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:	2668
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.
#	Content
1	/*
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	}