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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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#include <cmath> |
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|
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#include "nonbonded/MAW.hpp" |
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#include "utils/simError.h" |
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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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MAW::MAW() : name_("MAW"), initialized_(false), forceField_(NULL), |
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shiftedPot_(false), shiftedFrc_(false) {} |
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|
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void MAW::initialize() { |
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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->isMAW()) { |
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pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes(); |
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|
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GenericData* data = nbt->getPropertyByName("MAW"); |
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if (data == NULL) { |
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sprintf( painCave.errMsg, "MAW::initialize could not find\n" |
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"\tMAW 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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MAWData* mawData = dynamic_cast<MAWData*>(data); |
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if (mawData == NULL) { |
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sprintf( painCave.errMsg, |
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"MAW::initialize could not convert GenericData to\n" |
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"\tMAWData 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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MAWParam mawParam = mawData->getData(); |
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|
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RealType De = mawParam.De; |
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RealType beta = mawParam.beta; |
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RealType Re = mawParam.Re; |
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RealType ca1 = mawParam.ca1; |
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RealType cb1 = mawParam.cb1; |
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|
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addExplicitInteraction(atypes.first, atypes.second, |
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De, beta, Re, ca1, cb1); |
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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 MAW::addExplicitInteraction(AtomType* atype1, AtomType* atype2, |
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RealType De, RealType beta, RealType Re, |
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RealType ca1, RealType cb1) { |
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|
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MAWInteractionData mixer; |
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mixer.De = De; |
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mixer.beta = beta; |
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mixer.Re = Re; |
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mixer.ca1 = ca1; |
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mixer.cb1 = cb1; |
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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 MAW::calcForce(InteractionData idat) { |
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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(idat.atype1, idat.atype2); |
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map<pair<AtomType*, AtomType*>, MAWInteractionData>::iterator it; |
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it = MixingMap.find(key); |
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if (it != MixingMap.end()) { |
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MAWInteractionData mixer = (*it).second; |
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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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RealType D_e = mixer.De; |
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RealType R_e = mixer.Re; |
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RealType beta = mixer.beta; |
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RealType ca1 = mixer.ca1; |
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RealType cb1 = mixer.cb1; |
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|
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bool j_is_Metal = idat.atype2->isMetal(); |
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|
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Vector3d r; |
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RotMat3x3d Atrans; |
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if (j_is_Metal) { |
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// rotate the inter-particle separation into the two different |
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// body-fixed coordinate systems: |
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r = idat.A1 * idat.d; |
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Atrans = idat.A1.transpose(); |
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} else { |
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// negative sign because this is the vector from j to i: |
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r = -idat.A2 * idat.d; |
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Atrans = idat.A2.transpose(); |
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} |
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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 - R_e); |
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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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myPot = D_e * (expfnc2 - 2.0 * expfnc); |
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myDeriv = 2.0 * D_e * beta * (expfnc - expfnc2); |
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|
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if (MAW::shiftedPot_ || MAW::shiftedFrc_) { |
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exptC = -beta*(idat.rcut - R_e); |
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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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if (MAW::shiftedPot_) { |
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myPotC = D_e * (expfnc2C - 2.0 * expfncC); |
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myDerivC = 0.0; |
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} else if (MAW::shiftedFrc_) { |
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myPotC = D_e * (expfnc2C - 2.0 * expfncC); |
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myDerivC = 2.0 * D_e * 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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RealType x = r.x(); |
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RealType y = r.y(); |
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RealType z = r.z(); |
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RealType x2 = x * x; |
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RealType y2 = y * y; |
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RealType z2 = z * z; |
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|
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RealType r3 = idat.r2 * idat.rij; |
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RealType r4 = idat.r2 * idat.r2; |
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|
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// angular modulation of morse part of potential to approximate |
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// the squares of the two HOMO lone pair orbitals in water: |
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//********************** old form************************* |
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// s = 1 / (4 pi) |
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// ta1 = (s - pz)^2 = (1 - sqrt(3)*cos(theta))^2 / (4 pi) |
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// b1 = px^2 = 3 * (sin(theta)*cos(phi))^2 / (4 pi) |
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//********************** old form************************* |
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// we'll leave out the 4 pi for now |
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|
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// new functional form just using the p orbitals. |
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// Vmorse(r)*[a*p_x + b p_z + (1-a-b)] |
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// which is |
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// Vmorse(r)*[a sin^2(theta) cos^2(phi) + b cos(theta) + (1-a-b)] |
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// Vmorse(r)*[a*x2/r2 + b*z/r + (1-a-b)] |
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|
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RealType Vmorse = (myPot - myPotC); |
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RealType Vang = ca1 * x2 / idat.r2 + cb1 * z / idat.rij + (0.8 - ca1 / 3.0); |
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|
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RealType pot_temp = idat.vdwMult * Vmorse * Vang; |
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idat.vpair += pot_temp; |
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idat.pot += idat.sw * pot_temp; |
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|
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Vector3d dVmorsedr = (myDeriv - myDerivC) * Vector3d(x, y, z) / idat.rij; |
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|
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Vector3d dVangdr = Vector3d(-2.0 * ca1 * x2 * x / r4 + 2.0 * ca1 * x / idat.r2 - cb1 * x * z / r3, |
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-2.0 * ca1 * x2 * y / r4 - cb1 * z * y / r3, |
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-2.0 * ca1 * x2 * z / r4 + cb1 / idat.rij - cb1 * z2 / r3); |
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|
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// chain rule to put these back on x, y, z |
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|
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Vector3d dvdr = Vang * dVmorsedr + Vmorse * dVangdr; |
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|
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// Torques for Vang using method of Price: |
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// S. L. Price, A. J. Stone, and M. Alderton, Mol. Phys. 52, 987 (1984). |
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|
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Vector3d dVangdu = Vector3d(cb1 * y / idat.rij, |
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2.0 * ca1 * x * z / idat.r2 - cb1 * x / idat.rij, |
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-2.0 * ca1 * y * x / idat.r2); |
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|
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// do the torques first since they are easy: |
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// remember that these are still in the body fixed axes |
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|
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Vector3d trq = idat.vdwMult * Vmorse * dVangdu * idat.sw; |
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|
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// go back to lab frame using transpose of rotation matrix: |
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|
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if (j_is_Metal) { |
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idat.t1 += Atrans * trq; |
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} else { |
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idat.t2 += Atrans * trq; |
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} |
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|
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// Now, on to the forces (still in body frame of water) |
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|
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Vector3d ftmp = idat.vdwMult * idat.sw * dvdr; |
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|
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// rotate the terms back into the lab frame: |
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Vector3d flab; |
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if (j_is_Metal) { |
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flab = Atrans * ftmp; |
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} else { |
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flab = - Atrans * ftmp; |
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} |
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|
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idat.f1 += flab; |
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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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RealType MAW::getSuggestedCutoffRadius(AtomType* at1, AtomType* at2) { |
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if (!initialized_) initialize(); |
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pair<AtomType*, AtomType*> key = make_pair(at1, at2); |
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map<pair<AtomType*, AtomType*>, MAWInteractionData>::iterator it; |
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it = MixingMap.find(key); |
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if (it == MixingMap.end()) |
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return 0.0; |
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else { |
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MAWInteractionData mixer = (*it).second; |
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|
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RealType R_e = mixer.Re; |
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RealType beta = mixer.beta; |
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// This value of the r corresponds to an energy about 1.48% of |
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// the energy at the bottom of the Morse well. For comparison, the |
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// Lennard-Jones function is about 1.63% of it's minimum value at |
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// a distance of 2.5 sigma. |
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return (4.9 + beta * R_e) / beta; |
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} |
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} |
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} |
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|
