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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 |
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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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/* Uses the Helfand-moment method for calculating thermal |
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* conductivity using the relation kappa = (N,V)lim(t)->inf 1/(2*k_B*T^2*V*t) <[G_K(t)-G_K(0)]^2> |
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* where G_K is the Helfand moment for thermal conductivity definded as |
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* G_K(t) = sum_{a=1}{^N} x_a(E_a-<E_a>) and E_a is defined to be |
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* E_a = p_2^2/(2*m)+1/2 sum_{b.ne.a} u(r_ab) where p is momentum and u is pot energy for the |
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* particle pair a-b. This routine calculates E_a, <E_a> and does the correlation |
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* <[G_K(t)-G_K(0)]^2>. |
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* See Viscardy et al. JCP 126, 184513 (2007) |
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*/ |
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#ifndef APPLICATIONS_DYNAMICPROPS_ENERGYCORRFUNC_HPP |
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#define APPLICATIONS_DYNAMICPROPS_ENERGYCORRFUNC_HPP |
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#include "applications/dynamicProps/FrameTimeCorrFunc.hpp" |
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namespace oopse { |
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class EnergyCorrFunc : public FrameTimeCorrFunc { |
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public: |
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EnergyCorrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2); |
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private: |
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virtual void correlateFrames(int frame1, int frame2); |
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virtual RealType calcCorrVal(int frame1, int frame2) { return 0.0; } |
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virtual void writeCorrelate(); |
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protected: |
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virtual void preCorrelate(); |
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virtual void postCorrelate(); |
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std::vector< Vector3d > histogram_; |
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std::vector< std::vector< RealType > > E_a_; |
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std::vector< RealType > AvgE_a_; |
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std::vector< Vector3d > G_t_; |
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}; |
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} |
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#endif //ENERGYCORRFUNC |
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