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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/Sticky.hpp" |
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#include "nonbonded/LJ.hpp" |
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#include "utils/simError.h" |
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using namespace std; |
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namespace OpenMD { |
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gezelter |
1502 |
Sticky::Sticky() : name_("Sticky"), initialized_(false), forceField_(NULL) {} |
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gezelter |
1485 |
|
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StickyParam Sticky::getStickyParam(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->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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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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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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return stickyData->getData(); |
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} |
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void Sticky::initialize() { |
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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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// Sticky handles all of the Sticky-Sticky interactions |
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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->isSticky() || at->isStickyPower()) |
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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 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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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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RealType w0i, v0i, v0pi, rli, rui, rlpi, rupi; |
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StickyParam sticky1 = getStickyParam(atomType); |
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// Now, iterate over all known types and add to the mixing map: |
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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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AtomType* atype2 = (*it).second; |
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StickyParam sticky2 = getStickyParam(atype2); |
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StickyInteractionData mixer; |
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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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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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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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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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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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} |
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gezelter |
1502 |
/** |
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* This function does the sticky portion of the SSD potential |
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* [Chandra and Ichiye, Journal of Chemical Physics 111, 2701 |
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* (1999)]. The Lennard-Jones and dipolar interaction must be |
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* handled separately. We assume that the rotation matrices have |
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* already been calculated and placed in the A1 & A2 entries in the |
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* idat structure. |
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*/ |
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void Sticky::calcForce(InteractionData idat) { |
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if (!initialized_) initialize(); |
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pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2); |
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map<pair<AtomType*, AtomType*>, StickyInteractionData>::iterator it; |
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it = MixingMap.find(key); |
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if (it != MixingMap.end()) { |
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gezelter |
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1505 |
StickyInteractionData mixer = (*it).second; |
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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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if (idat.rij <= rbig) { |
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RealType r3 = idat.r2 * idat.rij; |
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RealType r5 = r3 * idat.r2; |
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RotMat3x3d A1trans = idat.A1.transpose(); |
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RotMat3x3d A2trans = idat.A2.transpose(); |
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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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Vector3d ri = idat.A1 * idat.d; |
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// negative sign because this is the vector from j to i: |
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Vector3d rj = - idat.A2 * idat.d; |
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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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RealType xj = rj.x(); |
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RealType yj = rj.y(); |
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RealType zj = rj.z(); |
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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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RealType xj2 = xj * xj; |
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RealType yj2 = yj * yj; |
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RealType zj2 = zj * zj; |
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// calculate the switching info. from the splines |
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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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if (idat.rij < ru) { |
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if (idat.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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pair<RealType, RealType> res = mixer.s->getValueAndDerivativeAt(idat.rij); |
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s = res.first; |
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dsdr = res.second; |
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} |
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gezelter |
1485 |
} |
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gezelter |
1505 |
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if (idat.rij < rup) { |
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if (idat.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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pair<RealType, RealType> res =mixer.sp->getValueAndDerivativeAt(idat.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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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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RealType zif = zi/idat.rij - 0.6; |
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RealType zis = zi/idat.rij + 0.8; |
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RealType zjf = zj/idat.rij - 0.6; |
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RealType zjs = zj/idat.rij + 0.8; |
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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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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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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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RealType uglyi = zif*zif*zis + zif*zis*zis; |
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RealType uglyj = zjf*zjf*zjs + zjf*zjs*zjs; |
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gezelter |
1485 |
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gezelter |
1505 |
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/idat.rij - zi2/r3)*uglyi); |
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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/idat.rij - zj2/r3)*uglyj); |
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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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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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Vector3d dwipdu(2.0*yi*uglyi/idat.rij, |
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-2.0*xi*uglyi/idat.rij, |
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0.0); |
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Vector3d dwjpdu(2.0*yj*uglyj/idat.rij, |
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-2.0*xj*uglyj/idat.rij, |
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0.0); |
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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; |
| 338 |
|
|
dwidu = frac1*3.0*wi2*dwidu + frac2*dwidu; |
| 339 |
|
|
dwidu = frac1*3.0*wj2*dwjdu + frac2*dwjdu; |
| 340 |
|
|
dwipdu = V3Zero; |
| 341 |
|
|
dwjpdu = V3Zero; |
| 342 |
|
|
sp = 0.0; |
| 343 |
gezelter |
1485 |
dspdr = 0.0; |
| 344 |
|
|
} |
| 345 |
gezelter |
1505 |
|
| 346 |
|
|
idat.vpair += 0.5*(v0*s*w + v0p*sp*wp); |
| 347 |
|
|
idat.pot += 0.5*(v0*s*w + v0p*sp*wp)*idat.sw; |
| 348 |
|
|
|
| 349 |
|
|
// do the torques first since they are easy: |
| 350 |
|
|
// remember that these are still in the body-fixed axes |
| 351 |
|
|
|
| 352 |
|
|
Vector3d ti = 0.5*idat.sw*(v0*s*dwidu + v0p*sp*dwipdu); |
| 353 |
|
|
Vector3d tj = 0.5*idat.sw*(v0*s*dwjdu + v0p*sp*dwjpdu); |
| 354 |
|
|
|
| 355 |
|
|
// go back to lab frame using transpose of rotation matrix: |
| 356 |
|
|
|
| 357 |
|
|
idat.t1 += A1trans * ti; |
| 358 |
|
|
idat.t2 += A2trans * tj; |
| 359 |
|
|
|
| 360 |
|
|
// Now, on to the forces: |
| 361 |
|
|
|
| 362 |
|
|
// first rotate the i terms back into the lab frame: |
| 363 |
|
|
|
| 364 |
|
|
Vector3d radcomi = (v0 * s * dwi + v0p * sp * dwip) * idat.sw; |
| 365 |
|
|
Vector3d radcomj = (v0 * s * dwj + v0p * sp * dwjp) * idat.sw; |
| 366 |
|
|
|
| 367 |
|
|
Vector3d fii = A1trans * radcomi; |
| 368 |
|
|
Vector3d fjj = A2trans * radcomj; |
| 369 |
|
|
|
| 370 |
|
|
// now assemble these with the radial-only terms: |
| 371 |
|
|
|
| 372 |
|
|
idat.f1 += 0.5 * ((v0*dsdr*w + v0p*dspdr*wp) * idat.d / |
| 373 |
|
|
idat.rij + fii - fjj); |
| 374 |
|
|
|
| 375 |
gezelter |
1485 |
} |
| 376 |
|
|
} |
| 377 |
|
|
|
| 378 |
gezelter |
1505 |
return; |
| 379 |
gezelter |
1485 |
} |
| 380 |
gezelter |
1505 |
|
| 381 |
|
|
RealType Sticky::getSuggestedCutoffRadius(AtomType* at1, AtomType* at2) { |
| 382 |
|
|
if (!initialized_) initialize(); |
| 383 |
|
|
pair<AtomType*, AtomType*> key = make_pair(at1, at2); |
| 384 |
|
|
map<pair<AtomType*, AtomType*>, StickyInteractionData>::iterator it; |
| 385 |
|
|
it = MixingMap.find(key); |
| 386 |
|
|
if (it == MixingMap.end()) |
| 387 |
|
|
return 0.0; |
| 388 |
|
|
else { |
| 389 |
|
|
StickyInteractionData mixer = (*it).second; |
| 390 |
|
|
return mixer.rbig; |
| 391 |
|
|
} |
| 392 |
|
|
} |
| 393 |
gezelter |
1485 |
} |
