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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. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. 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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* 3. 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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|
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#include "integrators/RNEMD.hpp" |
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#include "math/SquareMatrix3.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "primitives/StuntDouble.hpp" |
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|
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#ifndef IS_MPI |
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#include "math/SeqRandNumGen.hpp" |
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#else |
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#include "math/ParallelRandNumGen.hpp" |
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#endif |
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|
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/* Remove me after testing*/ |
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/* |
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#include <cstdio> |
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#include <iostream> |
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*/ |
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/*End remove me*/ |
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|
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namespace oopse { |
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|
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RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info) { |
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|
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int seedValue; |
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Globals * simParams = info->getSimParams(); |
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|
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stringToEnumMap_["Kinetic"] = rnemdKinetic; |
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stringToEnumMap_["Px"] = rnemdPx; |
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stringToEnumMap_["Py"] = rnemdPy; |
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stringToEnumMap_["Pz"] = rnemdPz; |
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stringToEnumMap_["Unknown"] = rnemdUnknown; |
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|
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rnemdObjectSelection_ = simParams->getRNEMD_objectSelection(); |
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|
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std::cerr << "calling evaluator with " << rnemdObjectSelection_ << "\n"; |
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evaluator_.loadScriptString(rnemdObjectSelection_); |
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std::cerr << "done"; |
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|
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const std::string st = simParams->getRNEMD_swapType(); |
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|
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std::map<std::string, RNEMDTypeEnum>::iterator i; |
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i = stringToEnumMap_.find(st); |
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rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second; |
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|
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set_RNEMD_swapTime(simParams->getRNEMD_swapTime()); |
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set_RNEMD_nBins(simParams->getRNEMD_nBins()); |
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exchangeSum_ = 0.0; |
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|
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#ifndef IS_MPI |
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if (simParams->haveSeed()) { |
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seedValue = simParams->getSeed(); |
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randNumGen_ = new SeqRandNumGen(seedValue); |
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}else { |
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randNumGen_ = new SeqRandNumGen(); |
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} |
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#else |
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if (simParams->haveSeed()) { |
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seedValue = simParams->getSeed(); |
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randNumGen_ = new ParallelRandNumGen(seedValue); |
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}else { |
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randNumGen_ = new ParallelRandNumGen(); |
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} |
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#endif |
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} |
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|
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RNEMD::~RNEMD() { |
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delete randNumGen_; |
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} |
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|
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void RNEMD::doSwap() { |
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std::cerr << "in RNEMD!\n"; |
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std::cerr << "nBins = " << nBins_ << "\n"; |
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std::cerr << "swapTime = " << swapTime_ << "\n"; |
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std::cerr << "exchangeSum = " << exchangeSum_ << "\n"; |
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std::cerr << "swapType = " << rnemdType_ << "\n"; |
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std::cerr << "selection = " << rnemdObjectSelection_ << "\n"; |
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|
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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|
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std::cerr << "selectionCount = " << seleMan_.getSelectionCount() << "\n\n"; |
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|
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int i; |
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StuntDouble* sd; |
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|
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for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) { |
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Vector3d pos = sd->getPos(); |
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//wrap the stuntdoubles into a cell |
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if (usePeriodicBoundaryConditions_) |
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info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos); |
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int binNo = int(nBins_ * (pos.z()) / hmat(2,2)); |
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sliceSDLists_[binNo].push_back(sd); |
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} |
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|
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} |
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} |
