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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 |
| 6 |
< |
* redistribute this software in source and binary code form, provided |
| 7 |
< |
* 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 |
| 23 |
< |
* documentation and/or other materials provided with the |
| 24 |
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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, |
| 29 |
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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 |
| 32 |
< |
* using, modifying or distributing the software or its |
| 33 |
< |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
< |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
< |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
< |
* damages, however caused and regardless of the theory of liability, |
| 37 |
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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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|
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/* Creates orientational bond order parameters as outlined by |
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* Bond-orientaional order in liquids and glasses, Steinhart,Nelson,Ronchetti |
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* Phys Rev B, 28,784,1983 |
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* |
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*/ |
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|
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#include "applications/staticProps/BondOrderParameter.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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#include "math/RealSphericalHarmonic.hpp" |
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namespace oopse { |
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|
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|
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BondOrderParameter::BondOrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1, |
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const std::string& sele2, double rCut, int lNumber) |
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: StaticAnalyser(info, filename), |
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selectionScript1_(sele1), evaluator1_(info), |
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seleMan1_(info){ |
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|
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setOutputName(getPrefix(filename) + ".obo"); |
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|
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evaluator1_.loadScriptString(sele1); |
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evaluator2_.loadScriptString(sele2); |
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|
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if (!evaluator1_.isDynamic()) { |
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seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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}else { |
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sprintf( painCave.errMsg, |
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"--sele1 must be static selection\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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/* Set up cutoff radius and type of order parameter we are calcuating*/ |
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lNumber_ = lNumber; |
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rCut_ = rCut; |
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mSize_ = 2*lNumber_+1; |
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|
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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 = seleMan1_.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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|
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sdPairs_.push_back(std::make_pair(sd1, sd2)); |
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} |
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|
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|
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} |
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|
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void BondOrderParameter::process() { |
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Molecule* mol; |
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RigidBody* rb; |
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SimInfo::MoleculeIterator mi; |
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Molecule::RigidBodyIterator rbIter; |
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RealType theta; |
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RealType phi; |
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RealType r; |
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RealType dist; |
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RealType* QBar_lm; |
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int nBonds; |
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RealSphericalHarmonic sphericalHarmonic; |
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|
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|
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader.getNFrames(); |
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|
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/*Set the l for the spherical harmonic, it doesn't change*/ |
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sphericalHarmonic.setL(lNumber_); |
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|
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for (int i = 0; i < nFrames; i += step_) { |
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reader.readFrame(i); |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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nBonds = 0; |
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|
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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//change the positions of atoms which belong to the rigidbodies |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; 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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|
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/* Calculate "bonds" and build Q_lm(r) where Q_lm = Y_lm(theta(r),phi(r)) */ |
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for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
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Vector3d vec = j->first->getPos() - j->second->getPos(); |
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currentSnapshot_->wrapVector(vec); |
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/* The spherical harmonics are wrt any arbitray coordiate sysetm, |
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* we choose standard spherical coordinates */ |
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r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2)); |
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|
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/* Check to see if neighbor is in bond cuttoff*/ |
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if (r<rCut_){ |
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theta = atan(vec.y()/vec.x()); |
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phi = acos(vec.z()/r); |
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for(int m = -lNumber_; m <= lNumber_; m++){ |
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sphericalHarmonic.setM(m); |
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QBar_lm(m) += sphericalHarmonic.getValueAt(theta,phi); |
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} |
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nBonds++; |
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} |
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} |
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|
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/*Normalize Qbar*/ |
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for (int m = -lNumber_;m <= lNumber_; m++){ |
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QBar_lm(m) = QBar_lm(m)/nBonds; |
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} |
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|
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|
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} |
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|
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/*Normalize by number of frames*/ |
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for (int m = -lNumber_;m <= lNumber_; m++){ |
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QBar_lm(m) = QBar_lm(m)/nFrames; |
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} |
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|
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|
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|
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/* Find second order invariant Q_l*/ |
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|
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for (int m = -lNumber_;m <= lNumber_; m++){ |
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QSq_l += pow(QBar_lm(m),2); |
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} |
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Q_l = sqrt((4*NumericConstant::PI/lNumber_+1)*QSq_l); |
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|
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/* Find Third Order Invariant W_l*/ |
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for (int m = -lNumber_;m<= lNumber_;m++){ |
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|
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|
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} |
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|
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|
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writeOrderParameter(); |
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|
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} |
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|
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void BondOrderParameter::initalizeHistogram() { |
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std::fill(histogram_.begin(), histogram_.end(), 0); |
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} |
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|
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void BondOrderParameter::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 = ( 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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RealType rLower = i * deltaR_; |
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RealType rUpper = rLower + deltaR_; |
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RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); |
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RealType nIdeal = volSlice * pairConstant; |
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|
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avgGofr_[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 BondOrderParameter::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->getPos(); |
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Vector3d pos2 = sd2->getPos(); |
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Vector3d r12 = pos2 - pos1; |
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currentSnapshot_->wrapVector(r12); |
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|
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RealType 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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|
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|
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|
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|
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void BondOrderParameter::writeOrderParameter() { |
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|
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std::ofstream os(getOutputFileName().c_str()); |
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os << "#radial distribution function\n"; |
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os<< "#selection1: (" << selectionScript1_ << ")\t"; |
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os << "selection2: (" << selectionScript2_ << ")\n"; |
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os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n"; |
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|
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for (std::size_t i = 0; i < orderParams_.size(); ++i) { |
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os << orderParams_[i].p2 << "\t" |
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<< orderParams_[i].director[0] << "\t" |
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<< orderParams_[i].director[1] << "\t" |
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<< orderParams_[i].director[2] << "\t" |
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<< orderParams_[i].angle << "\n"; |
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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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/* |
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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 |
| 5 |
> |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
> |
* redistribute this software in source and binary code form, provided |
| 7 |
> |
* that the following conditions are met: |
| 8 |
> |
* |
| 9 |
> |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
> |
* publication of scientific results based in part on use of the |
| 11 |
> |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
> |
* the article in which the program was described (Matthew |
| 13 |
> |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
> |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
> |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
> |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
> |
* |
| 18 |
> |
* 2. Redistributions of source code must retain the above copyright |
| 19 |
> |
* notice, this list of conditions and the following disclaimer. |
| 20 |
> |
* |
| 21 |
> |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
> |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
> |
* documentation and/or other materials provided with the |
| 24 |
> |
* distribution. |
| 25 |
> |
* |
| 26 |
> |
* This software is provided "AS IS," without a warranty of any |
| 27 |
> |
* kind. All express or implied conditions, representations and |
| 28 |
> |
* warranties, including any implied warranty of merchantability, |
| 29 |
> |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
> |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
> |
* be liable for any damages suffered by licensee as a result of |
| 32 |
> |
* using, modifying or distributing the software or its |
| 33 |
> |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
> |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
> |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
> |
* damages, however caused and regardless of the theory of liability, |
| 37 |
> |
* arising out of the use of or inability to use software, even if the |
| 38 |
> |
* University of Notre Dame has been advised of the possibility of |
| 39 |
> |
* such damages. |
| 40 |
> |
*/ |
| 41 |
> |
|
| 42 |
> |
|
| 43 |
> |
/* Creates orientational bond order parameters as outlined by |
| 44 |
> |
* Bond-orientaional order in liquids and glasses, Steinhart,Nelson,Ronchetti |
| 45 |
> |
* Phys Rev B, 28,784,1983 |
| 46 |
> |
* |
| 47 |
> |
*/ |
| 48 |
> |
|
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> |
#include "applications/staticProps/BondOrderParameter.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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> |
#include "math/RealSphericalHarmonic.hpp" |
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> |
namespace oopse { |
| 56 |
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|
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|
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BondOrderParameter::BondOrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1, |
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const std::string& sele2, double rCut, int lNumber) |
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: StaticAnalyser(info, filename), |
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selectionScript1_(sele1), evaluator1_(info), |
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seleMan1_(info){ |
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|
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setOutputName(getPrefix(filename) + ".obo"); |
| 65 |
> |
|
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evaluator1_.loadScriptString(sele1); |
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evaluator2_.loadScriptString(sele2); |
| 68 |
> |
|
| 69 |
> |
if (!evaluator1_.isDynamic()) { |
| 70 |
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seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
| 71 |
> |
}else { |
| 72 |
> |
sprintf( painCave.errMsg, |
| 73 |
> |
"--sele1 must be static selection\n"); |
| 74 |
> |
painCave.severity = OOPSE_ERROR; |
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> |
painCave.isFatal = 1; |
| 76 |
> |
simError(); |
| 77 |
> |
} |
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> |
|
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/* Set up cutoff radius and type of order parameter we are calcuating*/ |
| 80 |
> |
lNumber_ = lNumber; |
| 81 |
> |
rCut_ = rCut; |
| 82 |
> |
mSize_ = 2*lNumber_+1; |
| 83 |
> |
|
| 84 |
> |
int i; |
| 85 |
> |
int j; |
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> |
StuntDouble* sd1; |
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> |
StuntDouble* sd2; |
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> |
for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan1_.beginSelected(j); |
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sd1 != NULL && sd2 != NULL; |
| 90 |
> |
sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) { |
| 91 |
> |
for (sd2 = seleMan1_.beginSelected(j),sd2 |
| 92 |
> |
sdPairs_.push_back(std::make_pair(sd1, sd2)); |
| 93 |
> |
} |
| 94 |
> |
|
| 95 |
> |
|
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> |
} |
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> |
|
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> |
void BondOrderParameter::process |
| 99 |
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() { |
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> |
Molecule* mol; |
| 101 |
> |
RigidBody* rb; |
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> |
SimInfo::MoleculeIterator mi; |
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> |
Molecule::RigidBodyIterator rbIter; |
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> |
RealType theta; |
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> |
RealType phi; |
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> |
RealType r; |
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> |
RealType dist; |
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> |
RealType* QBar_lm; |
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> |
RealType QSq_l; |
| 110 |
> |
int nBonds; |
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> |
int m, m_index; |
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> |
RealSphericalHarmonic sphericalHarmonic; |
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> |
|
| 114 |
> |
|
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> |
DumpReader reader(info_, dumpFilename_); |
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> |
int nFrames = reader.getNFrames(); |
| 117 |
> |
|
| 118 |
> |
/*Set the l for the spherical harmonic, it doesn't change*/ |
| 119 |
> |
sphericalHarmonic.setL(lNumber_); |
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> |
|
| 121 |
> |
for (int i = 0; i < nFrames; i += step_) { |
| 122 |
> |
reader.readFrame(i); |
| 123 |
> |
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 124 |
> |
nBonds = 0; |
| 125 |
> |
|
| 126 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 127 |
> |
//change the positions of atoms which belong to the rigidbodies |
| 128 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 129 |
> |
rb->updateAtoms(); |
| 130 |
> |
} |
| 131 |
> |
|
| 132 |
> |
} |
| 133 |
> |
|
| 134 |
> |
|
| 135 |
> |
/* Setup QBar */ |
| 136 |
> |
QBar_lm = new double[mSize_]; |
| 137 |
> |
|
| 138 |
> |
/* Calculate "bonds" and build Q_lm(r) where Q_lm = Y_lm(theta(r),phi(r)) */ |
| 139 |
> |
for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
| 140 |
> |
Vector3d vec = j->first->getPos() - j->second->getPos(); |
| 141 |
> |
currentSnapshot_->wrapVector(vec); |
| 142 |
> |
/* The spherical harmonics are wrt any arbitray coordiate sysetm, |
| 143 |
> |
* we choose standard spherical coordinates */ |
| 144 |
> |
r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2)); |
| 145 |
> |
|
| 146 |
> |
/* Check to see if neighbor is in bond cuttoff*/ |
| 147 |
> |
if (r<rCut_){ |
| 148 |
> |
theta = atan(vec.y()/vec.x()); |
| 149 |
> |
phi = acos(vec.z()/r); |
| 150 |
> |
for(int m_index = 0; m_index < mSize_; m_index++){ |
| 151 |
> |
sphericalHarmonic.setM(m_index-lNumber_); |
| 152 |
> |
QBar_lm(m_index) += sphericalHarmonic.getValueAt(theta,phi); |
| 153 |
> |
} |
| 154 |
> |
nBonds++; |
| 155 |
> |
} |
| 156 |
> |
} |
| 157 |
> |
|
| 158 |
> |
/*Normalize Qbar by number of Bonds*/ |
| 159 |
> |
for ( int m_index = 0;m_index < mSize_; m_index++){ |
| 160 |
> |
QBar_lm(m_index) = QBar_lm(m_index)/nBonds; |
| 161 |
> |
} |
| 162 |
> |
|
| 163 |
> |
|
| 164 |
> |
} |
| 165 |
> |
|
| 166 |
> |
/*Normalize by number of frames*/ |
| 167 |
> |
for ( int m_index = 0;m_index < mSize_; m_index++){ |
| 168 |
> |
QBar_lm(m_index) = QBar_lm(m_index)/nFrames; |
| 169 |
> |
} |
| 170 |
> |
|
| 171 |
> |
|
| 172 |
> |
|
| 173 |
> |
/* Find second order invariant Q_l*/ |
| 174 |
> |
|
| 175 |
> |
for (int m_index = 0 ;m_index <= sizeM_; m++){ |
| 176 |
> |
QSq_l += pow(QBar_lm(m),2); |
| 177 |
> |
} |
| 178 |
> |
Q_l_ = sqrt((4*NumericConstant::PI/lNumber_+1)*QSq_l); |
| 179 |
> |
|
| 180 |
> |
/* Find Third Order Invariant W_l*/ |
| 181 |
> |
|
| 182 |
> |
/* Make arrays for Wigner3jm */ |
| 183 |
> |
double* THRCOF = new double[mSize_]; |
| 184 |
> |
/* Variables for Wigner routine */ |
| 185 |
> |
double l_ = (double)lNumber_; |
| 186 |
> |
double m2Min; |
| 187 |
> |
double m2Max; |
| 188 |
> |
int error; |
| 189 |
> |
int m1; |
| 190 |
> |
int m2; |
| 191 |
> |
int m3; |
| 192 |
> |
|
| 193 |
> |
for (int m1 = -lNumber_;m <= lNumber_;m1++){ |
| 194 |
> |
/* Zero work array */ |
| 195 |
> |
for (i=0; i<mSize_;i++){ |
| 196 |
> |
THRCOF[i] = 0.0; |
| 197 |
> |
} |
| 198 |
> |
/* Get wigner coefficients */ |
| 199 |
> |
Wigner3jm(&l_,&l_,&l_,&(double)m1,&m2Min,&m2Max&,THRCOF,&mSize_,&error); |
| 200 |
> |
for (m_index=1; i<(m2Max-M2Min-1.0);m_index++){ |
| 201 |
> |
m2 = floor(m2Min) + m_index - 1; |
| 202 |
> |
m3 = -m1-m2; |
| 203 |
> |
W_l_ += THRCOF(m_index)*QBar_lm(m1+lNumber_)*QBar_lm(m2+lNumber_)*QBar_lm(m3+lNumber_); |
| 204 |
> |
} |
| 205 |
> |
} |
| 206 |
> |
|
| 207 |
> |
|
| 208 |
> |
writeOrderParameter(); |
| 209 |
> |
|
| 210 |
> |
} |
| 211 |
> |
|
| 212 |
> |
|
| 213 |
> |
void BondOrderParameter::writeOrderParameter() { |
| 214 |
> |
|
| 215 |
> |
std::ofstream os(getOutputFileName().c_str()); |
| 216 |
> |
os << "#radial distribution function\n"; |
| 217 |
> |
os<< "#selection1: (" << selectionScript1_ << ")\t"; |
| 218 |
> |
os << "selection2: (" << selectionScript2_ << ")\n"; |
| 219 |
> |
os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n"; |
| 220 |
> |
|
| 221 |
> |
for (std::size_t i = 0; i < orderParams_.size(); ++i) { |
| 222 |
> |
os << orderParams_[i].p2 << "\t" |
| 223 |
> |
<< orderParams_[i].director[0] << "\t" |
| 224 |
> |
<< orderParams_[i].director[1] << "\t" |
| 225 |
> |
<< orderParams_[i].director[2] << "\t" |
| 226 |
> |
<< orderParams_[i].angle << "\n"; |
| 227 |
> |
|
| 228 |
> |
} |
| 229 |
> |
|
| 230 |
> |
} |
| 231 |
> |
|
| 232 |
> |
} |
| 233 |
> |
|
