applications/dynamicProps/LegendreCorrFunc.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/LegendreCorrFunc.hpp"
#include "math/LegendrePolynomial.hpp"
#include "utils/simError.h"

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

      setCorrFuncType("Legendre Correlation Function");
      setOutputName(getPrefix(dumpFilename_) + ".lcorr");
      histogram_.resize(nTimeBins_); 
      count_.resize(nTimeBins_);
      nSelected_ =   seleMan1_.getSelectionCount();  
      std::cout << "sele1 = " << sele1 << "\n";
      std::cout << "sele2 = " << sele2 << "\n";
      std::cout << "nSelected = " << nSelected_ << "\n";
      assert(  nSelected_ == seleMan2_.getSelectionCount());

      LegendrePolynomial polynomial(order);
      legendre_ = polynomial.getLegendrePolynomial(order);
    }

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

  void LegendreCorrFunc::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 LegendreCorrFunc::calcCorrVals(int frame1, int frame2, StuntDouble* sd1,  StuntDouble* sd2) {
    
    // 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.
    // Similar identites give the 0th and 1st rows of A for
    // the lab vectors associated with body-fixed x- and y- axes.

    Vector3d v1x = sd1->getA(frame1).getRow(0);
    Vector3d v2x = sd2->getA(frame2).getRow(0);
    Vector3d v1y = sd1->getA(frame1).getRow(1);
    Vector3d v2y = sd2->getA(frame2).getRow(1);
    Vector3d v1z = sd1->getA(frame1).getRow(2);
    Vector3d v2z = sd2->getA(frame2).getRow(2);

    RealType uxprod = legendre_.evaluate(dot(v1x, v2x)/(v1x.length()*v2x.length()));
    RealType uyprod = legendre_.evaluate(dot(v1y, v2y)/(v1y.length()*v2y.length()));
    RealType uzprod = legendre_.evaluate(dot(v1z, v2z)/(v1z.length()*v2z.length()));

    return Vector3d(uxprod, uyprod, uzprod);

  }


  void LegendreCorrFunc::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,
                "LegendreCorrFunc::validateSelection Error: selected atoms are not Directional\n");
        painCave.isFatal = 1;
        simError();        
      }
    }
    
  }

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

    if (ofs.is_open()) {

      ofs << "#" << getCorrFuncType() << "\n";
      ofs << "#time\tPn(costheta_x)\tPn(costheta_y)\tPn(costheta_z)\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,
              "LegendreCorrFunc::writeCorrelate Error: fail to open %s\n", getOutputFileName().c_str());
      painCave.isFatal = 1;
      simError();        
    }
    ofs.close();    
  }
}
Revision:	1629
Committed:	Wed Sep 14 21:15:17 2011 UTC (14 years, 1 month ago) by gezelter
File size:	6446 byte(s)
Log Message:	Merging changes from old branch into development branch
#	User	Rev	Content
1	tim	876	/*
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	876	* 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	876	* 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	tim	876	*/
41
42			#include "applications/dynamicProps/LegendreCorrFunc.hpp"
43			#include "math/LegendrePolynomial.hpp"
44			#include "utils/simError.h"
45
46	gezelter	1390	namespace OpenMD {
47	gezelter	1629	LegendreCorrFunc::LegendreCorrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, int order, long long int memSize)
48			: ParticleTimeCorrFunc(info, filename, sele1, sele2, DataStorage::dslAmat \| DataStorage::dslElectroFrame, memSize){
49	tim	876
50			setCorrFuncType("Legendre Correlation Function");
51			setOutputName(getPrefix(dumpFilename_) + ".lcorr");
52	xsun	1183	histogram_.resize(nTimeBins_);
53			count_.resize(nTimeBins_);
54			nSelected_ = seleMan1_.getSelectionCount();
55			std::cout << "sele1 = " << sele1 << "\n";
56			std::cout << "sele2 = " << sele2 << "\n";
57			std::cout << "nSelected = " << nSelected_ << "\n";
58			assert( nSelected_ == seleMan2_.getSelectionCount());
59
60	tim	876	LegendrePolynomial polynomial(order);
61			legendre_ = polynomial.getLegendrePolynomial(order);
62	xsun	1183	}
63	tim	876
64	xsun	1183	void LegendreCorrFunc::correlateFrames(int frame1, int frame2) {
65			Snapshot* snapshot1 = bsMan_->getSnapshot(frame1);
66			Snapshot* snapshot2 = bsMan_->getSnapshot(frame2);
67			assert(snapshot1 && snapshot2);
68
69			RealType time1 = snapshot1->getTime();
70			RealType time2 = snapshot2->getTime();
71
72			int timeBin = int ((time2 - time1) /deltaTime_ + 0.5);
73			count_[timeBin] += nSelected_;
74
75			int i;
76			int j;
77			StuntDouble* sd1;
78			StuntDouble* sd2;
79
80			for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j);
81			sd1 != NULL && sd2 != NULL;
82			sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) {
83
84			Vector3d corrVals = calcCorrVals(frame1, frame2, sd1, sd2);
85			histogram_[timeBin] += corrVals;
86	tim	876	}
87	xsun	1183
88			}
89	tim	876
90	xsun	1183	void LegendreCorrFunc::postCorrelate() {
91			for (int i =0 ; i < nTimeBins_; ++i) {
92			if (count_[i] > 0) {
93			histogram_[i] /= count_[i];
94			}
95			}
96			}
97	tim	876
98	xsun	1183	void LegendreCorrFunc::preCorrelate() {
99			// Fill the histogram with empty Vector3d:
100			std::fill(histogram_.begin(), histogram_.end(), Vector3d(0.0));
101			// count array set to zero
102			std::fill(count_.begin(), count_.end(), 0);
103	tim	876	}
104
105
106	xsun	1183
107			Vector3d LegendreCorrFunc::calcCorrVals(int frame1, int frame2, StuntDouble* sd1, StuntDouble* sd2) {
108	xsun	1213
109			// The lab frame vector corresponding to the body-fixed
110			// z-axis is simply the second column of A.transpose()
111			// or, identically, the second row of A itself.
112			// Similar identites give the 0th and 1st rows of A for
113			// the lab vectors associated with body-fixed x- and y- axes.
114	xsun	1183
115	xsun	1213	Vector3d v1x = sd1->getA(frame1).getRow(0);
116			Vector3d v2x = sd2->getA(frame2).getRow(0);
117			Vector3d v1y = sd1->getA(frame1).getRow(1);
118			Vector3d v2y = sd2->getA(frame2).getRow(1);
119			Vector3d v1z = sd1->getA(frame1).getRow(2);
120			Vector3d v2z = sd2->getA(frame2).getRow(2);
121
122	xsun	1183	RealType uxprod = legendre_.evaluate(dot(v1x, v2x)/(v1x.length()*v2x.length()));
123			RealType uyprod = legendre_.evaluate(dot(v1y, v2y)/(v1y.length()*v2y.length()));
124			RealType uzprod = legendre_.evaluate(dot(v1z, v2z)/(v1z.length()*v2z.length()));
125
126			return Vector3d(uxprod, uyprod, uzprod);
127
128			}
129
130
131	tim	876	void LegendreCorrFunc::validateSelection(const SelectionManager& seleMan) {
132			StuntDouble* sd;
133			int i;
134			for (sd = seleMan1_.beginSelected(i); sd != NULL; sd = seleMan1_.nextSelected(i)) {
135			if (!sd->isDirectionalAtom()) {
136			sprintf(painCave.errMsg,
137	xsun	1183	"LegendreCorrFunc::validateSelection Error: selected atoms are not Directional\n");
138	tim	876	painCave.isFatal = 1;
139			simError();
140			}
141			}
142
143			}
144
145	xsun	1183	void LegendreCorrFunc::writeCorrelate() {
146			std::ofstream ofs(getOutputFileName().c_str());
147	tim	876
148	xsun	1183	if (ofs.is_open()) {
149	tim	876
150	xsun	1183	ofs << "#" << getCorrFuncType() << "\n";
151			ofs << "#time\tPn(costheta_x)\tPn(costheta_y)\tPn(costheta_z)\n";
152	tim	876
153	xsun	1183	for (int i = 0; i < nTimeBins_; ++i) {
154			ofs << time_[i] << "\t" <<
155			histogram_[i](0) << "\t" <<
156			histogram_[i](1) << "\t" <<
157			histogram_[i](2) << "\t" << "\n";
158			}
159
160			} else {
161			sprintf(painCave.errMsg,
162			"LegendreCorrFunc::writeCorrelate Error: fail to open %s\n", getOutputFileName().c_str());
163			painCave.isFatal = 1;
164			simError();
165			}
166			ofs.close();
167			}
168			}