applications/dynamicProps/SystemDipoleCorrFunc.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/SystemDipoleCorrFunc.hpp"
#include "utils/PhysicalConstants.hpp"
#include "brains/ForceManager.hpp"
#include "brains/Thermo.hpp"

namespace OpenMD {

  // Just need the dipole of the system for each frame
  SystemDipoleCorrFunc::SystemDipoleCorrFunc(SimInfo* info, const std::string& filename, 
                                 const std::string& sele1, 
                                 const std::string& sele2,
                                 long long int memSize)
    : FrameTimeCorrFunc(info, filename, sele1, sele2, 
                        DataStorage::dslPosition | 
                        DataStorage::dslVelocity |
                        DataStorage::dslParticlePot,
                        memSize){

      setCorrFuncType("SystemDipoleCorrFunc");
      setOutputName(getPrefix(dumpFilename_) + ".sysdipcorr");
      histogram_.resize(nTimeBins_); 
      count_.resize(nTimeBins_);
    }

  void SystemDipoleCorrFunc::correlateFrames(int frame1, int frame2) {
    Snapshot* snapshot1 = bsMan_->getSnapshot(frame1);
    assert(snapshot1);
    Vector3d dipoleMoment1 = thermo_->getSystemDipole();

    Snapshot* snapshot2 = bsMan_->getSnapshot(frame2);
    assert(snapshot2);
    Vector3d dipoleMoment2 = thermo_->getSystemDipole();
    assert(snapshot1 && snapshot2);

    RealType time1 = snapshot1->getTime();
    RealType time2 = snapshot2->getTime();
       
    int timeBin = int ((time2 - time1) /deltaTime_ + 0.5);

    histogram_[timeBin] += dot(dipoleMoment1, dipoleMoment2);
    
    count_[timeBin]++;
    
  }

  void SystemDipoleCorrFunc::postCorrelate() {
    for (int i =0 ; i < nTimeBins_; ++i) {
      if (count_[i] > 0) {
        histogram_[i] /= count_[i];
      }
    }
  }

  void SystemDipoleCorrFunc::preCorrelate() {
    // Fill the histogram with zeroes, 0.0
    std::fill(histogram_.begin(), histogram_.end(), 0.0);
    // count array set to zero
    std::fill(count_.begin(), count_.end(), 0);
    thermo_ = new Thermo(info_);
  }   


  void SystemDipoleCorrFunc::writeCorrelate() {
    std::ofstream ofs(getOutputFileName().c_str());

    if (ofs.is_open()) {

      ofs << "#" << getCorrFuncType() << "\n";
      ofs << "#time\tnormalizedTau\n";

      for (int i = 0; i < nTimeBins_; ++i) {
        ofs << time_[i] << "\t" << 
              histogram_[i] << "\n";
      }
            
    } else {
      sprintf(painCave.errMsg,
              "SystemDipoleCorrFunc::writeCorrelate Error: fail to open %s\n", getOutputFileName().c_str());
      painCave.isFatal = 1;
      simError();        
    }

    ofs.close();    
    
  }

}
Revision:	1850
Committed:	Wed Feb 20 15:39:39 2013 UTC (12 years, 3 months ago) by gezelter
File size:	4651 byte(s)
Log Message:	Fixed a widespread typo in the license
#	User	Rev	Content
1	gezelter	1629	/*
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. Redistributions of source code must retain the above copyright
10			* notice, this list of conditions and the following disclaimer.
11			*
12			* 2. Redistributions in binary form must reproduce the above copyright
13			* 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			*
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	gezelter	1629	*/
42
43
44
45			#include "applications/dynamicProps/SystemDipoleCorrFunc.hpp"
46			#include "utils/PhysicalConstants.hpp"
47			#include "brains/ForceManager.hpp"
48			#include "brains/Thermo.hpp"
49
50			namespace OpenMD {
51
52			// Just need the dipole of the system for each frame
53			SystemDipoleCorrFunc::SystemDipoleCorrFunc(SimInfo* info, const std::string& filename,
54			const std::string& sele1,
55			const std::string& sele2,
56			long long int memSize)
57			: FrameTimeCorrFunc(info, filename, sele1, sele2,
58			DataStorage::dslPosition \|
59			DataStorage::dslVelocity \|
60			DataStorage::dslParticlePot,
61			memSize){
62
63			setCorrFuncType("SystemDipoleCorrFunc");
64			setOutputName(getPrefix(dumpFilename_) + ".sysdipcorr");
65			histogram_.resize(nTimeBins_);
66			count_.resize(nTimeBins_);
67			}
68
69			void SystemDipoleCorrFunc::correlateFrames(int frame1, int frame2) {
70			Snapshot* snapshot1 = bsMan_->getSnapshot(frame1);
71			assert(snapshot1);
72	gezelter	1764	Vector3d dipoleMoment1 = thermo_->getSystemDipole();
73	gezelter	1629
74			Snapshot* snapshot2 = bsMan_->getSnapshot(frame2);
75			assert(snapshot2);
76	gezelter	1764	Vector3d dipoleMoment2 = thermo_->getSystemDipole();
77	gezelter	1629	assert(snapshot1 && snapshot2);
78
79			RealType time1 = snapshot1->getTime();
80			RealType time2 = snapshot2->getTime();
81
82			int timeBin = int ((time2 - time1) /deltaTime_ + 0.5);
83
84			histogram_[timeBin] += dot(dipoleMoment1, dipoleMoment2);
85
86			count_[timeBin]++;
87
88			}
89
90			void SystemDipoleCorrFunc::postCorrelate() {
91			for (int i =0 ; i < nTimeBins_; ++i) {
92			if (count_[i] > 0) {
93			histogram_[i] /= count_[i];
94			}
95			}
96			}
97
98			void SystemDipoleCorrFunc::preCorrelate() {
99			// Fill the histogram with zeroes, 0.0
100			std::fill(histogram_.begin(), histogram_.end(), 0.0);
101			// count array set to zero
102			std::fill(count_.begin(), count_.end(), 0);
103			thermo_ = new Thermo(info_);
104			}
105
106
107			void SystemDipoleCorrFunc::writeCorrelate() {
108			std::ofstream ofs(getOutputFileName().c_str());
109
110			if (ofs.is_open()) {
111
112			ofs << "#" << getCorrFuncType() << "\n";
113			ofs << "#time\tnormalizedTau\n";
114
115			for (int i = 0; i < nTimeBins_; ++i) {
116			ofs << time_[i] << "\t" <<
117			histogram_[i] << "\n";
118			}
119
120			} else {
121			sprintf(painCave.errMsg,
122			"SystemDipoleCorrFunc::writeCorrelate Error: fail to open %s\n", getOutputFileName().c_str());
123			painCave.isFatal = 1;
124			simError();
125			}
126
127			ofs.close();
128
129			}
130
131			}