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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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#include "perturbations/ElectricField.hpp" |
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#include "types/FixedChargeAdapter.hpp" |
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#include "types/FluctuatingChargeAdapter.hpp" |
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#include "types/MultipoleAdapter.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "nonbonded/NonBondedInteraction.hpp" |
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|
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namespace OpenMD { |
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|
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ElectricField::ElectricField(SimInfo* info) : info_(info), |
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doElectricField(false), |
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doParticlePot(false), |
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initialized(false) { |
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simParams = info_->getSimParams(); |
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} |
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|
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void ElectricField::initialize() { |
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if (simParams->haveElectricField()) { |
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doElectricField = true; |
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EF = simParams->getElectricField(); |
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} |
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int storageLayout_ = info_->getSnapshotManager()->getStorageLayout(); |
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if (storageLayout_ & DataStorage::dslParticlePot) doParticlePot = true; |
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initialized = true; |
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} |
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|
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void ElectricField::applyPerturbation() { |
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if (!initialized) initialize(); |
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|
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SimInfo::MoleculeIterator i; |
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Molecule::AtomIterator j; |
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Molecule* mol; |
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Atom* atom; |
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potVec longRangePotential(0.0); |
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Vector3d dip; |
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Vector3d trq; |
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Vector3d EFfrc; |
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Vector3d pos; |
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RealType chrg; |
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RealType pot, fieldPot, moment; |
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RealType chrgToKcal = 23.0609; |
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RealType debyeToKcal = 4.8018969509; |
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bool isCharge; |
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|
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if (doElectricField) { |
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fieldPot = 0.0; |
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|
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for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
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for (atom = mol->beginAtom(j); atom != NULL; |
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atom = mol->nextAtom(j)) { |
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isCharge = false; |
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chrg = 0.0; |
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|
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FixedChargeAdapter fca = FixedChargeAdapter(atom->getAtomType()); |
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if ( fca.isFixedCharge() ) { |
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isCharge = true; |
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chrg = fca.getCharge(); |
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} |
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|
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FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atom->getAtomType()); |
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if ( fqa.isFluctuatingCharge() ) { |
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isCharge = true; |
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chrg += atom->getFlucQPos(); |
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} |
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|
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if (isCharge) { |
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EFfrc = EF*chrg; |
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EFfrc *= chrgToKcal; |
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atom->addFrc(EFfrc); |
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// totally ad-hoc choice of the origin for potential calculation |
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pos = atom->getPos(); |
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pot = -dot(pos, EFfrc); |
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if (doParticlePot) { |
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atom->addParticlePot(pot); |
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} |
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fieldPot += pot; |
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} |
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|
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MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType()); |
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if (ma.isDipole() ) { |
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Vector3d u_i = atom->getElectroFrame().getColumn(2); |
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moment = ma.getDipoleMoment(); |
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moment *= debyeToKcal; |
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dip = u_i * moment; |
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trq = cross(dip, EF); |
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//cerr << "dip = " << dip << "\n"; |
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// cerr << "trq = " << trq << "\n"; |
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atom->addTrq(trq); |
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pot = -dot(dip, EF); |
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//cerr << "pot = " << pot << "\n"; |
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if (doParticlePot) { |
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atom->addParticlePot(pot); |
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} |
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fieldPot += pot; |
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} |
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} |
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} |
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#ifdef IS_MPI |
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MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &fieldPot, 1, MPI::REALTYPE, |
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MPI::SUM); |
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#endif |
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Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
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longRangePotential = snap->getLongRangePotentials(); |
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// << "longRangePotential = " << longRangePotential << "\n"; |
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longRangePotential[ELECTROSTATIC_FAMILY] += fieldPot; |
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//cerr << "longRangePotential[ELECTROSTATIC_FAMILY] = " << longRangePotential[ELECTROSTATIC_FAMILY] << "\n"; |
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snap->setLongRangePotential(longRangePotential); |
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} |
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} |
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|
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} |
