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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 <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/Morse.hpp" |
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#include "utils/simError.h" |
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#include "types/NonBondedInteractionType.hpp" |
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|
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using namespace std; |
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|
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namespace OpenMD { |
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|
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Morse::Morse() : name_("Morse"), initialized_(false), forceField_(NULL), |
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shiftedPot_(false), shiftedFrc_(false) {} |
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|
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void Morse::initialize() { |
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|
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stringToEnumMap_["shiftedMorse"] = shiftedMorse; |
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stringToEnumMap_["repulsiveMorse"] = repulsiveMorse; |
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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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|
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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->isMorse()) { |
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|
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pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes(); |
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|
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GenericData* data = nbt->getPropertyByName("Morse"); |
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if (data == NULL) { |
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sprintf( painCave.errMsg, "Morse::initialize could not find\n" |
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"\tMorse parameters for %s - %s interaction.\n", |
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atypes.first->getName().c_str(), |
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atypes.second->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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MorseData* morseData = dynamic_cast<MorseData*>(data); |
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if (morseData == NULL) { |
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sprintf( painCave.errMsg, |
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"Morse::initialize could not convert GenericData to\n" |
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"\tMorseData for %s - %s interaction.\n", |
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atypes.first->getName().c_str(), |
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atypes.second->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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MorseParam morseParam = morseData->getData(); |
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|
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RealType De = morseParam.De; |
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RealType Re = morseParam.Re; |
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RealType beta = morseParam.beta; |
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string interactionType = morseParam.interactionType; |
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|
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toUpper(interactionType); |
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map<string, MorseInteractionType>::iterator i; |
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i = stringToEnumMap_.find(interactionType); |
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if (i != stringToEnumMap_.end()) { |
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addExplicitInteraction(atypes.first, atypes.second, |
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De, Re, beta, i->second ); |
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} else { |
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sprintf( painCave.errMsg, |
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"Morse::initialize found unknown Morse interaction type\n" |
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"\t(%s) for %s - %s interaction.\n", |
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morseParam.interactionType.c_str(), |
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atypes.first->getName().c_str(), |
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atypes.second->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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} |
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initialized_ = true; |
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} |
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|
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void Morse::addExplicitInteraction(AtomType* atype1, AtomType* atype2, |
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RealType De, RealType Re, RealType beta, |
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MorseInteractionType mit) { |
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|
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MorseInteractionData mixer; |
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mixer.De = De; |
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mixer.Re = Re; |
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mixer.beta = beta; |
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mixer.interactionType = mit; |
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|
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pair<AtomType*, AtomType*> key1, key2; |
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key1 = make_pair(atype1, atype2); |
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key2 = make_pair(atype2, atype1); |
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|
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MixingMap[key1] = mixer; |
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if (key2 != key1) { |
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MixingMap[key2] = mixer; |
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} |
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} |
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|
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void Morse::calcForce(InteractionData idat) { |
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|
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if (!initialized_) initialize(); |
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|
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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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pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2); |
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MorseInteractionData mixer = MixingMap[key]; |
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|
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RealType De = mixer.De; |
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RealType Re = mixer.Re; |
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RealType beta = mixer.beta; |
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MorseInteractionType interactionType = mixer.interactionType; |
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|
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// V(r) = D_e exp(-a(r-re)(exp(-a(r-re))-2) |
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|
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RealType expt = -beta*(idat.rij - Re); |
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RealType expfnc = exp(expt); |
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RealType expfnc2 = expfnc*expfnc; |
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|
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RealType exptC = 0.0; |
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RealType expfncC = 0.0; |
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RealType expfnc2C = 0.0; |
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|
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if (Morse::shiftedPot_ || Morse::shiftedFrc_) { |
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exptC = -beta*(idat.rcut - Re); |
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expfncC = exp(exptC); |
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expfnc2C = expfncC*expfncC; |
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} |
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|
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|
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switch(interactionType) { |
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case shiftedMorse : { |
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|
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myPot = De * (expfnc2 - 2.0 * expfnc); |
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myDeriv = 2.0 * De * beta * (expfnc - expfnc2); |
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|
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if (Morse::shiftedPot_) { |
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myPotC = De * (expfnc2C - 2.0 * expfncC); |
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myDerivC = 0.0; |
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} else if (Morse::shiftedFrc_) { |
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myPotC = De * (expfnc2C - 2.0 * expfncC); |
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myDerivC = 2.0 * De * beta * (expfnc2C - expfnc2C); |
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myPotC += myDerivC * (idat.rij - idat.rcut); |
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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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break; |
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} |
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case repulsiveMorse : { |
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|
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myPot = De * expfnc2; |
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myDeriv = -2.0 * De * beta * expfnc2; |
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|
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if (Morse::shiftedPot_) { |
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myPotC = De * expfnc2C; |
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myDerivC = 0.0; |
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} else if (Morse::shiftedFrc_) { |
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myPotC = De * expfnc2C; |
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myDerivC = -2.0 * De * beta * expfnc2C; |
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myPotC += myDerivC * (idat.rij - idat.rcut); |
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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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break; |
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} |
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} |
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|
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RealType pot_temp = idat.vdwMult * (myPot - myPotC); |
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idat.vpair += pot_temp; |
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|
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RealType dudr = idat.sw * idat.vdwMult * (myDeriv - myDerivC); |
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|
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idat.pot += 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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|
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} |
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|
