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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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#ifndef PARALLEL_FORCEMATRIXDECOMPOSITION_HPP |
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#define PARALLEL_FORCEMATRIXDECOMPOSITION_HPP |
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|
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#include "parallel/ForceDecomposition.hpp" |
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#include "math/SquareMatrix3.hpp" |
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#include "brains/Snapshot.hpp" |
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|
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#ifdef IS_MPI |
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#include "parallel/Communicator.hpp" |
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#endif |
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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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class ForceMatrixDecomposition : public ForceDecomposition { |
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public: |
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ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan); |
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|
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void distributeInitialData(); |
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void zeroWorkArrays(); |
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void distributeData(); |
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void collectIntermediateData(); |
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void distributeIntermediateData(); |
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void collectData(); |
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|
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// neighbor list routines |
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vector<pair<int, int> > buildNeighborList(); |
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// neighbor list routines based on Rapaport |
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vector<vector<CutoffGroup *> > buildLayerBasedNeighborList(); |
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|
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// group bookkeeping |
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groupCutoffs getGroupCutoffs(int cg1, int cg2); |
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|
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// Group->atom bookkeeping |
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vector<int> getAtomsInGroupRow(int cg1); |
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vector<int> getAtomsInGroupColumn(int cg2); |
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Vector3d getAtomToGroupVectorRow(int atom1, int cg1); |
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Vector3d getAtomToGroupVectorColumn(int atom2, int cg2); |
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RealType getMassFactorRow(int atom1); |
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RealType getMassFactorColumn(int atom2); |
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|
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// spatial data |
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Vector3d getIntergroupVector(int cg1, int cg2); |
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Vector3d getIntergroupVector(CutoffGroup *cg1, CutoffGroup *cg2); |
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Vector3d getInteratomicVector(int atom1, int atom2); |
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|
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// atom bookkeeping |
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int getNAtomsInRow(); |
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int getTopologicalDistance(int atom1, int atom2); |
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vector<int> getExcludesForAtom(int atom1); |
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bool skipAtomPair(int atom1, int atom2); |
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bool excludeAtomPair(int atom1, int atom2); |
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void addForceToAtomRow(int atom1, Vector3d fg); |
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void addForceToAtomColumn(int atom2, Vector3d fg); |
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|
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// filling interaction blocks with pointers |
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void fillInteractionData(InteractionData &idat, int atom1, int atom2); |
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void unpackInteractionData(InteractionData &idat, int atom1, int atom2); |
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|
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// memory reordering |
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void reorderGroupCutoffs(vector<int> &order); |
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void reorderPosition(vector<int> &order); |
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void reorderGroupList(vector<int> &order); |
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void reorderMemory(vector<vector<CutoffGroup *> > &H_c_l); |
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|
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private: |
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void createGtypeCutoffMap(); |
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|
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int nLocal_; |
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int nGroups_; |
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vector<int> AtomLocalToGlobal; |
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vector<int> cgLocalToGlobal; |
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vector<RealType> groupCutoff; |
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vector<int> groupToGtype; |
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|
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/* XXX */ |
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int neighborListReorderFreq; |
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int reorderFreqCounter; |
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|
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#ifdef IS_MPI |
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DataStorage atomRowData; |
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DataStorage atomColData; |
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DataStorage cgRowData; |
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DataStorage cgColData; |
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|
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int nAtomsInRow_; |
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int nAtomsInCol_; |
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int nGroupsInRow_; |
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int nGroupsInCol_; |
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|
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Communicator<Row> rowComm; |
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Communicator<Column> colComm; |
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|
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Plan<int>* AtomPlanIntRow; |
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Plan<RealType>* AtomPlanRealRow; |
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Plan<Vector3d>* AtomPlanVectorRow; |
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Plan<Mat3x3d>* AtomPlanMatrixRow; |
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Plan<potVec>* AtomPlanPotRow; |
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|
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Plan<int>* AtomPlanIntColumn; |
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Plan<RealType>* AtomPlanRealColumn; |
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Plan<Vector3d>* AtomPlanVectorColumn; |
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Plan<Mat3x3d>* AtomPlanMatrixColumn; |
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Plan<potVec>* AtomPlanPotColumn; |
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|
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Plan<int>* cgPlanIntRow; |
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Plan<Vector3d>* cgPlanVectorRow; |
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Plan<int>* cgPlanIntColumn; |
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Plan<Vector3d>* cgPlanVectorColumn; |
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|
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// work arrays for assembling potential energy |
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vector<potVec> pot_row; |
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vector<potVec> pot_col; |
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|
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vector<int> identsRow; |
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vector<int> identsCol; |
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|
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vector<AtomType*> atypesRow; |
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vector<AtomType*> atypesCol; |
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|
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vector<int> AtomRowToGlobal; |
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vector<int> AtomColToGlobal; |
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|
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vector<int> cgRowToGlobal; |
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vector<int> cgColToGlobal; |
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|
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vector<RealType> groupCutoffRow; |
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vector<RealType> groupCutoffCol; |
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vector<int> groupColToGtype; |
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vector<int> groupRowToGtype; |
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|
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vector<vector<int> > cellListRow_; |
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vector<vector<int> > cellListCol_; |
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|
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vector<vector<int> > groupListRow_; |
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vector<vector<int> > groupListCol_; |
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|
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vector<RealType> massFactorsRow; |
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vector<RealType> massFactorsCol; |
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#endif |
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|
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}; |
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|
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} |
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#endif |
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|
