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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, 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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#include "applications/dynamicProps/LegendreCorrFuncZ.hpp" |
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#include "math/LegendrePolynomial.hpp" |
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#include "utils/simError.h" |
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namespace OpenMD { |
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LegendreCorrFuncZ::LegendreCorrFuncZ(SimInfo* info, |
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const std::string& filename, |
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const std::string& sele1, |
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const std::string& sele2, |
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int order, int nZbins, |
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long long int memSize) |
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: ParticleTimeCorrFunc(info, filename, sele1, sele2, |
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DataStorage::dslAmat, memSize), nZBins_(nZbins) { |
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setCorrFuncType("Legendre Correlation Function of Z"); |
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setOutputName(getPrefix(dumpFilename_) + ".lcorrZ"); |
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histogram_.resize(nTimeBins_); |
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counts_.resize(nTimeBins_); |
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for (int i = 0; i < nTimeBins_; i++) { |
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histogram_[i].resize(nZBins_); |
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counts_[i].resize(nZBins_); |
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} |
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LegendrePolynomial polynomial(order); |
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legendre_ = polynomial.getLegendrePolynomial(order); |
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} |
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void LegendreCorrFuncZ::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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Mat3x3d hmat = snapshot1->getHmat(); |
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RealType halfBoxZ_ = hmat(2,2) / 2.0; |
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RealType time1 = snapshot1->getTime(); |
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RealType time2 = snapshot2->getTime(); |
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int timeBin = int ((time2 - time1) /deltaTime_ + 0.5); |
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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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for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j); |
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sd1 != NULL && sd2 != NULL; |
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sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) { |
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Vector3d pos = sd1->getPos(); |
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if (info_->getSimParams()->getUsePeriodicBoundaryConditions()) |
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snapshot1->wrapVector(pos); |
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int zBin = int(nZBins_ * (halfBoxZ_ + pos.z()) / hmat(2,2)); |
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Vector3d corrVals = calcCorrVals(frame1, frame2, sd1, sd2); |
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histogram_[timeBin][zBin] += corrVals; |
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counts_[timeBin][zBin]++; |
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} |
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} |
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void LegendreCorrFuncZ::postCorrelate() { |
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for (int i =0 ; i < nTimeBins_; ++i) { |
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for (int j = 0; j < nZBins_; ++j) { |
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if (counts_[i][j] > 0) { |
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histogram_[i][j] /= counts_[i][j]; |
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} |
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} |
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} |
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} |
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void LegendreCorrFuncZ::preCorrelate() { |
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for (int i = 0; i < nTimeBins_; i++) { |
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std::fill(histogram_[i].begin(), histogram_[i].end(), Vector3d(0.0)); |
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std::fill(counts_[i].begin(), counts_[i].end(), 0); |
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} |
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} |
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Vector3d LegendreCorrFuncZ::calcCorrVals(int frame1, int frame2, StuntDouble* sd1, StuntDouble* sd2) { |
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// The lab frame vector corresponding to the body-fixed |
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// z-axis is simply the second column of A.transpose() |
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// or, identically, the second row of A itself. |
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// Similar identites give the 0th and 1st rows of A for |
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// the lab vectors associated with body-fixed x- and y- axes. |
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Vector3d v1x = sd1->getA(frame1).getRow(0); |
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Vector3d v2x = sd2->getA(frame2).getRow(0); |
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Vector3d v1y = sd1->getA(frame1).getRow(1); |
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Vector3d v2y = sd2->getA(frame2).getRow(1); |
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Vector3d v1z = sd1->getA(frame1).getRow(2); |
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Vector3d v2z = sd2->getA(frame2).getRow(2); |
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RealType uxprod = legendre_.evaluate(dot(v1x, v2x)/(v1x.length()*v2x.length())); |
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RealType uyprod = legendre_.evaluate(dot(v1y, v2y)/(v1y.length()*v2y.length())); |
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RealType uzprod = legendre_.evaluate(dot(v1z, v2z)/(v1z.length()*v2z.length())); |
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return Vector3d(uxprod, uyprod, uzprod); |
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} |
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void LegendreCorrFuncZ::validateSelection(const SelectionManager& seleMan) { |
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StuntDouble* sd; |
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int i; |
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for (sd = seleMan1_.beginSelected(i); sd != NULL; sd = seleMan1_.nextSelected(i)) { |
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if (!sd->isDirectionalAtom()) { |
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sprintf(painCave.errMsg, |
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"LegendreCorrFunc::validateSelection Error: selected atoms are not Directional\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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} |
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void LegendreCorrFuncZ::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\tPn(costheta_z)\n"; |
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for (int i = 0; i < nTimeBins_; ++i) { |
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ofs << time_[i]; |
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for (int j = 0; j < nZBins_; ++j) { |
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ofs << "\t" << histogram_[i][j](2); |
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} |
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ofs << "\n"; |
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} |
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} else { |
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sprintf(painCave.errMsg, |
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"LegendreCorrFuncZ::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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} |