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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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#include "applications/dynamicProps/ActionCorrFunc.hpp" |
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#include "utils/OOPSEConstant.hpp" |
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#include "brains/ForceManager.hpp" |
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#include "brains/Thermo.hpp" |
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namespace oopse { |
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// We need all of the positions, velocities, etc. so that we can |
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// recalculate pressures and actions on the fly: |
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ActionCorrFunc::ActionCorrFunc(SimInfo* info, const std::string& filename, |
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const std::string& sele1, |
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const std::string& sele2) |
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: FrameTimeCorrFunc(info, filename, sele1, sele2, |
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DataStorage::dslPosition | |
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DataStorage::dslVelocity | |
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DataStorage::dslForce ){ |
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setCorrFuncType("ActionCorrFunc"); |
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setOutputName(getPrefix(dumpFilename_) + ".action"); |
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histogram_.resize(nTimeBins_); |
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count_.resize(nTimeBins_); |
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} |
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void ActionCorrFunc::correlateFrames(int frame1, int frame2) { |
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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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RealType time1 = snapshot1->getTime(); |
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RealType time2 = snapshot2->getTime(); |
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RealType vol1 = snapshot1->getVolume(); |
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RealType vol2 = snapshot2->getVolume(); |
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int timeBin = int ((time2 - time1) /deltaTime_ + 0.5); |
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//std::cerr << "times = " << time1 << " " << time2 << "\n"; |
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//std::cerr << "vols = " << vol1 << " " << vol2 << "\n"; |
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int i; |
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int j; |
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StuntDouble* sd1; |
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Mat3x3d actionTensor1(0.0); |
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//std::cerr << "at1 = " << actionTensor1 << "\n"; |
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Mat3x3d actionTensor2(0.0); |
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//std::cerr << "at2 = " << actionTensor2 << "\n"; |
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for (sd1 = seleMan1_.beginSelected(i); sd1 != NULL; |
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sd1 = seleMan1_.nextSelected(i)) { |
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//std::cerr << "found a SD\n"; |
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Vector3d r1 = sd1->getPos(frame1); |
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//std::cerr << "r1 = " << r1 << "\n"; |
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Vector3d v1 = sd1->getVel(frame1); |
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//std::cerr << "v1 = " << v1 << "\n"; |
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Vector3d r2 = sd1->getPos(frame2); |
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//std::cerr << "r2 = " << r2 << "\n"; |
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Vector3d v2 = sd1->getVel(frame2); |
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//std::cerr << "v2 = " << v2 << "\n"; |
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RealType m = sd1->getMass(); |
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//std::cerr << "m = " << m << "\n"; |
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actionTensor1 += m*outProduct(r1, v1); |
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actionTensor2 += m*outProduct(r2, v2); |
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} |
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actionTensor1 /= vol1; |
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//std::cerr << "at1 = " << actionTensor1 << "\n"; |
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actionTensor2 /= vol2; |
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//std::cerr << "at2 = " << actionTensor2 << "\n"; |
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Mat3x3d corrTensor(0.0); |
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//std::cerr << "ct = " << corrTensor << "\n"; |
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RealType thisTerm; |
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for (i = 0; i < 3; i++) { |
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for (j = 0; j < 3; j++) { |
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//std::cerr << "i, j = " << i << " " << j << "\n"; |
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if (i == j) { |
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thisTerm = (actionTensor2(i, j) - actionTensor1(i, j) - avePress_ *(time2-time1)); |
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std::cerr << "at1, at2 = " << actionTensor1(i,j) << " " << actionTensor2(i,j) << " p = " << avePress_ << "\n"; |
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} else { |
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thisTerm = (actionTensor2(i, j) - actionTensor1(i, j)); |
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} |
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//std::cerr << "thisTerm = " << thisTerm << "\n"; |
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corrTensor(i, j) += thisTerm * thisTerm; |
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} |
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} |
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//std::cerr << "ct = " << corrTensor << "\n"; |
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//std::cerr << "hist = " << histogram_[timeBin] << "\n"; |
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histogram_[timeBin] += corrTensor; |
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count_[timeBin]++; |
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} |
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void ActionCorrFunc::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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void ActionCorrFunc::preCorrelate() { |
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// Fill the histogram with empty 3x3 matrices: |
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std::fill(histogram_.begin(), histogram_.end(), Mat3x3d(0.0)); |
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// count array set to zero |
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std::fill(count_.begin(), count_.end(), 0); |
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SimInfo::MoleculeIterator mi; |
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Molecule* mol; |
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Molecule::AtomIterator ai; |
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Atom* atom; |
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// We'll need the force manager to compute forces for the average pressure |
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ForceManager* forceMan = new ForceManager(info_); |
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forceMan->init(); |
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// We'll need thermo to compute the pressures from the virial |
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Thermo* thermo = new Thermo(info_); |
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// prepare the averages |
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RealType pSum = 0.0; |
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RealType vSum = 0.0; |
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int nsamp = 0; |
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// dump files can be enormous, so read them in block-by-block: |
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int nblocks = bsMan_->getNBlocks(); |
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for (int i = 0; i < nblocks; ++i) { |
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std::cerr << "block = " << i << "\n"; |
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bsMan_->loadBlock(i); |
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assert(bsMan_->isBlockActive(i)); |
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SnapshotBlock block1 = bsMan_->getSnapshotBlock(i); |
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for (int j = block1.first; j < block1.second; ++j) { |
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// go snapshot-by-snapshot through this block: |
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Snapshot* snap = bsMan_->getSnapshot(j); |
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// update the positions and velocities of the atoms belonging |
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// to rigid bodies: |
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updateFrame(j); |
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// do the forces: |
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forceMan->calcForces(true, true); |
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// call thermo to get the pressure and volume. |
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pSum += thermo->getPressure(); |
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vSum += thermo->getVolume(); |
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nsamp++; |
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} |
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bsMan_->unloadBlock(i); |
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} |
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avePress_ = pSum / ( OOPSEConstant::pressureConvert * (RealType)nsamp); |
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aveVol_ = vSum / (RealType)nsamp; |
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std::cout << "pAve = " << avePress_ << " vAve = " << aveVol_ << "\n"; |
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} |
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void ActionCorrFunc::writeCorrelate() { |
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std::ofstream ofs(getOutputFileName().c_str()); |
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if (ofs.is_open()) { |
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ofs << "#" << getCorrFuncType() << "\n"; |
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ofs << "#time\tcorrTensor\txx\txy\txz\tyx\tyy\tyz\tzx\tzy\tzz\n"; |
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for (int i = 0; i < nTimeBins_; ++i) { |
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ofs << time_[i] << "\t" << |
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histogram_[i](0,0) << "\t" << |
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histogram_[i](0,1) << "\t" << |
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histogram_[i](0,2) << "\t" << |
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histogram_[i](1,0) << "\t" << |
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histogram_[i](1,1) << "\t" << |
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histogram_[i](1,2) << "\t" << |
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histogram_[i](2,0) << "\t" << |
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histogram_[i](2,1) << "\t" << |
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histogram_[i](2,2) << "\t" << "\n"; |
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} |
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} else { |
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sprintf(painCave.errMsg, |
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"ActionCorrFunc::writeCorrelate Error: fail to open %s\n", getOutputFileName().c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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ofs.close(); |
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} |
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} |