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

#include "applications/dynamicProps/DipoleCorrFunc.hpp"
#include "utils/simError.h"

namespace OpenMD {
  DipoleCorrFunc::DipoleCorrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, long long int memSize)
    : ParticleTimeCorrFunc(info, filename, sele1, sele2, DataStorage::dslElectroFrame, memSize){

      setCorrFuncType("Dipole Correlation Function");
      setOutputName(getPrefix(dumpFilename_) + ".dcorr");

    }

  RealType DipoleCorrFunc::calcCorrVal(int frame1, int frame2, StuntDouble* sd1,  StuntDouble* sd2) {
    Vector3d v1 =sd1->getElectroFrame(frame1).getColumn(2);
    Vector3d v2 = sd2->getElectroFrame(frame2).getColumn(2);

    return dot(v1, v2)/(v1.length()*v2.length());
  }


  void DipoleCorrFunc::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,
                "DipoleCorrFunc::validateSelection Error: selected atoms do not have dipole moment\n");
        painCave.isFatal = 1;
        simError();        
      }
    }
    
  }

}


Revision:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 6 months ago) by gezelter
File size:	3376 byte(s)
Log Message:	updated copyright notices
#	User	Rev	Content
1	tim	318	/*
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	tim	318	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	318	* 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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	318	*/
42
43			#include "applications/dynamicProps/DipoleCorrFunc.hpp"
44			#include "utils/simError.h"
45
46	gezelter	1390	namespace OpenMD {
47	gezelter	1629	DipoleCorrFunc::DipoleCorrFunc(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::dslElectroFrame, memSize){
49	tim	318
50	gezelter	507	setCorrFuncType("Dipole Correlation Function");
51			setOutputName(getPrefix(dumpFilename_) + ".dcorr");
52	tim	318
53	gezelter	507	}
54	tim	318
55	tim	963	RealType DipoleCorrFunc::calcCorrVal(int frame1, int frame2, StuntDouble* sd1, StuntDouble* sd2) {
56	tim	884	Vector3d v1 =sd1->getElectroFrame(frame1).getColumn(2);
57			Vector3d v2 = sd2->getElectroFrame(frame2).getColumn(2);
58	tim	318
59	tim	922	return dot(v1, v2)/(v1.length()*v2.length());
60	gezelter	507	}
61	tim	318
62
63	gezelter	507	void DipoleCorrFunc::validateSelection(const SelectionManager& seleMan) {
64	tim	318	StuntDouble* sd;
65			int i;
66			for (sd = seleMan1_.beginSelected(i); sd != NULL; sd = seleMan1_.nextSelected(i)) {
67	gezelter	507	if (!sd->isDirectionalAtom()) {
68			sprintf(painCave.errMsg,
69	tim	318	"DipoleCorrFunc::validateSelection Error: selected atoms do not have dipole moment\n");
70	gezelter	507	painCave.isFatal = 1;
71			simError();
72			}
73	tim	318	}
74
75	gezelter	507	}
76	tim	318
77			}
78
79