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, long long int memSize)
    : ParticleTimeCorrFunc(info, filename, sele1, sele2, DataStorage::dslPosition, memSize){

      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:	1596
Committed:	Mon Jul 25 17:30:53 2011 UTC (14 years, 1 month ago) by gezelter
File size:	3165 byte(s)
Log Message:	Updated the BlockSnapshotManager to use a specified memory footprint in constructor and not to rely on physmem and residentMem to figure out free memory. DynamicProps is the only program that uses the BlockSnapshotManager, so substantial changes were needed there as well.
#	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	gezelter	1596	RadialRCorrFunc::RadialRCorrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, long long int memSize)
47			: ParticleTimeCorrFunc(info, filename, sele1, sele2, DataStorage::dslPosition, memSize){
48	chuckv	1096
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			}