applications/dynamicProps/LegendreCorrFunc.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/LegendreCorrFunc.hpp"
#include "math/LegendrePolynomial.hpp"
#include "utils/simError.h"

namespace oopse {
  LegendreCorrFunc::LegendreCorrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, int order)
    : ParticleTimeCorrFunc(info, filename, sele1, sele2, DataStorage::dslElectroFrame){

      setCorrFuncType("Legendre Correlation Function");
      setOutputName(getPrefix(dumpFilename_) + ".lcorr");
      LegendrePolynomial polynomial(order);
      legendre_ = polynomial.getLegendrePolynomial(order);
      

    }

  double LegendreCorrFunc::calcCorrVal(int frame1, int frame2, StuntDouble* sd1,  StuntDouble* sd2) {
    Vector3d v1 =sd1->getA(frame1).getColumn(2);
    Vector3d v2 = sd2->getA(frame2).getColumn(2);

    return legendre_.evaluate(dot(v1, v2));
  }


  void LegendreCorrFunc::validateSelection(const SelectionManager& seleMan) {
    StuntDouble* sd;
    int i;    
    for (sd = seleMan1_.beginSelected(i); sd != NULL; sd = seleMan1_.nextSelected(i)) {
      if (!sd->isDirectionalAtom()) {
        sprintf(painCave.errMsg,
                "LegendreCorrFunc::validateSelection Error: selected atoms do not Directional\n");
        painCave.isFatal = 1;
        simError();        
      }
    }
    
  }

}


Revision:	887
Committed:	Fri Feb 10 15:45:02 2006 UTC (19 years, 3 months ago) by kdaily
Original Path:	*trunk/src/applications/dynamicProps/LegendreCorrFunc.cpp*
File size:	3374 byte(s)
Log Message:	* empty log message *
#	User	Rev	Content
1	tim	876	/*
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/LegendreCorrFunc.hpp"
43			#include "math/LegendrePolynomial.hpp"
44			#include "utils/simError.h"
45
46			namespace oopse {
47			LegendreCorrFunc::LegendreCorrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, int order)
48			: ParticleTimeCorrFunc(info, filename, sele1, sele2, DataStorage::dslElectroFrame){
49
50			setCorrFuncType("Legendre Correlation Function");
51			setOutputName(getPrefix(dumpFilename_) + ".lcorr");
52			LegendrePolynomial polynomial(order);
53			legendre_ = polynomial.getLegendrePolynomial(order);
54
55
56			}
57
58			double LegendreCorrFunc::calcCorrVal(int frame1, int frame2, StuntDouble* sd1, StuntDouble* sd2) {
59	kdaily	887	Vector3d v1 =sd1->getA(frame1).getColumn(2);
60			Vector3d v2 = sd2->getA(frame2).getColumn(2);
61	tim	876
62			return legendre_.evaluate(dot(v1, v2));
63			}
64
65
66			void LegendreCorrFunc::validateSelection(const SelectionManager& seleMan) {
67			StuntDouble* sd;
68			int i;
69			for (sd = seleMan1_.beginSelected(i); sd != NULL; sd = seleMan1_.nextSelected(i)) {
70			if (!sd->isDirectionalAtom()) {
71			sprintf(painCave.errMsg,
72	kdaily	887	"LegendreCorrFunc::validateSelection Error: selected atoms do not Directional\n");
73	tim	876	painCave.isFatal = 1;
74			simError();
75			}
76			}
77
78			}
79
80			}
81
82
83