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gezelter |
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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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#include <stdio.h> |
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#include <string.h> |
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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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using namespace std; |
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namespace OpenMD { |
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bool Morse::initialized_ = false; |
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bool Morse::shiftedPot_ = false; |
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bool Morse::shiftedFrc_ = false; |
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ForceField* Morse::forceField_ = NULL; |
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map<int, AtomType*> Morse::MorseMap; |
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map<pair<AtomType*, AtomType*>, MorseInteractionData> Morse::MixingMap; |
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map<string, MorseInteractionType> Morse::stringToEnumMap_; |
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Morse* Morse::_instance = NULL; |
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Morse* Morse::Instance() { |
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if (!_instance) { |
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_instance = new Morse(); |
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} |
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return _instance; |
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} |
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void Morse::initialize() { |
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stringToEnumMap_["shiftedMorse"] = shiftedMorse; |
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stringToEnumMap_["repulsiveMorse"] = repulsiveMorse; |
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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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for (nbt = nbiTypes->beginType(j); nbt != NULL; |
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nbt = nbiTypes->nextType(j)) { |
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if (nbt->isMorse()) { |
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pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes(); |
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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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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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MorseParam morseParam = morseData->getData(); |
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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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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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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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AtomTypeProperties atp = atype1->getATP(); |
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MorseMap.insert( pair<int, AtomType*>(atp.ident, atype1) ); |
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atp = atype2->getATP(); |
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MorseMap.insert( pair<int, AtomType*>(atp.ident, atype2) ); |
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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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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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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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void Morse::calcForce(AtomType* at1, AtomType* at2, Vector3d d, |
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RealType r, RealType r2, RealType rcut, RealType sw, |
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RealType vdwMult, RealType &vpair, RealType &pot, |
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Vector3d &f1) { |
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if (!initialized_) initialize(); |
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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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pair<AtomType*, AtomType*> key = make_pair(at1, at2); |
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MorseInteractionData mixer = MixingMap[key]; |
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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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// V(r) = D_e exp(-a(r-re)(exp(-a(r-re))-2) |
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RealType expt = -beta*(r - Re); |
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RealType expfnc = exp(expt); |
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RealType expfnc2 = expfnc*expfnc; |
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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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if (Morse::shiftedPot_ || Morse::shiftedFrc_) { |
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exptC = -beta*(rcut - Re); |
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expfncC = exp(exptC); |
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expfnc2C = expfncC*expfncC; |
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} |
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switch(interactionType) { |
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case shiftedMorse : { |
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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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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 * (r - 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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break; |
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} |
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case repulsiveMorse : { |
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myPot = De * expfnc2; |
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myDeriv = -2.0 * De * beta * expfnc2; |
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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 * (r - 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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break; |
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} |
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} |
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RealType pot_temp = vdwMult * (myPot - myPotC); |
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vpair += pot_temp; |
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RealType dudr = sw * vdwMult * (myDeriv - myDerivC); |
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pot += sw * pot_temp; |
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f1 = d * dudr / r; |
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return; |
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} |
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void Morse::do_morse_pair(int *atid1, int *atid2, RealType *d, |
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RealType *rij, RealType *r2, RealType *rcut, |
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RealType *sw, RealType *vdwMult, |
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RealType *vpair, RealType *pot, RealType *f1) { |
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if (!initialized_) initialize(); |
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AtomType* atype1 = MorseMap[*atid1]; |
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AtomType* atype2 = MorseMap[*atid2]; |
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Vector3d disp(d[0], d[1], d[2]); |
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Vector3d frc(f1[0], f1[1], f1[2]); |
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calcForce(atype1, atype2, disp, *rij, *r2, *rcut, *sw, *vdwMult, *vpair, |
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*pot, frc); |
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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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return; |
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} |
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void Morse::setMorseDefaultCutoff(RealType *thisRcut, int *sP, int *sF) { |
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shiftedPot_ = (bool)(*sP); |
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shiftedFrc_ = (bool)(*sF); |
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} |
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} |
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extern "C" { |
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#define fortranSetMorseCutoff FC_FUNC(setmorsedefaultcutoff, SETMORSEDEFAULTCUTOFF) |
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#define fortranDoMorsePair FC_FUNC(do_morse_pair, DO_MORSE_PAIR) |
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void fortranSetMorseCutoff(RealType *rcut, int *shiftedPot, int *shiftedFrc) { |
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return OpenMD::Morse::Instance()->setMorseDefaultCutoff(rcut, shiftedPot, |
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shiftedFrc); |
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} |
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void fortranDoMorsePair(int *atid1, int *atid2, RealType *d, RealType *rij, |
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RealType *r2, RealType *rcut, RealType *sw, |
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RealType *vdwMult, RealType* vpair, RealType* pot, |
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RealType *f1){ |
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return OpenMD::Morse::Instance()->do_morse_pair(atid1, atid2, d, rij, r2, |
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rcut, sw, vdwMult, vpair, |
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pot, f1); |
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} |
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} |