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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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#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() : initialized_(false), forceField_(NULL), name_("MAW") {} |
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|
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void MAW::initialize() { |
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|
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MAWtypes.clear(); |
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MAWtids.clear(); |
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MixingMap.clear(); |
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MAWtids.resize( forceField_->getNAtomType(), -1); |
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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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ForceField::NonBondedInteractionTypeContainer::KeyType keys; |
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NonBondedInteractionType* nbt; |
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int mtid1, mtid2; |
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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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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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int atid1 = at1->getIdent(); |
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if (MAWtids[atid1] == -1) { |
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mtid1 = MAWtypes.size(); |
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MAWtypes.insert(atid1); |
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MAWtids[atid1] = mtid1; |
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} |
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int atid2 = at2->getIdent(); |
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if (MAWtids[atid2] == -1) { |
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mtid2 = MAWtypes.size(); |
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MAWtypes.insert(atid2); |
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MAWtids[atid2] = mtid2; |
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} |
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|
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MAWInteractionType* mit = dynamic_cast<MAWInteractionType*>(nbt); |
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|
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if (mit == NULL) { |
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sprintf( painCave.errMsg, |
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"MAW::initialize could not convert NonBondedInteractionType\n" |
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"\tto MAWInteractionType 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 De = mit->getD(); |
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RealType beta = mit->getBeta(); |
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RealType Re = mit->getR(); |
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RealType ca1 = mit->getCA1(); |
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RealType cb1 = mit->getCB1(); |
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|
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addExplicitInteraction(at1, at2, |
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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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mixer.j_is_Metal = atype2->isMetal(); |
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|
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int mtid1 = MAWtids[atype1->getIdent()]; |
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int mtid2 = MAWtids[atype2->getIdent()]; |
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int nM = MAWtypes.size(); |
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|
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MixingMap.resize(nM); |
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MixingMap[mtid1].resize(nM); |
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|
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MixingMap[mtid1][mtid2] = mixer; |
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if (mtid2 != mtid1) { |
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MixingMap[mtid2].resize(nM); |
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mixer.j_is_Metal = atype1->isMetal(); |
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MixingMap[mtid2][mtid1] = 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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MAWInteractionData &mixer = MixingMap[MAWtids[idat.atid1]][MAWtids[idat.atid2]]; |
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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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Vector3d r; |
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RotMat3x3d Atrans; |
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if (mixer.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 (idat.shiftedPot || idat.shiftedForce) { |
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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 (idat.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 (idat.shiftedForce) { |
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myPotC = D_e * (expfnc2C - 2.0 * expfncC); |
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myDerivC = 2.0 * D_e * beta * (expfncC - 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 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) + |
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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))[VANDERWAALS_FAMILY] += *(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 (mixer.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 (mixer.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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RealType MAW::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
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if (!initialized_) initialize(); |
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int atid1 = atypes.first->getIdent(); |
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int atid2 = atypes.second->getIdent(); |
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int mtid1 = MAWtids[atid1]; |
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int mtid2 = MAWtids[atid2]; |
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|
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if ( mtid1 == -1 || mtid2 == -1) return 0.0; |
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else { |
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MAWInteractionData mixer = MixingMap[mtid1][mtid2]; |
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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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|
