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/* |
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* Copyright (c) 2007 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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* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * |
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* Created by J. Daniel Gezelter on 07/27/07. |
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* @author J. Daniel Gezelter |
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* @version $Id$ |
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* |
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*/ |
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|
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#include "applications/staticProps/BondAngleDistribution.hpp" |
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#include "utils/simError.h" |
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#include "io/DumpReader.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/NumericConstant.hpp" |
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|
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using namespace std; |
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namespace OpenMD { |
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|
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BondAngleDistribution::BondAngleDistribution(SimInfo* info, |
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const string& filename, |
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const string& sele, |
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double rCut, int nbins) |
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: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), |
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seleMan_(info) { |
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|
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setOutputName(getPrefix(filename) + ".bad"); |
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|
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evaluator_.loadScriptString(sele); |
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if (!evaluator_.isDynamic()) { |
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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} |
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|
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// Set up cutoff radius and order of the Legendre Polynomial: |
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|
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rCut_ = rCut; |
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nBins_ = nbins; |
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|
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|
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// Theta can take values from 0 to 180 |
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deltaTheta_ = (180.0) / nBins_; |
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histogram_.resize(nBins_); |
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} |
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|
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BondAngleDistribution::~BondAngleDistribution() { |
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histogram_.clear(); |
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} |
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|
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void BondAngleDistribution::initializeHistogram() { |
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for (int bin = 0; bin < nBins_; bin++) { |
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histogram_[bin] = 0; |
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} |
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} |
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|
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void BondAngleDistribution::process() { |
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Molecule* mol; |
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Atom* atom; |
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RigidBody* rb; |
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int myIndex; |
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SimInfo::MoleculeIterator mi; |
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Molecule::RigidBodyIterator rbIter; |
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Molecule::AtomIterator ai; |
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StuntDouble* sd; |
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Vector3d vec; |
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std::vector<Vector3d> bondvec; |
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RealType r; |
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int nBonds; |
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int i; |
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|
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader.getNFrames(); |
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frameCounter_ = 0; |
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|
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nTotBonds_ = 0; |
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|
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for (int istep = 0; istep < nFrames; istep += step_) { |
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reader.readFrame(istep); |
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frameCounter_++; |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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|
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if (evaluator_.isDynamic()) { |
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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} |
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|
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// update the positions of atoms which belong to the rigidbodies |
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|
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
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rb = mol->nextRigidBody(rbIter)) { |
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rb->updateAtoms(); |
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} |
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} |
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|
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// outer loop is over the selected StuntDoubles: |
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|
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for (sd = seleMan_.beginSelected(i); sd != NULL; |
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sd = seleMan_.nextSelected(i)) { |
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|
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myIndex = sd->getGlobalIndex(); |
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nBonds = 0; |
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bondvec.clear(); |
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|
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// inner loop is over all other atoms in the system: |
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|
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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for (atom = mol->beginAtom(ai); atom != NULL; |
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atom = mol->nextAtom(ai)) { |
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|
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if (atom->getGlobalIndex() != myIndex) { |
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|
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vec = sd->getPos() - atom->getPos(); |
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|
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(vec); |
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|
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// Calculate "bonds" and make a pair list |
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|
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r = vec.length(); |
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|
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// Check to see if neighbor is in bond cutoff |
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|
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if (r < rCut_) { |
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// Add neighbor to bond list's |
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bondvec.push_back(vec); |
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nBonds++; |
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nTotBonds_++; |
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} |
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} |
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} |
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|
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|
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for (int i = 0; i < nBonds-1; i++ ){ |
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Vector3d vec1 = bondvec[i]; |
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vec1.normalize(); |
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for(int j = i+1; j < nBonds; j++){ |
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Vector3d vec2 = bondvec[j]; |
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|
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vec2.normalize(); |
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|
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RealType theta = acos(dot(vec1,vec2))*180.0/NumericConstant::PI; |
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|
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|
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if (theta > 180.0){ |
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theta = 360.0 - theta; |
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} |
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int whichBin = int(theta/deltaTheta_); |
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|
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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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} |
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|
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|
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writeBondAngleDistribution(); |
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} |
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|
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|
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void BondAngleDistribution::writeBondAngleDistribution() { |
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|
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std::ofstream osbad(getOutputFileName().c_str()); |
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|
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|
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RealType norm = (RealType)nTotBonds_*((RealType)nTotBonds_-1.0)/2.0; |
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if (osbad.is_open()) { |
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|
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// Normalize by number of frames and write it out: |
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for (int i = 0; i < nBins_; ++i) { |
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RealType Thetaval = i * deltaTheta_; |
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osbad << Thetaval; |
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osbad << "\t" << (RealType)histogram_[i]/norm/frameCounter_; |
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|
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osbad << "\n"; |
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} |
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|
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osbad.close(); |
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|
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} else { |
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sprintf(painCave.errMsg, "BondAngleDistribution: unable to open %s\n", |
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(getOutputFileName() + "q").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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} |
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} |
