applications/dynamicProps/ThetaCorrFunc.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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#include "applications/dynamicProps/ThetaCorrFunc.hpp"


namespace OpenMD {
  ThetaCorrFunc::ThetaCorrFunc(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("ThetaCorrFunc");
      setOutputName(getPrefix(dumpFilename_) + ".tcorr");

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

  RealType ThetaCorrFunc::calcCorrVal(int frame1, int frame2, StuntDouble* sd1, StuntDouble* sd2) {
    RealType r0;
    RealType rt;
    RealType csth;
    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));

    csth = dot(coord_t0,coord_t)/(r0*rt);
    return csth;
  }

}
Revision:	1850
Committed:	Wed Feb 20 15:39:39 2013 UTC (12 years, 3 months ago) by gezelter
File size:	3271 byte(s)
Log Message:	Fixed a widespread typo in the license
#	User	Rev	Content
1	chuckv	1114	/*
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	1114	* 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	1114	* 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	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	chuckv	1114	*/
42
43			#include "applications/dynamicProps/ThetaCorrFunc.hpp"
44
45
46	gezelter	1390	namespace OpenMD {
47	gezelter	1629	ThetaCorrFunc::ThetaCorrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, long long int memSize)
48			: ParticleTimeCorrFunc(info, filename, sele1, sele2, DataStorage::dslPosition, memSize){
49	chuckv	1114
50			setCorrFuncType("ThetaCorrFunc");
51			setOutputName(getPrefix(dumpFilename_) + ".tcorr");
52
53			// Turn on COM calculation in block snapshot
54			bool ncp = true;
55			bsMan_->needCOMprops(ncp);
56			}
57
58			RealType ThetaCorrFunc::calcCorrVal(int frame1, int frame2, StuntDouble* sd1, StuntDouble* sd2) {
59			RealType r0;
60			RealType rt;
61			RealType csth;
62			Vector3d coord_t0;
63			Vector3d coord_t;
64
65			Vector3d r1 = sd1->getPos(frame1);
66			Vector3d r2 = sd2->getPos(frame2);
67			Vector3d com1 = sd1->getCOM(frame1);
68			Vector3d com2 = sd2->getCOM(frame2);
69
70			coord_t0 = r1 - com1;
71			coord_t = r2 - com2;
72
73			r0 = sqrt(dot(coord_t0, coord_t0));
74			rt = sqrt(dot(coord_t,coord_t));
75
76			csth = dot(coord_t0,coord_t)/(r0*rt);
77			return csth;
78			}
79
80			}