applications/dynamicProps/DirectionalRCorrFunc.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/DirectionalRCorrFunc.hpp"

namespace OpenMD {
  DirectionalRCorrFunc::DirectionalRCorrFunc(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("DirectionalRCorrFunc");
      setOutputName(getPrefix(dumpFilename_) + ".drcorr");
      histogram_.resize(nTimeBins_); 
      count_.resize(nTimeBins_);
      nSelected_ =   seleMan1_.getSelectionCount();  
      assert(  nSelected_ == seleMan2_.getSelectionCount());
    }

  void DirectionalRCorrFunc::correlateFrames(int frame1, int frame2) {
    Snapshot* snapshot1 = bsMan_->getSnapshot(frame1);
    Snapshot* snapshot2 = bsMan_->getSnapshot(frame2);
    assert(snapshot1 && snapshot2);

    RealType time1 = snapshot1->getTime();
    RealType time2 = snapshot2->getTime();

    int timeBin = int ((time2 - time1) /deltaTime_ + 0.5);
    count_[timeBin] += nSelected_;    

    int i;
    int j;
    StuntDouble* sd1;
    StuntDouble* sd2;

    for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j);
         sd1 != NULL && sd2 != NULL;
         sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) {

      Vector3d corrVals = calcCorrVals(frame1, frame2, sd1, sd2);
      histogram_[timeBin] += corrVals; 
    }
    
  }

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

  void DirectionalRCorrFunc::preCorrelate() {
    // Fill the histogram with empty Vector3d:
    std::fill(histogram_.begin(), histogram_.end(), Vector3d(0.0));
    // count array set to zero
    std::fill(count_.begin(), count_.end(), 0);
  }


  Vector3d DirectionalRCorrFunc::calcCorrVals(int frame1, int frame2, StuntDouble* sd1, StuntDouble* sd2) {
    Vector3d r1 = sd1->getPos(frame1);
    Vector3d r2 = sd2->getPos(frame2);

    // The lab frame vector corresponding to the body-fixed 
    // z-axis is simply the second column of A.transpose()
    // or, identically, the second row of A itself.
  
    Vector3d u1 = sd1->getA(frame1).getRow(2);
    RealType u1l = u1.length();

    RealType rsq = (r2-r1).lengthSquare();
    RealType rpar = dot( (r2-r1), u1)/u1l;
    RealType rpar2 = rpar*rpar;
    RealType rperp2 = rsq - rpar2;

    return Vector3d(rsq, rpar2, rperp2);
  }

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

    if (ofs.is_open()) {

      ofs << "#" << getCorrFuncType() << "\n";
      ofs << "#time\tr2\trparallel\trperpendicular\n";

      for (int i = 0; i < nTimeBins_; ++i) {
        ofs << time_[i] << "\t" << 
          histogram_[i](0) << "\t" <<
          histogram_[i](1) << "\t" <<
          histogram_[i](2) << "\t" << "\n";
      }
            
    } else {
      sprintf(painCave.errMsg,
              "DirectionalRCorrFunc::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:	5352 byte(s)
Log Message:	Fixed a widespread typo in the license
#	User	Rev	Content
1	xsun	1183	/*
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	xsun	1183	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	xsun	1183	* 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	xsun	1183	*/
42
43			#include "applications/dynamicProps/DirectionalRCorrFunc.hpp"
44
45	gezelter	1390	namespace OpenMD {
46	gezelter	1629	DirectionalRCorrFunc::DirectionalRCorrFunc(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	xsun	1183
49			setCorrFuncType("DirectionalRCorrFunc");
50			setOutputName(getPrefix(dumpFilename_) + ".drcorr");
51			histogram_.resize(nTimeBins_);
52			count_.resize(nTimeBins_);
53			nSelected_ = seleMan1_.getSelectionCount();
54			assert( nSelected_ == seleMan2_.getSelectionCount());
55			}
56
57			void DirectionalRCorrFunc::correlateFrames(int frame1, int frame2) {
58			Snapshot* snapshot1 = bsMan_->getSnapshot(frame1);
59			Snapshot* snapshot2 = bsMan_->getSnapshot(frame2);
60			assert(snapshot1 && snapshot2);
61
62			RealType time1 = snapshot1->getTime();
63			RealType time2 = snapshot2->getTime();
64
65			int timeBin = int ((time2 - time1) /deltaTime_ + 0.5);
66			count_[timeBin] += nSelected_;
67
68			int i;
69			int j;
70			StuntDouble* sd1;
71			StuntDouble* sd2;
72
73			for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j);
74			sd1 != NULL && sd2 != NULL;
75			sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) {
76
77			Vector3d corrVals = calcCorrVals(frame1, frame2, sd1, sd2);
78			histogram_[timeBin] += corrVals;
79			}
80
81			}
82
83			void DirectionalRCorrFunc::postCorrelate() {
84			for (int i =0 ; i < nTimeBins_; ++i) {
85			if (count_[i] > 0) {
86			histogram_[i] /= count_[i];
87			}
88			}
89			}
90
91			void DirectionalRCorrFunc::preCorrelate() {
92			// Fill the histogram with empty Vector3d:
93			std::fill(histogram_.begin(), histogram_.end(), Vector3d(0.0));
94			// count array set to zero
95			std::fill(count_.begin(), count_.end(), 0);
96			}
97
98
99			Vector3d DirectionalRCorrFunc::calcCorrVals(int frame1, int frame2, StuntDouble* sd1, StuntDouble* sd2) {
100			Vector3d r1 = sd1->getPos(frame1);
101			Vector3d r2 = sd2->getPos(frame2);
102
103	xsun	1213	// The lab frame vector corresponding to the body-fixed
104			// z-axis is simply the second column of A.transpose()
105			// or, identically, the second row of A itself.
106
107			Vector3d u1 = sd1->getA(frame1).getRow(2);
108			RealType u1l = u1.length();
109
110	xsun	1183	RealType rsq = (r2-r1).lengthSquare();
111	xsun	1213	RealType rpar = dot( (r2-r1), u1)/u1l;
112	xsun	1183	RealType rpar2 = rpar*rpar;
113			RealType rperp2 = rsq - rpar2;
114
115			return Vector3d(rsq, rpar2, rperp2);
116			}
117
118			void DirectionalRCorrFunc::writeCorrelate() {
119			std::ofstream ofs(getOutputFileName().c_str());
120
121			if (ofs.is_open()) {
122
123			ofs << "#" << getCorrFuncType() << "\n";
124			ofs << "#time\tr2\trparallel\trperpendicular\n";
125
126			for (int i = 0; i < nTimeBins_; ++i) {
127			ofs << time_[i] << "\t" <<
128			histogram_[i](0) << "\t" <<
129			histogram_[i](1) << "\t" <<
130			histogram_[i](2) << "\t" << "\n";
131			}
132
133			} else {
134			sprintf(painCave.errMsg,
135			"DirectionalRCorrFunc::writeCorrelate Error: fail to open %s\n", getOutputFileName().c_str());
136			painCave.isFatal = 1;
137			simError();
138			}
139
140			ofs.close();
141			}
142
143
144			}