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, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */


#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_->getBoxDipole();

    Snapshot* snapshot2 = bsMan_->getSnapshot(frame2);
    assert(snapshot2);
    Vector3d dipoleMoment2 = thermo_->getBoxDipole();
    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:	1606
Committed:	Mon Aug 8 19:02:58 2011 UTC (14 years ago) by jmichalk
File size:	4578 byte(s)
Log Message:	Forgot to svn add the SystemDipoleCorrFunc.hpp/cpp. Should be done adding/committing for now though. -JRM
#	User	Rev	Content
1	jmichalk	1606	/*
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			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40			*/
41
42
43
44			#include "applications/dynamicProps/SystemDipoleCorrFunc.hpp"
45			#include "utils/PhysicalConstants.hpp"
46			#include "brains/ForceManager.hpp"
47			#include "brains/Thermo.hpp"
48
49			namespace OpenMD {
50
51			// Just need the dipole of the system for each frame
52			SystemDipoleCorrFunc::SystemDipoleCorrFunc(SimInfo* info, const std::string& filename,
53			const std::string& sele1,
54			const std::string& sele2,
55			long long int memSize)
56			: FrameTimeCorrFunc(info, filename, sele1, sele2,
57			DataStorage::dslPosition \|
58			DataStorage::dslVelocity \|
59			DataStorage::dslParticlePot,
60			memSize){
61
62			setCorrFuncType("SystemDipoleCorrFunc");
63			setOutputName(getPrefix(dumpFilename_) + ".sysdipcorr");
64			histogram_.resize(nTimeBins_);
65			count_.resize(nTimeBins_);
66			}
67
68			void SystemDipoleCorrFunc::correlateFrames(int frame1, int frame2) {
69			Snapshot* snapshot1 = bsMan_->getSnapshot(frame1);
70			assert(snapshot1);
71			Vector3d dipoleMoment1 = thermo_->getBoxDipole();
72
73			Snapshot* snapshot2 = bsMan_->getSnapshot(frame2);
74			assert(snapshot2);
75			Vector3d dipoleMoment2 = thermo_->getBoxDipole();
76			assert(snapshot1 && snapshot2);
77
78			RealType time1 = snapshot1->getTime();
79			RealType time2 = snapshot2->getTime();
80
81			int timeBin = int ((time2 - time1) /deltaTime_ + 0.5);
82
83			histogram_[timeBin] += dot(dipoleMoment1, dipoleMoment2);
84
85			count_[timeBin]++;
86
87			}
88
89			void SystemDipoleCorrFunc::postCorrelate() {
90			for (int i =0 ; i < nTimeBins_; ++i) {
91			if (count_[i] > 0) {
92			histogram_[i] /= count_[i];
93			}
94			}
95			}
96
97			void SystemDipoleCorrFunc::preCorrelate() {
98			// Fill the histogram with zeroes, 0.0
99			std::fill(histogram_.begin(), histogram_.end(), 0.0);
100			// count array set to zero
101			std::fill(count_.begin(), count_.end(), 0);
102			thermo_ = new Thermo(info_);
103			}
104
105
106			void SystemDipoleCorrFunc::writeCorrelate() {
107			std::ofstream ofs(getOutputFileName().c_str());
108
109			if (ofs.is_open()) {
110
111			ofs << "#" << getCorrFuncType() << "\n";
112			ofs << "#time\tnormalizedTau\n";
113
114			for (int i = 0; i < nTimeBins_; ++i) {
115			ofs << time_[i] << "\t" <<
116			histogram_[i] << "\n";
117			}
118
119			} else {
120			sprintf(painCave.errMsg,
121			"SystemDipoleCorrFunc::writeCorrelate Error: fail to open %s\n", getOutputFileName().c_str());
122			painCave.isFatal = 1;
123			simError();
124			}
125
126			ofs.close();
127
128			}
129
130			}