applications/dynamicProps/RadialRCorrFunc.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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */

#include "applications/dynamicProps/RadialRCorrFunc.hpp"


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

      setCorrFuncType("RadialRCorrFunc");
      setOutputName(getPrefix(dumpFilename_) + ".r_rcorr");

// Turn on COM calculation in block snapshot
      bool ncp = true;
      bsMan_->needCOMprops(ncp);
    }

  RealType RadialRCorrFunc::calcCorrVal(int frame1, int frame2, StuntDouble* sd1, StuntDouble* sd2) {
    RealType r0;
    RealType rt;
    Vector3d coord_t0;
    Vector3d coord_t;

    Vector3d r1 = sd1->getPos(frame1);
    Vector3d r2 = sd2->getPos(frame2);
    Vector3d com1 = sd1->getCOM(frame1);
    Vector3d com2 = sd2->getCOM(frame2);

    coord_t0 = r1 - com1;
    coord_t  = r2 - com2;
    
    r0 = sqrt(dot(coord_t0, coord_t0));
    rt = sqrt(dot(coord_t,coord_t));

    return pow(rt - r0,2);
  }

}
Revision:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 6 months ago) by gezelter
Original Path:	*trunk/src/applications/dynamicProps/RadialRCorrFunc.cpp*
File size:	3133 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	User	Rev	Content
1	chuckv	1096	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	chuckv	1096	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	chuckv	1096	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40	chuckv	1096	*/
41
42			#include "applications/dynamicProps/RadialRCorrFunc.hpp"
43
44
45	gezelter	1390	namespace OpenMD {
46	chuckv	1096	RadialRCorrFunc::RadialRCorrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
47			: ParticleTimeCorrFunc(info, filename, sele1, sele2, DataStorage::dslPosition){
48
49			setCorrFuncType("RadialRCorrFunc");
50			setOutputName(getPrefix(dumpFilename_) + ".r_rcorr");
51
52	chuckv	1112	// Turn on COM calculation in block snapshot
53			bool ncp = true;
54			bsMan_->needCOMprops(ncp);
55	chuckv	1096	}
56
57			RealType RadialRCorrFunc::calcCorrVal(int frame1, int frame2, StuntDouble* sd1, StuntDouble* sd2) {
58			RealType r0;
59			RealType rt;
60			Vector3d coord_t0;
61			Vector3d coord_t;
62
63			Vector3d r1 = sd1->getPos(frame1);
64			Vector3d r2 = sd2->getPos(frame2);
65	chuckv	1112	Vector3d com1 = sd1->getCOM(frame1);
66			Vector3d com2 = sd2->getCOM(frame2);
67	chuckv	1096
68			coord_t0 = r1 - com1;
69			coord_t = r2 - com2;
70
71	chuckv	1112	r0 = sqrt(dot(coord_t0, coord_t0));
72			rt = sqrt(dot(coord_t,coord_t));
73
74			return pow(rt - r0,2);
75	chuckv	1096	}
76
77			}