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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] 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/RepulsivePower.hpp" |
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#include "utils/simError.h" |
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#include "types/RepulsivePowerInteractionType.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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RepulsivePower::RepulsivePower() : name_("RepulsivePower"), |
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initialized_(false), forceField_(NULL) {} |
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|
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void RepulsivePower::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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ForceField::NonBondedInteractionTypeContainer::KeyType keys; |
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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->isRepulsivePower()) { |
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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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|
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RepulsivePowerInteractionType* rpit = dynamic_cast<RepulsivePowerInteractionType*>(nbt); |
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|
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if (rpit == NULL) { |
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sprintf( painCave.errMsg, |
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"RepulsivePower::initialize could not convert NonBondedInteractionType\n" |
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"\tto RepulsivePowerInteractionType 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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|
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RealType sigma = rpit->getSigma(); |
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RealType epsilon = rpit->getEpsilon(); |
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int nRep = rpit->getNrep(); |
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|
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addExplicitInteraction(at1, at2, sigma, epsilon, nRep); |
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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 RepulsivePower::addExplicitInteraction(AtomType* atype1, |
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AtomType* atype2, |
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RealType sigma, |
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RealType epsilon, |
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int nRep) { |
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|
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RPInteractionData 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.nRep = nRep; |
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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 RepulsivePower::calcForce(InteractionData &idat) { |
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|
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if (!initialized_) initialize(); |
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|
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map<pair<AtomType*, AtomType*>, RPInteractionData>::iterator it; |
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it = MixingMap.find( idat.atypes ); |
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|
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if (it != MixingMap.end()) { |
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|
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RPInteractionData mixer = (*it).second; |
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RealType sigmai = mixer.sigmai; |
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RealType epsilon = mixer.epsilon; |
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int nRep = mixer.nRep; |
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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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getNRepulsionFunc(ros, nRep, 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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getNRepulsionFunc(rcos, nRep, 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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getNRepulsionFunc(rcos, nRep, 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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|
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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 RepulsivePower::getNRepulsionFunc(RealType r, int n, RealType &pot, RealType &deriv) { |
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|
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RealType ri = 1.0 / r; |
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RealType rin = pow(ri, n); |
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RealType rin1 = rin * ri; |
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|
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pot = rin; |
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deriv = -n * rin1; |
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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 RepulsivePower::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
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if (!initialized_) initialize(); |
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map<pair<AtomType*, AtomType*>, RPInteractionData>::iterator it; |
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it = MixingMap.find(atypes); |
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if (it == MixingMap.end()) |
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return 0.0; |
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else { |
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RPInteractionData mixer = (*it).second; |
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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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} |
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|
