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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 "applications/dynamicProps/CorrelationFunction.hpp" |
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#include "utils/simError.h" |
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#include "primitives/Molecule.hpp" |
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namespace oopse { |
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|
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CorrelationFunction::CorrelationFunction(SimInfo* info, const std::string& filename, |
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const std::string& sele1, const std::string& sele2, int storageLayout) |
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: info_(info), storageLayout_(storageLayout), dumpFilename_(filename), selectionScript1_(sele1), |
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selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), seleMan1_(info), seleMan2_(info){ |
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|
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int nAtoms = info->getNGlobalAtoms(); |
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int nRigidBodies = info->getNGlobalRigidBodies(); |
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int nStuntDoubles = nAtoms + nRigidBodies; |
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|
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std::set<AtomType*> atomTypes = info->getUniqueAtomTypes(); |
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std::set<AtomType*>::iterator i; |
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bool hasDirectionalAtom = false; |
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bool hasMultipole = false; |
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for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
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if ((*i)->isDirectional()){ |
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hasDirectionalAtom = true; |
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} |
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if ((*i)->isMultipole()){ |
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hasMultipole = true; |
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} |
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} |
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|
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if (nRigidBodies > 0 || hasDirectionalAtom) { |
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storageLayout_ |= DataStorage::dslAmat; |
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} |
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if (hasMultipole) { |
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storageLayout_ |= DataStorage::dslElectroFrame; |
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if (nRigidBodies > 0) { |
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storageLayout_ |= DataStorage::dslAngularMomentum; |
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} |
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} |
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|
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bsMan_ = new BlockSnapshotManager(info, dumpFilename_, storageLayout_); |
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info_->setSnapshotManager(bsMan_); |
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|
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//if selection is static, we only need to evaluate it once |
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if (!evaluator1_.isDynamic()) { |
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seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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validateSelection(seleMan1_); |
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} |
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if (!evaluator2_.isDynamic()) { |
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seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
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validateSelection(seleMan2_); |
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} |
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|
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/**@todo Fixed Me */ |
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Globals* simParams = info_->getSimParams(); |
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if (simParams->haveSampleTime()){ |
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deltaTime_ = simParams->getSampleTime(); |
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} else { |
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sprintf(painCave.errMsg, |
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"CorrelationFunction::writeCorrelate Error: can not figure out deltaTime\n"); |
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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 nframes = bsMan_->getNFrames(); |
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nTimeBins_ = nframes; |
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histogram_.resize(nTimeBins_); |
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count_.resize(nTimeBins_); |
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time_.resize(nTimeBins_); |
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|
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for (int i = 0; i < nTimeBins_; ++i) { |
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time_[i] = i * deltaTime_; |
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} |
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|
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} |
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|
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|
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void CorrelationFunction::doCorrelate() { |
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preCorrelate(); |
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|
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int nblocks = bsMan_->getNBlocks(); |
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|
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for (int i = 0; i < nblocks; ++i) { |
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bsMan_->loadBlock(i); |
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for (int j = i; j < nblocks; ++j) { |
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bsMan_->loadBlock(j); |
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correlateBlocks(i, j); |
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|
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if (i != j) { |
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//if i equals to j, the block is still used, should not unload it |
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bsMan_->unloadBlock(j); |
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} |
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} |
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bsMan_->unloadBlock(i); |
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} |
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|
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postCorrelate(); |
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|
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writeCorrelate(); |
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} |
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|
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void CorrelationFunction::correlateBlocks(int block1, int block2) { |
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|
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int jstart, jend; |
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|
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assert(bsMan_->isBlockActive(block1) && bsMan_->isBlockActive(block2)); |
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|
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SnapshotBlock snapshotBlock1 = bsMan_->getSnapshotBlock(block1); |
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SnapshotBlock snapshotBlock2 = bsMan_->getSnapshotBlock(block2); |
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|
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jend = snapshotBlock2.second; |
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|
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for (int i = snapshotBlock1.first; i < snapshotBlock1.second; ++i) { |
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|
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//evaluate selection if it is dynamic |
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if (evaluator1_.isDynamic()) { |
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seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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validateSelection(seleMan1_); |
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} |
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|
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//update the position or velocity of the atoms belong to rigid bodies |
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updateFrame(i); |
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|
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// if the two blocks are the same, we don't want to correlate |
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// backwards in time, so start j at the same frame as i |
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|
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if (block1 == block2) |
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jstart = i; |
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else |
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jstart = snapshotBlock2.first; |
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|
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for(int j = jstart; j < jend; ++j) { |
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//evaluate selection |
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if (!evaluator2_.isDynamic()) { |
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seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
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validateSelection(seleMan2_); |
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} |
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//update the position or velocity of the atoms belong to rigid bodies |
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updateFrame(j); |
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|
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correlateFrames(i, j); |
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} |
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} |
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} |
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|
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|
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void CorrelationFunction::correlateFrames(int frame1, int frame2) { |
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int count = seleMan1_.getSelectionCount(); |
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assert( count == seleMan2_.getSelectionCount()); |
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|
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Snapshot* snapshot1 = bsMan_->getSnapshot(frame1); |
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Snapshot* snapshot2 = bsMan_->getSnapshot(frame2); |
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assert(snapshot1 && snapshot2); |
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|
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double time1 = snapshot1->getTime(); |
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double time2 = snapshot2->getTime(); |
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|
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if (time2 < time1) { printf("BARF ON NON POSITIVE DT!\n"); stop;} |
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|
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int timeBin = int ((time2 - time1) /deltaTime_ + 0.5); |
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count_[timeBin] += count; |
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|
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int i; |
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int j; |
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StuntDouble* sd1; |
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StuntDouble* sd2; |
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|
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switch (correlationFunctionType()) { |
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|
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case frame: |
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double corrVal = calcCorrVal(frame1, frame2); |
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histogram_[timeBin] += corrVal; |
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count_[timeBin] += 1; |
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break; |
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|
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case particle: |
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for (sd1 = seleMan1_.beginSelected(i), sd1 != NULL; |
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sd1 = seleMan1_.nextSelected(i)) { |
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double corrVal = calcCorrVal(frame1, frame2, sd); |
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histogram_[timeBin] += corrVal; |
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count_[timeBin] += 1; |
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} |
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break; |
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|
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case cross: |
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for (sd1 = seleMan1_.beginSelected(i); sd1 != NULL; sd1 = seleMan1_.nextSelected(i)) { |
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|
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for (sd2 = seleMan2_.beginSelected(j); sd2 != NULL; sd2 = seleMan2_.nextSelected(j)) { |
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double corrVal = calcCorrVal(frame1, frame2, sd1, sd2); |
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histogram_[timeBin] += corrVal; |
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count_[timeBin] += 1; |
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} |
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} |
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break; |
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|
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default: |
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return NULL; |
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|
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} |
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} |
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|
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|
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void CorrelationFunction::updateFrame(int frame){ |
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Molecule* mol; |
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RigidBody* rb; |
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SimInfo::MoleculeIterator mi; |
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Molecule::RigidBodyIterator rbIter; |
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|
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/** @todo need improvement */ |
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if (storageLayout_ & DataStorage::dslPosition) { |
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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|
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//change the positions of atoms which belong to the rigidbodies |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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rb->updateAtoms(frame); |
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} |
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} |
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} |
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|
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if (storageLayout_ & DataStorage::dslVelocity) { |
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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|
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//change the positions of atoms which belong to the rigidbodies |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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rb->updateAtomVel(frame); |
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} |
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} |
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|
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} |
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|
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} |
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|
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|
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void CorrelationFunction::preCorrelate() { |
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std::fill(histogram_.begin(), histogram_.end(), 0.0); |
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std::fill(count_.begin(), count_.end(), 0); |
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} |
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|
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void CorrelationFunction::postCorrelate() { |
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for (int i =0 ; i < nTimeBins_; ++i) { |
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if (count_[i] > 0) { |
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histogram_[i] /= count_[i]; |
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} |
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} |
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} |
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|
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|
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void CorrelationFunction::writeCorrelate() { |
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std::ofstream ofs(outputFilename_.c_str()); |
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|
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if (ofs.is_open()) { |
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|
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ofs << "#" << getCorrFuncType() << "\n"; |
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ofs << "#selection script1: \"" << selectionScript1_ <<"\"\tselection script2: \"" << selectionScript2_ << "\"\n"; |
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ofs << "#extra information: " << extra_ << "\n"; |
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ofs << "#time\tcorrVal\n"; |
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|
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for (int i = 0; i < nTimeBins_; ++i) { |
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ofs << time_[i] << "\t" << histogram_[i] << "\n"; |
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} |
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|
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} else { |
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sprintf(painCave.errMsg, |
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"CorrelationFunction::writeCorrelate Error: fail to open %s\n", outputFilename_.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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ofs.close(); |
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} |
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|
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} |
