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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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* RhoZ.cpp |
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* OOPSE-2.0 |
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* |
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* Created by Charles F. Vardeman II on 11/26/05. |
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* @author Charles F. Vardeman II |
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* @version $Id: RhoZ.cpp,v 1.1 2005-11-30 21:00:39 chuckv Exp $ |
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* |
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*/ |
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|
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/* Calculates Rho(Z) for density profile of liquid slab. */ |
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|
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#include <algorithm> |
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#include <fstream> |
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#include "applications/staticProps/RhoZ.hpp" |
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#include "utils/simError.h" |
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|
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namespace oopse { |
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|
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RhoZ::RhoZ(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len, int nrbins) |
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: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins){ |
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|
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deltaR_ = len_ /nRBins_; |
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|
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histogram_.resize(nRBins_); |
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avgRhoZ_.resize(nRBins_); |
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|
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setOutputName(getPrefix(filename) + ".RhoZ"); |
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} |
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|
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|
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void RhoZ::preProcess() { |
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std::fill(avgRhoZ_.begin(), avgRhoZ_.end(), 0.0); |
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} |
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|
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void RhoZ::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 RhoZ::processHistogram() { |
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|
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int nPairs = getNPairs(); |
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double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
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double pairDensity = nPairs /volume * 2.0; |
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double pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0; |
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|
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for(int i = 0 ; i < histogram_.size(); ++i){ |
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|
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double rLower = i * deltaR_; |
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double rUpper = rLower + deltaR_; |
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double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); |
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double nIdeal = volSlice * pairConstant; |
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|
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avgRhoZ_[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 RhoZ::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
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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->getPosZ(); |
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Vector3d pos2 = sd2->getPosZ(); |
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Vector3d r12 = pos2 - pos1; |
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currentSnapshot_->wrapVector(r12); |
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|
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double distance = r12.length(); |
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|
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if (distance < len_) { |
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int whichBin = distance / deltaR_; |
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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 RhoZ::writeRdf() { |
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std::ofstream rdfStream(outputFilename_.c_str()); |
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if (rdfStream.is_open()) { |
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rdfStream << "#radial 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 < avgRhoZ_.size(); ++i) { |
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double r = deltaR_ * (i + 0.5); |
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rdfStream << r << "\t" << avgRhoZ_[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, "RhoZ: 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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