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/* |
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* copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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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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* |
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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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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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* @file SimCreator.cpp |
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* @author tlin |
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* @date 11/03/2004 |
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* @time 13:51am |
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* @version 1.0 |
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*/ |
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#include <exception> |
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MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode); |
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#endif |
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SimplePreprocessor preprocessor; |
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preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, |
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ppStream); |
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preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream); |
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#ifdef IS_MPI |
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//brocasting the stream size |
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streamSize = ppStream.str().size() +1; |
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MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode); |
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MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), |
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streamSize, MPI::CHAR, masterNode); |
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MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI::CHAR, masterNode); |
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} else { |
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MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode); |
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//get stream size |
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ppStream.str(buf); |
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delete [] buf; |
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} |
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#endif |
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// Create a scanner that reads from the input stream |
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int metaDataBlockStart = -1; |
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int metaDataBlockEnd = -1; |
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int i, j; |
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streamoff mdOffset(0); |
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streamoff mdOffset; |
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int mdFileVersion; |
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// Create a string for embedding the version information in the MetaData |
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#ifdef IS_MPI |
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void SimCreator::divideMolecules(SimInfo *info) { |
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RealType numerator; |
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RealType denominator; |
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RealType precast; |
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RealType x; |
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RealType y; |
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RealType a; |
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int old_atoms; |
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int add_atoms; |
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int new_atoms; |
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int nTarget; |
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int done; |
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int i; |
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int loops; |
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int which_proc; |
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int nProcessors; |
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std::vector<int> atomsPerProc; |
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int nGlobalMols = info->getNGlobalMolecules(); |
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std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition: |
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std::vector<int> molToProcMap(nGlobalMols, -1); // default to an |
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// error |
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// condition: |
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nProcessors = MPI::COMM_WORLD.Get_size(); |
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|
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"\tthe number of molecules. This will not result in a \n" |
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"\tusable division of atoms for force decomposition.\n" |
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"\tEither try a smaller number of processors, or run the\n" |
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"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols); |
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"\tsingle-processor version of OpenMD.\n", nProcessors, |
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nGlobalMols); |
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|
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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int seedValue; |
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Globals * simParams = info->getSimParams(); |
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SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator |
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SeqRandNumGen* myRandom; //divide labor does not need Parallel |
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//random number generator |
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if (simParams->haveSeed()) { |
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seedValue = simParams->getSeed(); |
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int seedValue = simParams->getSeed(); |
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myRandom = new SeqRandNumGen(seedValue); |
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}else { |
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myRandom = new SeqRandNumGen(); |
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atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0); |
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|
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if (worldRank == 0) { |
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numerator = info->getNGlobalAtoms(); |
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denominator = nProcessors; |
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precast = numerator / denominator; |
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nTarget = (int)(precast + 0.5); |
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|
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for(i = 0; i < nGlobalMols; i++) { |
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RealType numerator = info->getNGlobalAtoms(); |
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RealType denominator = nProcessors; |
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RealType precast = numerator / denominator; |
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int nTarget = (int)(precast + 0.5); |
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for(int i = 0; i < nGlobalMols; i++) { |
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done = 0; |
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loops = 0; |
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int done = 0; |
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int loops = 0; |
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while (!done) { |
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loops++; |
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// Pick a processor at random |
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which_proc = (int) (myRandom->rand() * nProcessors); |
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int which_proc = (int) (myRandom->rand() * nProcessors); |
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//get the molecule stamp first |
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int stampId = info->getMoleculeStampId(i); |
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MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId); |
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// How many atoms does this processor have so far? |
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old_atoms = atomsPerProc[which_proc]; |
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add_atoms = moleculeStamp->getNAtoms(); |
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new_atoms = old_atoms + add_atoms; |
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int old_atoms = atomsPerProc[which_proc]; |
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int add_atoms = moleculeStamp->getNAtoms(); |
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int new_atoms = old_atoms + add_atoms; |
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// If we've been through this loop too many times, we need |
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// to just give up and assign the molecule to this processor |
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// Pacc(x) = exp(- a * x) |
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// where a = penalty / (average atoms per molecule) |
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x = (RealType)(new_atoms - nTarget); |
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y = myRandom->rand(); |
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RealType x = (RealType)(new_atoms - nTarget); |
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RealType y = myRandom->rand(); |
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if (y < exp(- a * x)) { |
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molToProcMap[i] = which_proc; |
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set<AtomType*>::iterator i; |
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bool hasDirectionalAtoms = false; |
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bool hasFixedCharge = false; |
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bool hasMultipoles = false; |
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bool hasDipoles = false; |
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bool hasQuadrupoles = false; |
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bool hasPolarizable = false; |
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bool hasFluctuatingCharge = false; |
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bool hasMetallic = false; |
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if (da.isDirectional()){ |
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hasDirectionalAtoms = true; |
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} |
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if (ma.isMultipole()){ |
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hasMultipoles = true; |
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if (ma.isDipole()){ |
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hasDipoles = true; |
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} |
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if (ma.isQuadrupole()){ |
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hasQuadrupoles = true; |
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} |
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if (ea.isEAM() || sca.isSuttonChen()){ |
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hasMetallic = true; |
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} |
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storageLayout |= DataStorage::dslTorque; |
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} |
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} |
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if (hasMultipoles) { |
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storageLayout |= DataStorage::dslElectroFrame; |
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if (hasDipoles) { |
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storageLayout |= DataStorage::dslDipole; |
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} |
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if (hasQuadrupoles) { |
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storageLayout |= DataStorage::dslQuadrupole; |
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} |
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if (hasFixedCharge || hasFluctuatingCharge) { |
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storageLayout |= DataStorage::dslSkippedCharge; |
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} |
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} |
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} |
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if (simParams->getOutputElectricField()) { |
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if (simParams->getOutputElectricField() | simParams->haveElectricField()) { |
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storageLayout |= DataStorage::dslElectricField; |
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} |
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if (simParams->getOutputFluctuatingCharges()) { |
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storageLayout |= DataStorage::dslFlucQPosition; |
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storageLayout |= DataStorage::dslFlucQVelocity; |
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storageLayout |= DataStorage::dslFlucQForce; |
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} |
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info->setStorageLayout(storageLayout); |
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return storageLayout; |
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} |
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} |
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void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) { |
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DumpReader reader(info, mdFileName); |
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int nframes = reader.getNFrames(); |
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if (nframes > 0) { |
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reader.readFrame(nframes - 1); |
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} else { |
