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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] Vardeman & Gezelter, in progress (2009). |
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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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bool InteractionManager::initialized_ = false; |
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ForceField* InteractionManager::forceField_ = NULL; |
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InteractionManager* InteractionManager::_instance = NULL; |
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map<int, AtomType*> InteractionManager::typeMap_; |
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map<pair<AtomType*, AtomType*>, set<NonBondedInteraction*> > InteractionManager::interactions_; |
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|
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InteractionManager* InteractionManager::Instance() { |
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if (!_instance) { |
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_instance = new InteractionManager(); |
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} |
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return _instance; |
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} |
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|
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void InteractionManager::initialize() { |
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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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eam_ = new EAM(); |
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sc_ = new SC(); |
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morse_ = new Morse(); |
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electrostatic_ = new Electrostatic(); |
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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_->setForceField(forceField_); |
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|
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ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes(); |
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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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pair<AtomType*, AtomType*> key; |
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pair<set<NonBondedInteraction*>::iterator, bool> ret; |
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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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// add it to the map: |
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AtomTypeProperties atp = atype1->getATP(); |
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|
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pair<map<int,AtomType*>::iterator,bool> ret; |
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ret = typeMap_.insert( pair<int, AtomType*>(atp.ident, 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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atp.ident); |
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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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// 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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|
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for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) { |
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atype2 = (*it2).second; |
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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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key = make_pair(atype1, atype2); |
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|
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if (atype1->isLennardJones() && atype2->isLennardJones()) { |
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interactions_[key].insert(lj_); |
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} |
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if (atype1->isElectrostatic() && atype2->isElectrostatic() ) { |
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interactions_[key].insert(electrostatic_); |
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} |
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if (atype1->isSticky() && atype2->isSticky() ) { |
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interactions_[key].insert(sticky_); |
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} |
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if (atype1->isStickyPower() && atype2->isStickyPower() ) { |
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interactions_[key].insert(sticky_); |
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} |
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if (atype1->isEAM() && atype2->isEAM() ) { |
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interactions_[key].insert(eam_); |
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} |
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if (atype1->isSC() && atype2->isSC() ) { |
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interactions_[key].insert(sc_); |
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} |
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if (atype1->isGayBerne() && atype2->isGayBerne() ) { |
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interactions_[key].insert(gb_); |
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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_[key].insert(gb_); |
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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->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_[key].begin(); it != interactions_[key].end(); ++it) { |
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InteractionFamily ifam = (*it)->getFamily(); |
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if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it); |
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} |
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interactions_[key].insert(lj_); |
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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 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_[key].begin(); it != interactions_[key].end(); ++it) { |
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InteractionFamily ifam = (*it)->getFamily(); |
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if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it); |
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} |
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interactions_[key].insert(morse_); |
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vdwExplicit = true; |
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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_[key].begin(); it != interactions_[key].end(); ++it) { |
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InteractionFamily ifam = (*it)->getFamily(); |
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if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it); |
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} |
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interactions_[key].insert(eam_); |
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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 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_[key].begin(); it != interactions_[key].end(); ++it) { |
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InteractionFamily ifam = (*it)->getFamily(); |
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if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it); |
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} |
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interactions_[key].insert(sc_); |
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metExplicit = true; |
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} |
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} |
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} |
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|
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// make sure every pair of atom types has a non-bonded interaction: |
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for (atype1 = atomTypes->beginType(i1); atype1 != NULL; |
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atype1 = atomTypes->nextType(i1)) { |
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for (atype2 = atomTypes->beginType(i2); atype2 != NULL; |
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atype2 = atomTypes->nextType(i2)) { |
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key = make_pair(atype1, atype2); |
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|
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if (interactions_[key].size() == 0) { |
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sprintf( painCave.errMsg, |
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"InteractionManager unable to find an appropriate non-bonded\n" |
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"\tinteraction 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_INFO; |
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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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} |
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|
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|
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void InteractionManager::doPrePair(AtomType* atype1, |
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AtomType* atype2, |
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RealType rij, |
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RealType &rho_i_at_j, |
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RealType &rho_j_at_i) { |
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|
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} |
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|
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void InteractionManager::doPreForce(AtomType* atype, |
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RealType rho, |
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RealType &frho, |
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RealType &dfrhodrho) { |
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} |
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|
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void InteractionManager::doSkipCorrection(AtomType* atype1, |
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AtomType* atype2, |
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Vector3d d, |
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RealType rij, |
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RealType &skippedCharge1, |
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RealType &skippedCharge2, |
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RealType sw, |
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RealType electroMult, |
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RealType &pot, |
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RealType &vpair, |
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Vector3d &f1, |
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Mat3x3d eFrame1, |
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Mat3x3d eFrame2, |
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Vector3d &t1, |
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Vector3d &t2) { |
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} |
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|
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void InteractionManager::doSelfCorrection(AtomType* atype, |
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Mat3x3d eFrame, |
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RealType skippedCharge, |
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RealType &pot, |
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Vector3d &t) { |
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} |
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|
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void InteractionManager::do_prepair(int *atid1, int *atid2, RealType *rij, RealType *rho_i_at_j, RealType *rho_j_at_i){ |
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|
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if (!initialized_) initialize(); |
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AtomType* atype1 = typeMap_[*atid1]; |
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AtomType* atype2 = typeMap_[*atid2]; |
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|
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doPrePair(atype1, atype2, *rij, *rho_i_at_j, *rho_j_at_i); |
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|
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return; |
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} |
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|
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void InteractionManager::do_preforce(int *atid, RealType *rho, RealType *frho, RealType *dfrhodrho){ |
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|
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if (!initialized_) initialize(); |
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AtomType* atype = typeMap_[*atid]; |
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|
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doPreForce(atype, *rho, *frho, *dfrhodrho); |
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|
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return; |
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} |
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|
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void InteractionManager::do_pair(int *atid1, int *atid2, RealType *d, RealType *r, RealType *r2, RealType *rcut, RealType *sw, RealType *vdwMult,RealType *electroMult, RealType *pot, RealType *vpair, RealType *f1, RealType *eFrame1, RealType *eFrame2, RealType *A1, RealType *A2, RealType *t1, RealType *t2, RealType *rho1, RealType *rho2, RealType *dfrho1, RealType *dfrho2, RealType *fshift1, RealType *fshift2){ |
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|
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if (!initialized_) initialize(); |
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|
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InteractionData idat; |
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|
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idat.atype1 = typeMap_[*atid1]; |
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idat.atype2 = typeMap_[*atid2]; |
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idat.d = Vector3d(d); |
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idat.rij = *r; |
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idat.r2 = *r2; |
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idat.rcut = *rcut; |
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idat.sw = *sw; |
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idat.vdwMult = *vdwMult; |
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idat.electroMult = *electroMult; |
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idat.pot = *pot; |
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idat.vpair = *vpair; |
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idat.f1 = Vector3d(f1); |
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idat.eFrame1 = Mat3x3d(eFrame1); |
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idat.eFrame2 = Mat3x3d(eFrame2); |
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idat.A1 = RotMat3x3d(A1); |
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idat.A2 = RotMat3x3d(A2); |
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idat.t1 = Vector3d(t1); |
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idat.t2 = Vector3d(t2); |
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idat.rho1 = *rho1; |
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idat.rho2 = *rho2; |
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idat.dfrho1 = *dfrho1; |
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idat.dfrho2 = *dfrho2; |
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idat.fshift1 = *fshift1; |
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idat.fshift2 = *fshift2; |
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|
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pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2); |
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set<NonBondedInteraction*>::iterator it; |
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|
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for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) |
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(*it)->calcForce(idat); |
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|
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f1[0] = idat.f1.x(); |
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f1[1] = idat.f1.y(); |
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f1[2] = idat.f1.z(); |
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|
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t1[0] = idat.t1.x(); |
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t1[1] = idat.t1.y(); |
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t1[2] = idat.t1.z(); |
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|
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t2[0] = idat.t2.x(); |
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t2[1] = idat.t2.y(); |
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t2[2] = idat.t2.z(); |
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|
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return; |
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} |
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|
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void InteractionManager::do_skip_correction(int *atid1, int *atid2, RealType *d, RealType *r, RealType *skippedCharge1, RealType *skippedCharge2, RealType *sw, RealType *electroMult, RealType *pot, RealType *vpair, RealType *f1, RealType *eFrame1, RealType *eFrame2, RealType *t1, RealType *t2){ |
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|
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if (!initialized_) initialize(); |
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|
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AtomType* atype1 = typeMap_[*atid1]; |
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AtomType* atype2 = typeMap_[*atid2]; |
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Vector3d disp(d); |
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Vector3d frc(f1); |
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Vector3d trq1(t1); |
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Vector3d trq2(t2); |
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Mat3x3d eFi(eFrame1); |
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Mat3x3d eFj(eFrame2); |
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|
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doSkipCorrection(atype1, atype2, disp, *r, *skippedCharge1, *skippedCharge2, *sw, |
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*electroMult, *pot, *vpair, frc, eFi, eFj, trq1, trq2); |
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|
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f1[0] = frc.x(); |
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f1[1] = frc.y(); |
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f1[2] = frc.z(); |
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|
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t1[0] = trq1.x(); |
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t1[1] = trq1.y(); |
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t1[2] = trq1.z(); |
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|
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t2[0] = trq2.x(); |
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t2[1] = trq2.y(); |
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t2[2] = trq2.z(); |
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|
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return; |
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} |
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|
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void InteractionManager::do_self_correction(int *atid, RealType *eFrame, RealType *skippedCharge, RealType *pot, RealType *t){ |
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|
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if (!initialized_) initialize(); |
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|
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AtomType* atype = typeMap_[*atid]; |
| 383 |
Mat3x3d eFi(eFrame); |
| 384 |
Vector3d trq1(t); |
| 385 |
|
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doSelfCorrection(atype, eFi, *skippedCharge, *pot, trq1); |
| 387 |
|
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t[0] = trq1.x(); |
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t[1] = trq1.y(); |
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t[2] = trq1.z(); |
| 391 |
|
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return; |
| 393 |
} |
| 394 |
|
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} //end namespace OpenMD |
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|
| 397 |
extern "C" { |
| 398 |
|
| 399 |
#define fortranDoPrePair FC_FUNC(do_prepair, DO_PREPAIR) |
| 400 |
#define fortranDoPreForce FC_FUNC(do_preforce, DO_PREFORCE) |
| 401 |
#define fortranDoPair FC_FUNC(do_pair, DO_PAIR) |
| 402 |
#define fortranDoSkipCorrection FC_FUNC(do_skip_correction, DO_SKIP_CORRECTION) |
| 403 |
#define fortranDoSelfCorrection FC_FUNC(do_self_correction, DO_SELF_CORRECTION) |
| 404 |
#define fortranGetCutoff FC_FUNC(get_cutoff, GET_CUTOFF) |
| 405 |
|
| 406 |
void fortranDoPrePair(int *atid1, int *atid2, RealType *rij, |
| 407 |
RealType *rho_i_at_j, RealType *rho_j_at_i) { |
| 408 |
|
| 409 |
return OpenMD::InteractionManager::Instance()->do_prepair(atid1, atid2, rij, |
| 410 |
rho_i_at_j, |
| 411 |
rho_j_at_i); |
| 412 |
} |
| 413 |
void fortranDoPreforce(int *atid, RealType *rho, RealType *frho, |
| 414 |
RealType *dfrhodrho) { |
| 415 |
|
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return OpenMD::InteractionManager::Instance()->do_preforce(atid, rho, frho, |
| 417 |
dfrhodrho); |
| 418 |
} |
| 419 |
|
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void fortranDoPair(int *atid1, int *atid2, RealType *d, RealType *r, |
| 421 |
RealType *r2, RealType *rcut, RealType *sw, RealType *vdwMult, |
| 422 |
RealType *electroMult, RealType *pot, RealType *vpair, RealType *f1, |
| 423 |
RealType *eFrame1, RealType *eFrame2, RealType *A1, RealType *A2, |
| 424 |
RealType *t1, RealType *t2, |
| 425 |
RealType *rho1, RealType *rho2, RealType *dfrho1, RealType *dfrho2, |
| 426 |
RealType *fshift1, RealType *fshift2){ |
| 427 |
|
| 428 |
return OpenMD::InteractionManager::Instance()->do_pair(atid1, atid2, d, r, r2, rcut, |
| 429 |
sw, vdwMult, electroMult, pot, |
| 430 |
vpair, f1, eFrame1, eFrame2, |
| 431 |
A1, A2, t1, t2, rho1, rho2, |
| 432 |
dfrho1, dfrho2, fshift1, fshift2); |
| 433 |
} |
| 434 |
|
| 435 |
void fortranDoSkipCorrection(int *atid1, int *atid2, RealType *d, RealType *r, |
| 436 |
RealType *skippedCharge1, RealType *skippedCharge2, |
| 437 |
RealType *sw, RealType *electroMult, RealType *pot, |
| 438 |
RealType *vpair, RealType *f1, |
| 439 |
RealType *eFrame1, RealType *eFrame2, |
| 440 |
RealType *t1, RealType *t2){ |
| 441 |
|
| 442 |
return OpenMD::InteractionManager::Instance()->do_skip_correction(atid1, atid2, d, r, |
| 443 |
skippedCharge1, |
| 444 |
skippedCharge2, |
| 445 |
sw, electroMult, pot, |
| 446 |
vpair, f1, eFrame1, |
| 447 |
eFrame2, t1, t2); |
| 448 |
} |
| 449 |
|
| 450 |
void fortranDoSelfCorrection(int *atid, RealType *eFrame, RealType *skippedCharge, |
| 451 |
RealType *pot, RealType *t) { |
| 452 |
|
| 453 |
return OpenMD::InteractionManager::Instance()->do_self_correction(atid, eFrame, |
| 454 |
skippedCharge, |
| 455 |
pot, t); |
| 456 |
} |
| 457 |
RealType fortranGetCutoff() { |
| 458 |
return OpenMD::InteractionManager::Instance()->getCutoff(); |
| 459 |
} |
| 460 |
} |
