applications/dynamicProps/RMSD.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */

#include "applications/dynamicProps/RMSD.hpp"

namespace oopse {
  RMSD::RMSD(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
    : ParticleTimeCorrFunc(info, filename, sele1, sele2, DataStorage::dslPosition){

      setCorrFuncType("RMSD");
      setOutputName(getPrefix(dumpFilename_) + ".rmsd");

    }

  double RMSD::calcCorrVal(int frame1, int frame2, StuntDouble* sd1, StuntDouble* sd2) {
    Vector3d r1 =sd1->getPos(frame1);
    Vector3d r2 = sd2->getPos(frame2);

    return (r2-r1).lengthSquare();
  }

}
Revision:	916
Committed:	Fri Mar 24 16:49:09 2006 UTC (19 years, 1 month ago) by tim
File size:	2639 byte(s)
Log Message:	Adding position correlation function. The command line option for DynamicProps is now changed. --rcorr is for position correlation and --rmsd is for mean square displacement.
#	User	Rev	Content
1	tim	916	/*
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			#include "applications/dynamicProps/RMSD.hpp"
43
44			namespace oopse {
45			RMSD::RMSD(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
46			: ParticleTimeCorrFunc(info, filename, sele1, sele2, DataStorage::dslPosition){
47
48			setCorrFuncType("RMSD");
49			setOutputName(getPrefix(dumpFilename_) + ".rmsd");
50
51			}
52
53			double RMSD::calcCorrVal(int frame1, int frame2, StuntDouble* sd1, StuntDouble* sd2) {
54			Vector3d r1 =sd1->getPos(frame1);
55			Vector3d r2 = sd2->getPos(frame2);
56
57			return (r2-r1).lengthSquare();
58			}
59
60			}