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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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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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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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void InteractionManager::initialize() { |
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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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|
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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 != NULL) { |
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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(); |
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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 " |
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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_[key].begin(); |
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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(); |
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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 " |
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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_[key].begin(); |
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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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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_[key].begin(); |
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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(maw_); |
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vdwExplicit = true; |
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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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// 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. |
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|
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set<AtomType*> simTypes = info_->getSimulatedAtomTypes(); |
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set<AtomType*>::iterator it, jt; |
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|
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for (it = simTypes.begin(); it != simTypes.end(); ++it) { |
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atype1 = (*it); |
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for (jt = it; jt != simTypes.end(); ++jt) { |
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atype2 = (*jt); |
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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 could not find a matching non-bonded\n" |
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"\tinteraction for atom types %s - %s\n" |
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"\tProceeding without this interaction.\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 = 0; |
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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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initialized_ = true; |
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} |
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|
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void InteractionManager::setCutoffRadius(RealType rcut) { |
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|
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electrostatic_->setCutoffRadius(rcut); |
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eam_->setCutoffRadius(rcut); |
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} |
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|
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void InteractionManager::setSwitchingRadius(RealType rswitch) { |
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electrostatic_->setSwitchingRadius(rswitch); |
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} |
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|
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void InteractionManager::doPrePair(InteractionData idat){ |
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// printf("%s\tERROR!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", __FUNCTION__); |
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if (!initialized_) initialize(); |
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|
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// excluded interaction, so just return |
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if (idat.excluded) return; |
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|
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set<NonBondedInteraction*>::iterator it; |
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|
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for (it = interactions_[ idat.atypes ].begin(); |
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it != interactions_[ idat.atypes ].end(); ++it){ |
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if ((*it)->getFamily() == METALLIC_FAMILY) { |
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dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat); |
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} |
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} |
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|
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return; |
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} |
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|
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void InteractionManager::initializeOMP() { |
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if (!initialized_) initialize(); |
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} |
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|
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void InteractionManager::doPrePairOMP(InteractionDataPrv idatThread){ |
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InteractionData idat; |
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// excluded interaction, so just return |
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if (idat.excluded) return; |
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|
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wrapData(idatThread, idat); |
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|
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set<NonBondedInteraction*>::iterator it; |
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|
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for (it = interactions_[ idat.atypes ].begin(); |
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it != interactions_[ idat.atypes ].end(); ++it){ |
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if ((*it)->getFamily() == METALLIC_FAMILY) { |
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dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat); |
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} |
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} |
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|
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return; |
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} |
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|
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void InteractionManager::doPreForce(SelfData sdat){ |
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|
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if (!initialized_) initialize(); |
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|
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pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype); |
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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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if ((*it)->getFamily() == METALLIC_FAMILY) { |
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dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat); |
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} |
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} |
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|
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return; |
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} |
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|
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void InteractionManager::initNonbondedForces() { |
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pair<AtomType*, AtomType*> key; |
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set<AtomType*> simTypes = info_->getSimulatedAtomTypes(); |
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set<AtomType*>::iterator it, jt; |
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set<NonBondedInteraction*>::iterator kt; |
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AtomType* atype1; |
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AtomType* atype2; |
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|
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for (it = simTypes.begin(); it != simTypes.end(); ++it) { |
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atype1 = (*it); |
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for (jt = it; jt != simTypes.end(); ++jt) { |
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atype2 = (*jt); |
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key = make_pair(atype1, atype2); |
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|
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for (kt = interactions_[ key ].begin(); |
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kt != interactions_[ key ].end(); ++kt) { |
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|
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(*kt)->initForce(); |
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} |
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} |
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} |
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|
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/* lj_->initForce(); |
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electrostatic_->initForce(); |
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sticky_->initForce(); |
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eam_->initForce(); |
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sc_->initForce(); |
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gb_->initForce();*/ |
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|
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return; |
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} |
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|
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void InteractionManager::doPair(InteractionData idat){ |
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// printf("%s\tERROR!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", __FUNCTION__); |
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if (!initialized_) initialize(); |
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|
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set<NonBondedInteraction*>::iterator it; |
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|
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for (it = interactions_[ idat.atypes ].begin(); |
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it != interactions_[ idat.atypes ].end(); ++it) { |
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|
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// electrostatics still has to worry about indirect |
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// contributions from excluded pairs of atoms: |
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|
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if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) { |
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(*it)->calcForce(idat); |
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} |
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} |
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|
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return; |
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} |
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|
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void InteractionManager::wrapData(InteractionDataPrv &src, InteractionData &dst) { |
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dst.A1 = src.A1; |
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dst.A2 = src.A2; |
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dst.atypes = src.atypes; |
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dst.d = &src.d; |
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dst.dfrho1 = src.dfrho1; |
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dst.dfrho2 = src.dfrho2; |
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dst.eFrame1 = src.eFrame1; |
| 401 |
dst.eFrame2 = src.eFrame2; |
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dst.electroMult = &src.electroMult; |
| 403 |
dst.excluded = src.excluded; |
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dst.f1 = &src.f1; |
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dst.frho1 = src.frho1; |
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dst.frho2 = src.frho2; |
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dst.particlePot1 = src.particlePot1; |
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dst.particlePot2 = src.particlePot2; |
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dst.pot = &src.pot; |
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dst.r2 = &src.r2; |
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dst.rcut = &src.rcut; |
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dst.rho1 = src.rho1; |
| 413 |
dst.rho2 = src.rho2; |
| 414 |
dst.rij = &src.rij; |
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dst.shiftedForce = src.shiftedForce; |
| 416 |
dst.shiftedPot = src.shiftedPot; |
| 417 |
dst.skippedCharge1 = src.skippedCharge1; |
| 418 |
dst.skippedCharge2 = src.skippedCharge2; |
| 419 |
dst.sw = &src.sw; |
| 420 |
dst.t1 = src.t1; |
| 421 |
dst.t2 = src.t2; |
| 422 |
dst.topoDist = src.topoDist; |
| 423 |
dst.vdwMult = &src.vdwMult; |
| 424 |
dst.vpair = &src.vpair; |
| 425 |
} |
| 426 |
|
| 427 |
void InteractionManager::doPairOMP(InteractionDataPrv &idatThread){ |
| 428 |
set<NonBondedInteraction*>::iterator it; |
| 429 |
InteractionData idat; |
| 430 |
|
| 431 |
wrapData(idatThread, idat); |
| 432 |
|
| 433 |
for (it = interactions_[ idat.atypes ].begin(); |
| 434 |
it != interactions_[ idat.atypes ].end(); ++it) { |
| 435 |
|
| 436 |
// electrostatics still has to worry about indirect |
| 437 |
// contributions from excluded pairs of atoms: |
| 438 |
|
| 439 |
if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) { |
| 440 |
(*it)->calcForce(idat); |
| 441 |
} |
| 442 |
} |
| 443 |
|
| 444 |
return; |
| 445 |
} |
| 446 |
|
| 447 |
void InteractionManager::doSelfCorrection(SelfData sdat){ |
| 448 |
|
| 449 |
if (!initialized_) initialize(); |
| 450 |
|
| 451 |
pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype); |
| 452 |
set<NonBondedInteraction*>::iterator it; |
| 453 |
|
| 454 |
for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){ |
| 455 |
if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) { |
| 456 |
dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat); |
| 457 |
} |
| 458 |
} |
| 459 |
|
| 460 |
return; |
| 461 |
} |
| 462 |
|
| 463 |
RealType InteractionManager::getSuggestedCutoffRadius(int *atid) { |
| 464 |
if (!initialized_) initialize(); |
| 465 |
|
| 466 |
AtomType* atype = typeMap_[*atid]; |
| 467 |
|
| 468 |
pair<AtomType*, AtomType*> key = make_pair(atype, atype); |
| 469 |
set<NonBondedInteraction*>::iterator it; |
| 470 |
RealType cutoff = 0.0; |
| 471 |
|
| 472 |
for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) |
| 473 |
cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key)); |
| 474 |
return cutoff; |
| 475 |
} |
| 476 |
|
| 477 |
RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) { |
| 478 |
if (!initialized_) initialize(); |
| 479 |
|
| 480 |
pair<AtomType*, AtomType*> key = make_pair(atype, atype); |
| 481 |
set<NonBondedInteraction*>::iterator it; |
| 482 |
RealType cutoff = 0.0; |
| 483 |
|
| 484 |
for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) |
| 485 |
cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key)); |
| 486 |
return cutoff; |
| 487 |
} |
| 488 |
} //end namespace OpenMD |
