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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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|
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#include "applications/dynamicProps/RadialRCorrFunc.hpp" |
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|
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|
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namespace oopse { |
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RadialRCorrFunc::RadialRCorrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) |
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: ParticleTimeCorrFunc(info, filename, sele1, sele2, DataStorage::dslPosition){ |
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|
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setCorrFuncType("RadialRCorrFunc"); |
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setOutputName(getPrefix(dumpFilename_) + ".r_rcorr"); |
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|
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// Turn on COM calculation in block snapshot |
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bool ncp = true; |
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bsMan_->needCOMprops(ncp); |
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} |
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|
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RealType RadialRCorrFunc::calcCorrVal(int frame1, int frame2, StuntDouble* sd1, StuntDouble* sd2) { |
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RealType r0; |
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RealType rt; |
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Vector3d coord_t0; |
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Vector3d coord_t; |
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|
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Vector3d r1 = sd1->getPos(frame1); |
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Vector3d r2 = sd2->getPos(frame2); |
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Vector3d com1 = sd1->getCOM(frame1); |
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Vector3d com2 = sd2->getCOM(frame2); |
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|
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coord_t0 = r1 - com1; |
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coord_t = r2 - com2; |
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|
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r0 = sqrt(dot(coord_t0, coord_t0)); |
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rt = sqrt(dot(coord_t,coord_t)); |
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|
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return pow(rt - r0,2); |
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} |
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|
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} |
