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gezelter |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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#include <stdio.h> |
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#include <string.h> |
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#include <cmath> |
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#include "nonbonded/SC.hpp" |
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#include "utils/simError.h" |
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#include "types/NonBondedInteractionType.hpp" |
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namespace OpenMD { |
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bool SC::initialized_ = false; |
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RealType SC::scRcut_ = 0.0; |
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int SC::np_ = 3000; |
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ForceField* SC::forceField_ = NULL; |
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map<int, AtomType*> SC::SClist; |
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map<AtomType*, SCAtomData> SC::SCMap; |
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map<pair<AtomType*, AtomType*>, SCInteractionData> SC::MixingMap; |
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SC* SC::_instance = NULL; |
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SC* SC::Instance() { |
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if (!_instance) { |
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_instance = new SC(); |
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} |
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return _instance; |
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} |
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SCParam SC::getSCParam(AtomType* atomType) { |
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// Do sanity checking on the AtomType we were passed before |
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// building any data structures: |
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if (!atomType->isSC()) { |
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sprintf( painCave.errMsg, |
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"SC::getSCParam was passed an atomType (%s) that does not\n" |
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"\tappear to be a Sutton-Chen (SC) atom.\n", |
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atomType->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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GenericData* data = atomType->getPropertyByName("SC"); |
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if (data == NULL) { |
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sprintf( painCave.errMsg, "SC::getSCParam could not find SC\n" |
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"\tparameters for atomType %s.\n", |
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atomType->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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SCParamGenericData* scData = dynamic_cast<SCParamGenericData*>(data); |
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if (scData == NULL) { |
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sprintf( painCave.errMsg, |
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"SC::getSCParam could not convert GenericData to SCParamGenericData\n" |
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"\tfor atom type %s\n", atomType->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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return scData->getData(); |
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} |
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RealType SC::getC(AtomType* atomType) { |
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SCParam scParam = getSCParam(atomType); |
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return scParam.c; |
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} |
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RealType SC::getM(AtomType* atomType) { |
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SCParam scParam = getSCParam(atomType); |
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return scParam.m; |
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} |
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RealType SC::getM(AtomType* atomType1, AtomType* atomType2) { |
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RealType m1 = getM(atomType1); |
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RealType m2 = getM(atomType2); |
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return 0.5 * (m1 + m2); |
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} |
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RealType SC::getN(AtomType* atomType) { |
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SCParam scParam = getSCParam(atomType); |
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return scParam.n; |
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} |
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RealType SC::getN(AtomType* atomType1, AtomType* atomType2) { |
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RealType n1 = getN(atomType1); |
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RealType n2 = getN(atomType2); |
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return 0.5 * (n1 + n2); |
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} |
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RealType SC::getAlpha(AtomType* atomType) { |
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SCParam scParam = getSCParam(atomType); |
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return scParam.alpha; |
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} |
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RealType SC::getAlpha(AtomType* atomType1, AtomType* atomType2) { |
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RealType alpha1 = getAlpha(atomType1); |
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RealType alpha2 = getAlpha(atomType2); |
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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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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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RealType SC::getEpsilon(AtomType* atomType) { |
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SCParam scParam = getSCParam(atomType); |
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return scParam.epsilon; |
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} |
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RealType SC::getEpsilon(AtomType* atomType1, AtomType* atomType2) { |
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RealType epsilon1 = getEpsilon(atomType1); |
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RealType epsilon2 = getEpsilon(atomType2); |
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return sqrt(epsilon1 * epsilon2); |
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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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for (at = atomTypes->beginType(i); at != NULL; |
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at = atomTypes->nextType(i)) { |
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if (at->isSC()) |
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addType(at); |
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} |
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initialized_ = true; |
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} |
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void SC::addType(AtomType* atomType){ |
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SCAtomData scAtomData; |
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scAtomData.c = getC(atomType); |
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scAtomData.m = getM(atomType); |
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scAtomData.n = getN(atomType); |
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scAtomData.alpha = getAlpha(atomType); |
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scAtomData.epsilon = getEpsilon(atomType); |
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scAtomData.rCut = 2.0 * scAtomData.alpha; |
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// add it to the map: |
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AtomTypeProperties atp = atomType->getATP(); |
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pair<map<int,AtomType*>::iterator,bool> ret; |
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ret = SClist.insert( pair<int, AtomType*>(atp.ident, 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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atp.ident); |
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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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SCMap[atomType] = scAtomData; |
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// Now, iterate over all known types and add to the mixing map: |
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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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AtomType* atype2 = (*it).first; |
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SCInteractionData mixer; |
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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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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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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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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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mixer.vCut = mixer.epsilon * pow(mixer.alpha/mixer.rCut, mixer.n); |
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CubicSpline* V = new CubicSpline(); |
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V->addPoints(rvals, vvals); |
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CubicSpline* phi = new CubicSpline(); |
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phi->addPoints(rvals, phivals); |
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mixer.V = V; |
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mixer.phi = phi; |
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mixer.explicitlySet = false; |
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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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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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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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// 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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SCInteractionData mixer; |
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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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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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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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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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mixer.vCut = mixer.epsilon * pow(mixer.alpha/mixer.rCut, mixer.n); |
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CubicSpline* V = new CubicSpline(); |
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V->addPoints(rvals, vvals); |
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CubicSpline* phi = new CubicSpline(); |
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phi->addPoints(rvals, phivals); |
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mixer.V = V; |
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mixer.phi = phi; |
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mixer.explicitlySet = true; |
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pair<AtomType*, AtomType*> key1, key2; |
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key1 = make_pair(atype1, atype2); |
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key2 = make_pair(atype2, atype1); |
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MixingMap[key1] = mixer; |
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if (key2 != key1) { |
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MixingMap[key2] = mixer; |
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} |
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return; |
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} |
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void SC::calcDensity(AtomType* at1, AtomType* at2, const RealType rij, |
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RealType &rho_i_at_j, RealType &rho_j_at_i) { |
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| 321 |
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if (!initialized_) initialize(); |
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SCInteractionData mixer = MixingMap[make_pair(at1, at2)]; |
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rho_i_at_j = mixer.phi->getValueAt(rij); |
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rho_j_at_i = rho_i_at_j; |
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return; |
| 329 |
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} |
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void SC::calcFunctional(AtomType* at1, RealType rho, RealType &frho, |
| 332 |
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RealType &dfrhodrho) { |
| 333 |
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| 334 |
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if (!initialized_) initialize(); |
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SCAtomData data1 = SCMap[at1]; |
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frho = - data1.c * data1.epsilon * sqrt(rho); |
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dfrhodrho = 0.5 * frho / rho; |
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return; |
| 342 |
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} |
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| 345 |
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void SC::calcForce(AtomType* at1, AtomType* at2, Vector3d d, |
| 346 |
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RealType rij, RealType r2, RealType sw, |
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RealType &vpair, RealType &pot, Vector3d &f1, |
| 348 |
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RealType rho_i, RealType rho_j, |
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RealType dfrhodrho_i, RealType dfrhodrho_j, |
| 350 |
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RealType &fshift_i, RealType &fshift_j) { |
| 351 |
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| 352 |
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if (!initialized_) initialize(); |
| 353 |
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| 354 |
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SCAtomData data1 = SCMap[at1]; |
| 355 |
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SCAtomData data2 = SCMap[at1]; |
| 356 |
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| 357 |
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SCInteractionData mixer = MixingMap[make_pair(at1, at2)]; |
| 358 |
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| 359 |
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RealType rcij = mixer.rCut; |
| 360 |
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RealType vcij = mixer.vCut; |
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| 362 |
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pair<RealType, RealType> res; |
| 363 |
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| 364 |
|
|
res = mixer.phi->getValueAndDerivativeAt(rij); |
| 365 |
|
|
RealType rhtmp = res.first; |
| 366 |
|
|
RealType drhodr = res.second; |
| 367 |
|
|
|
| 368 |
|
|
res = mixer.V->getValueAndDerivativeAt(rij); |
| 369 |
|
|
RealType vptmp = res.first; |
| 370 |
|
|
RealType dvpdr = res.second; |
| 371 |
|
|
|
| 372 |
|
|
RealType pot_temp = vptmp - vcij; |
| 373 |
|
|
vpair += pot_temp; |
| 374 |
|
|
|
| 375 |
|
|
RealType dudr = drhodr * (dfrhodrho_i + dfrhodrho_j) + dvpdr; |
| 376 |
|
|
|
| 377 |
|
|
f1 += d * dudr / rij; |
| 378 |
|
|
|
| 379 |
|
|
// particle_pot is the difference between the full potential |
| 380 |
|
|
// and the full potential without the presence of a particular |
| 381 |
|
|
// particle (atom1). |
| 382 |
|
|
// |
| 383 |
|
|
// This reduces the density at other particle locations, so |
| 384 |
|
|
// we need to recompute the density at atom2 assuming atom1 |
| 385 |
|
|
// didn't contribute. This then requires recomputing the |
| 386 |
|
|
// density functional for atom2 as well. |
| 387 |
|
|
// |
| 388 |
|
|
// Most of the particle_pot heavy lifting comes from the |
| 389 |
|
|
// pair interaction, and will be handled by vpair. |
| 390 |
|
|
|
| 391 |
|
|
fshift_i = - data1.c * data1.epsilon * sqrt(rho_i - rhtmp); |
| 392 |
|
|
fshift_j = - data2.c * data2.epsilon * sqrt(rho_j - rhtmp); |
| 393 |
|
|
|
| 394 |
|
|
pot += pot_temp; |
| 395 |
|
|
|
| 396 |
|
|
return; |
| 397 |
|
|
} |
| 398 |
|
|
|
| 399 |
|
|
|
| 400 |
|
|
void SC::calc_sc_prepair_rho(int *atid1, int *atid2, RealType *rij, |
| 401 |
|
|
RealType* rho_i_at_j, RealType* rho_j_at_i){ |
| 402 |
|
|
|
| 403 |
|
|
if (!initialized_) initialize(); |
| 404 |
|
|
|
| 405 |
|
|
AtomType* atype1 = SClist[*atid1]; |
| 406 |
|
|
AtomType* atype2 = SClist[*atid2]; |
| 407 |
|
|
|
| 408 |
|
|
calcDensity(atype1, atype2, *rij, *rho_i_at_j, *rho_j_at_i); |
| 409 |
|
|
|
| 410 |
|
|
return; |
| 411 |
|
|
} |
| 412 |
|
|
|
| 413 |
|
|
void SC::calc_sc_preforce_Frho(int *atid1, RealType *rho, RealType *frho, |
| 414 |
|
|
RealType *dfrhodrho) { |
| 415 |
|
|
|
| 416 |
|
|
if (!initialized_) initialize(); |
| 417 |
|
|
|
| 418 |
|
|
AtomType* atype1 = SClist[*atid1]; |
| 419 |
|
|
|
| 420 |
|
|
calcFunctional(atype1, *rho, *frho, *dfrhodrho); |
| 421 |
|
|
|
| 422 |
|
|
return; |
| 423 |
|
|
} |
| 424 |
|
|
|
| 425 |
|
|
RealType SC::getSCcut(int *atid1) { |
| 426 |
|
|
|
| 427 |
|
|
if (!initialized_) initialize(); |
| 428 |
|
|
|
| 429 |
|
|
AtomType* atype1 = SClist[*atid1]; |
| 430 |
|
|
|
| 431 |
|
|
return 2.0 * getAlpha(atype1); |
| 432 |
|
|
} |
| 433 |
|
|
|
| 434 |
|
|
void SC::do_sc_pair(int *atid1, int *atid2, RealType *d, RealType *rij, |
| 435 |
|
|
RealType *r2, RealType *sw, RealType *vpair, |
| 436 |
|
|
RealType *pot, RealType *f1, RealType *rho1, |
| 437 |
|
|
RealType *rho2, RealType *dfrho1, RealType *dfrho2, |
| 438 |
|
|
RealType *fshift1, RealType *fshift2) { |
| 439 |
|
|
|
| 440 |
|
|
if (!initialized_) initialize(); |
| 441 |
|
|
|
| 442 |
|
|
AtomType* atype1 = SClist[*atid1]; |
| 443 |
|
|
AtomType* atype2 = SClist[*atid2]; |
| 444 |
|
|
|
| 445 |
|
|
Vector3d disp(d[0], d[1], d[2]); |
| 446 |
|
|
Vector3d frc(f1[0], f1[1], f1[2]); |
| 447 |
|
|
|
| 448 |
|
|
calcForce(atype1, atype2, disp, *rij, *r2, *sw, *vpair, *pot, frc, |
| 449 |
|
|
*rho1, *rho2, *dfrho1, *dfrho2, *fshift1, *fshift2); |
| 450 |
|
|
|
| 451 |
|
|
f1[0] = frc.x(); |
| 452 |
|
|
f1[1] = frc.y(); |
| 453 |
|
|
f1[2] = frc.z(); |
| 454 |
|
|
|
| 455 |
|
|
return; |
| 456 |
|
|
} |
| 457 |
|
|
|
| 458 |
|
|
void SC::setCutoffSC(RealType *thisRcut) { |
| 459 |
|
|
scRcut_ = *thisRcut; |
| 460 |
|
|
} |
| 461 |
|
|
} |
| 462 |
|
|
|
| 463 |
|
|
extern "C" { |
| 464 |
|
|
|
| 465 |
|
|
#define fortranCalcDensity FC_FUNC(calc_sc_prepair_rho, CALC_SC_PREPAIR_RHO) |
| 466 |
|
|
#define fortranCalcFunctional FC_FUNC(calc_sc_preforce_frho, CALC_SC_PREFORCE_FRHO) |
| 467 |
|
|
#define fortranCalcForce FC_FUNC(do_sc_pair, DO_SC_PAIR) |
| 468 |
|
|
#define fortranSetCutoffSC FC_FUNC(setcutoffsc, SETCUTOFFSC) |
| 469 |
|
|
#define fortranGetSCcut FC_FUNC(getsccut, GETSCCUT) |
| 470 |
|
|
|
| 471 |
|
|
|
| 472 |
|
|
void fortranCalcDensity(int *atid1, int *atid2, RealType *rij, |
| 473 |
|
|
RealType *rho_i_at_j, RealType *rho_j_at_i) { |
| 474 |
|
|
|
| 475 |
|
|
return OpenMD::SC::Instance()->calc_sc_prepair_rho(atid1, atid2, rij, |
| 476 |
|
|
rho_i_at_j, |
| 477 |
|
|
rho_j_at_i); |
| 478 |
|
|
} |
| 479 |
|
|
void fortranCalcFunctional(int *atid1, RealType *rho, RealType *frho, |
| 480 |
|
|
RealType *dfrhodrho) { |
| 481 |
|
|
|
| 482 |
|
|
return OpenMD::SC::Instance()->calc_sc_preforce_Frho(atid1, rho, frho, |
| 483 |
|
|
dfrhodrho); |
| 484 |
|
|
|
| 485 |
|
|
} |
| 486 |
|
|
void fortranSetCutoffSC(RealType *rcut) { |
| 487 |
|
|
return OpenMD::SC::Instance()->setCutoffSC(rcut); |
| 488 |
|
|
} |
| 489 |
|
|
void fortranCalcForce(int *atid1, int *atid2, RealType *d, RealType *rij, |
| 490 |
|
|
RealType *r2, RealType *sw, RealType *vpair, |
| 491 |
|
|
RealType *pot, RealType *f1, RealType *rho1, |
| 492 |
|
|
RealType *rho2, RealType *dfrho1, RealType *dfrho2, |
| 493 |
|
|
RealType *fshift1, RealType *fshift2){ |
| 494 |
|
|
|
| 495 |
|
|
return OpenMD::SC::Instance()->do_sc_pair(atid1, atid2, d, rij, |
| 496 |
|
|
r2, sw, vpair, |
| 497 |
|
|
pot, f1, rho1, |
| 498 |
|
|
rho2, dfrho1, dfrho2, |
| 499 |
|
|
fshift1, fshift2); |
| 500 |
|
|
} |
| 501 |
|
|
RealType fortranGetSCcut(int* atid) { |
| 502 |
|
|
return OpenMD::SC::Instance()->getSCcut(atid); |
| 503 |
|
|
} |
| 504 |
|
|
|
| 505 |
|
|
} |
