gezelter	2020	atom->addElectricField(EF * PhysicalConstants::chargeFieldConvert);
132	gezelter	1879	}
133
134			FixedChargeAdapter fca = FixedChargeAdapter(atype);
135	jmarr	1780	if ( fca.isFixedCharge() ) {
136			isCharge = true;
137	gezelter	2020	C = fca.getCharge();
138	jmarr	1780	}
139
140	gezelter	1879	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype);
141	jmarr	1780	if ( fqa.isFluctuatingCharge() ) {
142			isCharge = true;
143	gezelter	2020	C += atom->getFlucQPos();
144			atom->addFlucQFrc( dot(r, EF)
145			* PhysicalConstants::chargeFieldConvert );
146	jmarr	1780	}
147
148			if (isCharge) {
149	gezelter	2020	f = EF * C * PhysicalConstants::chargeFieldConvert;
150			atom->addFrc(f);
151			U = -dot(r, f);
152
153	jmarr	1780	if (doParticlePot) {
154	gezelter	2020	atom->addParticlePot(U);
155	jmarr	1780	}
156	gezelter	2020	fPot += U;
157	jmarr	1780	}
158
159	gezelter	2020	MultipoleAdapter ma = MultipoleAdapter(atype);
160	jmarr	1780	if (ma.isDipole() ) {
161	gezelter	1879
162	gezelter	2020	D = atom->getDipole() * PhysicalConstants::dipoleFieldConvert;
163
164			t = cross(D, EF);
165			atom->addTrq(t);
166	gezelter	1879
167	gezelter	2020	U = -dot(D, EF);
168
169	jmarr	1780	if (doParticlePot) {
170	gezelter	2020	atom->addParticlePot(U);
171	jmarr	1780	}
172	gezelter	2020	fPot += U;
173	jmarr	1780	}
174			}
175			}
176	gezelter	2020
177	jmarr	1780	#ifdef IS_MPI
178	gezelter	2020	MPI_Allreduce(MPI_IN_PLACE, &fPot, 1, MPI_REALTYPE,
179	gezelter	1987	MPI_SUM, MPI_COMM_WORLD);
180	jmarr	1780	#endif
181	gezelter	2020
182	jmarr	1780	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
183			longRangePotential = snap->getLongRangePotentials();
184	gezelter	2020	longRangePotential[ELECTROSTATIC_FAMILY] += fPot;
185	jmarr	1780	snap->setLongRangePotential(longRangePotential);
186			}
187			}
188			}