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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 |
| 32 |
< |
* using, modifying or distributing the software or its |
| 33 |
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* derivatives. In no event will the University of Notre Dame or its |
| 34 |
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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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|
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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: |
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> |
* |
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> |
* 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 |
> |
* |
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> |
* 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 |
> |
* |
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> |
* 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 |
> |
* |
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> |
* BondOrderParameter.cpp |
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* OOPSE-4 |
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* |
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* Created by J. Daniel Gezelter on 09/26/06. |
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* @author J. Daniel Gezelter |
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* @version $Id: BondOrderParameter.cpp,v 1.20 2006-11-03 22:02:55 gezelter Exp $ |
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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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|
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namespace oopse { |
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|
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BondOrderParameter::BondOrderParameter(SimInfo* info, |
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const std::string& filename, |
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const std::string& sele, |
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double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ |
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|
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setOutputName(getPrefix(filename) + ".bo"); |
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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: |
| 71 |
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|
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rCut_ = rCut; |
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nBins_ = nbins; |
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Qcount_.resize(lMax_+1); |
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Wcount_.resize(lMax_+1); |
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|
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// Q can take values from 0 to 1 |
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> |
|
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MinQ_ = 0.0; |
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MaxQ_ = 1.1; |
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deltaQ_ = (MaxQ_ - MinQ_) / nbins; |
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|
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// W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll |
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// use values for MinW_ and MaxW_ that are slightly larger than this: |
| 85 |
> |
|
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MinW_ = -0.25; |
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MaxW_ = 0.25; |
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deltaW_ = (MaxW_ - MinW_) / nbins; |
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> |
|
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// Make arrays for Wigner3jm |
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> |
double* THRCOF = new double[2*lMax_+1]; |
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> |
// Variables for Wigner routine |
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> |
double lPass, m1Pass, m2m, m2M; |
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> |
int error, mSize; |
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> |
mSize = 2*lMax_+1; |
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> |
|
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> |
for (int l = 0; l <= lMax_; l++) { |
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> |
lPass = (double)l; |
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> |
for (int m1 = -l; m1 <= l; m1++) { |
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> |
m1Pass = (double)m1; |
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> |
|
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std::pair<int,int> lm = std::make_pair(l, m1); |
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> |
|
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// Zero work array |
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> |
for (int ii = 0; ii < 2*l + 1; ii++){ |
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THRCOF[ii] = 0.0; |
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> |
} |
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> |
|
| 109 |
> |
// Get Wigner coefficients |
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> |
Wigner3jm(&lPass, &lPass, &lPass, |
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&m1Pass, &m2m, &m2M, |
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> |
THRCOF, &mSize, &error); |
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> |
|
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> |
m2Min[lm] = (int)floor(m2m); |
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> |
m2Max[lm] = (int)floor(m2M); |
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> |
|
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> |
for (int mmm = 0; mmm < (int)(m2M - m2m); mmm++) { |
| 118 |
> |
w3j[lm].push_back(THRCOF[mmm]); |
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> |
} |
| 120 |
> |
} |
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> |
} |
| 122 |
> |
delete [] THRCOF; |
| 123 |
> |
THRCOF = NULL; |
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> |
} |
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> |
|
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> |
BondOrderParameter::~BondOrderParameter() { |
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> |
Q_histogram_.clear(); |
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> |
W_histogram_.clear(); |
| 129 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 130 |
> |
for (int m = -l; m <= l; m++) { |
| 131 |
> |
w3j[std::make_pair(l,m)].clear(); |
| 132 |
> |
} |
| 133 |
> |
} |
| 134 |
> |
w3j.clear(); |
| 135 |
> |
m2Min.clear(); |
| 136 |
> |
m2Max.clear(); |
| 137 |
> |
} |
| 138 |
> |
|
| 139 |
> |
void BondOrderParameter::initalizeHistogram() { |
| 140 |
> |
for (int bin = 0; bin < nBins_; bin++) { |
| 141 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 142 |
> |
Q_histogram_[std::make_pair(bin,l)] = 0; |
| 143 |
> |
W_histogram_[std::make_pair(bin,l)] = 0; |
| 144 |
> |
} |
| 145 |
> |
} |
| 146 |
> |
} |
| 147 |
> |
|
| 148 |
> |
void BondOrderParameter::process() { |
| 149 |
> |
Molecule* mol; |
| 150 |
> |
Atom* atom; |
| 151 |
> |
RigidBody* rb; |
| 152 |
> |
int myIndex; |
| 153 |
> |
SimInfo::MoleculeIterator mi; |
| 154 |
> |
Molecule::RigidBodyIterator rbIter; |
| 155 |
> |
Molecule::AtomIterator ai; |
| 156 |
> |
StuntDouble* sd; |
| 157 |
> |
Vector3d vec; |
| 158 |
> |
RealType costheta; |
| 159 |
> |
RealType phi; |
| 160 |
> |
RealType r; |
| 161 |
> |
RealType dist; |
| 162 |
> |
std::map<std::pair<int,int>,ComplexType> q; |
| 163 |
> |
std::vector<RealType> q_l; |
| 164 |
> |
std::vector<RealType> q2; |
| 165 |
> |
std::vector<ComplexType> w; |
| 166 |
> |
std::vector<ComplexType> w_hat; |
| 167 |
> |
std::map<std::pair<int,int>,ComplexType> QBar; |
| 168 |
> |
std::vector<RealType> Q2; |
| 169 |
> |
std::vector<RealType> Q; |
| 170 |
> |
std::vector<ComplexType> W; |
| 171 |
> |
std::vector<ComplexType> W_hat; |
| 172 |
> |
int nBonds, Nbonds; |
| 173 |
> |
SphericalHarmonic sphericalHarmonic; |
| 174 |
> |
int i, j; |
| 175 |
> |
|
| 176 |
> |
DumpReader reader(info_, dumpFilename_); |
| 177 |
> |
int nFrames = reader.getNFrames(); |
| 178 |
> |
frameCounter_ = 0; |
| 179 |
> |
|
| 180 |
> |
q_l.resize(lMax_+1); |
| 181 |
> |
q2.resize(lMax_+1); |
| 182 |
> |
w.resize(lMax_+1); |
| 183 |
> |
w_hat.resize(lMax_+1); |
| 184 |
> |
|
| 185 |
> |
Q2.resize(lMax_+1); |
| 186 |
> |
Q.resize(lMax_+1); |
| 187 |
> |
W.resize(lMax_+1); |
| 188 |
> |
W_hat.resize(lMax_+1); |
| 189 |
> |
|
| 190 |
> |
for (int istep = 0; istep < nFrames; istep += step_) { |
| 191 |
> |
reader.readFrame(istep); |
| 192 |
> |
frameCounter_++; |
| 193 |
> |
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 194 |
> |
|
| 195 |
> |
if (evaluator_.isDynamic()) { |
| 196 |
> |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 197 |
> |
} |
| 198 |
> |
|
| 199 |
> |
// update the positions of atoms which belong to the rigidbodies |
| 200 |
> |
|
| 201 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 202 |
> |
mol = info_->nextMolecule(mi)) { |
| 203 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 204 |
> |
rb = mol->nextRigidBody(rbIter)) { |
| 205 |
> |
rb->updateAtoms(); |
| 206 |
> |
} |
| 207 |
> |
} |
| 208 |
> |
|
| 209 |
> |
// outer loop is over the selected StuntDoubles: |
| 210 |
> |
|
| 211 |
> |
for (sd = seleMan_.beginSelected(i); sd != NULL; |
| 212 |
> |
sd = seleMan_.nextSelected(i)) { |
| 213 |
> |
|
| 214 |
> |
myIndex = sd->getGlobalIndex(); |
| 215 |
> |
nBonds = 0; |
| 216 |
> |
|
| 217 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 218 |
> |
for (int m = -l; m <= l; m++) { |
| 219 |
> |
q[std::make_pair(l,m)] = 0.0; |
| 220 |
> |
} |
| 221 |
> |
} |
| 222 |
> |
|
| 223 |
> |
// inner loop is over all other atoms in the system: |
| 224 |
> |
|
| 225 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 226 |
> |
mol = info_->nextMolecule(mi)) { |
| 227 |
> |
for (atom = mol->beginAtom(ai); atom != NULL; |
| 228 |
> |
atom = mol->nextAtom(ai)) { |
| 229 |
> |
|
| 230 |
> |
if (atom->getGlobalIndex() != myIndex) { |
| 231 |
> |
|
| 232 |
> |
vec = sd->getPos() - atom->getPos(); |
| 233 |
> |
|
| 234 |
> |
if (usePeriodicBoundaryConditions_) |
| 235 |
> |
currentSnapshot_->wrapVector(vec); |
| 236 |
> |
|
| 237 |
> |
// Calculate "bonds" and build Q_lm(r) where |
| 238 |
> |
// Q_lm = Y_lm(theta(r),phi(r)) |
| 239 |
> |
// The spherical harmonics are wrt any arbitrary coordinate |
| 240 |
> |
// system, we choose standard spherical coordinates |
| 241 |
> |
|
| 242 |
> |
r = vec.length(); |
| 243 |
> |
|
| 244 |
> |
// Check to see if neighbor is in bond cutoff |
| 245 |
> |
|
| 246 |
> |
if (r < rCut_) { |
| 247 |
> |
costheta = vec.z() / r; |
| 248 |
> |
phi = atan2(vec.y(), vec.x()); |
| 249 |
> |
|
| 250 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 251 |
> |
sphericalHarmonic.setL(l); |
| 252 |
> |
for(int m = -l; m <= l; m++){ |
| 253 |
> |
sphericalHarmonic.setM(m); |
| 254 |
> |
q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi); |
| 255 |
> |
} |
| 256 |
> |
} |
| 257 |
> |
nBonds++; |
| 258 |
> |
} |
| 259 |
> |
} |
| 260 |
> |
} |
| 261 |
> |
} |
| 262 |
> |
|
| 263 |
> |
|
| 264 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 265 |
> |
q_l[l] = 0.0; |
| 266 |
> |
for(int m = -l; m <= l; m++) { |
| 267 |
> |
q_l[l] += norm(q[std::make_pair(l,m)]); |
| 268 |
> |
} |
| 269 |
> |
q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1); |
| 270 |
> |
q_l[l] = sqrt(q_l[l])/(RealType)nBonds; |
| 271 |
> |
} |
| 272 |
> |
|
| 273 |
> |
// Find second order invariant Q_l |
| 274 |
> |
|
| 275 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 276 |
> |
q2[l] = 0.0; |
| 277 |
> |
for (int m = -l; m <= l; m++){ |
| 278 |
> |
q2[l] += norm(q[std::make_pair(l,m)]); |
| 279 |
> |
} |
| 280 |
> |
q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / |
| 281 |
> |
(RealType)(2*l + 1))/(RealType)nBonds; |
| 282 |
> |
} |
| 283 |
> |
|
| 284 |
> |
// Find Third Order Invariant W_l |
| 285 |
> |
|
| 286 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 287 |
> |
w[l] = 0.0; |
| 288 |
> |
for (int m1 = -l; m1 <= l; m1++) { |
| 289 |
> |
std::pair<int,int> lm = std::make_pair(l, m1); |
| 290 |
> |
for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) { |
| 291 |
> |
int m2 = m2Min[lm] + mmm; |
| 292 |
> |
int m3 = -m1-m2; |
| 293 |
> |
w[l] += w3j[lm][mmm] * q[lm] * |
| 294 |
> |
q[std::make_pair(l,m2)] * q[std::make_pair(l,m3)]; |
| 295 |
> |
} |
| 296 |
> |
} |
| 297 |
> |
|
| 298 |
> |
w_hat[l] = w[l] / pow(q2[l], 1.5); |
| 299 |
> |
} |
| 300 |
> |
|
| 301 |
> |
collectHistogram(q_l, w_hat); |
| 302 |
> |
|
| 303 |
> |
Nbonds += nBonds; |
| 304 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 305 |
> |
for (int m = -l; m <= l; m++) { |
| 306 |
> |
QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)]; |
| 307 |
> |
} |
| 308 |
> |
} |
| 309 |
> |
} |
| 310 |
> |
} |
| 311 |
> |
|
| 312 |
> |
// Normalize Qbar2 |
| 313 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 314 |
> |
for (int m = -l; m <= l; m++){ |
| 315 |
> |
QBar[std::make_pair(l,m)] /= Nbonds; |
| 316 |
> |
} |
| 317 |
> |
} |
| 318 |
> |
|
| 319 |
> |
// Find second order invariant Q_l |
| 320 |
> |
|
| 321 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 322 |
> |
Q2[l] = 0.0; |
| 323 |
> |
for (int m = -l; m <= l; m++){ |
| 324 |
> |
Q2[l] += norm(QBar[std::make_pair(l,m)]); |
| 325 |
> |
} |
| 326 |
> |
Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1)); |
| 327 |
> |
} |
| 328 |
> |
|
| 329 |
> |
// Find Third Order Invariant W_l |
| 330 |
> |
|
| 331 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 332 |
> |
W[l] = 0.0; |
| 333 |
> |
for (int m1 = -l; m1 <= l; m1++) { |
| 334 |
> |
std::pair<int,int> lm = std::make_pair(l, m1); |
| 335 |
> |
for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) { |
| 336 |
> |
int m2 = m2Min[lm] + mmm; |
| 337 |
> |
int m3 = -m1-m2; |
| 338 |
> |
W[l] += w3j[lm][mmm] * QBar[lm] * |
| 339 |
> |
QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)]; |
| 340 |
> |
} |
| 341 |
> |
} |
| 342 |
> |
|
| 343 |
> |
W_hat[l] = W[l] / pow(Q2[l], 1.5); |
| 344 |
> |
} |
| 345 |
> |
|
| 346 |
> |
writeOrderParameter(Q, W_hat); |
| 347 |
> |
} |
| 348 |
> |
|
| 349 |
> |
void BondOrderParameter::collectHistogram(std::vector<RealType> q, |
| 350 |
> |
std::vector<ComplexType> what) { |
| 351 |
> |
|
| 352 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 353 |
> |
if (q[l] >= MinQ_ && q[l] < MaxQ_) { |
| 354 |
> |
int qbin = (q[l] - MinQ_) / deltaQ_; |
| 355 |
> |
Q_histogram_[std::make_pair(qbin,l)] += 1; |
| 356 |
> |
Qcount_[l]++; |
| 357 |
> |
} else { |
| 358 |
> |
sprintf( painCave.errMsg, |
| 359 |
> |
"q_l value outside reasonable range\n"); |
| 360 |
> |
painCave.severity = OOPSE_ERROR; |
| 361 |
> |
painCave.isFatal = 1; |
| 362 |
> |
simError(); |
| 363 |
> |
} |
| 364 |
> |
} |
| 365 |
> |
|
| 366 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 367 |
> |
if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) { |
| 368 |
> |
int wbin = (real(what[l]) - MinW_) / deltaW_; |
| 369 |
> |
W_histogram_[std::make_pair(wbin,l)] += 1; |
| 370 |
> |
Wcount_[l]++; |
| 371 |
> |
} else { |
| 372 |
> |
sprintf( painCave.errMsg, |
| 373 |
> |
"Re[w_hat] value outside reasonable range\n"); |
| 374 |
> |
painCave.severity = OOPSE_ERROR; |
| 375 |
> |
painCave.isFatal = 1; |
| 376 |
> |
simError(); |
| 377 |
> |
} |
| 378 |
> |
} |
| 379 |
> |
|
| 380 |
> |
} |
| 381 |
> |
|
| 382 |
> |
|
| 383 |
> |
void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q, |
| 384 |
> |
std::vector<ComplexType> What) { |
| 385 |
> |
|
| 386 |
> |
std::ofstream osq((getOutputFileName() + "q").c_str()); |
| 387 |
> |
|
| 388 |
> |
if (osq.is_open()) { |
| 389 |
> |
|
| 390 |
> |
osq << "# Bond Order Parameters\n"; |
| 391 |
> |
osq << "# selection: (" << selectionScript_ << ")\n"; |
| 392 |
> |
osq << "# \n"; |
| 393 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 394 |
> |
osq << "# <Q_" << l << ">: " << Q[l] << "\n"; |
| 395 |
> |
} |
| 396 |
> |
// Normalize by number of frames and write it out: |
| 397 |
> |
for (int i = 0; i < nBins_; ++i) { |
| 398 |
> |
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
| 399 |
> |
osq << Qval; |
| 400 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 401 |
> |
osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]*deltaQ_/ |
| 402 |
> |
(RealType)Qcount_[l]; |
| 403 |
> |
} |
| 404 |
> |
osq << "\n"; |
| 405 |
> |
} |
| 406 |
> |
|
| 407 |
> |
osq.close(); |
| 408 |
> |
|
| 409 |
> |
} else { |
| 410 |
> |
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
| 411 |
> |
(getOutputFileName() + "q").c_str()); |
| 412 |
> |
painCave.isFatal = 1; |
| 413 |
> |
simError(); |
| 414 |
> |
} |
| 415 |
> |
|
| 416 |
> |
std::ofstream osw((getOutputFileName() + "w").c_str()); |
| 417 |
> |
|
| 418 |
> |
if (osw.is_open()) { |
| 419 |
> |
osw << "# Bond Order Parameters\n"; |
| 420 |
> |
osw << "# selection: (" << selectionScript_ << ")\n"; |
| 421 |
> |
osw << "# \n"; |
| 422 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 423 |
> |
osw << "# <W_" << l << ">: " << real(What[l]) << "\t" << imag(What[l]) << "\n"; |
| 424 |
> |
} |
| 425 |
> |
// Normalize by number of frames and write it out: |
| 426 |
> |
for (int i = 0; i < nBins_; ++i) { |
| 427 |
> |
RealType Wval = MinW_ + (i + 0.5) * deltaW_; |
| 428 |
> |
osw << Wval; |
| 429 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 430 |
> |
osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]*deltaW_/ |
| 431 |
> |
(RealType)Wcount_[l]; |
| 432 |
> |
} |
| 433 |
> |
osw << "\n"; |
| 434 |
> |
} |
| 435 |
> |
|
| 436 |
> |
osw.close(); |
| 437 |
> |
} else { |
| 438 |
> |
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
| 439 |
> |
(getOutputFileName() + "w").c_str()); |
| 440 |
> |
painCave.isFatal = 1; |
| 441 |
> |
simError(); |
| 442 |
> |
} |
| 443 |
> |
|
| 444 |
> |
} |
| 445 |
> |
} |
