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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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* 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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* 3. Redistributions in binary form must reproduce the above copyright |
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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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* 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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#ifndef APPLICATIONS_STATICPROPS_BONDORDERPARAMETER_HPP |
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#define APPLICATIONS_STATICPROPS_BONDORDERPARAMETER_HPP |
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#include "selection/SelectionEvaluator.hpp" |
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#include "selection/SelectionManager.hpp" |
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#include "applications/staticProps/StaticAnalyser.hpp" |
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#include "math/Vector3.hpp" |
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#include "math/Wigner3jm_interface.h" |
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#include "math/SphericalHarmonic.hpp" |
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|
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namespace oopse { |
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|
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namespace OpenMD { |
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|
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/** |
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* @class BondOrderParameter |
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* @brief Bond Order Parameter |
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* |
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* Computes orientational bond order parameters as outlined in: |
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* |
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* "Bond-orientaional order in liquids and glasses," by |
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* P. J. Steinhart, D. R. Nelson, and M. Ronchetti, |
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* Phys. Rev. B, 28, 784 (1983). |
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* |
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* A somewhat more useful reference which has formulae for these order |
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* parameters for individual atoms is: |
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* |
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* "Numerical calculation of the rate of crystal nucleation in a |
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* Lennard-Jones system at moderate undercooling," by |
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* Pieter Rein ten Wolde, Maria J. Ruiz-Montero, and Daan Frenkel, |
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* J. Chem. Phys. 104, pp. 9932-9947 (1996). |
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* |
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* Note that this version uses a single cutoff radius to decide |
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* membership in the list of neighbors, and does not have use a |
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* distance-dependent weighting as used in the second reference above. |
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* |
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* The selection script can be utilized to look at specific types of |
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* central atoms. A dynamic selector can also be utilized. By default, |
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* this class computes the Q_{l} and \hat{W}_{l} parameters up to l = 12. |
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* The completed configurational averages of these values as |
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* well as the distributions of atomic q_{l} and \hat{w}_{l} values |
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* are then placed in .boq and .bow files. |
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*/ |
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class BondOrderParameter : public StaticAnalyser{ |
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public: |
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BondOrderParameter(SimInfo* info, const std::string& filename, |
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const std::string& sele, double rCut, int lNumber, int nbins); |
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|
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const std::string& sele, double rCut, int nbins); |
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|
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virtual ~BondOrderParameter(); |
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virtual void process(); |
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|
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|
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private: |
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|
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void writeOrderParameter(); |
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virtual void initalizeHistogram(); |
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virtual void collectHistogram(RealType Q_l, RealType W_l_hat); |
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virtual void initializeHistogram(); |
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virtual void collectHistogram(std::vector<RealType> q, |
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std::vector<ComplexType> what); |
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void writeOrderParameter(std::vector<RealType> Q, |
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std::vector<ComplexType> What); |
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|
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Snapshot* currentSnapshot_; |
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– |
|
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std::string selectionScript_; |
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SelectionManager seleMan_; |
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SelectionEvaluator evaluator_; |
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|
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RealType rCut_; |
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int lNumber_; |
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int mSize_; |
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static const int lMax_ = 12; |
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int frameCounter_; |
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|
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int nBins_; |
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> |
|
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std::map<std::pair<int,int>,int> m2Min; |
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std::map<std::pair<int,int>,int> m2Max; |
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std::map<std::pair<int,int>,std::vector<RealType> > w3j; |
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|
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RealType MinQ_; |
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RealType MaxQ_; |
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RealType deltaQ_; |
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RealType sumQ_; |
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RealType sumQ2_; |
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int Qcount_; |
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std::vector<int> Q_histogram_; |
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std::vector<int> Qcount_; |
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std::map<std::pair<int,int>,int> Q_histogram_; |
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|
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RealType MinW_; |
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RealType MaxW_; |
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RealType deltaW_; |
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RealType sumW_; |
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RealType sumW2_; |
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int Wcount_; |
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std::vector<int> W_histogram_; |
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std::vector<int> Wcount_; |
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std::map<std::pair<int,int>,int> W_histogram_; |
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}; |
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} |
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|
