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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/SC.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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namespace OpenMD { |
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|
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|
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SC::SC() : name_("SC"), initialized_(false), forceField_(NULL), |
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scRcut_(0.0), np_(3000) {} |
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|
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RealType SC::getM(AtomType* atomType1, AtomType* atomType2) { |
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SuttonChenAdapter sca1 = SuttonChenAdapter(atomType1); |
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SuttonChenAdapter sca2 = SuttonChenAdapter(atomType2); |
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RealType m1 = sca1.getM(); |
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RealType m2 = sca2.getM(); |
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return 0.5 * (m1 + m2); |
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} |
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|
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RealType SC::getN(AtomType* atomType1, AtomType* atomType2) { |
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SuttonChenAdapter sca1 = SuttonChenAdapter(atomType1); |
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SuttonChenAdapter sca2 = SuttonChenAdapter(atomType2); |
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RealType n1 = sca1.getN(); |
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RealType n2 = sca2.getN(); |
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return 0.5 * (n1 + n2); |
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} |
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|
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RealType SC::getAlpha(AtomType* atomType1, AtomType* atomType2) { |
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SuttonChenAdapter sca1 = SuttonChenAdapter(atomType1); |
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SuttonChenAdapter sca2 = SuttonChenAdapter(atomType2); |
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RealType alpha1 = sca1.getAlpha(); |
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RealType alpha2 = sca2.getAlpha(); |
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|
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ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
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std::string DistanceMix = fopts.getDistanceMixingRule(); |
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toUpper(DistanceMix); |
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|
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if (DistanceMix == "GEOMETRIC") |
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return sqrt(alpha1 * alpha2); |
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else |
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return 0.5 * (alpha1 + alpha2); |
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} |
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|
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RealType SC::getEpsilon(AtomType* atomType1, AtomType* atomType2) { |
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SuttonChenAdapter sca1 = SuttonChenAdapter(atomType1); |
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SuttonChenAdapter sca2 = SuttonChenAdapter(atomType2); |
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RealType epsilon1 = sca1.getEpsilon(); |
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RealType epsilon2 = sca2.getEpsilon(); |
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return sqrt(epsilon1 * epsilon2); |
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} |
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|
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void SC::initialize() { |
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// find all of the SC atom Types: |
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ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes(); |
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ForceField::AtomTypeContainer::MapTypeIterator i; |
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AtomType* at; |
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|
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for (at = atomTypes->beginType(i); at != NULL; |
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at = atomTypes->nextType(i)) { |
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SuttonChenAdapter sca = SuttonChenAdapter(at); |
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if (sca.isSuttonChen()) |
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addType(at); |
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} |
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initialized_ = true; |
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} |
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|
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|
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|
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void SC::addType(AtomType* atomType){ |
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|
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SuttonChenAdapter sca = SuttonChenAdapter(atomType); |
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SCAtomData scAtomData; |
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|
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scAtomData.c = sca.getC(); |
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scAtomData.m = sca.getM(); |
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scAtomData.n = sca.getN(); |
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scAtomData.alpha = sca.getAlpha(); |
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scAtomData.epsilon = sca.getEpsilon(); |
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scAtomData.rCut = 2.0 * scAtomData.alpha; |
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|
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// add it to the map: |
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|
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pair<map<int,AtomType*>::iterator,bool> ret; |
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ret = SClist.insert( pair<int, AtomType*>(atomType->getIdent(), atomType) ); |
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if (ret.second == false) { |
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sprintf( painCave.errMsg, |
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"SC already had a previous entry with ident %d\n", |
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atomType->getIdent() ); |
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painCave.severity = OPENMD_INFO; |
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painCave.isFatal = 0; |
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simError(); |
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} |
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|
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SCMap[atomType] = scAtomData; |
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|
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// Now, iterate over all known types and add to the mixing map: |
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|
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map<AtomType*, SCAtomData>::iterator it; |
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for( it = SCMap.begin(); it != SCMap.end(); ++it) { |
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|
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AtomType* atype2 = (*it).first; |
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|
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SCInteractionData mixer; |
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|
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mixer.alpha = getAlpha(atomType, atype2); |
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mixer.rCut = 2.0 * mixer.alpha; |
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mixer.epsilon = getEpsilon(atomType, atype2); |
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mixer.m = getM(atomType, atype2); |
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mixer.n = getN(atomType, atype2); |
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|
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RealType dr = mixer.rCut / (np_ - 1); |
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vector<RealType> rvals; |
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vector<RealType> vvals; |
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vector<RealType> phivals; |
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|
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rvals.push_back(0.0); |
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vvals.push_back(0.0); |
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phivals.push_back(0.0); |
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|
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for (int k = 1; k < np_; k++) { |
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RealType r = dr * k; |
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rvals.push_back(r); |
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vvals.push_back( mixer.epsilon * pow(mixer.alpha/r, mixer.n) ); |
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phivals.push_back( pow(mixer.alpha/r, mixer.m) ); |
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} |
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|
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mixer.vCut = mixer.epsilon * pow(mixer.alpha/mixer.rCut, mixer.n); |
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|
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CubicSpline* V = new CubicSpline(); |
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V->addPoints(rvals, vvals); |
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|
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CubicSpline* phi = new CubicSpline(); |
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phi->addPoints(rvals, phivals); |
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|
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mixer.V = V; |
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mixer.phi = phi; |
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|
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mixer.explicitlySet = false; |
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|
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pair<AtomType*, AtomType*> key1, key2; |
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key1 = make_pair(atomType, atype2); |
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key2 = make_pair(atype2, atomType); |
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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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return; |
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} |
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|
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void SC::addExplicitInteraction(AtomType* atype1, AtomType* atype2, |
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RealType epsilon, RealType m, RealType n, |
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RealType alpha) { |
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|
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// in case these weren't already in the map |
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addType(atype1); |
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addType(atype2); |
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|
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SCInteractionData mixer; |
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|
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mixer.epsilon = epsilon; |
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mixer.m = m; |
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mixer.n = n; |
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mixer.alpha = alpha; |
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mixer.rCut = 2.0 * mixer.alpha; |
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|
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RealType dr = mixer.rCut / (np_ - 1); |
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vector<RealType> rvals; |
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vector<RealType> vvals; |
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vector<RealType> phivals; |
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|
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rvals.push_back(0.0); |
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vvals.push_back(0.0); |
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phivals.push_back(0.0); |
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|
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for (int k = 1; k < np_; k++) { |
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RealType r = dr * k; |
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rvals.push_back(r); |
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vvals.push_back( mixer.epsilon * pow(mixer.alpha/r, mixer.n) ); |
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phivals.push_back( pow(mixer.alpha/r, mixer.m) ); |
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} |
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|
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mixer.vCut = mixer.epsilon * pow(mixer.alpha/mixer.rCut, mixer.n); |
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|
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CubicSpline* V = new CubicSpline(); |
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V->addPoints(rvals, vvals); |
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|
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CubicSpline* phi = new CubicSpline(); |
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phi->addPoints(rvals, phivals); |
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|
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mixer.V = V; |
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mixer.phi = phi; |
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|
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mixer.explicitlySet = true; |
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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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return; |
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} |
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|
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void SC::calcDensity(InteractionData &idat) { |
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|
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if (!initialized_) initialize(); |
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|
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SCInteractionData mixer = MixingMap[ idat.atypes ]; |
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|
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RealType rcij = mixer.rCut; |
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|
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if ( *(idat.rij) < rcij) { |
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RealType rho = mixer.phi->getValueAt( *(idat.rij) ); |
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*(idat.rho1) += rho; |
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*(idat.rho2) += rho; |
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} |
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|
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return; |
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} |
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|
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void SC::calcFunctional(SelfData &sdat) { |
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|
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if (!initialized_) initialize(); |
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|
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SCAtomData data1 = SCMap[sdat.atype]; |
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|
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RealType u = - data1.c * data1.epsilon * sqrt( *(sdat.rho) ); |
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*(sdat.frho) = u; |
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*(sdat.dfrhodrho) = 0.5 * *(sdat.frho) / *(sdat.rho); |
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|
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(*(sdat.pot))[METALLIC_FAMILY] += u; |
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if (sdat.doParticlePot) { |
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*(sdat.particlePot) += u; |
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} |
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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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void SC::calcForce(InteractionData &idat) { |
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|
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if (!initialized_) initialize(); |
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|
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SCAtomData data1 = SCMap[idat.atypes.first]; |
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SCAtomData data2 = SCMap[idat.atypes.second]; |
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|
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SCInteractionData mixer = MixingMap[idat.atypes]; |
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|
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RealType rcij = mixer.rCut; |
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|
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if ( *(idat.rij) < rcij) { |
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RealType vcij = mixer.vCut; |
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|
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pair<RealType, RealType> res; |
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|
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res = mixer.phi->getValueAndDerivativeAt( *(idat.rij) ); |
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RealType rhtmp = res.first; |
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RealType drhodr = res.second; |
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|
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res = mixer.V->getValueAndDerivativeAt( *(idat.rij) ); |
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RealType vptmp = res.first; |
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RealType dvpdr = res.second; |
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|
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RealType pot_temp = vptmp - vcij; |
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*(idat.vpair) += pot_temp; |
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|
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RealType dudr = drhodr * ( *(idat.dfrho1) + *(idat.dfrho2) ) + dvpdr; |
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|
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*(idat.f1) += *(idat.d) * dudr / *(idat.rij) ; |
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|
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if (idat.doParticlePot) { |
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// particlePot is the difference between the full potential and |
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// the full potential without the presence of a particular |
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// particle (atom1). |
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// |
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// This reduces the density at other particle locations, so we |
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// need to recompute the density at atom2 assuming atom1 didn't |
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// contribute. This then requires recomputing the density |
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// functional for atom2 as well. |
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|
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*(idat.particlePot1) -= data2.c * data2.epsilon * |
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sqrt( *(idat.rho2) - rhtmp) + *(idat.frho2); |
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|
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*(idat.particlePot2) -= data1.c * data1.epsilon * |
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sqrt( *(idat.rho1) - rhtmp) + *(idat.frho1); |
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} |
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|
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(*(idat.pot))[METALLIC_FAMILY] += pot_temp; |
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} |
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|
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return; |
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} |
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|
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RealType SC::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) { |
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if (!initialized_) initialize(); |
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|
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map<pair<AtomType*, AtomType*>, SCInteractionData>::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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SCInteractionData mixer = (*it).second; |
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return mixer.rCut; |
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} |
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} |
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} |
