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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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#include <stdio.h> |
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#include <string.h> |
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|
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#include <cmath> |
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#include "nonbonded/Sticky.hpp" |
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#include "nonbonded/LJ.hpp" |
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#include "utils/simError.h" |
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|
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using namespace std; |
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namespace OpenMD { |
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|
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bool Sticky::initialized_ = false; |
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ForceField* Sticky::forceField_ = NULL; |
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map<int, AtomType*> Sticky::StickyMap; |
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map<pair<AtomType*, AtomType*>, StickyInteractionData> Sticky::MixingMap; |
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|
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Sticky* Sticky::_instance = NULL; |
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|
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Sticky* Sticky::Instance() { |
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if (!_instance) { |
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_instance = new Sticky(); |
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} |
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return _instance; |
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} |
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|
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StickyParam Sticky::getStickyParam(AtomType* atomType) { |
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|
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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->isSticky() && !atomType->isStickyPower()) { |
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sprintf( painCave.errMsg, |
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"Sticky::getStickyParam was passed an atomType (%s) that does\n" |
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"\tnot appear to be a Sticky 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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|
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DirectionalAtomType* daType = dynamic_cast<DirectionalAtomType*>(atomType); |
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GenericData* data = daType->getPropertyByName("Sticky"); |
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if (data == NULL) { |
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sprintf( painCave.errMsg, "Sticky::getStickyParam could not find\n" |
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"\tSticky parameters for atomType %s.\n", |
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daType->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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StickyParamGenericData* stickyData = dynamic_cast<StickyParamGenericData*>(data); |
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if (stickyData == NULL) { |
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sprintf( painCave.errMsg, |
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"Sticky::getStickyParam could not convert GenericData to\n" |
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"\tStickyParamGenericData for atom type %s\n", |
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daType->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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return stickyData->getData(); |
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} |
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|
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void Sticky::initialize() { |
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|
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ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
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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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// Sticky handles all of the Sticky-Sticky interactions |
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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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|
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if (at->isSticky() || at->isStickyPower()) |
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addType(at); |
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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 Sticky::addType(AtomType* atomType){ |
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// add it to the map: |
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AtomTypeProperties atp = atomType->getATP(); |
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|
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pair<map<int,AtomType*>::iterator,bool> ret; |
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ret = StickyMap.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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"Sticky 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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|
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RealType w0i, v0i, v0pi, rli, rui, rlpi, rupi; |
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|
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StickyParam sticky1 = getStickyParam(atomType); |
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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<int, AtomType*>::iterator it; |
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for( it = StickyMap.begin(); it != StickyMap.end(); ++it) { |
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|
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AtomType* atype2 = (*it).second; |
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|
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StickyParam sticky2 = getStickyParam(atype2); |
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|
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StickyInteractionData mixer; |
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|
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// Mixing two different sticky types is silly, but if you want 2 |
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// sticky types in your simulation, we'll let you do it with the |
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// Lorentz- Berthelot mixing rules (which happen to do the right thing |
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// when atomType and atype2 happen to be the same. |
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|
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mixer.rl = 0.5 * ( sticky1.rl + sticky2.rl ); |
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mixer.ru = 0.5 * ( sticky1.ru + sticky2.ru ); |
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mixer.rlp = 0.5 * ( sticky1.rlp + sticky2.rlp ); |
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mixer.rup = 0.5 * ( sticky1.rup + sticky2.rup ); |
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mixer.rbig = max(mixer.ru, mixer.rup); |
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mixer.w0 = sqrt( sticky1.w0 * sticky2.w0 ); |
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mixer.v0 = sqrt( sticky1.v0 * sticky2.v0 ); |
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mixer.v0p = sqrt( sticky1.v0p * sticky2.v0p ); |
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mixer.isPower = atomType->isStickyPower() && atype2->isStickyPower(); |
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|
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CubicSpline* s = new CubicSpline(); |
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s->addPoint(mixer.rl, 1.0); |
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s->addPoint(mixer.ru, 0.0); |
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mixer.s = s; |
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|
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CubicSpline* sp = new CubicSpline(); |
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sp->addPoint(mixer.rlp, 1.0); |
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sp->addPoint(mixer.rup, 0.0); |
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mixer.sp = sp; |
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|
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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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} |
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|
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RealType Sticky::getStickyCut(int atid) { |
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if (!initialized_) initialize(); |
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std::map<int, AtomType*> :: const_iterator it; |
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it = StickyMap.find(atid); |
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if (it == StickyMap.end()) { |
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sprintf( painCave.errMsg, |
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"Sticky::getStickyCut could not find atid %d in StickyMap\n", |
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(atid)); |
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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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AtomType* atype = it->second; |
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return MixingMap[make_pair(atype, atype)].rbig; |
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} |
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|
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|
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void Sticky::calcForce(AtomType* at1, AtomType* at2, Vector3d d, |
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RealType rij, RealType r2, RealType sw, |
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RealType &vpair, RealType &pot, |
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RotMat3x3d A1, RotMat3x3d A2, Vector3d &f1, |
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Vector3d &t1, Vector3d &t2) { |
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|
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// This routine does only the sticky portion of the SSD potential |
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// [Chandra and Ichiye, J. Chem. Phys. 111, 2701 (1999)]. |
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// The Lennard-Jones and dipolar interaction must be handled separately. |
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|
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// We assume that the rotation matrices have already been calculated |
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// and placed in the A array. |
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|
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if (!initialized_) initialize(); |
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|
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pair<AtomType*, AtomType*> key = make_pair(at1, at2); |
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StickyInteractionData mixer = MixingMap[key]; |
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|
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RealType w0 = mixer.w0; |
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RealType v0 = mixer.v0; |
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RealType v0p = mixer.v0p; |
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RealType rl = mixer.rl; |
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RealType ru = mixer.ru; |
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RealType rlp = mixer.rlp; |
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RealType rup = mixer.rup; |
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RealType rbig = mixer.rbig; |
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bool isPower = mixer.isPower; |
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|
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if (rij <= rbig) { |
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|
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RealType r3 = r2 * rij; |
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RealType r5 = r3 * r2; |
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|
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RotMat3x3d A1trans = A1.transpose(); |
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RotMat3x3d A2trans = A2.transpose(); |
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|
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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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|
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Vector3d ri = A1 * d; |
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|
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// negative sign because this is the vector from j to i: |
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|
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Vector3d rj = -A2 * d; |
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|
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RealType xi = ri.x(); |
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RealType yi = ri.y(); |
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RealType zi = ri.z(); |
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|
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RealType xj = rj.x(); |
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RealType yj = rj.y(); |
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RealType zj = rj.z(); |
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|
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RealType xi2 = xi * xi; |
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RealType yi2 = yi * yi; |
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RealType zi2 = zi * zi; |
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|
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RealType xj2 = xj * xj; |
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RealType yj2 = yj * yj; |
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RealType zj2 = zj * zj; |
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|
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// calculate the switching info. from the splines |
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|
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RealType s = 0.0; |
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RealType dsdr = 0.0; |
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RealType sp = 0.0; |
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RealType dspdr = 0.0; |
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|
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if (rij < ru) { |
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if (rij < rl) { |
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s = 1.0; |
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dsdr = 0.0; |
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} else { |
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// we are in the switching region |
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|
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pair<RealType, RealType> res = mixer.s->getValueAndDerivativeAt(rij); |
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s = res.first; |
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dsdr = res.second; |
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} |
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} |
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|
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if (rij < rup) { |
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if (rij < rlp) { |
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sp = 1.0; |
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dspdr = 0.0; |
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} else { |
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// we are in the switching region |
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|
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pair<RealType, RealType> res =mixer.sp->getValueAndDerivativeAt(rij); |
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sp = res.first; |
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dspdr = res.second; |
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} |
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} |
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|
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RealType wi = 2.0*(xi2-yi2)*zi / r3; |
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RealType wj = 2.0*(xj2-yj2)*zj / r3; |
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RealType w = wi+wj; |
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|
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|
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RealType zif = zi/rij - 0.6; |
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RealType zis = zi/rij + 0.8; |
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|
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RealType zjf = zj/rij - 0.6; |
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RealType zjs = zj/rij + 0.8; |
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|
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RealType wip = zif*zif*zis*zis - w0; |
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RealType wjp = zjf*zjf*zjs*zjs - w0; |
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RealType wp = wip + wjp; |
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|
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Vector3d dwi(4.0*xi*zi/r3 - 6.0*xi*zi*(xi2-yi2)/r5, |
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- 4.0*yi*zi/r3 - 6.0*yi*zi*(xi2-yi2)/r5, |
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2.0*(xi2-yi2)/r3 - 6.0*zi2*(xi2-yi2)/r5); |
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|
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Vector3d dwj(4.0*xj*zj/r3 - 6.0*xj*zj*(xj2-yj2)/r5, |
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- 4.0*yj*zj/r3 - 6.0*yj*zj*(xj2-yj2)/r5, |
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2.0*(xj2-yj2)/r3 - 6.0*zj2*(xj2-yj2)/r5); |
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|
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RealType uglyi = zif*zif*zis + zif*zis*zis; |
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RealType uglyj = zjf*zjf*zjs + zjf*zjs*zjs; |
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|
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Vector3d dwip(-2.0*xi*zi*uglyi/r3, |
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-2.0*yi*zi*uglyi/r3, |
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2.0*(1.0/rij - zi2/r3)*uglyi); |
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|
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Vector3d dwjp(-2.0*xj*zj*uglyj/r3, |
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-2.0*yj*zj*uglyj/r3, |
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2.0*(1.0/rij - zj2/r3)*uglyj); |
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|
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Vector3d dwidu(4.0*(yi*zi2 + 0.5*yi*(xi2-yi2))/r3, |
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4.0*(xi*zi2 - 0.5*xi*(xi2-yi2))/r3, |
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- 8.0*xi*yi*zi/r3); |
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|
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Vector3d dwjdu(4.0*(yj*zj2 + 0.5*yj*(xj2-yj2))/r3, |
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4.0*(xj*zj2 - 0.5*xj*(xj2-yj2))/r3, |
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- 8.0*xj*yj*zj/r3); |
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|
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Vector3d dwipdu(2.0*yi*uglyi/rij, |
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-2.0*xi*uglyi/rij, |
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0.0); |
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|
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Vector3d dwjpdu(2.0*yj*uglyj/rij, |
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-2.0*xj*uglyj/rij, |
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0.0); |
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|
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if (isPower) { |
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RealType frac1 = 0.25; |
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RealType frac2 = 0.75; |
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RealType wi2 = wi*wi; |
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RealType wj2 = wj*wj; |
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// sticky power has no w' function: |
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w = frac1 * wi * wi2 + frac2*wi + frac1*wj*wj2 + frac2*wj + v0p; |
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wp = 0.0; |
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dwi = frac1*3.0*wi2*dwi + frac2*dwi; |
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dwj = frac1*3.0*wj2*dwi + frac2*dwi; |
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dwip = V3Zero; |
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dwjp = V3Zero; |
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dwidu = frac1*3.0*wi2*dwidu + frac2*dwidu; |
| 367 |
dwidu = frac1*3.0*wj2*dwjdu + frac2*dwjdu; |
| 368 |
dwipdu = V3Zero; |
| 369 |
dwjpdu = V3Zero; |
| 370 |
sp = 0.0; |
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dspdr = 0.0; |
| 372 |
} |
| 373 |
|
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vpair += 0.5*(v0*s*w + v0p*sp*wp); |
| 375 |
pot += 0.5*(v0*s*w + v0p*sp*wp)*sw; |
| 376 |
|
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// do the torques first since they are easy: |
| 378 |
// remember that these are still in the body-fixed axes |
| 379 |
|
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Vector3d ti = 0.5*sw*(v0*s*dwidu + v0p*sp*dwipdu); |
| 381 |
Vector3d tj = 0.5*sw*(v0*s*dwjdu + v0p*sp*dwjpdu); |
| 382 |
|
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// go back to lab frame using transpose of rotation matrix: |
| 384 |
|
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t1 += A1trans * ti; |
| 386 |
t2 += A2trans * tj; |
| 387 |
|
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// Now, on to the forces: |
| 389 |
|
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// first rotate the i terms back into the lab frame: |
| 391 |
|
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Vector3d radcomi = (v0 * s * dwi + v0p * sp * dwip) * sw; |
| 393 |
Vector3d radcomj = (v0 * s * dwj + v0p * sp * dwjp) * sw; |
| 394 |
|
| 395 |
Vector3d fii = A1trans * radcomi; |
| 396 |
Vector3d fjj = A2trans * radcomj; |
| 397 |
|
| 398 |
// now assemble these with the radial-only terms: |
| 399 |
|
| 400 |
f1 += 0.5 * ((v0*dsdr*w + v0p*dspdr*wp) * d / rij + fii - fjj); |
| 401 |
|
| 402 |
} |
| 403 |
|
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return; |
| 405 |
|
| 406 |
} |
| 407 |
|
| 408 |
void Sticky::do_sticky_pair(int *atid1, int *atid2, RealType *d, |
| 409 |
RealType *r, RealType *r2, RealType *sw, |
| 410 |
RealType *vpair, RealType *pot, RealType *A1, |
| 411 |
RealType *A2, RealType *f1, |
| 412 |
RealType *t1, RealType *t2) { |
| 413 |
|
| 414 |
if (!initialized_) initialize(); |
| 415 |
|
| 416 |
AtomType* atype1 = StickyMap[*atid1]; |
| 417 |
AtomType* atype2 = StickyMap[*atid2]; |
| 418 |
|
| 419 |
Vector3d disp(d); |
| 420 |
Vector3d frc(f1); |
| 421 |
Vector3d trq1(t1); |
| 422 |
Vector3d trq2(t2); |
| 423 |
RotMat3x3d Ai(A1); |
| 424 |
RotMat3x3d Aj(A2); |
| 425 |
|
| 426 |
calcForce(atype1, atype2, disp, *r, *r2, *sw, *vpair, *pot, |
| 427 |
Ai, Aj, frc, trq1, trq2); |
| 428 |
|
| 429 |
f1[0] = frc.x(); |
| 430 |
f1[1] = frc.y(); |
| 431 |
f1[2] = frc.z(); |
| 432 |
|
| 433 |
t1[0] = trq1.x(); |
| 434 |
t1[1] = trq1.y(); |
| 435 |
t1[2] = trq1.z(); |
| 436 |
|
| 437 |
t2[0] = trq2.x(); |
| 438 |
t2[1] = trq2.y(); |
| 439 |
t2[2] = trq2.z(); |
| 440 |
|
| 441 |
return; |
| 442 |
} |
| 443 |
} |
| 444 |
|
| 445 |
extern "C" { |
| 446 |
|
| 447 |
#define fortranGetStickyCut FC_FUNC(getstickycut, GETSTICKYCUT) |
| 448 |
#define fortranDoStickyPair FC_FUNC(do_sticky_pair, DO_STICKY_PAIR) |
| 449 |
|
| 450 |
RealType fortranGetStickyCut(int* atid) { |
| 451 |
return OpenMD::Sticky::Instance()->getStickyCut(*atid); |
| 452 |
} |
| 453 |
|
| 454 |
void fortranDoStickyPair(int *atid1, int *atid2, RealType *d, RealType *r, |
| 455 |
RealType *r2, RealType *sw, RealType *vpair, RealType *pot, |
| 456 |
RealType *A1, RealType *A2, RealType *f1, |
| 457 |
RealType *t1, RealType *t2){ |
| 458 |
|
| 459 |
return OpenMD::Sticky::Instance()->do_sticky_pair(atid1, atid2, d, r, r2, |
| 460 |
sw, vpair, pot, A1, A2, |
| 461 |
f1, t1, t2); |
| 462 |
} |
| 463 |
} |
