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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 <stdio.h> |
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#include <string.h> |
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|
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#include <cmath> |
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#include "nonbonded/LJ.hpp" |
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#include "utils/simError.h" |
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#include "types/LennardJonesAdapter.hpp" |
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#include "types/LennardJonesInteractionType.hpp" |
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|
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namespace OpenMD { |
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|
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LJ::LJ() : name_("LJ"), initialized_(false), forceField_(NULL) {} |
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|
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RealType LJ::getSigma(AtomType* atomType1, AtomType* atomType2) { |
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|
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LennardJonesAdapter lja1 = LennardJonesAdapter(atomType1); |
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LennardJonesAdapter lja2 = LennardJonesAdapter(atomType2); |
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RealType sigma1 = lja1.getSigma(); |
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RealType sigma2 = lja2.getSigma(); |
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|
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ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
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string DistanceMix = fopts.getDistanceMixingRule(); |
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toUpper(DistanceMix); |
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|
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if (DistanceMix == "GEOMETRIC") |
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return sqrt(sigma1 * sigma2); |
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else |
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return 0.5 * (sigma1 + sigma2); |
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} |
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|
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RealType LJ::getEpsilon(AtomType* atomType1, AtomType* atomType2) { |
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LennardJonesAdapter lja1 = LennardJonesAdapter(atomType1); |
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LennardJonesAdapter lja2 = LennardJonesAdapter(atomType2); |
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|
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RealType epsilon1 = lja1.getEpsilon(); |
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RealType epsilon2 = lja2.getEpsilon(); |
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return sqrt(epsilon1 * epsilon2); |
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} |
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|
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void LJ::initialize() { |
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|
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LJtypes.clear(); |
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LJtids.clear(); |
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MixingMap.clear(); |
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nLJ_ = 0; |
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|
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LJtids.resize( forceField_->getNAtomType(), -1); |
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|
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set<AtomType*>::iterator at; |
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for (at = simTypes_.begin(); at != simTypes_.end(); ++at) { |
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if ((*at)->isLennardJones()) nLJ_++; |
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} |
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|
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MixingMap.resize(nLJ_); |
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|
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for (at = simTypes_.begin(); at != simTypes_.end(); ++at) { |
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if ((*at)->isLennardJones()) addType(*at); |
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} |
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|
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ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes(); |
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ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j; |
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NonBondedInteractionType* nbt; |
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ForceField::NonBondedInteractionTypeContainer::KeyType keys; |
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|
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for (nbt = nbiTypes->beginType(j); nbt != NULL; |
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nbt = nbiTypes->nextType(j)) { |
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|
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if (nbt->isLennardJones()) { |
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keys = nbiTypes->getKeys(j); |
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AtomType* at1 = forceField_->getAtomType(keys[0]); |
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AtomType* at2 = forceField_->getAtomType(keys[1]); |
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|
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LennardJonesInteractionType* ljit = dynamic_cast<LennardJonesInteractionType*>(nbt); |
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|
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if (ljit == NULL) { |
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sprintf( painCave.errMsg, |
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"LJ::initialize could not convert NonBondedInteractionType\n" |
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"\tto LennardJonesInteractionType for %s - %s interaction.\n", |
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at1->getName().c_str(), |
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at2->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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|
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RealType sigma = ljit->getSigma(); |
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RealType epsilon = ljit->getEpsilon(); |
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addExplicitInteraction(at1, at2, sigma, epsilon); |
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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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|
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void LJ::addType(AtomType* atomType){ |
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LennardJonesAdapter lja1 = LennardJonesAdapter(atomType); |
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|
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RealType sigma1 = lja1.getSigma(); |
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RealType epsilon1 = lja1.getEpsilon(); |
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|
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// add it to the map: |
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int atid = atomType->getIdent(); |
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int ljtid = LJtypes.size(); |
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|
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pair<set<int>::iterator,bool> ret; |
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ret = LJtypes.insert( atid ); |
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if (ret.second == false) { |
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sprintf( painCave.errMsg, |
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"LJ already had a previous entry with ident %d\n", |
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atid) ; |
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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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LJtids[atid] = ljtid; |
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MixingMap[ljtid].resize( nLJ_ ); |
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|
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// Now, iterate over all known types and add to the mixing map: |
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|
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std::set<int>::iterator it; |
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for( it = LJtypes.begin(); it != LJtypes.end(); ++it) { |
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|
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int ljtid2 = LJtids[ (*it) ]; |
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AtomType* atype2 = forceField_->getAtomType( (*it) ); |
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|
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LJInteractionData mixer; |
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mixer.sigma = getSigma(atomType, atype2); |
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mixer.epsilon = getEpsilon(atomType, atype2); |
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mixer.sigmai = 1.0 / mixer.sigma; |
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mixer.explicitlySet = false; |
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MixingMap[ljtid2].resize( nLJ_ ); |
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|
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MixingMap[ljtid][ljtid2] = mixer; |
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if (ljtid2 != ljtid) { |
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MixingMap[ljtid2][ljtid] = mixer; |
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} |
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} |
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} |
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|
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void LJ::addExplicitInteraction(AtomType* atype1, AtomType* atype2, RealType sigma, RealType epsilon){ |
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|
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LJInteractionData mixer; |
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mixer.sigma = sigma; |
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mixer.epsilon = epsilon; |
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mixer.sigmai = 1.0 / mixer.sigma; |
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mixer.explicitlySet = true; |
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|
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int atid1 = atype1->getIdent(); |
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int atid2 = atype2->getIdent(); |
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|
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int ljtid1, ljtid2; |
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|
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pair<set<int>::iterator,bool> ret; |
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ret = LJtypes.insert( atid1 ); |
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if (ret.second == false) { |
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// already had this type in the LJMap, just get the ljtid: |
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ljtid1 = LJtids[ atid1 ]; |
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} else { |
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// didn't already have it, so make a new one and assign it: |
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ljtid1 = nLJ_; |
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LJtids[atid1] = nLJ_; |
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nLJ_++; |
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} |
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|
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ret = LJtypes.insert( atid2 ); |
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if (ret.second == false) { |
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// already had this type in the LJMap, just get the ljtid: |
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ljtid2 = LJtids[ atid2 ]; |
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} else { |
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// didn't already have it, so make a new one and assign it: |
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ljtid2 = nLJ_; |
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LJtids[atid2] = nLJ_; |
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nLJ_++; |
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} |
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|
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MixingMap.resize(nLJ_); |
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MixingMap[ljtid1].resize(nLJ_); |
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|
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MixingMap[ljtid1][ljtid2] = mixer; |
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if (ljtid2 != ljtid1) { |
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MixingMap[ljtid2].resize(nLJ_); |
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MixingMap[ljtid2][ljtid1] = mixer; |
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} |
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} |
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|
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void LJ::calcForce(InteractionData &idat) { |
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if (!initialized_) initialize(); |
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|
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LJInteractionData &mixer = MixingMap[LJtids[idat.atid1]][LJtids[idat.atid2]]; |
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|
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RealType sigmai = mixer.sigmai; |
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RealType epsilon = mixer.epsilon; |
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|
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RealType ros; |
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RealType rcos; |
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RealType myPot = 0.0; |
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RealType myPotC = 0.0; |
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RealType myDeriv = 0.0; |
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RealType myDerivC = 0.0; |
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|
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ros = *(idat.rij) * sigmai; |
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|
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getLJfunc(ros, myPot, myDeriv); |
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|
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if (idat.shiftedPot) { |
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rcos = *(idat.rcut) * sigmai; |
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getLJfunc(rcos, myPotC, myDerivC); |
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myDerivC = 0.0; |
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} else if (idat.shiftedForce) { |
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rcos = *(idat.rcut) * sigmai; |
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getLJfunc(rcos, myPotC, myDerivC); |
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myPotC = myPotC + myDerivC * (*(idat.rij) - *(idat.rcut)) * sigmai; |
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} else { |
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myPotC = 0.0; |
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myDerivC = 0.0; |
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} |
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|
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RealType pot_temp = *(idat.vdwMult) * epsilon * (myPot - myPotC); |
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*(idat.vpair) += pot_temp; |
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|
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RealType dudr = *(idat.sw) * *(idat.vdwMult) * epsilon * (myDeriv - |
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myDerivC)*sigmai; |
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(*(idat.pot))[VANDERWAALS_FAMILY] += *(idat.sw) * pot_temp; |
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*(idat.f1) += *(idat.d) * dudr / *(idat.rij); |
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|
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return; |
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} |
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|
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void LJ::getLJfunc(RealType r, RealType &pot, RealType &deriv) { |
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|
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RealType ri = 1.0 / r; |
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RealType ri2 = ri * ri; |
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RealType ri6 = ri2 * ri2 * ri2; |
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RealType ri7 = ri6 * ri; |
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RealType ri12 = ri6 * ri6; |
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RealType ri13 = ri12 * ri; |
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|
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pot = 4.0 * (ri12 - ri6); |
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deriv = 24.0 * (ri7 - 2.0 * ri13); |
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|
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return; |
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} |
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|
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RealType LJ::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
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if (!initialized_) initialize(); |
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|
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int atid1 = atypes.first->getIdent(); |
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int atid2 = atypes.second->getIdent(); |
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int ljtid1 = LJtids[atid1]; |
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int ljtid2 = LJtids[atid2]; |
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|
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if (ljtid1 == -1 || ljtid2 == -1) return 0.0; |
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else { |
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LJInteractionData mixer = MixingMap[ljtid1][ljtid2]; |
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return 2.5 * mixer.sigma; |
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} |
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} |
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|
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} |
