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/* |
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* Copyright (c) 2014 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, 234107 (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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|
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#include "perturbations/UniformGradient.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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#include "utils/PhysicalConstants.hpp" |
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|
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namespace OpenMD { |
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|
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UniformGradient::UniformGradient(SimInfo* info) : info_(info), |
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doUniformGradient(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 UniformGradient::initialize() { |
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|
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bool haveA = false; |
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bool haveB = false; |
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bool haveG = false; |
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|
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if (simParams->haveUniformGradientDirection1()) { |
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std::vector<RealType> d1 = simParams->getUniformGradientDirection1(); |
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if (d1.size() != 3) { |
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sprintf(painCave.errMsg, |
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"uniformGradientDirection1: Incorrect number of parameters\n" |
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"\tspecified. There should be 3 parameters, but %lu were\n" |
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"\tspecified.\n", d1.size()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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a_.x() = d1[0]; |
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a_.y() = d1[1]; |
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a_.z() = d1[2]; |
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|
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a_.normalize(); |
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haveA = true; |
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} |
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|
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if (simParams->haveUniformGradientDirection2()) { |
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std::vector<RealType> d2 = simParams->getUniformGradientDirection2(); |
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if (d2.size() != 3) { |
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sprintf(painCave.errMsg, |
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"uniformGradientDirection2: Incorrect number of parameters\n" |
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"\tspecified. There should be 3 parameters, but %lu were\n" |
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"\tspecified.\n", d2.size()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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b_.x() = d2[0]; |
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b_.y() = d2[1]; |
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b_.z() = d2[2]; |
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|
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b_.normalize(); |
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haveB = true; |
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} |
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|
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if (simParams->haveUniformGradientStrength()) { |
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g_ = simParams->getUniformGradientStrength(); |
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haveG = true; |
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} |
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|
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if (haveA && haveB && haveG) { |
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doUniformGradient = true; |
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cpsi_ = dot(a_, b_); |
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|
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Grad_(0,0) = 2.0 * (a_.x()*b_.x() - cpsi_ / 3.0); |
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Grad_(0,1) = a_.x()*b_.y() + a_.y()*b_.x(); |
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Grad_(0,2) = a_.x()*b_.z() + a_.z()*b_.x(); |
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Grad_(1,0) = Grad_(0,1); |
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Grad_(1,1) = 2.0 * (a_.y()*b_.y() - cpsi_ / 3.0); |
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Grad_(1,2) = a_.y()*b_.z() + a_.z()*b_.y(); |
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Grad_(2,0) = Grad_(0,2); |
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Grad_(2,1) = Grad_(1,2); |
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Grad_(2,2) = 2.0 * (a_.z()*b_.z() - cpsi_ / 3.0); |
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|
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Grad_ *= g_ / 2.0; |
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} else { |
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if (!haveA) { |
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sprintf(painCave.errMsg, |
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"UniformGradient: uniformGradientDirection1 not specified.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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if (!haveB) { |
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sprintf(painCave.errMsg, |
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"UniformGradient: uniformGradientDirection2 not specified.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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if (!haveG) { |
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sprintf(painCave.errMsg, |
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"UniformGradient: uniformGradientStrength not specified.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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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 UniformGradient::applyPerturbation() { |
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|
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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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AtomType* atype; |
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potVec longRangePotential(0.0); |
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|
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RealType C; |
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Vector3d D; |
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Mat3x3d Q; |
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|
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RealType U; |
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RealType fPot; |
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Vector3d t; |
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Vector3d f; |
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|
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Vector3d r; |
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Vector3d EF; |
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|
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bool isCharge; |
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|
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if (doUniformGradient) { |
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|
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U = 0.0; |
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fPot = 0.0; |
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|
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for (mol = info_->beginMolecule(i); mol != NULL; |
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mol = info_->nextMolecule(i)) { |
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|
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for (atom = mol->beginAtom(j); atom != NULL; |
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atom = mol->nextAtom(j)) { |
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|
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isCharge = false; |
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C = 0.0; |
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|
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atype = atom->getAtomType(); |
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|
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r = atom->getPos(); |
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EF = Grad_ * r; |
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|
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if (atype->isElectrostatic()) { |
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atom->addElectricField(EF * PhysicalConstants::chargeFieldConvert); |
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} |
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|
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FixedChargeAdapter fca = FixedChargeAdapter(atype); |
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if ( fca.isFixedCharge() ) { |
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isCharge = true; |
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C = fca.getCharge(); |
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} |
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|
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FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype); |
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if ( fqa.isFluctuatingCharge() ) { |
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isCharge = true; |
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C += atom->getFlucQPos(); |
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atom->addFlucQFrc( dot(r, EF) |
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* PhysicalConstants::chargeFieldConvert ); |
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} |
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|
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if (isCharge) { |
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f = EF * C * PhysicalConstants::chargeFieldConvert; |
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atom->addFrc(f); |
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|
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U = -dot(r, f); |
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if (doParticlePot) { |
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atom->addParticlePot(U); |
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} |
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fPot += U; |
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} |
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|
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MultipoleAdapter ma = MultipoleAdapter(atype); |
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if (ma.isDipole() ) { |
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D = atom->getDipole() * PhysicalConstants::dipoleFieldConvert; |
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|
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f = D * Grad_; |
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atom->addFrc(f); |
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|
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t = cross(D, EF); |
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atom->addTrq(t); |
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|
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U = -dot(D, EF); |
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if (doParticlePot) { |
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atom->addParticlePot(U); |
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} |
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fPot += U; |
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} |
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|
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if (ma.isQuadrupole() ) { |
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Q = atom->getQuadrupole() * PhysicalConstants::dipoleFieldConvert; |
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|
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t = 2.0 * mCross(Q, Grad_); |
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atom->addTrq(t); |
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|
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U = -doubleDot(Q, Grad_); |
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if (doParticlePot) { |
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atom->addParticlePot(U); |
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} |
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fPot += U; |
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} |
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} |
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} |
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|
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#ifdef IS_MPI |
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MPI_Allreduce(MPI_IN_PLACE, &fPot, 1, MPI_REALTYPE, |
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MPI_SUM, MPI_COMM_WORLD); |
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#endif |
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|
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Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
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longRangePotential = snap->getLongRangePotentials(); |
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longRangePotential[ELECTROSTATIC_FAMILY] += fPot; |
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snap->setLongRangePotential(longRangePotential); |
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} |
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} |
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} |
