1 |
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/* |
2 |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
3 |
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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 |
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* Parallel Simulation Engine for Molecular Dynamics," |
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< |
* 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 |
< |
* |
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< |
* 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 |
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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 |
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* University of Notre Dame has been advised of the possibility of |
39 |
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* such damages. |
40 |
< |
*/ |
41 |
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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 |
45 |
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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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|
1 |
> |
/* |
2 |
> |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
3 |
> |
* |
4 |
> |
* 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 |
> |
|
49 |
> |
#include "applications/staticProps/BondOrderParameter.hpp" |
50 |
> |
#include "utils/simError.h" |
51 |
> |
#include "io/DumpReader.hpp" |
52 |
> |
#include "primitives/Molecule.hpp" |
53 |
> |
#include "utils/NumericConstant.hpp" |
54 |
> |
#include "math/RealSphericalHarmonic.hpp" |
55 |
> |
namespace oopse { |
56 |
> |
|
57 |
> |
|
58 |
> |
BondOrderParameter::BondOrderParameter(SimInfo* info, |
59 |
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const std::string& filename, |
60 |
> |
const std::string& sele, |
61 |
> |
double rCut, int lNumber, int nbins) |
62 |
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: StaticAnalyser(info, filename), selectionScript_(sele), |
63 |
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evaluator_(info), seleMan_(info){ |
64 |
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|
65 |
> |
setOutputName(getPrefix(filename) + ".obo"); |
66 |
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|
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evaluator_.loadScriptString(sele); |
68 |
> |
if (!evaluator_.isDynamic()) { |
69 |
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
70 |
> |
} |
71 |
> |
|
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// Set up cutoff radius and order of the Legendre Polynomial: |
73 |
> |
|
74 |
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lNumber_ = lNumber; |
75 |
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rCut_ = rCut; |
76 |
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mSize_ = 2*lNumber_+1; |
77 |
> |
|
78 |
> |
// Set the l for the spherical harmonic, it doesn't change |
79 |
> |
|
80 |
> |
sphericalHarmonic.setL(lNumber_); |
81 |
> |
|
82 |
> |
delta_Q = 1.0 / nbins; |
83 |
> |
delta_W = 2.0 / nbins; |
84 |
> |
|
85 |
> |
Q_histogram_.resize(nbins); |
86 |
> |
W_histogram_.resize(nbins); |
87 |
> |
|
88 |
> |
} |
89 |
> |
|
90 |
> |
void BondOrderParameter::initalizeHistogram() { |
91 |
> |
std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0); |
92 |
> |
std::fill(W_histogram_.begin(), W_histogram_.end(), 0); |
93 |
> |
} |
94 |
> |
|
95 |
> |
void BondOrderParameter::process() { |
96 |
> |
Molecule* mol; |
97 |
> |
Atom* atom; |
98 |
> |
RigidBody* rb; |
99 |
> |
SimInfo::MoleculeIterator mi; |
100 |
> |
Molecule::RigidBodyIterator rbIter; |
101 |
> |
Molecule::AtomIterator ai; |
102 |
> |
StuntDouble* sd; |
103 |
> |
RealType theta; |
104 |
> |
RealType phi; |
105 |
> |
RealType r; |
106 |
> |
RealType dist; |
107 |
> |
std::map<int, RealType> QBar_lm; |
108 |
> |
RealType QSq_l; |
109 |
> |
RealType Q_l; |
110 |
> |
int nBonds; |
111 |
> |
RealSphericalHarmonic sphericalHarmonic; |
112 |
> |
int i, j; |
113 |
> |
|
114 |
> |
|
115 |
> |
DumpReader reader(info_, dumpFilename_); |
116 |
> |
int nFrames = reader.getNFrames(); |
117 |
> |
|
118 |
> |
|
119 |
> |
for (int istep = 0; istep < nFrames; istep += step_) { |
120 |
> |
reader.readFrame(istep); |
121 |
> |
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
122 |
> |
|
123 |
> |
if (evaluator_.isDynamic()) { |
124 |
> |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
125 |
> |
} |
126 |
> |
|
127 |
> |
// update the positions of atoms which belong to the rigidbodies |
128 |
> |
|
129 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
130 |
> |
mol = info_->nextMolecule(mi)) { |
131 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
132 |
> |
rb = mol->nextRigidBody(rbIter)) { |
133 |
> |
rb->updateAtoms(); |
134 |
> |
} |
135 |
> |
} |
136 |
> |
|
137 |
> |
// outer loop is over the selected StuntDoubles: |
138 |
> |
|
139 |
> |
for (sd = seleMan_.beginSelected(i); sd != NULL; |
140 |
> |
sd = seleMan_.nextSelected(i)) { |
141 |
> |
|
142 |
> |
// For this central atom, zero out nBonds and QBar_lm |
143 |
> |
|
144 |
> |
nBonds = 0; |
145 |
> |
|
146 |
> |
for (int m = -lNumber_; m <= lNumber_; m++) { |
147 |
> |
QBar_lm[m] = 0.0; |
148 |
> |
} |
149 |
> |
|
150 |
> |
// inner loop is over all other atoms in the system: |
151 |
> |
|
152 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
153 |
> |
mol = info_->nextMolecule(mi)) { |
154 |
> |
for (atom = mol->beginAtom(ai); atom != NULL; |
155 |
> |
atom = mol->nextAtom(ai)) { |
156 |
> |
|
157 |
> |
|
158 |
> |
Vector3d vec = sd->getPos() - atom->getPos(); |
159 |
> |
currentSnapshot_->wrapVector(vec); |
160 |
> |
|
161 |
> |
// Calculate "bonds" and build Q_lm(r) where |
162 |
> |
// Q_lm = Y_lm(theta(r),phi(r)) |
163 |
> |
// The spherical harmonics are wrt any arbitrary coordinate |
164 |
> |
// system, we choose standard spherical coordinates |
165 |
> |
|
166 |
> |
r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2)); |
167 |
> |
|
168 |
> |
// Check to see if neighbor is in bond cutoff |
169 |
> |
|
170 |
> |
if (r < rCut_) { |
171 |
> |
theta = atan2(vec.y(), vec.x()); |
172 |
> |
phi = acos(vec.z()/r); |
173 |
> |
for(int m = -lNumber_; m <= lNumber_; m++){ |
174 |
> |
sphericalHarmonic.setM(m); |
175 |
> |
QBar_lm[m] += sphericalHarmonic.getValueAt(theta,phi); |
176 |
> |
} |
177 |
> |
nBonds++; |
178 |
> |
} |
179 |
> |
} |
180 |
> |
} |
181 |
> |
|
182 |
> |
// Normalize Qbar |
183 |
> |
for (int m = -lNumber_;m <= lNumber_; m++){ |
184 |
> |
QBar_lm[m] /= nBonds; |
185 |
> |
} |
186 |
> |
|
187 |
> |
// Find second order invariant Q_l |
188 |
> |
|
189 |
> |
QSq_l = 0.0; |
190 |
> |
for (int m = -lNumber_; m <= lNumber_; m++){ |
191 |
> |
QSq_l += pow(QBar_lm[m], 2); |
192 |
> |
} |
193 |
> |
Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1))); |
194 |
> |
|
195 |
> |
// Find Third Order Invariant W_l |
196 |
> |
|
197 |
> |
// Make arrays for Wigner3jm |
198 |
> |
double* THRCOF = new double[mSize_]; |
199 |
> |
// Variables for Wigner routine |
200 |
> |
double l_ = (double)lNumber_; |
201 |
> |
double m2Min, m2Max; |
202 |
> |
int error, m1, m2, m3; |
203 |
> |
|
204 |
> |
W_l_ = 0.0; |
205 |
> |
for (int m1 = -lNumber_; m1 <= lNumber_; m1++) { |
206 |
> |
// Zero work array |
207 |
> |
for (int ii = 0; ii < mSize_; ii+){ |
208 |
> |
THRCOF[i] = 0.0; |
209 |
> |
} |
210 |
> |
// Get Wigner coefficients |
211 |
> |
Wigner3jm(&l_, &l_, &l_, &(double)m1, &m2Min, &m2Max, THRCOF, &mSize_, &error); |
212 |
> |
for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) { |
213 |
> |
m2 = floor(m2Min) + m_index - 1; |
214 |
> |
m3 = -m1-m2; |
215 |
> |
W_l_ += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_]; |
216 |
> |
} |
217 |
> |
} |
218 |
> |
|
219 |
> |
W_l_hat = W_l_ / pow(QSq_l, 1.5); |
220 |
> |
|
221 |
> |
// accumulate histogram data for Q_l and W_l_hat: |
222 |
> |
|
223 |
> |
collectHistogram(Q_l, W_l_hat); |
224 |
> |
|
225 |
> |
} |
226 |
> |
} |
227 |
> |
|
228 |
> |
// Normalize by number of frames |
229 |
> |
for (int m = -lNumber_; m <= lNumber_; m++){ |
230 |
> |
QBar_lm[m] /= nFrames; |
231 |
> |
} |
232 |
> |
|
233 |
> |
|
234 |
> |
|
235 |
> |
|
236 |
> |
|
237 |
> |
writeOrderParameter(); |
238 |
> |
|
239 |
> |
} |
240 |
> |
|
241 |
> |
|
242 |
> |
void BondOrderParameter::processHistogram() { |
243 |
> |
|
244 |
> |
int nPairs = getNPairs(); |
245 |
> |
RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
246 |
> |
RealType pairDensity = nPairs /volume * 2.0; |
247 |
> |
RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0; |
248 |
> |
|
249 |
> |
for(int i = 0 ; i < histogram_.size(); ++i){ |
250 |
> |
|
251 |
> |
RealType rLower = i * deltaR_; |
252 |
> |
RealType rUpper = rLower + deltaR_; |
253 |
> |
RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); |
254 |
> |
RealType nIdeal = volSlice * pairConstant; |
255 |
> |
|
256 |
> |
avgGofr_[i] += histogram_[i] / nIdeal; |
257 |
> |
} |
258 |
> |
|
259 |
> |
} |
260 |
> |
|
261 |
> |
void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) { |
262 |
> |
|
263 |
> |
if (Q_l < Max_Q) { |
264 |
> |
int whichBin = Q_l / deltaQ_; |
265 |
> |
Q_histogram_[whichBin] += 1; |
266 |
> |
} |
267 |
> |
if (W_l_hat < Max_W) { |
268 |
> |
int whichBin = W_l_hat / deltaW_; |
269 |
> |
W_histogram_[whichBin] += 1; |
270 |
> |
} |
271 |
> |
} |
272 |
> |
|
273 |
> |
|
274 |
> |
void BondOrderParameter::writeOrderParameter() { |
275 |
> |
|
276 |
> |
std::ofstream os(getOutputFileName().c_str()); |
277 |
> |
os << "#Bond Order Parameter\n"; |
278 |
> |
os << "#selection: (" << selectionScript_ << ")\n"; |
279 |
> |
|
280 |
> |
for (std::size_t i = 0; i < orderParams_.size(); ++i) { |
281 |
> |
os << orderParams_[i].p2 << "\t" |
282 |
> |
<< orderParams_[i].director[0] << "\t" |
283 |
> |
<< orderParams_[i].director[1] << "\t" |
284 |
> |
<< orderParams_[i].director[2] << "\t" |
285 |
> |
<< orderParams_[i].angle << "\n"; |
286 |
> |
|
287 |
> |
} |
288 |
> |
} |
289 |
> |
|
290 |
> |
|
291 |
> |
|
292 |
> |
} |