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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. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * |
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* Created by J. Daniel Gezelter on 09/26/06. |
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* @author J. Daniel Gezelter |
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* @version $Id$ |
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* |
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*/ |
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|
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#include "applications/staticProps/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/Wigner3jm.hpp" |
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|
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using namespace MATPACK; |
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namespace OpenMD { |
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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: |
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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: |
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|
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MinW_ = -1.1; |
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MaxW_ = 1.1; |
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deltaW_ = (MaxW_ - MinW_) / nbins; |
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|
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// Make arrays for Wigner3jm |
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RealType* THRCOF = new RealType[2*lMax_+1]; |
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// Variables for Wigner routine |
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RealType 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 = (RealType)l; |
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for (int m1 = -l; m1 <= l; m1++) { |
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m1Pass = (RealType)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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|
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// 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++) { |
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w3j[lm].push_back(THRCOF[mmm]); |
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} |
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} |
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} |
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delete [] THRCOF; |
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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(); |
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for (int l = 0; l <= lMax_; l++) { |
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for (int m = -l; m <= l; m++) { |
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w3j[std::make_pair(l,m)].clear(); |
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} |
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} |
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w3j.clear(); |
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m2Min.clear(); |
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m2Max.clear(); |
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} |
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|
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void BondOrderParameter::initalizeHistogram() { |
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for (int bin = 0; bin < nBins_; bin++) { |
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for (int l = 0; l <= lMax_; l++) { |
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Q_histogram_[std::make_pair(bin,l)] = 0; |
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W_histogram_[std::make_pair(bin,l)] = 0; |
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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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Atom* atom; |
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RigidBody* rb; |
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int myIndex; |
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SimInfo::MoleculeIterator mi; |
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Molecule::RigidBodyIterator rbIter; |
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Molecule::AtomIterator ai; |
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StuntDouble* sd; |
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Vector3d vec; |
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RealType costheta; |
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RealType phi; |
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RealType r; |
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RealType dist; |
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std::map<std::pair<int,int>,ComplexType> q; |
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std::vector<RealType> q_l; |
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std::vector<RealType> q2; |
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std::vector<ComplexType> w; |
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std::vector<ComplexType> w_hat; |
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std::map<std::pair<int,int>,ComplexType> QBar; |
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std::vector<RealType> Q2; |
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std::vector<RealType> Q; |
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std::vector<ComplexType> W; |
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std::vector<ComplexType> W_hat; |
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int nBonds, Nbonds; |
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SphericalHarmonic sphericalHarmonic; |
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int i, j; |
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|
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader.getNFrames(); |
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frameCounter_ = 0; |
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|
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q_l.resize(lMax_+1); |
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q2.resize(lMax_+1); |
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w.resize(lMax_+1); |
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w_hat.resize(lMax_+1); |
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|
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Q2.resize(lMax_+1); |
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Q.resize(lMax_+1); |
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W.resize(lMax_+1); |
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W_hat.resize(lMax_+1); |
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Nbonds = 0; |
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|
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for (int istep = 0; istep < nFrames; istep += step_) { |
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reader.readFrame(istep); |
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frameCounter_++; |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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|
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if (evaluator_.isDynamic()) { |
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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} |
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|
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// update the positions of atoms which belong to the rigidbodies |
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|
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
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rb = mol->nextRigidBody(rbIter)) { |
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rb->updateAtoms(); |
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} |
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} |
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|
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// outer loop is over the selected StuntDoubles: |
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|
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for (sd = seleMan_.beginSelected(i); sd != NULL; |
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sd = seleMan_.nextSelected(i)) { |
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|
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myIndex = sd->getGlobalIndex(); |
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nBonds = 0; |
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|
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for (int l = 0; l <= lMax_; l++) { |
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for (int m = -l; m <= l; m++) { |
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q[std::make_pair(l,m)] = 0.0; |
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} |
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} |
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|
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// inner loop is over all other atoms in the system: |
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|
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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for (atom = mol->beginAtom(ai); atom != NULL; |
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atom = mol->nextAtom(ai)) { |
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|
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if (atom->getGlobalIndex() != myIndex) { |
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|
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vec = sd->getPos() - atom->getPos(); |
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|
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(vec); |
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|
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// Calculate "bonds" and build Q_lm(r) where |
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// Q_lm = Y_lm(theta(r),phi(r)) |
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// The spherical harmonics are wrt any arbitrary coordinate |
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// system, we choose standard spherical coordinates |
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|
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r = vec.length(); |
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|
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// Check to see if neighbor is in bond cutoff |
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|
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if (r < rCut_) { |
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costheta = vec.z() / r; |
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phi = atan2(vec.y(), vec.x()); |
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|
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for (int l = 0; l <= lMax_; l++) { |
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sphericalHarmonic.setL(l); |
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for(int m = -l; m <= l; m++){ |
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sphericalHarmonic.setM(m); |
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q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi); |
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} |
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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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} |
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|
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|
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for (int l = 0; l <= lMax_; l++) { |
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q2[l] = 0.0; |
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for (int m = -l; m <= l; m++){ |
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q[std::make_pair(l,m)] /= (RealType)nBonds; |
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q2[l] += norm(q[std::make_pair(l,m)]); |
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} |
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q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1)); |
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} |
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|
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// Find Third Order Invariant W_l |
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|
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for (int l = 0; l <= lMax_; l++) { |
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w[l] = 0.0; |
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for (int m1 = -l; m1 <= l; m1++) { |
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std::pair<int,int> lm = std::make_pair(l, m1); |
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for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) { |
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int m2 = m2Min[lm] + mmm; |
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int m3 = -m1-m2; |
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w[l] += w3j[lm][mmm] * q[lm] * |
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q[std::make_pair(l,m2)] * q[std::make_pair(l,m3)]; |
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} |
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} |
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|
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w_hat[l] = w[l] / pow(q2[l], 1.5); |
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} |
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|
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collectHistogram(q_l, w_hat); |
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|
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Nbonds += nBonds; |
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for (int l = 0; l <= lMax_; l++) { |
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for (int m = -l; m <= l; m++) { |
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QBar[std::make_pair(l,m)] += (RealType)nBonds*q[std::make_pair(l,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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// Normalize Qbar2 |
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for (int l = 0; l <= lMax_; l++) { |
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for (int m = -l; m <= l; m++){ |
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QBar[std::make_pair(l,m)] /= Nbonds; |
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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 l = 0; l <= lMax_; l++) { |
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Q2[l] = 0.0; |
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for (int m = -l; m <= l; m++){ |
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Q2[l] += norm(QBar[std::make_pair(l,m)]); |
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} |
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Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1)); |
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} |
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|
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// Find Third Order Invariant W_l |
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|
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for (int l = 0; l <= lMax_; l++) { |
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W[l] = 0.0; |
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for (int m1 = -l; m1 <= l; m1++) { |
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std::pair<int,int> lm = std::make_pair(l, m1); |
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for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) { |
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int m2 = m2Min[lm] + mmm; |
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int m3 = -m1-m2; |
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W[l] += w3j[lm][mmm] * QBar[lm] * |
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QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)]; |
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} |
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} |
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|
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W_hat[l] = W[l] / pow(Q2[l], 1.5); |
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} |
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|
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writeOrderParameter(Q, W_hat); |
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} |
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|
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void BondOrderParameter::collectHistogram(std::vector<RealType> q, |
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std::vector<ComplexType> what) { |
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|
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for (int l = 0; l <= lMax_; l++) { |
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if (q[l] >= MinQ_ && q[l] < MaxQ_) { |
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int qbin = (q[l] - MinQ_) / deltaQ_; |
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Q_histogram_[std::make_pair(qbin,l)] += 1; |
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Qcount_[l]++; |
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} else { |
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sprintf( painCave.errMsg, |
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"q_l value outside reasonable range\n"); |
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painCave.severity = OPENMD_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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|
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for (int l = 0; l <= lMax_; l++) { |
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if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) { |
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int wbin = (real(what[l]) - MinW_) / deltaW_; |
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W_histogram_[std::make_pair(wbin,l)] += 1; |
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Wcount_[l]++; |
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} else { |
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sprintf( painCave.errMsg, |
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"Re[w_hat] value (%lf) outside reasonable range\n", real(what[l])); |
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painCave.severity = OPENMD_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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|
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} |
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|
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|
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void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q, |
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std::vector<ComplexType> What) { |
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|
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std::ofstream osq((getOutputFileName() + "q").c_str()); |
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|
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if (osq.is_open()) { |
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|
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osq << "# Bond Order Parameters\n"; |
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osq << "# selection: (" << selectionScript_ << ")\n"; |
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osq << "# \n"; |
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for (int l = 0; l <= lMax_; l++) { |
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osq << "# <Q_" << l << ">: " << Q[l] << "\n"; |
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} |
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// Normalize by number of frames and write it out: |
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for (int i = 0; i < nBins_; ++i) { |
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RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
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osq << Qval; |
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for (int l = 0; l <= lMax_; l++) { |
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|
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osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_; |
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} |
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osq << "\n"; |
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} |
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|
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osq.close(); |
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|
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} else { |
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sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
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(getOutputFileName() + "q").c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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std::ofstream osw((getOutputFileName() + "w").c_str()); |
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|
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if (osw.is_open()) { |
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osw << "# Bond Order Parameters\n"; |
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osw << "# selection: (" << selectionScript_ << ")\n"; |
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osw << "# \n"; |
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for (int l = 0; l <= lMax_; l++) { |
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osw << "# <W_" << l << ">: " << real(What[l]) << "\t" << imag(What[l]) << "\n"; |
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} |
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// Normalize by number of frames and write it out: |
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for (int i = 0; i < nBins_; ++i) { |
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RealType Wval = MinW_ + (i + 0.5) * deltaW_; |
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osw << Wval; |
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for (int l = 0; l <= lMax_; l++) { |
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|
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osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_; |
| 421 |
} |
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osw << "\n"; |
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} |
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|
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osw.close(); |
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} else { |
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sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
| 428 |
(getOutputFileName() + "w").c_str()); |
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painCave.isFatal = 1; |
| 430 |
simError(); |
| 431 |
} |
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|
| 433 |
} |
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} |
