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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, 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 "nonbonded/InteractionManager.hpp" |
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|
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namespace OpenMD { |
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|
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InteractionManager::InteractionManager() { |
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|
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initialized_ = false; |
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|
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lj_ = new LJ(); |
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gb_ = new GB(); |
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sticky_ = new Sticky(); |
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morse_ = new Morse(); |
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repulsivePower_ = new RepulsivePower(); |
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eam_ = new EAM(); |
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sc_ = new SC(); |
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electrostatic_ = new Electrostatic(); |
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maw_ = new MAW(); |
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} |
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|
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InteractionManager::~InteractionManager() { |
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delete lj_; |
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delete gb_; |
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delete sticky_; |
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delete morse_; |
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delete repulsivePower_; |
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delete eam_; |
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delete sc_; |
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delete electrostatic_; |
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delete maw_; |
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} |
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|
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void InteractionManager::initialize() { |
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|
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if (initialized_) return; |
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|
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ForceField* forceField_ = info_->getForceField(); |
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|
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lj_->setForceField(forceField_); |
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gb_->setForceField(forceField_); |
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sticky_->setForceField(forceField_); |
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eam_->setForceField(forceField_); |
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sc_->setForceField(forceField_); |
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morse_->setForceField(forceField_); |
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electrostatic_->setSimInfo(info_); |
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electrostatic_->setForceField(forceField_); |
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maw_->setForceField(forceField_); |
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repulsivePower_->setForceField(forceField_); |
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|
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ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes(); |
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int nTypes = atomTypes->size(); |
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sHash_.resize(nTypes); |
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iHash_.resize(nTypes); |
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interactions_.resize(nTypes); |
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ForceField::AtomTypeContainer::MapTypeIterator i1, i2; |
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AtomType* atype1; |
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AtomType* atype2; |
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int atid1, atid2; |
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|
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// We only need to worry about the types that are actually in the simulation: |
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|
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set<AtomType*> atypes = info_->getSimulatedAtomTypes(); |
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|
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lj_->setSimulatedAtomTypes(atypes); |
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gb_->setSimulatedAtomTypes(atypes); |
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sticky_->setSimulatedAtomTypes(atypes); |
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eam_->setSimulatedAtomTypes(atypes); |
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sc_->setSimulatedAtomTypes(atypes); |
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morse_->setSimulatedAtomTypes(atypes); |
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electrostatic_->setSimInfo(info_); |
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electrostatic_->setSimulatedAtomTypes(atypes); |
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maw_->setSimulatedAtomTypes(atypes); |
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repulsivePower_->setSimulatedAtomTypes(atypes); |
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|
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set<AtomType*>::iterator at; |
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|
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for (at = atypes.begin(); at != atypes.end(); ++at) { |
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|
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//for (atype1 = atomTypes->beginType(i1); atype1 != NULL; |
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// atype1 = atomTypes->nextType(i1)) { |
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|
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atype1 = *at; |
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atid1 = atype1->getIdent(); |
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iHash_[atid1].resize(nTypes); |
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interactions_[atid1].resize(nTypes); |
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|
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// add it to the map: |
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pair<map<int,AtomType*>::iterator,bool> ret; |
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ret = typeMap_.insert( pair<int, AtomType*>(atid1, atype1) ); |
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if (ret.second == false) { |
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sprintf( painCave.errMsg, |
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"InteractionManager already had a previous entry with ident %d\n", |
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atype1->getIdent()); |
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painCave.severity = OPENMD_INFO; |
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painCave.isFatal = 0; |
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simError(); |
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} |
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} |
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|
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if (atype1->isLennardJones()) { |
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sHash_[atid1] |= LJ_INTERACTION; |
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} |
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if (atype1->isElectrostatic()) { |
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sHash_[atid1] |= ELECTROSTATIC_INTERACTION; |
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} |
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if (atype1->isSticky()) { |
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sHash_[atid1] |= STICKY_INTERACTION; |
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} |
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if (atype1->isStickyPower()) { |
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sHash_[atid1] |= STICKY_INTERACTION; |
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} |
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if (atype1->isEAM()) { |
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sHash_[atid1] |= EAM_INTERACTION; |
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} |
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if (atype1->isSC()) { |
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sHash_[atid1] |= SC_INTERACTION; |
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} |
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if (atype1->isGayBerne()) { |
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sHash_[atid1] |= GB_INTERACTION; |
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} |
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|
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// Now, iterate over all known types and add to the interaction map: |
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|
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map<int, AtomType*>::iterator it1, it2; |
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for (it1 = typeMap_.begin(); it1 != typeMap_.end(); ++it1) { |
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atype1 = (*it1).second; |
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atid1 = atype1->getIdent(); |
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|
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for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) { |
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atype2 = (*it2).second; |
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atid2 = atype2->getIdent(); |
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|
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iHash_[atid1][atid2] = 0; |
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|
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if (atype1->isLennardJones() && atype2->isLennardJones()) { |
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interactions_[atid1][atid2].insert(lj_); |
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iHash_[atid1][atid2] |= LJ_INTERACTION; |
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} |
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if (atype1->isElectrostatic() && atype2->isElectrostatic() ) { |
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interactions_[atid1][atid2].insert(electrostatic_); |
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iHash_[atid1][atid2] |= ELECTROSTATIC_INTERACTION; |
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} |
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if (atype1->isSticky() && atype2->isSticky() ) { |
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interactions_[atid1][atid2].insert(sticky_); |
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iHash_[atid1][atid2] |= STICKY_INTERACTION; |
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} |
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if (atype1->isStickyPower() && atype2->isStickyPower() ) { |
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interactions_[atid1][atid2].insert(sticky_); |
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iHash_[atid1][atid2] |= STICKY_INTERACTION; |
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} |
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if (atype1->isEAM() && atype2->isEAM() ) { |
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interactions_[atid1][atid2].insert(eam_); |
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iHash_[atid1][atid2] |= EAM_INTERACTION; |
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} |
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if (atype1->isSC() && atype2->isSC() ) { |
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interactions_[atid1][atid2].insert(sc_); |
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iHash_[atid1][atid2] |= SC_INTERACTION; |
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} |
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if (atype1->isGayBerne() && atype2->isGayBerne() ) { |
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interactions_[atid1][atid2].insert(gb_); |
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iHash_[atid1][atid2] |= GB_INTERACTION; |
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} |
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if ((atype1->isGayBerne() && atype2->isLennardJones()) |
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|| (atype1->isLennardJones() && atype2->isGayBerne())) { |
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interactions_[atid1][atid2].insert(gb_); |
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iHash_[atid1][atid2] |= GB_INTERACTION; |
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} |
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|
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// look for an explicitly-set non-bonded interaction type using the |
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// two atom types. |
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NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName()); |
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|
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if (nbiType != NULL) { |
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|
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bool vdwExplicit = false; |
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bool metExplicit = false; |
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// bool hbExplicit = false; |
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|
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if (nbiType->isLennardJones()) { |
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// We found an explicit Lennard-Jones interaction. |
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// override all other vdw entries for this pair of atom types: |
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set<NonBondedInteraction*>::iterator it; |
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for (it = interactions_[atid1][atid2].begin(); |
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it != interactions_[atid1][atid2].end(); ++it) { |
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InteractionFamily ifam = (*it)->getFamily(); |
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if (ifam == VANDERWAALS_FAMILY) { |
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interactions_[atid1][atid2].erase(*it); |
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iHash_[atid1][atid2] ^= (*it)->getHash(); |
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} |
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} |
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interactions_[atid1][atid2].insert(lj_); |
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iHash_[atid1][atid2] |= LJ_INTERACTION; |
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vdwExplicit = true; |
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} |
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|
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if (nbiType->isMorse()) { |
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if (vdwExplicit) { |
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sprintf( painCave.errMsg, |
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"InteractionManager::initialize found more than one " |
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"explicit \n" |
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"\tvan der Waals interaction for atom types %s - %s\n", |
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atype1->getName().c_str(), atype2->getName().c_str()); |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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// We found an explicit Morse interaction. |
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// override all other vdw entries for this pair of atom types: |
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set<NonBondedInteraction*>::iterator it; |
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for (it = interactions_[atid1][atid2].begin(); |
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it != interactions_[atid1][atid2].end(); ++it) { |
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InteractionFamily ifam = (*it)->getFamily(); |
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if (ifam == VANDERWAALS_FAMILY) { |
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interactions_[atid1][atid2].erase(*it); |
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iHash_[atid1][atid2] ^= (*it)->getHash(); |
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} |
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} |
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interactions_[atid1][atid2].insert(morse_); |
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iHash_[atid1][atid2] |= MORSE_INTERACTION; |
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vdwExplicit = true; |
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} |
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|
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if (nbiType->isRepulsivePower()) { |
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if (vdwExplicit) { |
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sprintf( painCave.errMsg, |
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"InteractionManager::initialize found more than one " |
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"explicit \n" |
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"\tvan der Waals interaction for atom types %s - %s\n", |
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atype1->getName().c_str(), atype2->getName().c_str()); |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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// We found an explicit RepulsivePower interaction. |
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// override all other vdw entries for this pair of atom types: |
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set<NonBondedInteraction*>::iterator it; |
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for (it = interactions_[atid1][atid2].begin(); |
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it != interactions_[atid1][atid2].end(); ++it) { |
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InteractionFamily ifam = (*it)->getFamily(); |
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if (ifam == VANDERWAALS_FAMILY) { |
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interactions_[atid1][atid2].erase(*it); |
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iHash_[atid1][atid2] ^= (*it)->getHash(); |
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} |
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} |
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interactions_[atid1][atid2].insert(repulsivePower_); |
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iHash_[atid1][atid2] |= REPULSIVEPOWER_INTERACTION; |
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vdwExplicit = true; |
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} |
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|
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|
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if (nbiType->isEAM()) { |
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// We found an explicit EAM interaction. |
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// override all other metallic entries for this pair of atom types: |
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set<NonBondedInteraction*>::iterator it; |
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for (it = interactions_[atid1][atid2].begin(); |
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it != interactions_[atid1][atid2].end(); ++it) { |
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InteractionFamily ifam = (*it)->getFamily(); |
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if (ifam == METALLIC_FAMILY) { |
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interactions_[atid1][atid2].erase(*it); |
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iHash_[atid1][atid2] ^= (*it)->getHash(); |
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} |
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} |
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interactions_[atid1][atid2].insert(eam_); |
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iHash_[atid1][atid2] |= EAM_INTERACTION; |
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metExplicit = true; |
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} |
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|
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if (nbiType->isSC()) { |
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if (metExplicit) { |
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sprintf( painCave.errMsg, |
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"InteractionManager::initialize found more than one " |
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"explicit\n" |
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"\tmetallic interaction for atom types %s - %s\n", |
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atype1->getName().c_str(), atype2->getName().c_str()); |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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// We found an explicit Sutton-Chen interaction. |
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// override all other metallic entries for this pair of atom types: |
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set<NonBondedInteraction*>::iterator it; |
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for (it = interactions_[atid1][atid2].begin(); |
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it != interactions_[atid1][atid2].end(); ++it) { |
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InteractionFamily ifam = (*it)->getFamily(); |
| 326 |
if (ifam == METALLIC_FAMILY) { |
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interactions_[atid1][atid2].erase(*it); |
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iHash_[atid1][atid2] ^= (*it)->getHash(); |
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} |
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} |
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interactions_[atid1][atid2].insert(sc_); |
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iHash_[atid1][atid2] |= SC_INTERACTION; |
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metExplicit = true; |
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} |
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|
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if (nbiType->isMAW()) { |
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if (vdwExplicit) { |
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sprintf( painCave.errMsg, |
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"InteractionManager::initialize found more than one " |
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"explicit\n" |
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"\tvan der Waals interaction for atom types %s - %s\n", |
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atype1->getName().c_str(), atype2->getName().c_str()); |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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// We found an explicit MAW interaction. |
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// override all other vdw entries for this pair of atom types: |
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set<NonBondedInteraction*>::iterator it; |
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for (it = interactions_[atid1][atid2].begin(); |
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it != interactions_[atid1][atid2].end(); ++it) { |
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InteractionFamily ifam = (*it)->getFamily(); |
| 353 |
if (ifam == VANDERWAALS_FAMILY) { |
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interactions_[atid1][atid2].erase(*it); |
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iHash_[atid1][atid2] ^= (*it)->getHash(); |
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} |
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} |
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interactions_[atid1][atid2].insert(maw_); |
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iHash_[atid1][atid2] |= MAW_INTERACTION; |
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vdwExplicit = true; |
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} |
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} |
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} |
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} |
| 365 |
|
| 366 |
|
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// Make sure every pair of atom types in this simulation has a |
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// non-bonded interaction. If not, just inform the user. |
| 369 |
|
| 370 |
set<AtomType*> simTypes = info_->getSimulatedAtomTypes(); |
| 371 |
set<AtomType*>::iterator it, jt; |
| 372 |
|
| 373 |
for (it = simTypes.begin(); it != simTypes.end(); ++it) { |
| 374 |
atype1 = (*it); |
| 375 |
atid1 = atype1->getIdent(); |
| 376 |
for (jt = it; jt != simTypes.end(); ++jt) { |
| 377 |
atype2 = (*jt); |
| 378 |
atid1 = atype1->getIdent(); |
| 379 |
|
| 380 |
if (interactions_[atid1][atid2].size() == 0) { |
| 381 |
sprintf( painCave.errMsg, |
| 382 |
"InteractionManager could not find a matching non-bonded\n" |
| 383 |
"\tinteraction for atom types %s - %s\n" |
| 384 |
"\tProceeding without this interaction.\n", |
| 385 |
atype1->getName().c_str(), atype2->getName().c_str()); |
| 386 |
painCave.severity = OPENMD_INFO; |
| 387 |
painCave.isFatal = 0; |
| 388 |
simError(); |
| 389 |
} |
| 390 |
} |
| 391 |
} |
| 392 |
|
| 393 |
initialized_ = true; |
| 394 |
} |
| 395 |
|
| 396 |
void InteractionManager::setCutoffRadius(RealType rcut) { |
| 397 |
|
| 398 |
electrostatic_->setCutoffRadius(rcut); |
| 399 |
eam_->setCutoffRadius(rcut); |
| 400 |
} |
| 401 |
|
| 402 |
void InteractionManager::doPrePair(InteractionData &idat){ |
| 403 |
|
| 404 |
if (!initialized_) initialize(); |
| 405 |
|
| 406 |
// excluded interaction, so just return |
| 407 |
if (idat.excluded) return; |
| 408 |
|
| 409 |
int& iHash = iHash_[idat.atid1][idat.atid2]; |
| 410 |
|
| 411 |
if ((iHash & EAM_INTERACTION) != 0) eam_->calcDensity(idat); |
| 412 |
if ((iHash & SC_INTERACTION) != 0) sc_->calcDensity(idat); |
| 413 |
|
| 414 |
// set<NonBondedInteraction*>::iterator it; |
| 415 |
|
| 416 |
// for (it = interactions_[ idat.atypes ].begin(); |
| 417 |
// it != interactions_[ idat.atypes ].end(); ++it){ |
| 418 |
// if ((*it)->getFamily() == METALLIC_FAMILY) { |
| 419 |
// dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat); |
| 420 |
// } |
| 421 |
// } |
| 422 |
|
| 423 |
return; |
| 424 |
} |
| 425 |
|
| 426 |
void InteractionManager::doPreForce(SelfData &sdat){ |
| 427 |
|
| 428 |
if (!initialized_) initialize(); |
| 429 |
|
| 430 |
int& sHash = sHash_[sdat.atid]; |
| 431 |
|
| 432 |
if ((sHash & EAM_INTERACTION) != 0) eam_->calcFunctional(sdat); |
| 433 |
if ((sHash & SC_INTERACTION) != 0) sc_->calcFunctional(sdat); |
| 434 |
|
| 435 |
// set<NonBondedInteraction*>::iterator it; |
| 436 |
|
| 437 |
// for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){ |
| 438 |
// if ((*it)->getFamily() == METALLIC_FAMILY) { |
| 439 |
// dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat); |
| 440 |
// } |
| 441 |
// } |
| 442 |
|
| 443 |
return; |
| 444 |
} |
| 445 |
|
| 446 |
void InteractionManager::doPair(InteractionData &idat){ |
| 447 |
|
| 448 |
if (!initialized_) initialize(); |
| 449 |
|
| 450 |
int& iHash = iHash_[idat.atid1][idat.atid2]; |
| 451 |
|
| 452 |
if ((iHash & ELECTROSTATIC_INTERACTION) != 0) electrostatic_->calcForce(idat); |
| 453 |
|
| 454 |
// electrostatics still has to worry about indirect |
| 455 |
// contributions from excluded pairs of atoms, but nothing else does: |
| 456 |
|
| 457 |
if (idat.excluded) return; |
| 458 |
|
| 459 |
if ((iHash & LJ_INTERACTION) != 0) lj_->calcForce(idat); |
| 460 |
if ((iHash & GB_INTERACTION) != 0) gb_->calcForce(idat); |
| 461 |
if ((iHash & STICKY_INTERACTION) != 0) sticky_->calcForce(idat); |
| 462 |
if ((iHash & MORSE_INTERACTION) != 0) morse_->calcForce(idat); |
| 463 |
if ((iHash & REPULSIVEPOWER_INTERACTION) != 0) repulsivePower_->calcForce(idat); |
| 464 |
if ((iHash & EAM_INTERACTION) != 0) eam_->calcForce(idat); |
| 465 |
if ((iHash & SC_INTERACTION) != 0) sc_->calcForce(idat); |
| 466 |
if ((iHash & MAW_INTERACTION) != 0) maw_->calcForce(idat); |
| 467 |
|
| 468 |
// set<NonBondedInteraction*>::iterator it; |
| 469 |
|
| 470 |
// for (it = interactions_[ idat.atypes ].begin(); |
| 471 |
// it != interactions_[ idat.atypes ].end(); ++it) { |
| 472 |
|
| 473 |
// // electrostatics still has to worry about indirect |
| 474 |
// // contributions from excluded pairs of atoms: |
| 475 |
|
| 476 |
// if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) { |
| 477 |
// (*it)->calcForce(idat); |
| 478 |
// } |
| 479 |
// } |
| 480 |
|
| 481 |
return; |
| 482 |
} |
| 483 |
|
| 484 |
void InteractionManager::doSelfCorrection(SelfData &sdat){ |
| 485 |
|
| 486 |
if (!initialized_) initialize(); |
| 487 |
|
| 488 |
int& sHash = sHash_[sdat.atid]; |
| 489 |
|
| 490 |
if ((sHash & ELECTROSTATIC_INTERACTION) != 0) electrostatic_->calcSelfCorrection(sdat); |
| 491 |
|
| 492 |
// set<NonBondedInteraction*>::iterator it; |
| 493 |
|
| 494 |
// for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){ |
| 495 |
// if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) { |
| 496 |
// dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat); |
| 497 |
// } |
| 498 |
// } |
| 499 |
|
| 500 |
return; |
| 501 |
} |
| 502 |
|
| 503 |
void InteractionManager::doReciprocalSpaceSum(RealType &pot){ |
| 504 |
if (!initialized_) initialize(); |
| 505 |
electrostatic_->ReciprocalSpaceSum(pot); |
| 506 |
} |
| 507 |
|
| 508 |
RealType InteractionManager::getSuggestedCutoffRadius(int *atid) { |
| 509 |
if (!initialized_) initialize(); |
| 510 |
|
| 511 |
AtomType* atype = typeMap_[*atid]; |
| 512 |
|
| 513 |
set<NonBondedInteraction*>::iterator it; |
| 514 |
RealType cutoff = 0.0; |
| 515 |
|
| 516 |
for (it = interactions_[*atid][*atid].begin(); |
| 517 |
it != interactions_[*atid][*atid].end(); |
| 518 |
++it) |
| 519 |
cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype))); |
| 520 |
return cutoff; |
| 521 |
} |
| 522 |
|
| 523 |
RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) { |
| 524 |
if (!initialized_) initialize(); |
| 525 |
|
| 526 |
int atid = atype->getIdent(); |
| 527 |
|
| 528 |
set<NonBondedInteraction*>::iterator it; |
| 529 |
RealType cutoff = 0.0; |
| 530 |
|
| 531 |
for (it = interactions_[atid][atid].begin(); |
| 532 |
it != interactions_[atid][atid].end(); ++it) |
| 533 |
cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype))); |
| 534 |
return cutoff; |
| 535 |
} |
| 536 |
} //end namespace OpenMD |
