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

#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:	1596
Committed:	Mon Jul 25 17:30:53 2011 UTC (14 years, 1 month ago) by gezelter
File size:	5285 byte(s)
Log Message:	Updated the BlockSnapshotManager to use a specified memory footprint in constructor and not to rely on physmem and residentMem to figure out free memory. DynamicProps is the only program that uses the BlockSnapshotManager, so substantial changes were needed there as well.
#	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			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40	xsun	1183	*/
41
42			#include "applications/dynamicProps/DirectionalRCorrFunc.hpp"
43
44	gezelter	1390	namespace OpenMD {
45	gezelter	1596	DirectionalRCorrFunc::DirectionalRCorrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, long long int memSize)
46			: ParticleTimeCorrFunc(info, filename, sele1, sele2, DataStorage::dslPosition, memSize){
47	xsun	1183
48			setCorrFuncType("DirectionalRCorrFunc");
49			setOutputName(getPrefix(dumpFilename_) + ".drcorr");
50			histogram_.resize(nTimeBins_);
51			count_.resize(nTimeBins_);
52			nSelected_ = seleMan1_.getSelectionCount();
53			assert( nSelected_ == seleMan2_.getSelectionCount());
54			}
55
56			void DirectionalRCorrFunc::correlateFrames(int frame1, int frame2) {
57			Snapshot* snapshot1 = bsMan_->getSnapshot(frame1);
58			Snapshot* snapshot2 = bsMan_->getSnapshot(frame2);
59			assert(snapshot1 && snapshot2);
60
61			RealType time1 = snapshot1->getTime();
62			RealType time2 = snapshot2->getTime();
63
64			int timeBin = int ((time2 - time1) /deltaTime_ + 0.5);
65			count_[timeBin] += nSelected_;
66
67			int i;
68			int j;
69			StuntDouble* sd1;
70			StuntDouble* sd2;
71
72			for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j);
73			sd1 != NULL && sd2 != NULL;
74			sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) {
75
76			Vector3d corrVals = calcCorrVals(frame1, frame2, sd1, sd2);
77			histogram_[timeBin] += corrVals;
78			}
79
80			}
81
82			void DirectionalRCorrFunc::postCorrelate() {
83			for (int i =0 ; i < nTimeBins_; ++i) {
84			if (count_[i] > 0) {
85			histogram_[i] /= count_[i];
86			}
87			}
88			}
89
90			void DirectionalRCorrFunc::preCorrelate() {
91			// Fill the histogram with empty Vector3d:
92			std::fill(histogram_.begin(), histogram_.end(), Vector3d(0.0));
93			// count array set to zero
94			std::fill(count_.begin(), count_.end(), 0);
95			}
96
97
98			Vector3d DirectionalRCorrFunc::calcCorrVals(int frame1, int frame2, StuntDouble* sd1, StuntDouble* sd2) {
99			Vector3d r1 = sd1->getPos(frame1);
100			Vector3d r2 = sd2->getPos(frame2);
101
102	xsun	1213	// The lab frame vector corresponding to the body-fixed
103			// z-axis is simply the second column of A.transpose()
104			// or, identically, the second row of A itself.
105
106			Vector3d u1 = sd1->getA(frame1).getRow(2);
107			RealType u1l = u1.length();
108
109	xsun	1183	RealType rsq = (r2-r1).lengthSquare();
110	xsun	1213	RealType rpar = dot( (r2-r1), u1)/u1l;
111	xsun	1183	RealType rpar2 = rpar*rpar;
112			RealType rperp2 = rsq - rpar2;
113
114			return Vector3d(rsq, rpar2, rperp2);
115			}
116
117			void DirectionalRCorrFunc::writeCorrelate() {
118			std::ofstream ofs(getOutputFileName().c_str());
119
120			if (ofs.is_open()) {
121
122			ofs << "#" << getCorrFuncType() << "\n";
123			ofs << "#time\tr2\trparallel\trperpendicular\n";
124
125			for (int i = 0; i < nTimeBins_; ++i) {
126			ofs << time_[i] << "\t" <<
127			histogram_[i](0) << "\t" <<
128			histogram_[i](1) << "\t" <<
129			histogram_[i](2) << "\t" << "\n";
130			}
131
132			} else {
133			sprintf(painCave.errMsg,
134			"DirectionalRCorrFunc::writeCorrelate Error: fail to open %s\n", getOutputFileName().c_str());
135			painCave.isFatal = 1;
136			simError();
137			}
138
139			ofs.close();
140			}
141
142
143			}