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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, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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#include <algorithm> |
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#include <fstream> |
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#include "applications/staticProps/GofZ.hpp" |
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#include "utils/simError.h" |
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|
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namespace OpenMD { |
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|
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GofZ::GofZ(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins) |
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: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins){ |
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|
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deltaZ_ = len_ /nRBins_; |
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rC_ = len_ / 2.0; |
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|
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histogram_.resize(nRBins_); |
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avgGofz_.resize(nRBins_); |
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|
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setOutputName(getPrefix(filename) + ".gofz"); |
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} |
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|
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|
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void GofZ::preProcess() { |
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std::fill(avgGofz_.begin(), avgGofz_.end(), 0.0); |
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} |
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|
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void GofZ::initalizeHistogram() { |
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std::fill(histogram_.begin(), histogram_.end(), 0); |
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} |
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|
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|
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void GofZ::processHistogram() { |
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|
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int nPairs = getNPairs(); |
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RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
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RealType pairDensity = nPairs /volume * 2.0; |
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RealType pairConstant = ( 2.0 * NumericConstant::PI * pairDensity ); |
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|
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for(int i = 0 ; i < histogram_.size(); ++i){ |
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|
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RealType zLower = i * deltaZ_; |
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RealType zUpper = zLower + deltaZ_; |
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RealType cylSlice = (zUpper - zLower)*rC_*rC_; |
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RealType nIdeal = cylSlice * pairConstant; |
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|
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avgGofz_[i] += histogram_[i] / nIdeal; |
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} |
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|
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} |
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|
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void GofZ::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
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|
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RealType thisZ; |
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|
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if (sd1 == sd2) { |
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return; |
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} |
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|
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Vector3d pos1 = sd1->getPos(); |
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Vector3d pos2 = sd2->getPos(); |
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Vector3d r12 = pos2 - pos1; |
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(r12); |
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|
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RealType distance = r12.length(); |
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RealType z2 = r12.z()*r12.z(); |
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RealType xydist = sqrt(distance*distance - z2); |
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|
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if (xydist < rC_) { |
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thisZ = abs(r12.z()); |
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int whichBin = thisZ / deltaZ_; |
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histogram_[whichBin] += 2; |
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} |
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} |
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|
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|
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void GofZ::writeRdf() { |
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std::ofstream rdfStream(outputFilename_.c_str()); |
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if (rdfStream.is_open()) { |
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rdfStream << "#z-separation distribution function\n"; |
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rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
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rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
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rdfStream << "#r\tcorrValue\n"; |
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for (int i = 0; i < avgGofz_.size(); ++i) { |
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RealType z = deltaZ_ * (i + 0.5); |
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rdfStream << z << "\t" << avgGofz_[i]/nProcessed_ << "\n"; |
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} |
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|
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} else { |
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|
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sprintf(painCave.errMsg, "GofZ: unable 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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rdfStream.close(); |
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} |
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|
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} |
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|
